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

[Chinh Su Tran To]

Hi,

I fixed my silly mistake and solved the problem. Btw, I also found how to
convert mol2 back to pdb in chimera. Chimera is interesting.
Thank you very much.

Chinh

On Thu, Mar 21, 2013 at 11:12 AM, Chinh Su Tran To <chinh.sutranto at gmail.com
> wrote:

> Hi,
>
> 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.
>
> Chinh
>
>
> 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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