Hi Charles. Thanks for the help and clarifying the use of fixGeom. It looks like using addAtoms2.py worked only when I converted the downloaded pdb (X-ray structure) into a pdb in which the HETATOMS and water were removed and selenomet was changed to MET. I used both pdbs and the only correct output pdb was the one in which the converted pdb was used.
Valerie On Tue, Mar 24, 2009 at 10:08 AM, <Charles at schwieters.org> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > 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----- >
