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

Chinh Su Tran To chinh.sutranto at gmail.com
Wed Mar 20 20:12:24 PDT 2013


Attached is my mol2 file. It is the DOCK result containing 10 conformations
of docked ligand. It does show 10 conformations using GUI Chimera (they're
sub-model, aint they?), but when I run the piece of code below (just for
testing), the result was an empty list (i.e. []).

*import chimera*
*confor = chimera.openModels.list()*
*print confor*

>>> []

""" if I used *print confor[0]*

>>> IndexError: list index out of range"""

Thank you.


On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
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