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Hello Valerie-- > I am trying to change a residue (e.g., LYS) to CYS-MTSL. This was > previously discussed; however, what should I do if the pdb (X-ray > structure downloaded from pdb.org) does not have the CYS present > already? Is executing the addAtoms.py script supposed to work in this > case? The output generated from addAtoms.py and addAtoms2.py (this > fixes covalent geometry) from Xplor v. 2.22 is an incorrectly folded > structure. The demo works, so it must be my input info. I also tried > adding protocol.genExtendedStructure(sel="not known") or (sel="resid > xx"). Unfortunately, the tertiary structure is still incorrect. > eginput/PSF_generation/addAtoms2.py should work for you in this case. Note, the comment above the definition of fixGeom is incorrect: only atoms in fixGeom are moved. > I have not done any modifications to the downloaded pdb; could this be > the problem? > It should work fine. If you still have problems, I'd like to see the output of the script, so I can figure out what's going on. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFJySGVPK2zrJwS/lYRAj4PAJ0QGwZDI6Pb3Vop9MpnyCn9Uy2YzACfbH+3 sbxnspIRmMYLKckYo0SSkJs= =QWec -----END PGP SIGNATURE-----
