[Chimera-users] reading PDB-format alignment files

Eric Pettersen pett at cgl.ucsf.edu
Tue Dec 3 13:08:40 PST 2013

Okay, though in your example file the alignment is kind of trivial since the query and template are identical.  Nonetheless, here is a simple Python script that will read I-Tasser PDB files and show the alignment.  You run the script by giving Chimera the startup command-line arguments:  --script "tasser.py threading1.pdb" (assuming both the script and the PDB file are in the folder you are currently in).  You can also provide more than one of the PDB files if you want it to show several alignments.  For more info about starting Chimera from the command line, go to this page:



On Dec 3, 2013, at 12:28 PM, Tom Duncan <duncant at upstate.edu> wrote:

> Eric, 
> It's not the structural info I want to extract - just the sequence alignment info.
> See the remarks in the file header.
> Thanks,
> Tom
> -----------------------------------------------------
> Thomas M. Duncan, Ph.D.
> Associate Professor
> Dept Biochemistry & Molecular Biology
> SUNY Upstate Medical University
> Syracuse, NY
> On Dec 3, 2013, at 3:00 PM, chimera-users-request at cgl.ucsf.edu wrote:
>> Date: Tue, 3 Dec 2013 11:27:02 -0800
>> From: Eric Pettersen <pett at cgl.ucsf.edu>
>> To: Tom Duncan <duncant at upstate.edu>
>> Cc: chimera-users BB <chimera-users at cgl.ucsf.edu>
>> Subject: Re: [Chimera-users] reading PDB-format alignment files
>> Message-ID: <9EF6E8D1-3C93-4C30-AD51-2B110CF5C813 at cgl.ucsf.edu>
>> Content-Type: text/plain; charset="us-ascii"
>> On Dec 3, 2013, at 7:47 AM, Tom Duncan <duncant at upstate.edu> wrote:
>>> Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file.
>> Hi Tom,
>> 	Well, this "PDB" file doesn't conform to the PDB standard in a variety of ways, but the one you care about is the extra two columns on the ATOM records.  The presence of those columns causes Chimera to skip those records.  If you simply edit them out then Chimera displays the structure.  I've attached an edited version of your file.  I will open an enhancement-request ticket in our bug-tracking database for having Chimera ignore non-standard columns past the coordinate records (there are some standard columns that are supposed to be there!) and put you on the notification list for that ticket.
>> --Eric
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