Terribly useful Carsten!
I could easily do a loop and get the RMS along the trajectory:
k = []
for i in range(1,101): k.append(cmd.align("trj","pdb1",mobile_state=i))
for i in range(100): print k[i][0]
Cheers,
Albert
On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
> Hi Al,
>
> you would need to go through the Python API:
>
> python
> rms=cmd.align("mob////CA","tar////CA", quiet=0)
> print rms
> python end
>
> rms contains a tuple with various parameters related to the superposition.
> The first value in the tuple i.e. rms[0] should be the RMS value.
>
> HTH
>
> Carsten
>
> -----Original Message-----
> From: Albert Solernou [mailto:[email protected]]
> Sent: Wednesday, May 06, 2015 8:32 AM
> To: [email protected]
> Subject: [PyMOL] RMS over a MD trajectory.
>
> Hi,
> I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I
> can see that "align" does things correctly when:
> align trj, pdb1, mobile_state=1
> i. e., when I align the first snapshot of the trajectory with the PDB file. I
> also understand that PyMOL does compute the RMS along the trajectory if I
> simply:
> align trj, pdb1
> as it is told in:
> http://www.pymolwiki.org/index.php/Align
> However, I am unable to get the list of RMS values printed out. How could I
> do that?
>
> Thanks,
> Albert
>
> --
> ---------------------------------
> Dr Albert Solernou
> EPSRC Research Fellow,
> Department of Physics and Astronomy,
> University of Leeds
> Tel: +44 (0)1133 431451
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> PyMOL-users mailing list ([email protected])
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/[email protected]
--
---------------------------------
Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
Tel: +44 (0)1133 431451
------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
PyMOL-users mailing list ([email protected])
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/[email protected]
