Quips about greasy pockets

From: Gerard DVD Kleywegt


Hi all,

As you may recall, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly produces Quips, short stories about QUite Interesting Pdb Structures (pdbe.org/quips). Quips address biologically interesting aspects of one or more PDB entries, coupled with interactive graphics views and often a mini-tutorial or suggestions for further exploration using PDBe services and resources.

Today another Quips episode was released. It is about autotaxins, physiologically important proteins that are pursued as anti-cancer drug targets. This Quips was developed together with scientists from the Netherlands Cancer Institute (Tassos Perrakis and Wouter Moolenaar) to accompany their review paper in Nature Reviews Molecular Cell Biology on autotaxin structure and function that was also published today.

- For the Quips story ("Autotaxins: inhibiting a greasy pocket"), go to: http://pdbe.org/quips?story=Autotaxin

- For the review paper ("Insights into autotaxin: how to produce and present a lipid mediator"), go to: http://www.nature.com/nrm/journal/vaop/ncurrent/full/nrm3188.html

---

If you have an interesting structure whose story you would like to tell (with our help) in the form of a Quips episode, please contact us at pdbe@ebi.ac.uk

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK

crystallization of complex and ...

From: m zhang
Date: 16 September 2011 03:20

Dear all,

I have two questions:

First, I was trying to crystallize a complex of two proteins. Both proteins has been crystallized before. The two proteins bind to each other based on Biacore study, but they didn't form a single peak on gel filtration. When I mixed them at 1:1 ratio, the crystals I got contain only one of the two proteins. I was suggested to increase the ratio, for example 1.5:1, to increase the probability of co-crystallization which I will try. But I do want to hear if there are other possible ways to try. What would you try if you were in my situation? 

Second is about reusing of Ni-NTA resin. According to Qiagen's instruction, after using fresh Ni-NTA resin, one only needs to wash the used Ni resin first with 0.5M NaOH, then with your own buffer. After that the resin is ready to be reused until it needs being recharged. But my question is: Once immidazole competes with His-tagged protein and binds to Ni-resin, how can immidazole be rinsed off with the same buffer(usually pH is above 7) one uses to purify the protein?

Thank you for any suggestion or comment.

Min

----------
From: <alexander.pautsch

Dear Min,

regarding #1 some things come to my mind:

- What is the Kd that you got from the Biacore? And did you make sure that the sample is concentrated enough (both on gel filtration and in crystallization) to have a "sufficient"  amount  in the complex.

- did you use the same buffer systems? Your Kd might be different in different buffers.

Best

Alex

 

 

 

 

 

Dr. Alexander Pautsch
Boehringer Ingelheim Pharma GmbH & Co. KG
Dept. Lead Identific. and Optim. Sup. Ge

----------
From: Enrico Stura

Dear Min,

Regarding the stoichiometry that you should use in crystallizing two proteins
that form a complex. I have looked at this question before. See:
Stura, E.A., Graille, M., Taussig, M.J., Sutton, B.J. Gore, M.G., Silverman, G.J., Charbonnier, J.-B. (2001)
Crystallization of macromolecular complexes: Stoichiometric variation screening. J. Cryst. Growth 232:580-590.
http://www.sciencedirect.com/science/article/pii/S0022024801011721

Briefly: The stoichiometry can, and should, be varied in your screening.

The relative protein solubility of the two individual proteins and the solubility of the complex should be
analysed under various potential crystallization conditions. Conditions where the complex is less soluble
than the individual ptoteins should be chosen if the complex has a tendency to dissociate.

Since both  proteins have been crystallized before you may also use
crystals of both the free forms of the two proteins to stimulate nucleation of the complex
The final  composition of the asymmetric unit may include free poteins as
well as the complex.

The paper will give you a lot more methodology to use to obtain crystals of the complex, if
such complex really exists, is homegeneous and relatively stable.

Enrico.

----------
From: Ed Pozharski

Imidazole binds much weaker than a his-tag, and thus more of it goes
into the buffer when you wash the column.  In theory, if you wash a
column with protein bound long enough, it will all slowly come off.

--
"Hurry up before we all come back to our senses!"
                          Julian, King of Lemurs

----------
From: Artem Evdokimov

1 imidazole affinity is not high which is why you use 200 mM or more to elute. So it comes off by itself.
2 you can wash with low ph and then recharge this is somewhat easier on the resin

----------
From: m zhang

To all and Alex,

-The Kd is around 500nM from Biacore.
-One of my protein tends to precipitate and is only stable below 3mg/m. If I concentrated it to higher concentration, it will precipitate a lot after 1hr. And it was previously crystallized at low concentration. But when I inject on gel filtration, I do try to load large amount both proteins. Then this leads to another question: How high should the concentration of complex be in co-crystallization or gel filtration? I set mine at 6mg/ml for the complex and I get some precipitate. What concentration of complex would people start with to co-crystallize?
-Yes, I use the same buffer system for both proteins and complex.

Thank you all for your suggestions.

Min

Postdoc vacancy in Leicester on kinase structure-based design/mechanism

A postdoctoral research post is available to undertake translational structural biology work on a kinase target within my research group in the Department of Biochemistry. My group is located in the state-of-the-art Henry Wellcome Building with access to excellent facilities for biochemical studies, structural biology, cell culture, microscopy and computer analysis. The position is funded by Cancer Research UK and is available immediately for one year in the first instance, renewable for a further year depending on progress. Prospective candidates should hold a degree and Ph.D in biochemistry, or related discipline, and have expertise in X-ray crystallography. Applicants with experience in high-throughput crystallography applied to structure-based drug design would be at an advantage.

My team has an established track record in the study of protein kinases and in the development of kinase chemical inhibitors in drug discovery. See the group website for further information (http://web.me.com/baylisslab).

Informal enquiries can be directed to me via email (rb308@le.ac.uk).

The closing date for this post is midnight on 18th October 2011. For further details, and to apply for the job, use the University vacancy search site (http://www2.le.ac.uk/offices/jobs/opportunities/jobsearch),  reference is MBP00426.

