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

[Elaine Meng]

Hi Pascal,
Did you try clicking the edge line?  If you tried that but it’s not doing anything, maybe it is because the edges are too close together in the diagram.  Maybe drag the diagram window out of the main interface (so it is its own window), make that window as large as possible, and then try clicking the edge. 

I haven’t figured out a command to do exactly the same thing, because a command specifying the two chains (see example command from Tom G in message from March 6 2019 below) will also include any intra-chain pseudobonds, not just the inter-chain ones.   If that is OK with you, however, then you could use commands like that.

Elaine 

> On Mar 15, 2019, at 3:42 AM, Pascal Albanese <pascal.albanese at polito.it> 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