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

Francesco Pietra chiendarret at gmail.com
Mon Oct 16 00:29:58 PDT 2017


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> 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
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 15, 2017, at 10:40 AM, Francesco Pietra <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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