Paper describing the structure of LFA-1

From: Narayanan Ramasubbu

Dear All:
I would like to know the literature on the crystal structure of Leukocyte Function-Associated Antigen One (LFA-1, CD11a/CD18).
I have the structure of I domain but not for the entire molecule. I would greatly appreciate if people can point me to the right article/reference.

Thanks
Subbu

----------
From: Ed Pozharski

One way to get that kind of information is to run your sequence against
pdb using NCBI BLAST, and then follow up the papers associated with the
PDB entries that come up.

PubMed search is also not a bad starting point.  If all else fails,
there is always google.  I am sure that with right keywords (e.g.
"structure of Leukocyte Function-Associated Antigen One") a review
article will pop up (if it exists) among the first five or so hits.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                               Julian, King of Lemurs

Program announcement: Nautilus

From: Kevin Cowtan

Here's an alpha release of my nucleic acid model building program for the early adopters among you to try out. There's no GUI, there's only a Linux binary for now, the features are rather limited, and it's only been tested on synthetic data. On the other hand, it seems to work for me.

Feedback would be very welcome. Please try it out if you can and send me the logfile (with filenames and cell parameters redacted if you prefer). Anything it builds, you get to keep.

It is available from here:
http://www.ysbl.york.ac.uk/~cowtan/nautilus/nautilus.html

..

'Nautilus' is a program for automatic model building of nucleotide
structures in electron density maps. It will trace a map with no model,
extend an existing model, or add nucleotide chains to an existing
non-nucleotide model.

'nautilus' does not currently perform refinement - you will need to
refine and recycle for further model building yourself. Neither does
it assign sequence - the model is built as ploy-U.

This is an alpha release. It may not work at all. It has only
been tested on synthetic data with simulated errors.
The API will change significantly in subsequent releases.

DNA cif files

From: Gregory Bowman
Date: 16 September 2011 16:26

I have a question about the bond angle restraints in the DNA cif files. I recently submitted a protein-DNA complex to the PDB, and found out that many of the glycosidic bond angles (atoms O4'-C1'-N9/N1) were outside the accepted range. I switched from CCP4 6.1.13 to 6.2.0 (installed/updated with fink on Mac OSX 10.6.8), and this "fixed" the problem in that now there is a narrower distribution of bond angles, but the target/ideal values are different in these two CCP4 monomer libraries (108.4 versus 107.8):

=====

/sw64/lib/ccp4-6.1.13/data/monomers

file=a/AD.cif

Ad       A   'Adenosine                           ' DNA                32  21 .

Ad       N9     C1*    O4*     108.400    3.000

file=c/CD.cif

Cd       C   'Cytidine                            ' DNA                30  19 .

Cd       N1     C1*    O4*     108.400    3.000

file=g/GD.cif

Gd       G   'Guanosine                           ' DNA                33  22 .

Gd       N9     C1*    O4*     108.400    3.000

file=t/TD.cif

Td       T   'Thymidine                           ' DNA                32  20 .

Td       N1     C1*    O4*     108.400    3.000

=====

/sw64/lib/ccp4-6.2.0/data/monomers

file=d/DA.cif

DA       DA  '2'-DEOXYADENOSINE-5'-MONOPHOSPHATE  ' DNA                34  22 .

DA       "O4'"  "C1'"  N9      107.800    0.800

file=d/DC.cif

DC       DC  '2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE   ' DNA                32  20 .

DC       "O4'"  "C1'"  N1      107.800    0.800

file=d/DG.cif

DG       DG  '2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE  ' DNA                35  23 .

DG       "O4'"  "C1'"  N9      107.800    0.800

file=d/DT.cif

DT       DT  'THYMIDINE-5'-MONOPHOSPHATE          ' DNA                34  21 .

DT       "O4'"  "C1'"  N1      107.800    0.800

Why are these values different in the two libraries? Am I looking at the wrong files or the wrong bonds?

Thanks!

Greg

----------
From: Ian Tickle


Hi, it depends what you mean by 'different'.  The SUs of the new set are much lower than the old values (0.8 deg vs. 3.0) so one would assume that these are improved estimates based on new data.  The difference between the old and the new is (108.4 - 107.8) = 0.6 deg with a SU of the difference of sqrt(3^2 + 0.8^2) = 3.1 deg, so difference/SU = 0.6/3.1 = 0.2 sigma - hardly what one could call 'significantly different'.

Cheers

-- Ian

Silver staining Coomassie stained gels

From: K Singh

Dear All,
Can anyone suggest me a protocol for silver-staining the PAGE that is
already stained with Coomassie.
Kris

----------
From: Ed Pozharski

Just destain it and then use the standard silver-staining protocol.  If
for some reason you want to have both stainings superimposed, take two
pictures and then combine them - it should be easy to do by
superimposing the ladders, just make sure that pictures are of the same
size (maybe tricky if you don't have an imager, but nothing GIMP
couldn't overcome).

--
"Hurry up before we all come back to our senses!"
                          Julian, King of Lemurs

----------
From: Artem Evdokimov

Destain it really well. One easy peasy option is to put the gel in water and add 1 or 2 ml of cheap Q sepharose to it then boil. Gel will destain in 2-3 minutes of boiling.

----------
From: Soisson, Stephen M

Now that's a nifty trick I hadn't heard of before!

----------
From: Artem Evdokimov

It is nice indeed, that's how we stainand destain our gels in less than 8 minutes :-) there was at one time a proprietary product like tis called magic beads or somesuch. But regular resin works ;-)

----------
From: Dima Klenchin


There is absolutely nothing wrong with silver staining of a Coomassie-stained gel without destaining. It only prevents "blowout" of most intense bands already well-visible with Coomassie. The only thing to do is to equlibrate the gel in water before going with silver. At least that's my experinece with the silver staining protocol that is based on tungstosilicic acid (aka Bio-Rad Silver Stain Plus described here for DNA in agarose but works equally well for proteins in PAAG: http://www.ncbi.nlm.nih.gov/pubmed/2446526 ).

- Dima

about alternate conformations

From: Ming
Date: 16 September 2011 15:08

Hi,

I was using Refmac from CCP4 to refine a protein's crystal structure. The methionine has half selenium and half sulfur. I was trying to make alternate conformations and let refmac do the refinement. But it keeps giving me error message as follows:

There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.5.0109:  Problem with coordinate file

And here is my modified pdb file.

