From: Ed Pozharski
Date: 8 December 2011 15:39
Colleagues,
One recurring question on this bb is "I got this blob of density - is it
my ligand or what in the name of pink unicorns this is?" Often, a
screen snapshot is posted, which is very helpful. But it may be better
if those helping out could rotate density around in 3D. Understandably,
posting the full model/map is not the way to go. However, I'd see no
harm in posting just a small cutout of the map in the region of
interest. It's not a difficult task (fft/mapmask or perhaps some usf
magic), but is there some user-friendly approach to cutting out a small
map volume? One can use coot to mask the map and then export it, but
this seems to generate the ccp4-formatted map that covers more than just
the masked region, thus the files are fairly large. Does anyone know of
a simple solution other than placing dummy atoms in the region of
interest and running fft/mapmask combination? (Is there
phenix.cut_the_map_around_this_weird_blob ? :)
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
----------
From: Mark J van Raaij
posting these attachments as links rather than attachments in CCP4bb messages is the way to go I think.
many institutions offer this service (ours does), and there are also free and for-pay online ways to do this (for example www.yousendit.com, but there are many others).
Then it is also not a problem to send (sorry, link) even large files. The only disadvantage I can think of is that they expire after some time.
Mark J van Raaij
----------
From: <Herman.Schreuder
I am not sure that sending links is the way to go. Our company blocks many websites that it considers not of professionel interest and were employees may spend too much time. More often than not I find that I cannot open the link provided to the bullitin board. E.g. I just checked the yousendit site and it is blocked. I think what Ed proposed, a map of maybe 10 Å**3 plus a pdb file with only a few residues would be better. Also properly compressed pictures (jpeg) are not that big that they cannot be sent by email.
Herman
----------
From: Petr Leiman
What a brilliant idea! If only this could be implemented in academia. Our Ph.D. students would stop asking stupid questions on this BB but instead read books and journal articles. Yes, everything except PDB, sciencedirect, webofscience, pubmed and arxiv (this one is for real science geeks) must be blocked!
Petr
----------
From: Ed Pozharski
There is indeed the phenix.cut_out_density tool (by Tom Terwilliger)
which does a nice job of reducing the size of the output mtz-file (it
shifts the cutout region to the origin and reduces the unit cell).
On the link-versus-attachment issue, certainly the link is preferred,
but the aforementioned tool produced in my tests the mtz-file as small
as 50kb, which is not too bad.
--
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
----------
From: Petr Leiman
For the second time today I have to apologize. In no way I wanted to discourage anyone and especially people new to crystallography from posting questions to this BB. Especially good thoughtful questions.
Sincerely,
Petr
----------
From: James Stroud
Date: 8 December 2011 15:39
Colleagues,
One recurring question on this bb is "I got this blob of density - is it
my ligand or what in the name of pink unicorns this is?" Often, a
screen snapshot is posted, which is very helpful. But it may be better
if those helping out could rotate density around in 3D. Understandably,
posting the full model/map is not the way to go. However, I'd see no
harm in posting just a small cutout of the map in the region of
interest. It's not a difficult task (fft/mapmask or perhaps some usf
magic), but is there some user-friendly approach to cutting out a small
map volume? One can use coot to mask the map and then export it, but
this seems to generate the ccp4-formatted map that covers more than just
the masked region, thus the files are fairly large. Does anyone know of
a simple solution other than placing dummy atoms in the region of
interest and running fft/mapmask combination? (Is there
phenix.cut_the_map_around_this_weird_blob ? :)
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
----------
From: Mark J van Raaij
posting these attachments as links rather than attachments in CCP4bb messages is the way to go I think.
many institutions offer this service (ours does), and there are also free and for-pay online ways to do this (for example www.yousendit.com, but there are many others).
Then it is also not a problem to send (sorry, link) even large files. The only disadvantage I can think of is that they expire after some time.
Mark J van Raaij
----------
From: <Herman.Schreuder
I am not sure that sending links is the way to go. Our company blocks many websites that it considers not of professionel interest and were employees may spend too much time. More often than not I find that I cannot open the link provided to the bullitin board. E.g. I just checked the yousendit site and it is blocked. I think what Ed proposed, a map of maybe 10 Å**3 plus a pdb file with only a few residues would be better. Also properly compressed pictures (jpeg) are not that big that they cannot be sent by email.
Herman
----------
From: Petr Leiman
What a brilliant idea! If only this could be implemented in academia. Our Ph.D. students would stop asking stupid questions on this BB but instead read books and journal articles. Yes, everything except PDB, sciencedirect, webofscience, pubmed and arxiv (this one is for real science geeks) must be blocked!
Petr
----------
From: Ed Pozharski
There is indeed the phenix.cut_out_density tool (by Tom Terwilliger)
which does a nice job of reducing the size of the output mtz-file (it
shifts the cutout region to the origin and reduces the unit cell).
On the link-versus-attachment issue, certainly the link is preferred,
but the aforementioned tool produced in my tests the mtz-file as small
as 50kb, which is not too bad.
--
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
----------
From: Petr Leiman
For the second time today I have to apologize. In no way I wanted to discourage anyone and especially people new to crystallography from posting questions to this BB. Especially good thoughtful questions.
Sincerely,
Petr
----------
From: James Stroud
There's probably a slick program somewhere, but attached is a command line tool I made several years ago and still use all of the time. To use it, you need ccp4 and mapman from USF in your path. Running the script with "mapreg -h" yields the documentation below. It can cut a map using a box, extend or cut to the ASU, extend a map to a cell, or use a pdb file to make a box. It can also cull a map around a PDB.
To use it, the attachment needs to be untarred (tar zxvf mapreg.tar).
One of these days I may give it a web page.
James
**************************************************
*** mapreg version 0.02
*** output a region of a cns map
*** copyright James C. Stroud, 2008
*** distributed under the GNU Public License
**************************************************
Usage: mapreg [-h] [-c weight] [-b border] [-s symm] [-t type]
[-x 'a b c alpha beta gamma'] mapfile
[x1 y1 z1 x2 y2 z2 | ASU | CELL | pdbfile ]
Flags: -h print this help
-b border define a border if using a pdb file to define region
default is 5 (5 Angstroms)
-c weight culls according to a weighting factor between 0 and 1
-x cell the sides and angles *must* be in single quotes
-s symm usually symmetry number is needed (ispcgr number)
-t type type of input map - default is cns
-o outfile name of output file (name generated if not supplied)
Description: Mapreg takes a cns map as input and outputs a new
region of the map as specified at the command line.
The possible region specifiers are:
x1 y1 z1 x2 y2 z2 : the region defined by the two grid unit or
fractional coordinate points (x1,y1,z1) and (x2,y2,z2)
'ASU' : the CCP4 default asymmetric unit
'CELL' : the whole unit cell
pdbfile : a pdb file defining the limits of the region
if border is defined, then this will be the border
in Angstroms around pdbfile to define the region
If the region specifier is left out, then mapreg will
output the whole unit cell.
CULLING
=======
If a culling factor is supplied and a pdb file is used
for trimming, then culling will be attempted.
Culling trims the map to the the atoms of the pdb file
if supplied. Without the pdb file, the program terminates
with an error if a culling factor is supplied.
The culling weighting factor is, for all practical purposes,
arbitrary. Play with it to get the desired results.
Start with 0.1 and go up (tighter) or down (less tight).
Make sure you are aware of the caveats of culling
before you use this to make figures for publication.
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