[Chimera-users] Merge PDB Question

Jonathan Hilmer jkhilmer at gmail.com
Thu Sep 28 14:54:05 PDT 2006

On the issue of using Chimera to write PDB files, would it be possible
to change the format of the PDB output Chimera generates?  I'm not too
well-versed in the details of the pdb file format, but I ran into
issues using Chimera-generated structures with a Blender plugin that
used BioPython to handle parsing the files.  Although I can't remember
the details off the top of my head, it involved the use of multiple
'END' statements to separate models (in Chimera-generated files).  It
was easy enough to write a script to substitute 'MODEL', 'ENDMDL'
pairs, but I'm sure it would be better implemented in whatever library
handles the file IO in Chimera.


> Date: Thu, 28 Sep 2006 10:38:00 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Merge PDB Question
> To: "Jared Godar" <jared.godar at vanderbilt.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <4F99156D-A681-4EFB-AC6C-5A0C57D029E0 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
> Hi Jared,
> Currently you cannot bond different models, and the only way to
> "merge" is to put the atoms in the same file before opening it.
> There are actually other reasons your command wouldn't work:
> - seems to me that there is no model 1, only 1.1, 1.2, 1.3 and 1.4,
> so the first part would specify zero atoms
> - the ampersand & stands for intersection (logical AND, not english
> and) and should be omitted, e.g.
>    command: bond #1.1:504.b at c #1.1:505.b at n
> What I've done in the past to handle similar cases (splicing stuff
> from an NMR structure onto a Xray structure) is to first put the tail
> (with a few extra residues to overlap with residues that are already
> present) into a file by itself.  Then I open that new file, so it
> will be a new, separate model.  I then match that model onto the
> original model using atoms in the overlapping part.  Then, write out
> another PDB file of the tail relative to the untransformed original
> model.  Using text-editing, remove the part that overlaps since it
> was just there for positioning purposes.  FINALLY (text-editing
> again) make another PDB file that combines the new tail with the
> original protein.  They may need to have the same chain ID as well.
> Sorry this is such a long process.  If you think you can hand-
> position the tail sufficiently well you could skip the parts about
> having the extra atoms, using them for matching, and deleting them.
> If you remove any intervening TER, the bond will already be there
> when  you open the new file.
> I hope this helps,
> Elaine

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