[chimerax-users] Implement Crosslinks/pseudobond/distances subselections and/or export

[Elaine Meng]

P.S. I guess you could use the same process are you are already using now to save only the crosslink subset of interest to a pb file, convert just those to distance measurements, and then use distance save.

Depending on how many subsets you have, that might be better than making one giant set of distances, writing them all, and then post-processing to extract the subsets of interest.

Elaine

> On Mar 21, 2019, at 1:40 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Pascal,
> I should mention that Tom’s away for a few weeks.   
> 
> In the meanwhile, I don’t have any good suggestions.
> 
> One not-so-good idea is to initially define all these pseudobonds as distance monitors instead of generic pseudobonds.  I.e. instead of reading in a pb file that lists pairs of atoms, read in a ChimeraX command file (.cxc) with the same number of lines of pairs of atoms but with the word “distance” before each pair.  
> 
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
> 
> Then you could use “distance save” to save all the distances (automatically sorted from shortest to longest) to a text file, and then post-process the text file to get subsets of interest.  
> 
> If the pbonds weren’t originally from a pb file but defined in some other way (e.g. by a plugin) you can write them to a pb file using “save” with “format pseudobonds”
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html>
> 
> I realize it would not be very convenient, however — sorry!
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Mar 21, 2019, at 9:20 AM, Pascal Albanese <pascal.albanese at polito.it> wrote:
>> 
>> Thank you, 
>> the command works perfectly and it's easier to manage subsets of pseudobonds. 
>> 
>> I would have a last request to facilitate the analysis of crosslinks: is it possible to add a feature by which we can extract also the distances from the selected pseudobonds? even if added as a tab column in the exported .pb file. This is because with large datasets it is impossible to visualize distances with either the histogram or on the screen. 
>> 
>> Thanks a lot, 
>> Pascal
>> 
>> Il giorno ven 15 mar 2019 alle ore 22:24 Tom Goddard <goddard at sonic.net> ha scritto:
>> Hi Pascal,
>> 
>>  If you click an edge of the crosslink network graph then it will select just the crosslinks corresponding to that edge, for example the 8 crosslinks between chains C and D in the example image below.  I made that graph using command "crosslink network #2"  and clicking on the CD edge only selects the #2 crosslinks, not a different set of crosslinks such as model #3.  I tested this and it is working in the current ChimeraX.  You will probably need to zoom your graph so you can actually see an edge -- use shift drag on the graph to zoom it, and alt drag (or some similar modifier) to translate the graph so you can see it better.
>> 
>>  Now the trouble is in your example you wanted crosslinks involving 4 chains #1/r/R and #2/r/R with both upper and lowercase R chains.  When you click on an edge in the graph it selects only those crosslinks between 2 chains, all others are unselected.  So it won't do what you need.  Might be nice to let shift-click on an edge add to the selection, but that could get pretty tedious if you need to show connections between several chains.  So a command is a better choice.  Here are two commands to select the pseudobonds in crosslink model #5
>> 
>> 	select #1/r/R #2/r/R & #5 min 6 max 35
>> 
>> The "& #5" part means intersect with model #5.  Or maybe slightly clearer using 2 commands
>> 
>> 	select #1/r/R #2/r/R min 6 max 35
>> 	select intersect #5
>> 
>> These command approaches did not work in the current ChimeraX because of two separate bugs that I just fixed, so they will work in tomorrow's ChimeraX.
>> 
>> 	Tom
>> 
>> <Screen Shot 2019-03-15 at 2.14.46 PM.png>
>>> On Mar 15, 2019, at 3:42 AM, Pascal Albanese wrote:
>>> 
>>> Hi Elaine, 
>>> 
>>> Sorry for the late response. So I don't know if I maybe have some issue 
>>> I see the connecting edges in the network window, but I can only select chains (individual chains) and the subset of pbonds are not selected:
>>> <image.png>
>>> Probably is my system which is a bit complicated... somehow the pbonds can be related to individual chains or group of them? like: sel #2.1/R #2.1/r #1.1/R #1.1/r (to select the model) pbonds #3 min 6 max 35 (to select the corresponding pbonds, in which previous chains R and r are involved). And then i can save the subselection of pbonds?
>>> 
>>> thanks for your help, i can share session if needed, 
>>> 
>>> Pascal
>>> 
>>> Il giorno ven 8 mar 2019 alle 18:20 Elaine Meng <meng at cgl.ucsf.edu> ha scritto:
>>> Hi Pascal,
>>> On the crosslinks network, clicking the edge between two chains selects the corresponding pseudobonds (those between the two chains).  Is that what you mean?
>>> 
>>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#network>
>>> 
>>> Or if you meant all those between the two chains, plus the ones within each chain, then Tom’s example command selecting pseudobonds of chains A and B should work.
>>> 
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>>> On Mar 8, 2019, at 6:21 AM, Pascal Albanese <pascal.albanese at polito.it> wrote:
>>>> 
>>>> Dear Tom, 
>>>> Thank for the add, it works and is very useful. However, I don't know if I might haven't explained well: I have a complex set of pseudobonds (let's say #2) involving several Chains of #1. In the "crosslinks network" feature I'm able to subselect chains, but not subgroups of pseudobonds involving, for instance, chains A and B (can be either clicking on the network or with the command line). Would be possible to add this? 
>>>> Thanks!
>>>> Pascal
>>>> 
>>>> Il giorno mer 6 mar 2019 alle 21:33 Tom Goddard <goddard at sonic.net> ha scritto:
>>>> Hi Pascal,
>>>> 
>>>>  I added the ability to save pseudobond files (.pb suffix) in ChimeraX, will be in tonight's builds,
>>>> 
>>>>      select /A,B min 15 max 24
>>>>      save somelinks.pb selectedOnly true
>>>> 
>>>> This saves crosslinks between chains A and B with lengths between 15 and 24.  The link colors and radii are also saved.
>>>> 
>>>>      Tom
>>>> 
>>>>> On Mar 6, 2019, at 2:33 AM, Pascal Albanese wrote:
>>>>> 
>>>>> Dear ChimearX Users and developers, 
>>>>> I'm using ChimeraX for visualization and analysis of pseudobonds datasets from Crosslinking-MS and i found new features very useful (min max selection etc). 
>>>>> I think it would be useful (but i don't know how much effort will be required) to be able to select subsets of distances (e.g. form 15 to 24 Angstroms, or involving chain A and B) and being able to create and export these subsets. for instance i have a Complex of A, B and C and i want to select all pseudo-bonds involving A and B and export them as pb file (to be able to load them as a separate model lateron). Or to sel min 15 max 24, and then export them as pb file (with "save" function). 
>>>>> 
>>>>> I think it would be really useful for both crosslinks visualization and analysis (i work with datasets of thousands of crosslinks on big complexes which make difficult to subselect them, i have to do it with pymol, then generate subsets and reformat them as .pb files). 
>>>>> 
>>>>> i had a look to previous threads, but i didn't found similar topics. If i'm wrong my apologize.
>>>>> Thank you!
>>>>> Pascal
>>> 
> 
> 
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