[Chimera-users] saving nol2 files

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 20 10:54:49 PDT 2008

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):

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 at 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).

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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

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