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 ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
