[Chimera-users] split

John Mercer jmercer at duke.edu
Thu Jun 19 13:42:48 PDT 2014


It does. Thank you. -John


On Jun 19, 2014, at 4:39 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi John,
> You could use something like:
> 
> split #0  atoms  :.a-b  atoms  :.c:.e  atoms  :.d
> 
> ...to put chains A&B in one model #0.1, C&E in #0.2, D in #0.3, and any remaining atoms in #0.4.  This could be generalized to higher numbers of chains per group and/or more output models.  If your original structure were opened as some different main model number, that would carry over into the resulting model numbers.  For example, if it were opened as #1 instead of #0, the split results would be #1.1, #1.2, etc.  I guess your question is more about the "atom specification" syntax than split per se.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> 
> Then you could just specify the two models of interest in the "findclash" command, as in the tutorial.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
> 
> For example, to find contacts between #0.1 and #0.3, it could be etiher
> 
> findclash #0.1  test #0.3 [… other command options …] 
> or
> findclash #0.3  test #0.1 [… other command options …] 
> 
> … which are functionally identical assuming the other options are the same.  
> 
> To split differently, start from scratch with the original structure.  That's easier than trying to combine the pieces back  together in a single model before resplitting.
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jun 19, 2014, at 1:00 PM, John Mercer <jmercer at duke.edu> wrote:
> 
>> Hi All,
>> I understand the use of split as outlined in the tutorial describing how to find the contact region between two chains.  
>> 
>> file:///Applications/Bioinformatics/Chimera.app/Contents/Resources/share/chimera/helpdir/UsersGuide/frametut.html
>> 
>> I don’t know the proper syntax for models with more than two chains, e. g. A, B, C, D, and E where you might like to split the model either as:
>> 
>> A, B, D, and E in one group C in the other 
>> 
>> or
>> 
>> A, B, and D in one group and C and E in the other.
>> 
>> I would be grateful for a recommendation for the correct syntax to use in the argument list to form two groups to identify the contact surface after further processing
>> (in the same manner as the tutorial).
>> Thanks,
>> -John
> 




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