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

[Elaine Meng]

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