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

Eric Pettersen pett at cgl.ucsf.edu
Fri Oct 20 11:36:46 PDT 2017


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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#combinations>>
>> 
>> I hope this helps,
>> Elaine
>> 
>> > On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret at gmail.com <mailto:chiendarret at gmail.com>> wrote:
>> >
>> > Hi Elaine:
>> > That works fine. However, I was unable to extend your suggestions to pick up a specific residue within a specific chain. Neither "select :17 @/pdbSegment=A1" nor "select @/pdbSegment=A1 :17" are valid commands (obviously expected).
>> >
>> > On the other hand, with such complex situations, it is Xplor, with its segname features, that helps.
>> >
>> > Should you need a pdb fine with segname, I could attach a simple one, with a single chain.
>> >
>> > On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
>> > Hi Francesco,
>> > Although I don’t have an example file with segnames to try myself, I’m told you can specify by the atom attribute pdbSegment, e.g.
>> >
>> > select @/pdbSegment=A1
>> > color red @/pdbSegment=F3
>> >
>> > I hope this helps,
>> > Elaine
>> >
>> > > On Oct 15, 2017, at 10:40 AM, Francesco Pietra <chiendarret at gmail.com <mailto:chiendarret at gmail.com>> wrote:
>> > >
>> > > Hi Elaine:
>> > >
>> > > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote:
>> > >  and your answer:
>> > >
>> > > command: select :45.a-d > or > command: select :45.* > > Or, to select residue 45 in just chains A and D: > > command: select :45.a,45.d
>> > >
>> > > I have a more complex case, where chains are defined by segname,
>> > > for example
>> > >
>> > > A1 A2 A3 A4 A5 etc
>> > >
>> > > while the standard PDB definition is "A" for all them.
>> > >
>> > > The same for standard "B", "C" etc.
>> > >
>> > > As I want to display a movie of ligand pathways, where the ligand
>> > > moves from, say, "A1" to, say, "F3", I want in the first instance
>> > > become able to select particular residues in particular chains,
>> > > as defined by their segname.
>> > >
>> > > Could you imagine a simple way not requiring selection by atom numbers?
>> > > Thanks
>> > > francesco pietra
>> >
>> >
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>> 
>> 
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