[chimerax-users] Distinguishing between upper and lower case chain IDs before and after splitting chains

[Elaine Meng]

Hi Yazan,
After splitting, each chain is its own model, and case is only needed/used when both upper- and lowercase chains are in the same model.  
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#capitalization>

After splitting, you can specify by model number, e.g. “select #1.56”

About creating a model from a selection:
There isn’t a way to do it directly.  Instead you could simply delete the parts that are not selected (e.g. “delete ~sel”).

 The method you gave is not right because the “models” keyword can only be used with model number(s), e.g. “save myfile.cif models #1.5-8”  …not the current selection or the name of a saved selection.

(If you were saving PDB, you could used the “selectedOnly” keyword of the “save” command, but that is not yet available for saving mmCIF.)

Some bugs with saving mmCIF were recently fixed, so if you have any problems try getting tomorrow’s daily build.  The relModel option shown in the development documentation was just added:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mmcif>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 25, 2019, at 2:43 PM, Yazan Abbas <yazan.abbas at gmail.com> wrote:
> 
> Hi, 
> My model (cif format) contains 34 chains, and so I've been using upper case and lower case letters for chain IDs. When I read in my model, the select command distinguishes between upper case and lower case, but after applying the split command on my model ('split #1 chains'), the select command no longer distinguishes between upper and lower case. I.e. 'select #1/D' will select both chains D and d. The split command works correctly, producing models 1.1-1.34. 
> 
> Also, is it possible to create a model from a selection? I can't find such a command anywhere, and the only thing I can figure out is to do the following: 
> 
> 'save name format mmcif models selecion_name; open test.cif'
> 
> Thanks, 
> Yazan