[Chimera-users] Selecting residues in chains defined by segname

Eric Pettersen pett at cgl.ucsf.edu
Mon Oct 23 15:49:40 PDT 2017


Though segname is not preserved, Chimera automatically assigns chain IDs to the polymers in the trajectory, using A-Z, a-z, and 1-9,0 in that order.  The assignments are in the reply log.  Therefore you should be able to specify polymeric segments by chain ID, and ligands near a particular chain with the “zone” operator, e.g.:  ":O2 & :.C zr<7" for a ligand named O2 near chain C.

—Eric

> On Oct 20, 2017, at 2:49 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Francesco,
> Is it not possible to specify the ligand without using the segname?   You can use residue number, chain number, residue name…  are you saying that there is more than one residue in the same chain with both the same name and the same number?
> Elaine
> 
>> On Oct 20, 2017, at 2:37 PM, Francesco Pietra <chiendarret at gmail.com> wrote:
>> 
>> A pity, in my view. As more and more complex proteins are being examined (thanks to faster clusters), working without segname would be practically impossible in  the frame of today pdb files. For example, how visualizing the trajectory of a particular ligand in a 24-chain protein assembly? I can do that with vmd, but at the price of a less clear-cut trajectory and poorer graphics.
>> But I understand that there may be different viewpoints.
>> Cheers
>> francesco
>> 
>> On Fri, Oct 20, 2017 at 8:36 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> Realistically no.  Too many other priorities.  The gap will eventually get filled in in ChimeraX, but even that will be awhile.
>> 
>> —Eric
>> 
>>> On Oct 19, 2017, at 1:24 PM, Francesco Pietra <chiendarret at gmail.com> wrote:
>>> 
>>> Hi Eric:
>>> 
>>> Any plan to fill this gap?
>>> 
>>> thanks
>>> 
>>> francesco
>>> 
>>> On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>> Hi Francseco,
>>> 	Unfortunately, segment IDs are not preserved by the trajectory reader.
>>> 
>>> —Eric
>>> 
>>> 	Eric Pettersen
>>> 	UCSF Computer Graphics Lab
>>> 
>>> 
>>>> On Oct 19, 2017, at 9:53 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
>>>> 
>>>> Hi Elaine:
>>>> While, as I wrote, the commands for segname did work fine with .psf/.pdb namd files,
>>>> in contrast, with .psf/.dcd files (movie)
>>>> 
>>>> select @/pdbSegment=C1
>>>> 
>>>> selects all chains of the protein assembly, including ligands. The same occurs with
>>>> 
>>>> select @/pdbSegment=O2C1
>>>> 
>>>> where O2C1 is the segname of the molecule dioxygen associated with chain.
>>>> 
>>>> This occurs both on my desktop and on a large-memory nextscale cluster on remote visualization (the latter is the actual interest)
>>>> 
>>>> Do you know of any remedy?
>>>> 
>>>> thanks a lot
>>>> 
>>>> francesco
>>>> ---------- Forwarded message ----------
>>>> From: Francesco Pietra <chiendarret at gmail.com>
>>>> Date: Mon, Oct 16, 2017 at 7:12 PM
>>>> Subject: Re: [Chimera-users] Selecting residues in chains defined by segname
>>>> To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
>>>> 
>>>> 
>>>> Hi Elaine:
>>>> 
>>>> Great!
>>>> 
>>>> thank you
>>>> francesco
>>>> 
>>>> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>> Hi Francesco,
>>>> The symbol for intersection is “&” ... in other words, you could use
>>>> 
>>>> select :17 & @/pdbSegment=A1
>>>> 
>>>> Intersection and union symbols are explained here:
>>>> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#combinations>
>>>> 
>>>> I hope this helps,
>>>> Elaine
> 
> 
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