HETATM  403  N  AMSE A 129      ***           N 
HETATM  404  CA AMSE A 129      ***           C 
HETATM  405  CB AMSE A 129      ***           C 
HETATM  406  CG AMSE A 129      ***           C 
HETATM  407 SE  AMSE A 129      ***          SE 
HETATM  408  CE AMSE A 129      ***           C 
HETATM  409  C  AMSE A 129      ***           C 
HETATM  410  O  AMSE A 129      ***           O 
ATOM    411  N  BMET A 129      ***           N 
ATOM    412  CA BMET A 129      ***           C 
ATOM    413  CB BMET A 129      ***           C 
ATOM    414  CG BMET A 129      ***           C 
ATOM    415  SD BMET A 129      ***           S 
ATOM    416  CE BMET A 129      ***           C 
ATOM    417  C  BMET A 129      ***           C 
ATOM    418  O  BMET A 129      ***           O 

I already confirmed with pdb that this is the right format for this case. But refmac doesn't work with it. I wonder if there is any other changes I should make for refmac?

Thank you,


Ming

----------
From: Ed Pozharski



Do you have the evidence that your incorporation ration was 50%?

On a practical side, try giving the SeMET a different chain ID.  You can
change it back manually after refinement.  Assuming that the side chain
conformation is the same, you can probably just have the selenium atom
added and hope that due to partial occupancy refmac will not apply any
vdw terms.

--
"Hurry up before we all come back to our senses!"
                          Julian, King of Lemurs

----------
From: Kevin Jin

I did not make it clear. The protocol we used for protein expression always limit the occ of MSE as 0.75. You may estimate your occ of MSE by ED. You can check PDB for JCSG structures.

 

Cheers,

 

Kevin

Fwd: [ccp4bb] Why Does Cross-linking Mean Anything?

From: Jacob Keller
Date: 15 September 2011 21:10

Dear Crystallographers and Biochemists,

cross-linking, say with gluteraldehyde, is an oft-used method of
demonstrating a protein's oligomeric state in solution. I have a
difficulty with this, however: theoretically (and in practice!), one
can tune the amount of cross-linker to get what ever result is
desired, such that any protein with some exposed lysines can be
cross-linked in any oligomeric state. How, then, does one evaluate the
power of this evidence? Maybe one should do a gradient of
gluteraldehyde concentrations, then plot the deviation of the observed
cross-linked oligomerization from a theoretical null hypothesis? Seems
like this could be done, but I have never seen this in the
literature...

Best,

Jacob Keller

--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program


----------
From: Ed Pozharski
Date: 15 September 2011 21:18


Right - just do it side-by-side with a protein known to be monomeric of
roughly the same size/lysine content...  And what is the "critical
concentration" of gutaraldehyde at which the false positives appear in
your experience?

--
"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs

----------
From: Jacob Keller


The critical concentration depends on protein concentration, time of
reaction, brand of gluteraldehyde, day of week, color of my shirt....

No, I don't know--I have seen cross-linking gradients in Nature and
such in which several oligomeric states can be seen up to the one the
author asserts is the physiological one. This is a nice experiment for
proving one's point on paper, but maybe not for establishing the
truth? Maybe a control with some SDS would be appropriate (although
this would probably perturb the lysines). Or maybe the experiment
should be done in a lysate, and then western-blotted?

Jacob

----------
From: Herwig Schuler

Dear Jacob,

agree, it's a mess. From what I read, the glutataldehyde concentration should be low (<0.01%) and the x-linked complex that you get should not occur in high salt conditions (reasoning that 1.2M KCl would break the average complex apart). Have seen papers where more selective zero length crosslinkers have been used - the Pierce catalog used to have lots of them - it seems it boils down to the same problem, eventually you will find one that "works" but you will need independent evidence to convince yourself.

I typically make really nice MW size ladders with my monomeric negative control proteins, though.

Best, Herwig

* * * * * * * * * * * * * *
Herwig Schüler, PhD
PI, Structural Biochemistry
Structural Genomics Consortium, MBB
Karolinska Institutet
Scheeles väg 2
S-17177 Stockholm

----------
From: R. M. Garavito

Jacob,

One of the problems with glutaraldehyde is the its chemistry is so bizarre.  It actually forms quite long transient polymers in solution.  You also have to ask yourself why formaldehyde also "fixes" tissues.  This is why glutaraldehyde works so well for tissue fixation for EM as opposed to our usual bivalent crosslinkers we use in biochemistry experiments.  Check out the old EM literature about discussions of glutaraldehyde chemistry.

Moreover, the Schiff's base linkage glutaraldehyde is slowly reversible.  You need to reduce it to make it permanent.  I think that glutaraldehyde is a very poor choice for a precise bivalent crosslinker, but as a broad spectrum crosslinker (hitting lysines and a free amino terminii that are different distances apart), glutaraldehyde is great.  As it is highly volatile (its unique smell tells you you've had the bottle open too long), you can crosslink crystals by vapor diffusion in an hour.

So I would be cautious about interpreting any crosslinking results using glutaraldehyde, except the obvious (i.e., oligomers may indicate the native tertiary state of a protein or complex).

Cheers,

Michael

****************************************************************

R. Michael Garavito, Ph.D.

Professor of Biochemistry & Molecular Biology

513 Biochemistry Bldg.   

Michigan State University      

East Lansing, MI 48824-1319

****************************************************************

Fortran runtime error in Procheck on Mac OS X 10.6.8

From: Alexander Batyuk
Date: 15 September 2011 07:48


Dear colleagues,

I have a problem running procheck on Mac OS X 10.6.8. It stops with the following error:

..................................................................

Stereochemical quality plots and residue-by-residue listing

At line 2639 of file /sw64/src/fink.build/ccp4-6.2.0-101/ccp4-6.2.0/src/procheck/pplot.f (unit = 14, file = 'rama.sum')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE


I would appreciate any help.

Thank you and best wishes,

Alex


--
Alex Batyuk
The Plueckthun Lab
www.bioc.uzh.ch/plueckthun

----------
From: Saul Hazledine


Hello Alex,
 I know nothing about Procheck but the following may be of interest to you. There is a similar error message produced during ARP/wARP model building as described in the message below:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;30c74e5a.1109

This error was found to be caused by the behaviour of gfortran 4.6.x which is currently used by Fink.

