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

[Chinh Su Tran To]

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.

Thank you.

Chinh

On Sat, Mar 9, 2013 at 2:01 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Chinh,
> If you are able to write a Python script, you could use the info in the
> Chimera Programmer's Guide
>
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide
>
> to write a script to get the values.  There is a programmer's example
> specifically about atomic-level measurements such as angles and distances:
>
>
> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeasure.html
>
> Also, Python is reasonably easy to learn, especially if you already know
> how to program in another language.  There are links to Python tutorials in
> the Programmer's Guide.
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
> On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote:
>
> Hi Chinh,
> For scripting measurements (distance, angle, torsion) you can use
> commands: distance, angle
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
>
> These measurements are specified individually.  Chimera does not have an
> option to write out a Z-matrix, sorry.
>
> More info on writing Chimera scripts to process multiple data files:
> <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote:
>
> Hi,
>
> I have some results after running docking from DOCK.
>
> I'd like to obtain information of internal coordinates (bond, angle,
> torsion OR z-matrix).
>
>
> Could anyone please give me any suggestion how to do that in Chimera? Or
> if possible, please suggest me some references that can help me find it out.
>
>
> I have bunch of conformations, so I may not use the gui.
>
> Thank you.
>
> Chinh
>
>
>
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>
>
>
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