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: 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@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@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@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
- 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