[Chimera-users] reading PDB-format alignment files

Eric Pettersen pett at cgl.ucsf.edu
Tue Dec 3 11:27:02 PST 2013

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 Pettersen
                        UCSF Computer Graphics Lab

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