There is also intra_rms and instra_fit commands:
https://pymol.org/pymol-command-ref.html#intra_rms
https://pymol.org/pymol-command-ref.html#intra_fit
For example:
intra_fit name CA and resid 1326-1350, 0
Maybe they will be useful.
Best, Mat
On Mon, 19 Aug 2019 at 13:54, sunyeping wrote:
> He
Hi Sunyeping,
Besides using the scripting language in pymol, you might want to consider
the experimental PyMOL extension created by the PyMOL Fellows (me and Paul
Smith, https://pymol.org/fellowship/). The extension relies on the
MDAnalysis package and so far includes RMSD as an example. Here is t
Hi Yeping Sun,
A non-pymol solution to this would be to extract your first frame (in the
form of .gro) from the .xtc file, and then load your .xtc trajectory
starting from the 2nd frame.
To get the first frame as a new .gro, a similar command to this can be used:
gmx trjconv -f .xtc -s .tpr -e 1
Hi Nathan,
If you have access to pip2 (from python2), you can install python2 version
of PyMol. I've just done tried this on my computer with conda and python2
and it worked fine.
Hope this helps, Mat
On Mon, Jan 28, 2019 at 6:44 PM Nathan Guerin wrote:
> Hello,
>
> I use Fedora 29 and have in
, 2018 at 2:27 PM Stejskal, Lenka
wrote:
> Hi Mat,
>
>
> I have of course read that but I am still unable to load the trajectory. I
> was looking for an actual successful example not just a guide.
>
>
> Thanks
>
>
> Lenka
> ----------
> *Fr
Hi Lenka,
Let me first state that the command "help load_traj" points to the webpage
which in turns says that the .nc format is supported by pymol.
I come from the gromacs background. Once you load the topology/state of
your system (in my case .gro or .pdb), then use "load_traj", ie
*load_traj tr
Hi Mohammad,
Can you specify in more detail what it is that you want to do? I am not
sure what you mean by plotting a mutation of TP53.
Thanks, Mat
On Thu, Jul 19, 2018 at 4:38 PM Mohammad Goodarzi <
mohammad.goda...@gmail.com> wrote:
> Hello,
>
> How can one plot specific mutation of TP53?
> I
Dear Adarsh,
If you create selection, you will be able to toggle them on and off with a
single click (switching between ligands would take two clicks). If you
really need "one click" solution you might want to investigate writing a
script for pymol.
One non-pymolic way to create a video is to sav
