[Chimera-users] internal coordinates (z-matrix) in chimera

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 20 11:12:13 PDT 2013

On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote:

> Hello,
> I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY.
> When I ran it for Mol2 input, I could not get the angles I want. 
> With the piece of code:
> confor = chimera.openModels.list()
> it shows an empty list of models (for mol2 file)???
> Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)? 
> I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges. 
> Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious.

As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file.  chimera.openModels.list() cannot be empty if Chimera is actually showing any structures.  Is it? (when you open the Mol2 file normally)?  Maybe you need to send along your Mol2 file and your script...


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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