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Hello Si-- . I'm a beginner of xplor-nih. I'm trying to calculate the rmsd of the . structure generated by xplor-nih calculation and published x-ray structure. . I have tried both the script rmsdplot.inp (in xplor-nih-2.23/tutorial/ . geomanal/) and the script targetRMSD.in (in the xplor-nih-2.23/bin). . However, every time it reports error when I compare the calculated structure . and x-ray structure of my protein. . Before running the program for my own protein, I practiced the example in . xplor-nih-tutorial-2009/gb1_simple, in which how to get the rmsd between . calculated structure and x-ray structure is shown. . I found the g-xray.pdb file here has exactly the same atom definitions with . the calculated structure files in precalc/. > All the published x-ray pdb files of my protein defines less atoms > (They do not have Hs) in each residue than the xplor-nih generated pdb > files. But, I think we chose C, CA and N for the comparison, so the program > should not read other atoms like Hs. But it always shows error when reading > the pdb file. Should I make these two pdb files include the same amount of > atoms for each residue? Or how can I modified the script targetRMSD.in to > make it work? > You can use targetRMSD as is to compare PDBs with different numbers of atoms if you specify the -diffSeq flag. In that case, only the number (and order) of atoms specified by the -selection option need be the same. Also, the most recent version of Xplor-NIH is 2.26, you may have better results if you upgrade. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAky95hkACgkQPK2zrJwS/lZtkACaAmI3IG3qwWARNEhRm092cof4 r6IAoIJrpCQ3BBWvwanxWY/xRXl73SLP =DK7H -----END PGP SIGNATURE-----