If your problem is related to the ARP/wARP issue then you should be able work around it by installing CCP4 from the DMG file provided on the CCP4 site. This DMG file contains executables compiled by the Intel Fortran compiler.

Saul Hazledine

Structure problem

From: #HEW KAI LI KELLY#
Date: 13 September 2011 09:55

Hi,

I am facing some problems in solving my structure now, so I am wondering if anyone is able to give me any tips and tricks on this matter.

My protein-DNA complex structure diffracted to 1.5A. There are 4 missing residues, 2 on each terminal. There is no twinning in the data. The angles, the bonds, the rotamers and the Ramachandran plot are okay too. I am using molecular replacement for the phasing and the sequence homology between my protein and my homologous model is 33%. The electron density map for the protein looks very nice and there is also nice density for the DNA. Rfree converged from the initial 39%. However, Rfree refused to go down any further and it's still around 30-31%. Does anyone have any suggestions for me? Thank you in advance!

Warmest Regards,

Kelly Hew

----------
From: Eleanor Dodson


Are you absolutely sure of the spacegroup?

Eleanor

----------
From: Vellieux Frederic


Hi there,

In crystallography there are so many places where you can have problems (and need to solve these problems) that I cannot list them all.

"There is no twinning in the data" - you probably mean "the data does not seem to indicate the presence of twinning but there might be twinning"; what about the space group ? What about your crystal appearing to have one space group for one component (example the protein) but the space group for the other component (e.g. DNA, which could be partially disordered, that happens) being different - and you have processed the data in the apparent space group for the protein ? The crystal could contain the protein:DNA complex plus one of the components needed for the whole thing to pack (and form the crystals); the model might be sufficiently different from "your" structure that all the loops plus a good part of the core is improperly positioned - or you have domain and subdomain "motions" etc etc.

There is one symptom: R-free seems to be stuck. What the reason is for this is unknown. There are cases in the literature where molecular replacement leads to this behaviour and where the crystallographers have to use experimental phasing (and understand what the problem was with molecular replacement afterwards, when the structure is solved).

Fred.

*
*
*
*
*
*

----------
From: Ed Pozharski


And you have built the DNA already, right?


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                               Julian, King of Lemurs

----------
From: Kay Diederichs

density for the DNA. Rfree converged from the initial 39%. However,

Hi,

pls check out <http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement>

To get more specific help, you'll have to tell us much more - number of residues and bases, spacegroup, ... (at least) everything that would end up in "Table 1" of your paper describing the structure, and in the header of the PDB file.

HTH,

Kay
--
Kay Diederichs              .



----------
From: Yuri Pompeu


Just echoing what has been said.
I would make sure you have the right space group.
It may be worthwhile tyring to find a MR solution in different space groups with different compositions.
Another imporatant thing is how complete is your model?
Do you have all the protein and DNA modeled in? How many waters (you should see plenty at 1.5 A)
How good is the difference map?
These are all things that should be checked before panic sets in....

Cheers

refmac and DNA bond angles

From: Gregory Bowman
Date: 15 September 2011 00:10

I'm running into some geometry problems with my DNA model after refinement with refmac (version 5.5.0109), and would appreciate any feedback. 

The problem is that the angles for many of the glycosidic bonds are 2 to 4 degrees off of the ideal values, and so are several standard deviations outside what's expected. Our data (from MR) is ~2 Å, and the density is well defined for the DNA. I was thinking that perhaps refmac was not recognizing my DNA and so just taking the poor geometry from one model and enforcing it for the next, but in the log file it does not indicate that a new molecule has been found, and I do not feed in a cif file from previous runs. Another indication that refmac recognizes the DNA bases is that it says it is renaming them. The DNA bases are named DA, DC, DT, DG, and the header of the output pdb file says:

MODRES       DC B    1  Cd                                              RENAME
MODRES       DC B    2  Cd                                              RENAME
MODRES       DA B    3  Ad                                              RENAME
MODRES       DT B    4  Td                                              RENAME
(etc...)

In the output, strangely (to me), it is actually not renaming them. That is, it is keeping the "DC" etc names.

In coot, I'm measuring the glycosidic bond (O4'-C1'-N9) to be 104.6, whereas in AD.cif, it is listed as 108.4.

The bond lengths are fine, and there are no distortions of the protein model.

Thanks,

Greg

----------
From: Gregory Bowman

OK, I updated ccp4 to 6.2.0 (and refmac to 5.6.0117) and now the angles coming out close to the ideal values. Also, I see now the the "MODRES" in the pdb header from before was tell future refmac runs to rename those residues - which confused the newer refmac version as it thought the DT (renamed Td) were somehow "DY". By just deleting these MODRES lines it was fine.

--
Department of Biophysics
Johns Hopkins University
302 Jenkins Hall
3400 N. Charles St.
Baltimore, MD 21218

glycerol on three-fold axis

From: Jacqueline Vitali
Date: 14 September 2011 20:03

Dear colleagues,

Has anyone seen glycerol on a three-fold axis?

THis is possible as the glycerol can be disordered but I want to know if there is an actual case.

Any information would be greatly appreciated.

Jackie Vitali

Ramachandran plot difference between Coot and Morprobity (or Phenix)

From: Xiaopeng Hu
Date: 2011/9/30
Dear all,

I just notified that there is a big difference between the Ramachandran plot analysis results produced by Coot and Morprobity (or Phenix). For the structure I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%, favored 95.2%, whileas Coot gives out Outliers 1.24%, Allowed 5,14% and Prefered 93.62%.I am wondering if there is a simply explain for the difference which I don't know? Or I just made some silly mistakes?

Best wishes,

xiaopeng

----------
From: Edward A. Berry
What does ProCheck say?

----------
From: Frank von Delft

Oh god no don't ask Procheck , its Rama plot is a complete disaster zone - for one thing, it's * ancient*. Doesn't discriminate between amino avoid types. Grrr. To be avoided at all costs.

