[Xplor-nih] seq2psf and pdb2psf

[R.vanderWerf at nmr.ru.nl]

Hi Blanton,

I remember I had the same problem, the H2' and H2'' are swapped.
To fix this I made a backup of the topology file.
Then I swapped the names H2' and H2''

Rerun your sequence2psf and psf2pdb scripts, et voila!
When doing RNA, you don't need to bother about the H2'' anyhow.
I don't know whether this screws up generation of DNA psf and pdb files.
[Therefor the backup]

Kind regard,
Ramon van der Werf
Radboud University of Nijmegen

[And merry christmas, and best wishes for the new year]

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> Today's Topics:
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>    1. seq2psf and pdb2psf (Blanton Tolbert)
>    2. Re: seq2psf and pdb2psf (Charles at Schwieters.org)
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> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 21 Dec 2006 12:30:54 -0500
> From: "Blanton Tolbert" <btolbert at gmail.com>
> Subject: [Xplor-nih] seq2psf and pdb2psf
> To: xplor-nih at nmr.cit.nih.gov
> Message-ID:
> 	<b22d40e50612210930m4a5a9e59reb7f16c84972e75a at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hello
> 
> I am trying to use the pdb2psf and seq2psf utilities to generate structure
> files for an RNA.  Whenever I create the .psf file all H2's are called H2''s
> and the amino notations are denoted HN' and HN''.  I have been manually
> editing the .psf file to the correct atom notation.  However, I am convinced
> that I am mis-executing the utilities.  Can someone please provide me some
> insight into the correct execution of these utilities?  Thanks in advance.
> 
> 
> 
> -- 
> Blanton Tolbert, Ph.D.
> 8363 Tamar Drive, Apt. 841
> Columbia, MD 21045
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> ------------------------------
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> Message: 2
> Date: Thu, 21 Dec 2006 15:50:03 -0500
> From: Charles at Schwieters.org
> Subject: Re: [Xplor-nih] seq2psf and pdb2psf
> To: "Blanton Tolbert" <btolbert at gmail.com>
> Cc: xplor-nih at nmr.cit.nih.gov, Charles at Schwieters.org
> Message-ID: <19497.1166734203 at beige.cit.nih.gov>
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> 
> Hi Blanton--
> 
> > I am trying to use the pdb2psf and seq2psf utilities to generate structure
> > files for an RNA.  Whenever I create the .psf file all H2's are called
> H2''s
> 
> this is due to a small bug. You should be able to fix it using the -rna
> flag with seq2psf.
> 
> > and the amino notations are denoted HN' and HN''.  
> 
> this is due to explicit renaming in psfGen.py - around line 409. You can
> manually remove it if you would like. In the next release, this renaming
> will be made optional.
> 
> Sorry for the confusion.
> 
> regards--
> Charles
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