[Chimera-users] Selecting residues with zones when reference is absent

Carlos G. Oliver cgoliver at protonmail.com
Tue Oct 1 14:03:00 PDT 2019

Hi Elaine,

Sorry for not sending to the user-list and thanks for your quick response!

Yeah the problem is that I don't know the residue ID of the ligands beforehand so I need the `select ligand` call.

One workaround I guess would be to use `writesel`to write a list of ligand residues in a file, and then read the file and insert residue IDs individually, as you suggested, in the distance filter.

What would be ideal is a way of piping selections so that a selection can be based on something that was previously selected and not always on the whole model.

Anyway thank you for the ChimeraX suggestion I'll give it a try but with the amount of time I was waiting I feel it will still be too slow.

Thanks again for all the help!

Carlos G. Oliver

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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Tuesday, October 1, 2019 4:34 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> > On Oct 1, 2019, at 11:39 AM, Carlos G. Oliver cgoliver at protonmail.com wrote:
> > Hi Elaine,
> > I just have a follow-up question on this topic.
> > Specifically the command:
> > select ligand & nucleic acid z<10
> > I'm not sure how the & operator is working here but it seems that it considers the two selections independently and then takes the intersection.
> > However it would be faster to first select the ligands and then within the ligand atoms find the ones that satisfy the second condition.
> > When I tested it on 6s0z knowing beforehand the name of the residue:
> > select #0:ery z<10
> > The computation is much faster.
> > Wondering if there is a way to more efficiently combine the selection conditions similar to this.
> > Thanks again!
> > Best,
> > Carlos G. Oliver
> Hi Carlos,
> Sending questions to chimera-users (CC’d here) is recommended unless involving private data. Others may know the answer when I don’t, and messages may fall through the cracks if you them only to my individual address.
> I’m not a programmer and don’t know the code structure, so I don’t know if there is any ingenious way of structuring your specification to make it faster. There might not be a way.
> However, your two commands seem to be doing totally different things. Is ERY the ligand? In that case your second command is lacking the “nucleic acid” part. The documentation says that & has highest priority,
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combinations
> … so your second command
> > select ligand & nucleic acid z<10
> intersects ligand with all residues within 10 angstroms of nucleic acid. is that what you are trying to do, find all ligands within 10 A of nucleic acids? Naturally this is going to take much longer than your first command
> > select #0:ery z<10
> … which just finds all residues within 10 A of ligand ERY. It’s looking at a zone from one residue instead of a zone from many (hundreds?) of nucleic acid residues.
> The comparison should instead be to
> select #0:ery & nucleic acid z<10
> … which I suspect would be just as slow. There are various ways to split up the selection process but I don’t have any reason to believe that they would be faster.
> In general, ChimeraX is much faster than Chimera for working with large structures (say ribosome), at least in rendering, and allows using parentheses in command-line specifications so it’s clearer what you will get. In ChimeraX, the command could be something like
> select ligand & (nucleic :<10)
> ...which takes 1 second on my laptop with structure 6s0z, whereas Chimera with your first example command is just hanging on that same structure and had to be force-quit. However, maybe ChimeraX doesn’t do all of the other things you are currently trying to do.
> ChimeraX is available under similar licensing conditions as Chimera (free for noncommercial use):
> http://www.rbvi.ucsf.edu/chimerax/index.html
> I hope this helps,
> Elaine
> ----------------------------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco

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