[Chimera-users] Select by attribute value in a .psf file

[MARIA CLARA BLANES MIRA]

Thank you very much Elaine and Eric for making our work much easier and for your quick reply. 
Clara


> El 28 may 2019, a las 23:30, Eric Pettersen <pett at cgl.ucsf.edu> escribió:
> 
> Hi Clara,
> 	Chimera doesn’t preserve the segment information in the PSF file, and therefore her solution is the best you can do right now.  I realize that the procedure she outlines is kind of a pain, so I added code to the PSF reader to preserve the segment info.  Starting with tomorrow’s build, the segment information will be printed in the Reply Log when the trajectory is opened, and the segment name will be set as a residue attribute, so you can select a segment named XYZ with:
> 
> 	sel :/segment=XYZ
> 
> —Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
> 
>> On May 28, 2019, at 2:10 PM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
>> 
>> Hello Clara,
>> Well, the basic problem is that the PSF file doesn’t have segment IDs in it, as far as I know.
>> 
>> If the residue names and numbers are all the same for those four phospholipid molecules, maybe you could use the atom serial numbers instead to distinguish them.  The trick is figuring them out, which I believe you can do by showing them as labels (temporarily).  Then hide the labels and use the numbers as specifiers.
>> 
>> (A) show the serial numbers as labels.  Select the four residues, and then use commands:
>> 
>> labelopt info serialNumber
>> la sel
>> 
>> (B) write down the serial numbers of the atoms you want to specify individually (I’m hoping it is a consecutive range for a molecule), then hide labels:
>> 
>> ~la
>> 
>> (C) later you can specify by number, e.g. 
>> 
>> select @/serialNumber>136 and serialNumber<148
>> 
>> (unfortunately can’t just use “select @/serialNumber=137-147” but something like the above works for a consecutive range)
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On May 28, 2019, at 10:39 AM, MARIA CLARA BLANES MIRA <c.blanes at goumh.umh.es <mailto:c.blanes at goumh.umh.es>> wrote:
>>> 
>>> Hello Chimera users,
>>> I am trying to see the movement of some phospholipids in a lipid bilayer when a peptide is anchoring to this membrane. 
>>> I have a .pdb, .psf and several .dcd files.
>>> When I select one of these phospholipids I obtain four molecules selected (with the same name due to the segments). I have been trying with ’Select by attribute value’/atoms/pdbSegment and it works perfect because this way I can specify the segment where it is. But I can’t find the way to do the same with the .psf file. Could you tell me how should I do it?. 
>>> 
>>> Thank you very much,
>>> clara
>> 
>> 
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