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
----------
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
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
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
----------
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
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