[Chimera-users] segname

Francesco Pietra chiendarret at gmail.com
Thu Apr 2 11:30:23 PDT 2015


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
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>>
>>
>>
>>
>>
>>
> <miniSOG_O2_box_ion.pdb>
>
>
>
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