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@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@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

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users