-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Longfei,
exploding hydrogens are most likely a naming issue: the names of the hydrogens in the nucleic acid must match exactly the names in the restraints-files (cif-files). Check if the hydrogens are present there and if the names match. However, unless you are working on neutron data or X-ray data at _REALLY_ high resolution (0.5A, say), there is little point in loading a PDB file into coot with hydrogens present. You refinement program should not write them to the PDB-file. If you are refining with shelxl, you can simply switch off the displaying of the hydrogens (which is actually the default in coot, as far as I know) and ignore them floating around: shelxl ignores the coordinates of AFIX'ed atoms and simply regenerate them based on the AFIX type. Regards, Tim On 03/27/12 22:29, Longfei Wang wrote: > Hi there, > > I've received a bug report about coot. I think this is a good place to > report. > Here is the summary of the problem. If open a molecule and try to build a > new nucleotide, Coot crashes. This happened for the version of Coot 3936, > both in Linux and WinCoot. A labmate suspects that there are library issues > with regards to PDB version between Coot and REFMAC. An additional issue: > Protein residues with hydrogens present can be real space refined in Coot. > However, nucleic acid residues with hydrogens present cannot be real space > refined in Coot. Attempting to do this results in exploding hydrogens. > > > Best > Longfei > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPctiQUxlJ7aRr7hoRAseZAJ9gdIcTvmXc1IcE1DYBn1IFbDQMIQCfVh1p 3tEyZyWb/14kNZQwmq8Seyg= =AQPb -----END PGP SIGNATURE-----
