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@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@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@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@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@cgl.ucsf.edu>

Hi Elaine:

Great!

thank you

francesco

On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng@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

> On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret@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@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@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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