jort at nmr.mpibpc.mpg.de
Tue Nov 13 08:52:16 PST 2007
First thanks a lot for the great software you provide us!!!
I would like to compare structures after an MD simulation.
There is a function called match which can be used to calculate the
RMSD between selected atoms.
The protocol is the following;
I select atoms within 5 Angstrom to a reference atom in the structure
1: 300 atoms selected. I do the same for the structure 2 (reference
atom is the same): 311 atoms selected
The problem is then I can not use the match function since the atom
number is different.
I selected then residues (the one which are 5A away from the
reference atom) instead of atoms but it is a bit fastidious plus it
is not the same as a "zone selection" (some atoms are coming even if
they are at 5.6A)
I print out (from a pdb) the number of desired proton but the command
sel @123 do not work because atom selection is done by name and not
by number (if it is really the case then it would be nice to have
this possibility as well ;-)
The last solution would be really easy and quick to do if the
selection on atoms can also be done by number.
Is there any way to solve this? I need to use all the atoms, so the
matchMaker give me an RMSD but it does not use all of the atoms in
the calculation of the RMSD.
Basically I need the intersection of the two sets (two structures) of
In reality I have much more than 2 structures so the protocol should
also be scriptable, but I guess everything is scriptable in Chimera
thank in advance
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