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

[Pascal Albanese]

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 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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