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

[James Starlight]

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!