Sent from tiny silly touch screen

----------
From: Mario Sanches
Hi Xiaopeng,

If you are feeding both programs exactly the same file then you are not doing anything wrong. Notice that, if you calculate the Ramachandran plot on Molprobity and then you go on coot, do a round of manual refinement, and only then calculate the Ramachandran, then that can be the source of the difference. But I would bet that it is because different programs have their own definition of what is allowed and what is an outlier. 

I personally use the Ramachandran plot on coot just to guide my refinement, but use another program (Molprobity is pretty good) to do a thorough validation.

Good luck,

Mario Sanches

--
Mario Sanches
Postdoctoral Researcher
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
600 University Ave
Toronto - Ontario
Canada
M5G 1X5
http://ca.linkedin.com/in/mariosanches

----------
From: Nat Echols

It's not you - I believe that Coot and Molprobity/Phenix both use the Richardson lab's data, but this isn't the first complaint I've heard about discrepancies in the statistics, so I suspect that the cutoffs are slightly stricter in Coot.  Will check this later today.

-Nat

Workshop in Athens

INTERNATIONAL

WORKSHOP

on

Macromolecular crystal growth and optimisation methods

 

National Centre for Scientific Research "DEMOKRITOS"

Athens, GREECE

 

31^st October  - 3^rd November  2011

 

 

Tentative List of Speakers

 

Professor Naomi Chayen, Professor of Biomedical Sciences, Imperial College London, United Kingdom. In charge for the E.U. "TOPCRYST" project for Imperial College

The joys and challenges of crystallising proteins

 

Professor John R. Helliwell, Professor of Structural Chemistry and Chair, School of Chemistry, University of Manchester, United Kingdom

The lessons of diffraction resolution and the study of crustacyanin

 

Professor E. Eliopoulos, Professor in Biochemistry, Dept of Agricultural Biotechnology, Agricultural University of Athens, Athens, Greece

Bioinformatics as a tool for crystallisation of membrane proteins

 

Mr. Fabrice Gorrec, Automation Crystallization Scientist, Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom

Robotics, procedures and innovations for macromolecular crystallisation

 

Dr. Demetres D. Leonidas, Associate Professor of Biochemistry, Dept. of Biochemistry and Biotechnology, University of Thessaly, Greece.

High-throughput structure based drug design: crystallisation

 

Dr. Irene Margiolaki, Lecturer, Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, Greece and Visiting Scientist, European Synchrotron Radiation Facility (ESRF), Grenoble, France

Macromolecular powder diffraction: current status and future prospects

 

Dr. Kyriacos Petratos, Principal Researcher, Protein Structure &  Function division, IMBB-FoRTH, Heraklion, Greece

Experimental phasing of diffraction data

 

Dr. Roberto Steiner, Principal Investigator, Randall Division of Cell and Molecular Biophysics Group Leader, King's College London, United Kingdom

There's more than one way to skin a cat (and to crystallize proteins): simple alternative strategies that worked for us (hopefully for you as well)

 

Dr. Marcus Swann, Cchem, MRSC, Business Manager, Farfield Group Ltd, Manchester, United Kingdom. In charge for the E.U. "TOPCRYST" project for Farfield Group Ltd

Characterising biomolecular assemblies using Dual Polarisation Interferometry

 

Dr. Emmanuel Saridakis, Research Fellow, N.C.S.R. "Demokritos", Institute of Physical Chemistry, Athens, Greece. Co-ordinator of the E.U. "TOPCRYST" Project

Dual Polarisation Interferometry as a diagnostic tool for protein crystallisation

 

Professor Socrates Tzartos, Professor of Immunobiology, Dept. of Pharmacy, University of Patras, Greece & Head of the Laboratory of Molecular Neurobiology and Immunology, Department of Biochemistry, Hellenic Pasteur Institute. Athens

Membrane proteins: the paradigm of nicotinic acetylcholine receptors in muscle and nerve

 

Dr. Spyros E. Zographos, Researcher, National Hellenic Research Foundation , Institute of Organic & Pharmaceutical Chemistry, 11635 Athens, Greece

The purification of proteins: Objectives and strategy, choice of source, purification methods (an overview of chromatographic methods), and protein purification examples

 

Dr. Lata Govada, Research Associate, Crystallisation Group, Biomolecular Medicine, Imperial College London, United Kingdom

When we twist... so we twist ... for better diffracting crystals

 

Dr. Sahir Khurshid, Research Associate, Crystallisation Group, Biomolecular Medicine, Imperial College London, United Kingdom

Theory and practice of protein crystallisation

 

 

The Workshop will also comprise demonstrations of Dual Polarisation Interferometry, crystallisation setup methods and crystallisation robotics.

 

Lunch and some dinners will be provided.

Limited financial support will be available to the attendants.

 

Limited to 20 participants. Applications to be sent to:

Dr. Emmanuel Saridakis

Institute of Physical Chemistry, N.C.S.R. "Demokritos"

Athens 15310, Greece

 

esaridak@chem.demokritos.gr

fax: +30-210-6511766

 

Post-doctoral Position in Structural Biology and Membrane Trafficking: CIC bioGUNE, Bilbao, Spain

The position is available in the laboratory of Aitor Hierro to work in the area of structural
biology and membrane trafficking.

We study the interactions, in molecular mechanistic detail, that underlie the selectivity of
cargo transport vesicles for recognizing the correct target membrane. We do this using a
combination of structural, biochemical and biophysical approaches. The focus of the project
is on a series of soluble and membrane associated proteins (and their complexes), which
coordinate tethering and fusion of transport vesicles from endosomes to the Golgi apparatus
(for references, see PMDIs: 20615984; 21183348 and 17891154).

The position requires PhD. degree with a strong background in molecular biology for
heterologous recombinant protein expression in different hosts such Escherichia coli, insect
cell-baculovirus and mammalian cells. Previous experience in X-ray crystallography and the
use of biophysical or biochemical techniques for the characterization of protein complexes
would be an advantage.

