[chimerax-users] morph movie with secondary structure and dssp

[Elaine Meng]

One correction, in ChimeraX, setting is_helix true does automatically change is_strand to false, and vice versa.  It was Chimera that allowed both to be true at the same time.

Elaine

> On Apr 30, 2020, at 1:38 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Joel,
> The morph generates a new trajectory model and gives it the same secondary structure as the starting structure, as you noted.
> 
> Currently no to both questions, unfortunately.  That leaves choices:
> 
> (1) stick with the starting-structure secondary structure throughout
> 
> (2) reassign for the entire structure with "dssp" using the "computeSs" option of "coordset" (every frame) or the "perframe" approach explained at the bottom of the "coordset" page (every Nth frame)
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#ssnote>
> 
> (3) a more manual approach (well, still using commands but with more detailed and direct control) where you play to a specific frame and then change residue assignments and then continue playing.  That would be scripted with "coordset" playback and "setattr" to change residue assignments, for example:
> 
> setattr /a:22-24 res ss_type 0
> 
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
> <http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>
> 
> In the second link above,  you can see that there are also residue attributes named  is_helix and is_strand but they are not automatically mutually exclusive (you have to remember to both set one to true and the other to false, or both to false) whereas changing "ss_type" takes care of it in one shot: 0 for coil (neither helix nor strand), 1 for helix, 2 for strand.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Apr 30, 2020, at 1:15 PM, Joel Meyerson <jrm2008 at med.cornell.edu> wrote:
>> 
>> Hi,
>> I am making a morph between two PDB models representing two states of the same protein, and the overall secondary structure does not change much between the models. However, there is a region where the secondary structure does change. I would like to capture the secondary structure change in the morph and have a couple questions.
>> 
>> 1. It seems the morph uses the secondary structure from PDB #1. Is there a way to use the two different secondary structure headers from the two PDBs to define the secondary structure endpoints on the morph?
>> 
>> 2. If the above is not possible, is there a way to restrict DSSP to update only the region of interest (i.e. a residue range), and not change secondary structure throughout the molecule?
>> 
>> Thanks,
>> Joel
> 
> 
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