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

[Francesco Pietra]

Hi Elaine:
Yes, I could build a stereo-pair of the trajectory (of centroids) using
atomIDs, and coloring the subunits involved also trough atomIDs.

Thanks
francesco
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Sat, Oct 21, 2017 at 8:53 AM
Subject: Re: [Chimera-users] Selecting residues in chains defined by segname
To: chimera <chimera-users at cgl.ucsf.edu>


Hi Elaine:

Same residue name and number. Different segname and atom id. You are
probably correct correct that I could try to visualize the trajectories
with (with centroids) with atom id number even in this complex situation.
I'll try, thanks.

At any event, I maintain that segname is a powerful aid, making it easier,
for example, to assign different colors to the different chains. Therefore,
in my view, making chimera able to deal with segname in MD trajectories is
high priority.

frsncesco




On Fri, Oct 20, 2017 at 11:49 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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