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

[Eric Pettersen]

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 <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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