[Chimera-users] Merge PDB Question

[Eric Pettersen]

Hi Jonathan,
	Good point.  This is actually on my to-do list and there are two  
different entries in our bug database requesting this (#1549 and  
#2642).  I'll increase the priority of getting it done, but it  
probably won't get into this next release since we are freezing the  
code for testing this Monday.

--Eric

On Sep 28, 2006, at 2:54 PM, Jonathan Hilmer wrote:

> 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.
>
> Jonathan
>
>
>> 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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