[Chimera-users] segname

[Eric Pettersen]

I'm glad it's working for you.  Thanks for finding that problem!

--Eric

On Apr 2, 2015, at 11:30 AM, Francesco Pietra <chiendarret at gmail.com> wrote:

> Hi Eric:
> I tried with my files. Thanks a lot for allowing NAMD users to catch segname segments with CHIMERA
> 
> all the best
> 
> francesco
> 
> On Wed, Apr 1, 2015 at 8:12 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hmm, Chimera was being a bit of stickler in that it wasn't reading the columns that included the segment ID unless the ATOM records had a full 80 characters.  The ATOM records in your file are a little shorter (78 characters).  I have modified the Chimera code to be a little more flexible in that regard.  If you get tonight's daily build, it will process the segment IDs in your file.  Look for builds dated April 1 or later.
> 
> --Eric
> 
> On Apr 1, 2015, at 8:27 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
>> Hi Eric:
>> If I did correctly, it does not work.
>> 
>> Attached is a pdb file from work that I recently published. If relevant, I could also provide psf/dcd. In fact, my main interest is in describing the MD trajectory with chimera/centroid, while highlighting in different colors the various chains and residues of particular interest
>> 
>> Thanks a lot for your interest
>> 
>> francesco
>> 
>> define centroid 
>> 
>> 
>> 
>> On Mon, Mar 30, 2015 at 11:32 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> Hi Francesco,
>> 	It should be available as the atom attribute pdbSegment, e.g. "color red @/pdbSegment=XY2".  If that doesn't work, please let me know and attach a PDB file with segment info in it that I can use for testing.
>> 
>> --Eric
>> 
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu
>> 
>> On Mar 28, 2015, at 6:34 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
>> 
>>> Hello:
>>> 
>>> May I ask whether there is till a problem in having CHIMERA understanding segname? For those working with XPLOR (NAMD, for example) and multichain proteins, rendering results with CHIMERA becomes very tedious (having to use atom indexes)
>>> 
>>> Thanks
>>> francesco pietra
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
>> 
>> 
>> 
>> 
>> <miniSOG_O2_box_ion.pdb>
> 
> 

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