On Dec 17, 2004, at 1:50 AM, Andrea Spitaleri wrote:
Hi everyone,
I am quite new here (I have been reading your post in past...) and now
I decide to post a question (easy maybe). I couldn't find any answer
on Google.
I have got two complexes of (protein+ligand)1 and (protein+ligand)2
where the only difference between the two is the different orientation
of the ligand. My purpose is to overlay the protein (or maybe better
the binding site) and to calculate the rms of the ligand's mismatch.
The pdb file contains the protein+ligand. Do I need to create the
ligand object for doing that?
Hello Andrea,
There are several tools available in PyMol for doing what you want.
I would suggest using the fit or pair_fit commands:
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DESCRIPTION
"pair_fit" fits a set of atom pairs between two models. Each atom
in each pair must be specified individually, which can be tedious
to enter manually. Script files are recommended when using this
command.
USAGE
pair_fit (selection), (selection), [ (selection), (selection) [ ...]
]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DESCRIPTION
"fit" superimposes the model in the first selection on to the model
in the second selection. Only matching atoms in both selections
will be used for the fit.
USAGE
fit (selection), (target-selection)
EXAMPLES
fit ( mutant and name ca ), ( wildtype and name ca )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There are some other commands which you might find useful too like rms
or rms_cur for calculating the rms between your two ligands.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DESCRIPTION
"rms" computes a RMS fit between two atom selections, but does not
tranform the models after performing the fit.
USAGE
rms (selection), (target-selection)
EXAMPLES
fit ( mutant and name ca ), ( wildtype and name ca )
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DESCRIPTION
"rms_cur" computes the RMS difference between two atom
selections without performing any fitting.
USAGE
rms_cur (selection), (selection)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Best of luck,
Scott
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Scott Classen, Ph.D.
ACS Postdoctoral Fellow
Department of Molecular & Cell Biology
University of California, Berkeley
237 Hildebrand Hall #3206
Berkeley, CA 94720-3206
LAB 510.643.9491
FAX 510.643.9290
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