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

[Carlos G. Oliver]

Hi Conrad,

Yes, I overlooked the `sel` option. That works much better.

Thanks!

Carlos


Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Wednesday, October 2, 2019 2:23 PM, Conrad Huang <conrad at cgl.ucsf.edu> wrote:

> Sorry to jump in late.
>
> "select ligand & nucleic acid z<10" is slow for the reason you
> suspected: it computes the left and right sides independently, and the
> right side starts with lots of atoms and then has to find even more.
> You can get the same answer more quickly using two commands:
>
> select ligand z<10 & nucleic acid
> select sel z<10 & ligand
>
> The first command selects all nucleic acid residues that are near
> ligands; the second selects all ligands that are near those residues.
> Since "sel z<10" starts with only relevant nucleic acid residues, it is
> much quicker to compute than "nucleic acid z<10". I tried this on 6s0x
> (140K atoms, 153K bonds) and got the same answer for both methods. The
> original method took over 2 minutes on my desktop; the two-stage method
> took less than 10 seconds.
>
> Conrad
>
> On 10/2/2019 7:50 AM, Carlos G. Oliver wrote:
>
> > Hi Elaine,
> > You're right it seems with the current selection implementation we can't avoid scanning the whole molecule.
> > I will have to resort to biopython :(
> > Thanks again for all the help!
> > Best,
> > Carlos G. Oliver
> > Sent with ProtonMail Secure Email.
> > ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
> > On Tuesday, October 1, 2019 7:09 PM, Elaine Meng meng at cgl.ucsf.edu wrote:
> >
> > > Hi Carlos,
> > > I tried to explain it before but was probably unclear. Your two commands were not comparable because your second command omitted the "nucleic acid z<10” part, and that is the slow part since there may be many nucleic acid residues.
> > > I don’t expect the total time to be much different if you do the fair comparison:
> > >
> > > > select ligand & nucleic acid z<10
> > >
> > > vs.
> > > select #0:ery & nucleic acid z<10
> > > NOT
> > >
> > > > select #0:ery z<10
> > >
> > > At least in my test structure, ChimeraX took 1 second compared to ??? (infinity? because I had to force quit Chimera).
> > > Best,
> > > Elaine
> > >
> > > > On Oct 1, 2019, at 2:03 PM, Carlos G. Oliver cgoliver at protonmail.com wrote:
> > > > 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!
> > > > Best,
> > > > Carlos G. Oliver
> > > > Sent with ProtonMail Secure Email.
> > > > ‐‐‐‐‐‐‐ 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
> > > >
> > > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
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