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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