[chimerax-users] symmetric function from different template in chimera x

[Elaine Meng]

Hi Alexei,
I have no idea what you are trying to do.  

First, the “sym” command creates a homomultimer from a monomer using several symmetry options.  Are you trying to create a homomultimer from the monomer ppar.pdb?  If not, then “sym” is not relevant. Your 3dzu file has only one copy of PPAR-gamma in it anyway.  The rest of the structure is DNA and other different proteins/peptides.

My second guess is that you are trying to do homology modeling.  Sorry, ChimeraX does not have homology modeling. (Chimera does have a Modeller interface, but graphical interface, not command line.)  However, maybe this ppar.pdb file already looks like it was modeled from the ppar protein in 3dzu.  The ribbons are almost identifical in 3D, but I do see a few small differences in amino acid sequence.

Third guess: If you just want to make a new file that has all the other stuff from 3dzu except replacing its original PPAR-gamma chain (which was chain D) with the one from ppar.pdb, then all you have to do is open both, delete the ppar chain in 3dzu, and then combine what is left and write it out.  However, you’d have to use Chimera and not ChimeraX, because Chimera has the “combine” command that is not yet available in ChimeraX.

E.g. in CHIMERA (not ChimeraX), after opening first the 3dzu file and then the ppar file, commands:

delete #0:.d
combine #0#1 
write relative #0 #2 ~/Desktop/mymodel.pdb

If you ask more questions, please try to explain in more detail what you are trying to do.  :-)
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 9, 2018, at 8:26 AM, Alexei Hernandez <alexei5 at vt.edu> wrote:
> 
> Good morning,
> 
> I am currently utilizing chimera x for different modeling features.  Right now I am trying to use the symmetric option for a file created by a peer of mine titled ppar.pdb.  I added the file here and trying to use the sym function by using the template of a close protein blast result, one called 3DZU, also added it.  I want to use the template of the 3dzu to create a structure for ppar.  I am confused as to which command line to use out of all of them and if it is possible to use 3dzu as a template for the ppar file created.  Could you please help me with the command line.  Have a nice day...
> 
> Alexei Hernandez
> <ppar (1).pdb><3dzu (1).pdb>