Local resources at the institute include shared state-of-the-art facilities for high throughput
crystallization, and in-house X-ray data collection. We also have regular synchrotron
beamtime. Other biophysical instrumentation such DLS, ITC, DSC, CD, SEC-MALLS
and fluorescence spectrometers are also available. For testing our structural and in vitro
analyses we have complementary collaborations with leading laboratories in the cell biology
field. The institute is well-situated with numerous groups working in X-ray crystallography,
NMR and EM that form a critical mass in the area of structural biology. This position offers an
excellent opportunity for an experienced protein biochemist/biophysicist or cell biologist to
complement his or her expertise in X-ray crystallography working at the juncture between
structural biology and cell biology.

The position is available beginning December 2011 and funded for 3+2 years. Applications
will be accepted until the position is filled.

Interested candidates please email a cover letter, your CV, and names (including email
address) of at least two referees to rrhh@cicbiogune.es with ref. 3131 in the subject.

Employment Res Assoc/ Postdocs KU-Pharm and Tox

We are seeking highly motivated individuals to fill in Research Associate and Postdoctoral positions to study the structure and function of proteins involved in lipid metabolism or lipid signaling by means of X-ray crystallography in the laboratory of Dr. Alex Moise at the Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas http://midwestlipids.com. The positions are funded by NIH. The laboratory is well equipped to analyze lipid metabolism and study lipid signaling, cell and animal models with altered lipid signaling and to conduct protein expression and purification. Our funding and project oversight is from the KU COBRE Center in Protein Structure and Function http://psf.cobre.ku.edu/ which provides core services in protein purification, reagents and setup for crystallization screening, diffraction and structure determination by X-ray and NMR and use of equipment including a Rigaku RU-H3RHB X-ray generator with an R-axis IV++ imaging plate system, a Bruker Avance 800 MHz NMR instrument fitted with a TCI cryoprobe and a Bruker Avance III 600 MHz with a variety of probes, Biacore for label free studies. KU campus also hosts a High Throughput Screening Laboratory, a Center for Bioinfomatics and a Mass Spectrometry facility.  In addition, through our collaborators Scott Lovell and Kevin Battaile, we have regular access to synchrotron radiation beamlines at Argonne National Labs IMCA-CAT 17. The environment is excellent and there is a lot of good work to be done.

Successful candidates must have a Ph.D. in biochemistry or a related field with a strong background in purification of proteins, protein-ligand complexes and the use of structural methods to investigate enzyme mechanism and to develop modulators. A background in membrane protein purification or purification of lipid processing enzymes is preferred. For more information email alexmoise@ku.edu. Review of applications will begin shortly and will continue until the positions are filled. Salary will be commensurate with experience. If a candidate has more than five years post PhD than the candidate will be automatically considered for a Research Position as per HR. University of Kansas is an EO/AA Employer.

In 2011, KU School of Pharmacy ranked fourth in the nation among Schools of Pharmacy in the amount of National Institutes of Health funding; 2011 is the 10th consecutive year the school has been ranked in the top five receiving more than $18,400,000 in NIH research funding in fiscal year 2010. The KU School of Pharmacy is situated in Lawrence Kansas, which was named one of the top 10 US college towns along with Austin TX, Boulder CO, Madison WI, and Berkeley CA  by Parents &Colleges and also made the list of top college towns by the American Institute for Economic Research, MSN and MSNBC. Lawrence boasts a vibrant downtown, youthful attitude - nearly 50% of residents are younger than 24 years of age - and a multitude of outdoor activities at Clinton Lake, the Kansas River and the city's 50 parks. Kansas City, a 41 miles east of Lawrence is a major US city with a variety of renowned museums, athletic venues, dining and cultural institutions.

Staff scientist opening at MacCHESS

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to pursue the development of novel techniques in x-ray scattering as applied to structural biology, and to support users at MacCHESS.  There will also be opportunities to pursue projects in structural biology, using current crystallographic and SAXS methods.  Research areas of particular interest include structure solution from multiple crystals, developing a pipeline approach for microcrystals, phasing methods, and use of Laue diffraction.  A Ph.D. in structural biology, biophysics, or a related field, and at least 5 years of experience beyond the degree in a relevant field is required.  A solid publication record is essential, and experience as a staff member at a synchrotron facility is highly desirable.  Excellent communication skills are a must, including fluency in the English language.  Appointments are nominally for three years with the possibility for renewal, subject to mutual satisfaction and the availability of funds.

Located on an Ivy League university campus in picturesque upstate New York, the Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of structural biologists, chemists, physicists, and engineers.  MacCHESS is an NIH-supported National Resource providing support for structural biology at CHESS.  MacCHESS is a heavily team-oriented environment.

Please provide an application and have at least three letters of reference sent to:

Dr. Marian  Szebenyi, Chair
MacCHESS Staff Scientist Search Committee
c/o Peggy Steenrod
Newman Laboratory
Cornell University
Ithaca, NY  14853  USA

Applications should include a cover letter, curriculum vita, a publication list, and a detailed summary of research experience and interests.  Electronic submissions and inquiries may be addressed to search-CLASSE@cornell.edu. Complete applications will be considered immediately.  The starting date is negotiable.

Cornell is an equal opportunity, affirmative action educator and employer.

Lectureship in Structural Biology at the University of Adelaide, Australia

Applications are invited from scientists in the fields of X-ray crystallography or Structural Biology. You will have a strong commitment to excellence in research and teaching, be expected to develop an active, externally funded research group and contribute to the undergraduate teaching responsibilities of the School of Molecular and Biomedical Science at the University of Adelaide, Australia.

Further information about the position can be viewed at  http://www.adelaide.edu.au/jobs/current/16987/

or from the Head of School, Professor David Adelson, telephone +61 8 83135328 or email head.mbs at adelaide.edu.au

Applications close: 26 October 2011

best wishes
Grant Booker

Space Group Table

From: James Stroud
Date: 14 September 2011 18:16


Hello All,

Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count on major software packages to honor this mapping if present in a PDB file)? I notice that this web page was authored by a couple of prominent developers.

Thank you,

James

----------
From: Ethan Merritt


I'm not sure that's the right question.  I think you need to start with
the question "Is this the list used by PDB files?".
And I'm pretty sure the answer is no, if only because the table you
link to does not list rhombohedral/hexagonal settings as starting with "H"
or "R".

See the note on the definition of the PDB field contents:
 http://www.wwpdb.org/documentation/format33/sect8.html

See also many threads over the past several years about inconsistent
handling of H3/R3.

