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

Fri Mar 22 10:06:04 PDT 2019

Hi Eric,

this script works perfectly! thank you

P

Il giorno ven 22 mar 2019 alle ore 01:35 Eric Pettersen <pett at cgl.ucsf.edu>
ha scritto:

> Here’s a Python script that will write out the atoms and distances of
> currently selected pseudobonds to a file named “pb_info.txt” in your home
> directory.  Run it simply by opening it.
>
> —Eric
>
>
>
> > On Mar 21, 2019, at 1:49 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > P.S. I guess you could use the same process are you are already using
> now to save only the crosslink subset of interest to a pb file, convert
> just those to distance measurements, and then use distance save.
> >
> > Depending on how many subsets you have, that might be better than making
> one giant set of distances, writing them all, and then post-processing to
> extract the subsets of interest.
> >
> > Elaine
> >
> >> On Mar 21, 2019, at 1:40 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >>
> >> Hi Pascal,
> >> I should mention that Tom’s away for a few weeks.
> >>
> >> In the meanwhile, I don’t have any good suggestions.
> >>
> >> One not-so-good idea is to initially define all these pseudobonds as
> distance monitors instead of generic pseudobonds.  I.e. instead of reading
> in a pb file that lists pairs of atoms, read in a ChimeraX command file
> (.cxc) with the same number of lines of pairs of atoms but with the word
> “distance” before each pair.
> >>
> >> <
> http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
> >
> >> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
> >>
> >> Then you could use “distance save” to save all the distances
> (automatically sorted from shortest to longest) to a text file, and then
> post-process the text file to get subsets of interest.
> >>
> >> If the pbonds weren’t originally from a pb file but defined in some
> other way (e.g. by a plugin) you can write them to a pb file using “save”
> with “format pseudobonds”
> >> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html>
> >>
> >> I realize it would not be very convenient, however — sorry!
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.
> >> UCSF Chimera(X) team
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>
> >>> On Mar 21, 2019, at 9:20 AM, Pascal Albanese <
> pascal.albanese at polito.it> wrote:
> >>>
> >>> 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
> >>>
> >>> <Screen Shot 2019-03-15 at 2.14.46 PM.png>
> >>>> 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
> >>>>
> >>
> >>
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> >
> >
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>

-- 

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>
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