[Chimera-users] matchmaker question

[Elaine Meng]

Hi Marco,
(a) In our tests the matchmaker superpositions were slightly better if we recomputed secondary structure, so that is why it is the default.  However, you can say to use only the input secondary structure (do not run ksdssp) with "computeSS false",  for example:

mm #0 #1 computess false show true

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>

In ChimeraX, we improved matchmaker so that by default it uses a recomputed secondary structure but also keeps the original assignments on the structure.  However, this feature is not available in Chimera.

(b) I'm not sure what you mean by "whole alignment" -- more than 2 sequences?  The matchmaker process only creates pairwise alignments.  If you want to compute a multiple (>2) sequence alignment from the superposition, there is a separate tool Match->Align (in menu under Tools... Sequence). 
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html>

There is no command for that tool, so it may be difficult to script -- somebody else would have to advise on that.

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

> On Sep 26, 2022, at 1:19 AM, Marco Sette via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> I would like to write a script to compute structural alignment and show the actual, not the calculated by ksdspp, secondary structure of some pdb files.
> 
> My problems are:
> 
> a) mm #0 #1 show true 
> 
> shows the predicted secondary structure, not the actual. How this can be modified to show the actual secondary structure?
> 
> b) how the typical script provided in 
> 
> https://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGuide/basicPrimer.html
> 
> for fn in file_names: 
>     replyobj.status("Processing " + fn) # show what file we're working on 
>     rc("open " + fn) 
>     rc("mm #0 #1 ...  ?") # 
> 
> has to be modified to have the whole alignment in the same window?
> Thanks for your help,
> Marco Sette