       Ethan

--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Refinement with Low resolution data

From: Md Shaik
Date: 14 September 2011 15:34

Dear ccp4,

I am refining one structure at low resolution (3.5 A). I solved the structure in space group P622 by molecular replacement. The Rw/Rf after some cycle of rigid body refinement in Refmac5 is 34/37. But when I am trying to refine with Restrain refinement in Refmac the Rw is going down but the Rf is going up. This same happens with the phenix refinement. The protein is quite big 520 residues and one molecule is present in the crystal asymmetric unit. The maps are also not so bad except some region.

Please give me suggestion, what should I have to care during low resolution refinement? or is there any other tricks for this types of data?

Thanks in advance.

Md. Munan Shaik
PhD Student
Department of Biotehnology
School of Bioscience and Biotechnology
via G. Colombo 03
Padova 35131, Italy

----------
From: Pavel Afonine


Hi,

did you use refinement strategy suitable for low (3.5A) resolution (secondary structure restraints, Ramachandran plot restraints, proper ADP parameterization, SA, etc.... etc...)?

If you send me the data and model files off-list I will have a look.

Pavel

----------
From: Phil Evans


Are you sure of the space group? P622 is much rarer than P6(x)22 where x > 0
Phil

----------
From: Tim Gruene

Dear Md. Munan Shaik,
a couple of aspects you might check:
- - first build the model AS MUCH AS POSSIBLE before running the first
 refinement cycle
- - switch off automatic weight determination in refmac and use a low
 weight (e.g. 0.005) and many cycles of refinement
- - check that the geometry does not distort (rmsd angles and bond
 lengths reported in the refmac log-file must not go too high). if it
 does, lower the weight even further.

if your model stems from higher resolution data and is actually in good
agreement with the model you are going at, refinement might ruin the
good model if you use inappropriate settings, causing Rfree to go up.

Cheers, Tim

- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

neutron diffraction 'difference' map?

From: Francis E Reyes
Date: 13 September 2011 20:01


Hi all

Suppose you have a high resolution xtal structure (from usual x-ray diffraction) and you wanted to verify the location of a ligand. You can purchase a heavy atom isotope version of the ligand.

[1] Is it possible to do a neutron diffraction difference map (where you simply calculated Fobs(heavy) - Fobs(light) to verify the location of the ligand?

[1b] Suppose you couldn't measure the diffraction of the light version of the ligand. Can the x-ray data be combined with the neutron diffraction of the heavy atom isotope to unambiguously assign the ligand site?

[2] What would be the minimum resolution required from the neutron diffraction? (This is particularly important as you may be unable to grow high diffracting crystals or large crystals)


Note that you don't necessarily want to solve the structure of the structure from neutron diffraction from scratch, but rather you want to use it as a tool to verify the location of a ligand binding site.


Thanks!

F



---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

----------
From: Sean Seaver


Dear Francis,
It is possible, but would recommend exhausting all possibilities with X-ray crystallography.  The reason is that neutron crystallography as you mentioned has its own challenges/considerations such as possibly having to determine a new crystallization condition, crystal size, unit cell volume, symmetry, level of deuteration, data collection and processing (this table may serve as a good reference: http://1.usa.gov/qc5JoA ).  Of course, these can be overcome, but in the case of determining whether a ligand is present would stick with X-rays.  As a side note, I assume you've checked your possible isotope scatters neutrons well.
~2.2 Angstroms - this paper ( http://bit.ly/qgwHvI ) maybe handy see Table 3 on pg. 384, it compares the resolution of X-ray and neutron data collections.

Take Care,

Sean Seaver

P212121
http://store.p212121.com/

----------
From: Tim Gruene
Dear Francis,

ad [1]: if you are going for neutron diffraction, you probably want the
ligand to have its hydrogens replaced with deuteria, rather than a
'heavy atom derivative' of your ligand. The scattering power for
neutrons does not correlate with the weight of the nucleus und deuterium
scatters as strongly as O,C, ... (see ITCr, Vol. C, Chapter 4.4) In that
case you also do not need a difference map against the X-ray data
because the scattering of X-rays by hydrogens can be neglected.
ad [1b]: see [1]; remark: since we are doing science as opposed to math
or philosophy, there is no 'unambiguity'. There is only a model for the
experimental data which - depending on your means of validation - fits
the data more or less well.
ad [2]: That probably depends on whether your ligand site is fully
occupied and whether the ligand is disordered or not.

Cheers,
Tim

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

COOT on CentOS 6 (x86_64)

From: Yuri Pompeu
Date: 12 September 2011 00:05


Hello everyone,
Could anyone tell me (or point me to) how to get COOT running on CentOS6 64-bit?
It doesnt launch due to failed dependencies, it requires packages that CentOS6 has replaced...
At least that is what it looks like to me...
Cheers,

----------
From: Paul Emsley


I would try the centos5 binaries - if that didn't work, I'd try to compile it myself (build-it-gtk2-simple).  You can try to fiddle it by linking the new library so files with the old names in coot's lib directory - but that doesn't seem like the best solution to me.

Paul.

----------
From: Yuri Pompeu


Hi Paul,
I am running the centos5 build. After a couple of yum installs it seems to be happy...

Except I cannot maximize the window for some reason.
Thanks for the reply.

Yuri

Pointless problems

From: Emmanuel Saridakis
Date: 14 September 2011 19:06

Dear All,

I am having problems when trying to run Pointless with input from
Denzo/Scalepack.

(1) Pointless refuses to work from the .sca file. The error message is:

CCP4 library signal mtz:File not identified as MTZ (Error)
CCP4MTZfile: open_read - File missing or corrupted: rn7e222test.sca

or

The program run with command: /programs/CCP4/ccp4-6.1.1/bin/pointless
has failed with error message
child process exited abnormally

(when run from ccp4i)

(2) Scalepack2mtz refuses to convert a Scalepack file produced using the
command: "NO MERGE original index" (i.e. as instructed by the Pointless
instructions). It fails with the rather tactless message:

*  Resolution Range :
   0.00202    0.00485     (     22.256 -     14.357 A )
 * Sort Order :
     0     0     0     0     0
 * Space group = 'P 2 2 2' (number     16)

 SCALEPACK2MTZ:  Check your data!

