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

[Pascal Albanese]

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 ore 21:37 Pascal Albanese <
pascal.albanese at polito.it> ha scritto:

> This is great!
> Thanks,
>
> I’ll try tomorrow and give u some feedback.
>
> P
>
> 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
>>
>> --
>> Pascal Albanese, PhD
>> *Post-doc*, Politecnico di Torino
>> Dipartimento DISAT,
>>
>> BioSolar Lab at Environment Park
>>
>> Via Livorno 60
>> <https://maps.google.com/?q=Via+Livorno+60+10144+Torino&entry=gmail&source=g>
>>
>> 10144 Torino
>> <https://maps.google.com/?q=Via+Livorno+60+10144+Torino&entry=gmail&source=g>
>> e-mail: pascal.albanese at polito.it
>>
>> Phone number: +39 011 2257655 <+39%20011%20225%207655>
>>
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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>
>
>

-- 

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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