[Chimera-users] computed SS

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 31 08:10:12 PST 2018

Hi Hernando,
Here’s another way, slightly less painful … make aliases to save and restore the secondary structure, commands:

alias ^sskeep sel strand;namesel ostrand;sel helix;namesel ohelix;~sel

alias ^ssrestore setattr r isHelix false;setattr r isStrand false;setattr r isHelix true ohelix;setattr r isStrand true ostrand


Each alias command should be entered as one long line (even though the mailing-list software may decide to display them broken into multiple lines).  Then in Chimera, you have new commands “sskeep” and “ssrestore” that can be typed or run from the Aliases menu, and they are saved in the preferences file automatically so they should be available in later uses of Chimera.  

You would run sskeep one time before changing any assignments and then ssrestore any time you want to restore the ones that were saved with sskeep.  Matchmaker with “computeSS true” changes secondary structure assignments by running “ksdssp”, which you could also run separately.

The named selections (saved sets of residues) created by the aliases are saved in session files.

The approach outlined above just saves/restores secondary structure for all open models together.  A fancier appraoch would save different names for different models so they could be saved/restored independently, but that would probably require python (possibly could be done with “perframe” command) and I did not try it.

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

> On Jan 30, 2018, at 3:54 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hi Hernando,
> 	This is possible, but the only (non-Python) way I can think of to do it is kind of a pain.  You would use the Attribute Calculator (Tools->Structure Analysis) to define a residue attribute named ‘saveHelix’ using the formula ‘residue.isHelix’ and then the same with ‘saveStrand’ and ‘residue.isStrand’.  After the secondary assignments were later changed, you could revert to the originals by again using the Attribute Calculator, but by defining isHelix/isStrand with the formula residue.saveHelix/saveStrand.  Ugly.  Also, the saveHelix/Strand won’t be remembered in sessions unless you get tonight’s daily build.
> —Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>> On Jan 30, 2018, at 12:38 PM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
>> Dear UCSF-Chimera, 
>> I have several structures with their own defined secondary structures (SS) that are slightly different from the Chimera default assignments. I want to display them with their own assignment, not the chimera default so I am using the command mm with the option computeSS false which works as intended.   But my question is:  if at any point an alignment were done without using this option, is it possible to go back to display each structure with their own SS assignment?  I have tried but it seems that I can't go back.    Or a related question, is it possible to switch back and forth between structure-defined (when available) or Chimera-default SS assignments ?
>> Thank  you,
>> Best 
>> H.

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