Yes, when it comes to trajectory visualization, vmd is just much better
than Pymol.
intra_fit can be used for example this way:
print cmd.intra_fit("my-traj////CA", 1)
where my-traj is an object with all the frames and the macro in quotes can
be used to define any selection, in this example CA atoms. The 1 means fit
every state/frame on state number 1, and of course that can be any frame.
Istvan
On Wed, Nov 21, 2018 at 7:58 PM Floris van Eerden <
florisvaneer...@biken.osaka-u.ac.jp> wrote:
> Dear Ivan,
>
> Thanks for the suggestion. However it has the same result as what I tried
> before. The slider does the job, but is not responsive enough for intense
> scrolling through trajectories (not sure if it is because the rendering
> take to much CPU or because the slider is just not designed for that
> purpose). Anyway thanks for the suggestion.
>
> @Nese, there is the intra_fit command, you could try to use it on a
> selection only.
>
> On 22 Nov 2018, at 0:37, KurtYilmaz, Nese wrote:
>
> Hi,
>
> What is the best way to align the snapshots of a trajectory when viewing
> in pymol? Is it possible to align using a selection, say on a few selected
> residues?
>
> Nese
>
> ------------------------------
> *From:* Istvan Kolossvary [ikolos...@gmail.com]
> *Sent:* Tuesday, November 20, 2018 11:43 PM
> *To:* pymol-users@lists.sourceforge.net
> *Subject:* Re: [PyMOL] Viewing trajectories in pymol
>
> You can add a slider to the movie panel.
> # Set a movie slider
> set movie_panel=1
> #movie.add_state_sweep(1,0,start=1)
> movie.add_state_loop(1,0,start=1)
>
> Best,
>
> Istvan
>
> On Tue, Nov 20, 2018 at 5:02 AM Floris van Eerden <
> florisvaneer...@biken.osaka-u.ac.jp> wrote:
>
>> Dear Pymol community,
>>
>> Is there a way to *easily* view trajectories with pymol? In VMD there is
>> some kind of scrollbar, with which it is really easy to scroll through a
>> simulation. Is some similar functionality available somehow in pymol. The
>> only similar thing is the movie_panel in conjunction with the mset command.
>> However this does not provide as a smooth experience.
>>
>> Best wishes,
>>
>> Floris van Eerden
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