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

[Elaine Meng]

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
> 
> 
> 
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