Ok - thank you for your answer.
I was thinking if it is then possible to multiply the part of the molecule
(but with new atom numbers) that I want to give the highest priority in the
PDB file - would this bias the alignment towards the selected part of the
molecule?
Best regards
Magnus
Magnus,
With a little effort and the qkabsch.py file from the CEalign package
you can do this. It would take a little bit of programming, but you'd
only have to modify one line, I think.
IIRC, all you have to do is create the vector of weights and then
multiply that by the paired vectors making
Hi,
I noticed that pymol omits the headers (I mean the 5 first line) when you try
to write a pdb file. At this point I do it using this command line in my script
:
cmd.save(newName+.pdb,tmp)
Is there an implemeted way to avoid this behaviour or do I have to play around
with files ?
Thanks
Hi all --
I've been using pyMOL's fit and rmsd commands on small numbers of
structures but now I'd like to use these functions on large numbers of
molecules.
Does anybody know what algorithm is used in pyMOL to superimpose
molecular structures on top of other ones (i.e., pymol's fit
function).
