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

Thu Mar 21 09:20:28 PDT 2019

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
>
>
> 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
>>
>> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>
>
>

-- 

Pascal Albanese, PhD

*Post-doc*, Politecnico di Torino

Dipartimento DISAT,

BioSolar Lab at Environment Park

Via Livorno 60

10144 Torino

e-mail: pascal.albanese at polito.it

Phone number: +39 011 2257655 <+39%20011%20225%207655>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20190321/fa870d62/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2019-03-15 at 2.14.46 PM.png
Type: image/png
Size: 3139216 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20190321/fa870d62/attachment.png>