Hi again,
Joel, thank you for your additionnal help and suggestions. I unfortunately
cannot avoid deleting the structures, as there are far too many of them, and
having them all loaded at the same time really slows pymol down. I do seem
to have found a solution, and one last problem that I hope someone will be
able to help me with.
To consecutively load the session files that I had saved, I wrote a *.py
script which I call from a terminal with: pymol -l my_script.py
The script has the following structure:
from pymol import cmd
cmd.set("security", value=0)
cmd.load("/.../1st_session.pse")
raw_input() # wait until key pressed
cmd.load("/.../2nd_session.pse")
etc...
This alloys me to restore a saved session, then move onto the next one when
desired.
I would however like to make one last improvement, and here again ask for
advice: I want to be able to change the view while observing a session, then
obtain the same view for the next session. I have tried inserting:
my_view=cmd.get_view()
and:
cmd.set_view(my_view)
before and after cmd.load(), and this does work, but usually causes the next
structure to be loaded with its original view and then shifted to the
desired view (the protein appears to jump from one position to the next). I
say usually because this is not always the case even when running the same
file twice. Does anyone know how to avoid this, or how I could combine the
load and set commands as one, so as to load each structure in the right
position?
Thanks again for all the help. It is very much appreciated.
Nadine
Hi Nadine,
USing the scene/.psw files allows you to manipulate the structures as per
usual within the show. It pre4sents the graphical viwer in a full screen
mode without the right hand menu. So deleting molecules (probably a bad
thing)...it would be better if you could just undisplay them. I have just
tried doing this with two separate proteins (see attached) and the scene
function works fine. No sure about scripting.
Hope this helps
J
Nadine Atwood wrote:
Hi,
Thank you for your reply, Joel. I have followed that advice, downloaded
v0.98 and tried using the scene function, but I didn't mention yesterday
that I load and delete several dozen *.pdb files during the original movie
and this appears to be a problem as the scene function does not restore
deleted data. (Basically I want to take a few shots of the first
structure, then move on to the second and delete the first, take a few
more shots and move on to the third, etc. When I call the first scene,
after deleting the first structure, the result is empty.) Do you have any
other suggestions? I also did not specify that I am hoping to find a
solution that will allow the structures to be manipulated as usual (not
just a static representation of the structures at a given time). I do not
know if this is or is not the case when using a *.psw with embedded
scenes.
Would it maybe be possible to write a script containing load commands for
each of the different *.pse (or *.psw - I'm not sure of the difference
between the 2) files, seperated by some kind of "wait until key pressed"
command. If so, what is the second command?
As for the other problem I mentionned, it doesn't happen with v0.98.
Thanks again.
Nadine
Hi Nadine,
To answer the first part, there is a much easier way...use the scene
function in 0.98 version. This allows you to jump between individual
"screenshots". You can then save this as a .psw file and view it as full
screen or embed it in powerpoint. (See my previous post "Pymol scenes to
movies"). Essentaially you set up view 1 and hit append, then view 2 ,
append etc. you can then scroll thru your views.
The second question, can't help.
Cheers
J
Nadine Atwood wrote:
Hi,
I have come across a problem that I cannot find a way around and would
greatly appreciate some help. I have made a movie showing several
protein models and numerous distances to illustrate residue interactions
in different structures. This movie is rather long, and I wanted to make
a very short version containing certain "screenshots" of the original. I
have created *.pse files corresponding to the frames I would want in the
short movie, but cannot find a way of loading these in a script. (I can
view them "manually" by opening them one at a time through the command
line, but that rather defeats the point.) I wanted to load these using
mset and mdo commands, but of course, as soon as I load the first one,
PyMOL's memory returns to the state that was saved and the new movie is
deleted. I suppose I need to save these files in another format, but
have not been able to find anything that seems appropriate.
I have also encountered another small problem that I do not need a
solution to but thought I would mention as it might be a bug (though it
could be due to my very amateurish programming): when running the long
movie (which creates and deletes a large number of distances), if the
movie is stopped and then start again, some distances (I suppose
corresponding to commands given in frames where the movie was stopped)
are not deleted, whereas if the movie is run without interruption, all
distances are handled correctly. (I am using version 0.97)
I am not very computer literate, so a simple explanation would be
fantastic. ;)
Thanks for your advice.
Nadine
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