And, no my resolution range is not 22.2-14.3 A!!

(3) Pointless refuses to work with an .mtz file produced by Scalepack2mtz
from a .sca file obtained with the simple "NO MERGE" instruction (remember
the "NO MERGE original index" instruction is a no-go for Scalepack2mtz).
The error message in this case is quite simply:

HKLIN is merged and no HKLREF file is defined, SPACEGROUP or REINDEX.

I know the orthodox ccp4 reply would be "stop whining and use Mosflm!",
but is there an alternative if I really want to use Denzo/Scalepack? If
not, is there another way to check my point group/spacegroup starting from
Denzo/Scalepack?

Thanks a lot!

Emmanuel

----------
From: Ed Pozharski
If you are trying to choose the screw axes, you can always look at the
systematic absences. This script may be useful in extracting the (h00),
(0k0),(00l) and such (assuming you used P222 and thus scalepack kept
everything):
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Get_systematic_absences_from_.sca_file


Cheers,

Ed.

--
"Hurry up before we all come back to our senses!"
                          Julian, King of Lemurs

----------
From: Phil Evans
Pointless will read scalepack files. From ccp4i you need to select the "Scalepack file" option and give unit cell, see attached screen shot

Failing this you can do it from the command line

pointless << eof
scain file.sca
cel a b c alpha beta gamma
eof

Phil

Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening

Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening


Outstanding postdoctoral applicants to work jointly with Drs. Julia Kubakek, Mark Hay and Jeffrey Skolnick at the Georgia Institute of Technology are sought with the following qualifications:

* Extensive experience in enzyme kinetics studies, enzyme purification or other aspects of protein biology and enzyme activity. Experience in handling multiple protein systems would be a plus.
* A background in high throughput small molecule ligand screening is strongly preferred.
* Experience with or a desire to learn computational biology and molecular modeling of protein-ligand interactions.
* The ideal candidate is someone who gets satisfaction out of methods development and working through large data sets to see broad-scale patterns.


To apply, please email your CV to : skolnick at gatech.edu

Research Assistant Position in Molecular Biology at OPPF-UK

Research Assistant in Molecular Biology (Vacancy ID: 101125)
Wellcome Trust Centre for Human Genetics, Division of Structural Biology
Located at the Oxford Protein Production Facility - UK, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0FA
Grade 6: Salary £25,854 - £30,870 with a discretionary range to £33,734 p.a.

Applications are invited for a Research Assistant in Molecular Biology to join the Oxford Protein Production Facility- UK (OPPF-UK) team.

You will be responsible for carrying out cloning and expression screening of recombinant proteins as part of the services offered by the OPPF-UK to other academic groups (http://www.oppf.ox.ac.uk/). You will be involved in the development and automation of high throughput approaches to molecular biology and have the opportunity to undertake original research leading to academic publications as part of our own research projects.

You will have a BSc degree in biology, biochemistry or molecular biology and research experience in using recombinant DNA methods, including PCR, vector construction and transformation of E. coli. or experience of analysing protein expression by SDS-PAGE, Western blotting.

The position is funded by the Medical Research Council and is fixed term until 30th June 2013 in the first instance.

To apply for this role and for further details, including a job description and a person specification, please click on the link below:

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=101125

Only applications received before 12.00 midday on 24th October 2011 will be considered.

Please quote reference 101125 on all correspondence. You will be required to upload a CV and supporting statement as part of your online application.

refmac and DNA (and now RNA)

From: Francis E Reyes
Date: 12 September 2011 19:23
Is ' U ' now the standard vs '  U' ? I'm used to right justified letters for RNA residues in the residue field.

This is with a recent refinement with refmac 5.6.0117 .

And of course this switch in naming convention breaks compatibility with molprobity (which requires right justified letters in the residue field)

F


On Sep 8, 2011, at 7:35 AM, Ed Pozharski wrote:

> After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I
> have found a problem working with DNA that I have not seen with
> 6.1.13/5.5.0109.  Namely,
>
> - if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to
> output DNA as Ad/Td/Gd/Cd no matter what the input names were, refmac
> fails with the warning that it found a new monomer.  It appears that it
> stumbles upon the very first thymidine, but in a strange twist it
> reports the problematic residue having the name "DY"!
>
> - if I use the pdb file previously produced by refmac, which has the
> A/T/G/C as residue names, it fails too but now complains about the "new"
> monomer named "T".
>
> - the workaround I found is to rename all the thymidines to "DT".  It is
> a bit annoying since coot keeps renaming them (well, not refmac/ccp4
> problem per se) and I have to rename back (easily scripted task, of
> course).  What is peculiar is that Ad/Gd/Cd don't need to be renamed
> (does this have anything to do with thymidine being the only one that
> changes residue name in RNA?).
>
> Has anyone else seen this or it's something specific to my setup?
>
> Cheers,
>
> Ed.
>
> --
> After much deep and profound brain things inside my head,
> I have decided to thank you for bringing peace to our home.
>                                    Julian, King of Lemurs



---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

----------
From: Phoebe Rice
Is there finally, at long last, one convention for nucleic acids?  I wonder how many cumulative person-years of exasperation this @#$% issue has caused?

And please note, even Mother Nature herself, let alone synthetic chemists, occassionally attaches U to deoxyribose or T to plain ribose.

=====================================
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp

----------
From: Garib N Murshudov

Yes, new version of the dictionary uses U. Refmac will read right or left justified residue names, however pdb may use only one of them.

There are some backward compatibility code/dictionary elements. For example Ad/Ar are also accepted. However it is encouraged to use new pdb v2.3 residue/atom names. It will make sure that all software use same naming convention and moving between them is smooth. 

Hopefully we all will have one naming conventions.

regards

Garib

Garib N Murshudov
Structural Studies Division

MRC Laboratory of Molecular Biology

Hills Road 

Cambridge 

CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk

----------
From: Francis E Reyes
Hi Garib

Thanks for the quick reply!

Refmac  however is writing my pdb's as with the residue letter in the centered position.

Is the newest pdb requiring centered residue letters for RNA?

F

----------
From: Garib N Murshudov

Hi Francis

Is that newer version of refmac?

regards

Garib