Hi there, maybe the subject is a little bit misleading but i couldn’t find any better description. Basically I am trying to align two PDB structures, one is from the PDB directly and the other one is a file containing conformation information about a specific loop of the protein from the PDB. So I try to align this loop to the residues 211-220 of the PDB structures. My commands go like this:
fetch 1g68 load loop.pdb align 1g68 and chain A and n. CA+N+O+C and i. 211-220, loop instead of aligning on the 40 atoms as expected I align solely on 8, which are the N atoms. If I change the n. selection to O for instance I get ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). This is with the macports compiled version of pymol 1.7.7.2 and the PyMOLX11Hybrid 1.7.4. However, doing exactly the same in the Macpymol version 1.7.4 it works as expected. To even make it more weird if I use Python: import __main__ __main__.pymol_argv = [ 'pymol', ‘-qc'] # Quiet and no GUI -qc import pymol pymol.cmd.fetch('1g68’) pymol.cmd.load('loop.pdb’) pymol.cmd.align('loop', ‘1g68 and chain A and n. N+CA+O+C and i. 211-220, quiet=0) it works as well. Does anybody understands what is happening here? Thank you very much, Max PS: If you need the PDB files let me know. I don’t know if this list acceptes files ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ 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