On Aug 27, 2010, at 8:35 AM, Francesco Pietra wrote:
Hi: I have drawn a slightly modified small peptide (terminal phenylalanine changed to phenylalanine-amide) with an old, efficient package (PCMODEL). I have drawn from from either amino acid templates or atom-per-atom and then saved as pdb. In case of drawing atom-per-atom, I have edited the residue names, changing UNK to the appropriate standard amino acid name, except phenylalanine-amide, named PHA).
Opening the pdb file with an editor, the atoms are often scattered, not sequentially grouped together for a given amino acid.
Well, both the non-edited and the edited pdb files open correctly with either PCMODEL of VMD, not with CHIMERA. In the latter case, incorrect bonds between the atoms are seen, and the molecule is compressed. Deleting all CONECT generated by PCMODEL was even worse for CHIMERA.
With non peptidic molecules I never went into such troubles using the same packages.
Thanks for suggestions how to rearrange the pdb for CHIMERA.
Hi Francesco, Chimera has the connectivity of standard amino and nucleic acids "memorized" and will connect atoms based on their names for such residues regardless of their position in space. This doesn't quite seem like the problem you're having unless you accidentally swapped some of the atom names. Also, I don't really know what "the molecule is compressed" means exactly. I think your best option is to use "Help->Report a Bug" in Chimera to report the problem and attach a copy of the problematic PDB file so I can look into it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu