[chimerax-users] Orientation and pre-superimposition of the PDB

[James Starlight]

Yes, thank you so much Elaine!

I also thought about reference.pdb, which would be usefull for the
structural matching. Could you precise- what is 'hidden' reference?

Assuming that each time while looping pdbs, I load a new pdb (with
b-factors info) + the (same) reference pdb (which is going to be used
for matching of each pdb and should not be normally displayed, since I
am taking a screenshot at the end). Could you just show commands of
Chimera-X that mau be used as an example to

1) While having loaded 2 PDBs: to match target pdb (all of them have
the same suffix, called B-factors-*.pdb) to the reference.pdb e.g.
using C-alpha trace;
2) remove or hide reference pdb (not sure how to do it properly in
this case, since on the next step I take a screenshot of the aligned
PDB. probably I also should to focus camera on the aligned PDB.

Thank you in advance!

Gleb

чт, 27 июн. 2019 г. в 18:59, Elaine Meng <meng at cgl.ucsf.edu>:
>
> Hi James,
> The problem is how to tell ChimeraX (and the problem would be the same in Chimera) what orientation is the “same” … What I would do is keep one reference structure open at all times, but hide it.  Then when you open the different structures for display, you can match them to the (hidden) reference structure using whatever superposition method works best for you, either:
>
> - matchmaker command, which figures out the pairing for you based on sequence alignment
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
>
> - align command, for which you have to specify the atoms to pair yourself
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jun 27, 2019, at 2:08 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> >
> > Dear Chimera Users!
> >
> > I am dealing with some script that use Chimera X to make a very nice
> > images of the RMSF mapped to the PDB in B-factor column (produced by
> > gromacs as the result of MD simulation).
> >
> > The problem that when I map RMSF onto structure for several different
> > systems (e.g. the different conformations of the same protein) the pdb
> > produced by gmx rmsf in different orientation so Chimera use it for
> > image and the positions of the structure are not the same (thus not
> > being aligned, see the image for example!)
> >
> > Would it be possible by means of some Chimera-X comands to orient pdbs
> > in order to align them in the same way? E.g. I open (in bash loop)
> > many pdbs (the same protein but in different states, which are not
> > aligned before, but I need that on the final images the positions for
> > each PDB would be the same (thus to avoid pre-align the PDBs before
> > opening them in ChimeraX!
> >
> > Thanks in advance!
>