Dear Chao Wu, Determining atom types from elements and coordinates (as in PDB files) is actually a rather difficult and complicated process - for standard residues they can just be looked up, but for miscellaneous molecules such as ligands, it requires looking at all the bond lengths and angles, and even then the assignments may not be clear. Some of the ligands in the PDB have bad geometries such as bent aromatic rings. Further, there is not a one-to-one relationship between the atom types in Chimera and in mol2 (SYBYL). To summarize: It is a series of calculations and some errors are expected, especially if the input geometries are not ideal. Here is information on the first part of the calculation (input -> Chimera atom types): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html> I don't think there is a description of the second step (Chimera types -> mol2 types) other than in the python code itself, but it is mostly straightforward. We do not know what process SYBYL uses. SYBYL is commercial software, and as far as I know the process is not described in any publication. When I used SYBYL a very long time ago (20 years!) it made very little effort to figure out types from PDB input - it just made everything sp3 so it was usually necessary to change the types manually for nearly all atoms. Probably it has been improved since then, however! If you have a specific issue you would like to bring to our attention, however, you could send me ( meng@cgl.ucsf.edu ) a PDB of the ligand, the mol2 you get, and a description of which atoms should be different types or another mol2 with your corrected types. Also say what version of Chimera you are using (Help... About UCSF Chimera in the menu would show that). Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 20, 2008, at 2:49 AM, 吴超 wrote:
Hi, dear folks, I have some doubt about how chimera determines the atom type when you save mol2 files from ligand pdb files. Because when I opened the saved mol2 files, I found there were some mistakes about atom type. Does Chimera use the same procedure that Sybyl uses to determine the atom type? -- Chao Wu