[chimerax-users] alphafold contacts between 3 and more subunits

[Tom Goddard]

Hi André,

I added two options "replace" (default true) and "name" (default "PAE Contacts") to the alphafold contacts command. The replace option determines if existing contact pseudobonds (in the group with the specified or default name) are deleted. If replace is false the new contacts are just added to any existing ones. The name option gives the pseudobond model the specified name.  So you could use 

alphafold contacts /A to /B
alphafold contacts /B to /C replace false
alphafold contacts /A to /C replace false

to put all the contacts in one pseudobond submodel.  If instead you wanted them in 3 different models you could use

alphafold contacts /A to /B name "AB contacts"
alphafold contacts /B to /C name "BC contacts"
alphafold contacts /A to /C name "AC contacts"

This will be in tomorrow's (Oct 11) ChimeraX daily builds.

	Tom


> On Oct 10, 2022, at 12:38 PM, Michaelis, Andre Clemens <michaelis at biochem.mpg.de> wrote:
> 
> Awesome,
> Thank you so much!
> 
> Best 
> André
>   
>  
> ——————————————————
> 
> 
>> Am 10.10.2022 um 20:50 schrieb Tom Goddard <goddard at sonic.net>:
>> 
>>  Hi André,
>> 
>>   The "alphafold contacts" command creates a submodel of the atomic structure containing pseudobonds with the submodel named "PAE Contacts".  If you rename that submodel then it won't replace it when you do the second alphafold contacts command on the same structure.  For instance, if the structure is model #1.
>> 
>> alphafold contacts /A to /B
>> rename #1.1 "AB contacts"
>> alphafold contacts /B to /C
>> rename #1.2 "BC contacts"
>> alphafold contacts /A to /C
>> 
>> This should be easier to do.  I should add an option to the alphafold contacts command "replace false" that automatically uses new names for each group of pseudobonds.  I've made a request for this.
>> 
>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770>
>> 
>>   Tom
>> 
>>> On Oct 10, 2022, at 5:47 AM, Michaelis, Andre Clemens via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>> 
>>> Hi,
>>>  
>>> Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits?
>>> e.g.:
>>> alphafold contacts /A to /B
>>> AND
>>> alphafold contacts /B to /C
>>> AND
>>> alphafold contacts /A to /C
>>>  
>>> Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those
>>>  
>>> Thank you very much!
>>>  
>>> Best André
>>>  
>>>  
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