From: Thomas H. <sp...@us...> - 2011-09-04 17:07:42
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Hi Noloofar and Lina, >> I would like to calculate partial charges of my pdb. Is it possible to do it > > In pymol: > > Action-> compute -> partial charge sum this doesn't calculate partial charges, sorry. This does: Action -> generate -> vacuum electrostatics But better would be to use pdb2pqr: http://www.poissonboltzmann.org/pdb2pqr >> I have another question too, when aligning two structure in Pymol, there is >> a RMSD for the total structure, is there any command to calculate the RMSD >> for a specific region of the alignment. If the two structures have the same sequence (same atom identifiers) and you don't need an "alignment", you can use rms_cur. http://pymolwiki.org/index.php/Rms_Cur Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |