[Chimera-users] segname

Francesco Pietra chiendarret at gmail.com
Sat Apr 4 07:50:10 PDT 2015


Hi Eric:
It does not work with psf/dcd movie. Files attached (I also tried with
another psf/dcd couple)

On Thu, Apr 2, 2015 at 8:47 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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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