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@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@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/at om_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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