[PyMOL] Pymol and Matlab

2004-04-08 Thread Zach
Hello to all,

I have created a GUI for a particular application I am
developing in Matlab. I would love to be able to call 
Pymol and operate it from within this GUI.

My GUI does certain calculations on protein based structures and
I do need to visualize the results; in particular, I would
be interested in residue selection and their display over a
cartoon of the protein. Has anyone interfaced Matlab and
Pymol and can give me a push in the right direction to
do this?

I know I could create a script and load it from PyMol but
this would not be the best solution. Is PyMol for Win DDE
capable?

Thanks a lot for your help!

Zach Fernandez



[PyMOL] Re: Pymol debian package

2004-07-30 Thread Zach
Hello Vladimir,

May I request you turn off your virtual cards that come as
an attachment to every message you send to the list? I already
have a small collection of them :) Thanks.

Zach




[PyMOL] Questions about ray-tracing

2004-10-05 Thread Zach
Hello to all,

I am trying to ray trace a picture using pymol and I have a couple of questions:

a) I am using a cylindrical helix representation. Some of these helices have 
side
chains sticking out of them represented as sticks. The connection between the
alpha carbon (within the helix) and the beta atom (the first on the side chain) 
is
not connected and the residue seems to float. I know I can change the radius
of the cylinders through the cartoon_helix_radius setting but this would imply
making my helices fatter and I do not want to do this. As a matter of fact, what
I would like to do is to decrease the radii of the helices so that I can 
unclutter
the
picture but this would make the problem of floating residues even worse.
What can I do?

b) I would like to know how I can know the position of my light source with 
respect
to the object I am trying to render. I know I can change the position through 
the
light setting but I am not sure where it is located or what effect I will get by
changing
the coordinates of the light source. Trial and error is proving to be a 
difficult
choice
as I am not sure what I am doing.

Any help is really appreciated!

Zach




[PyMOL] cmd.translate

2009-06-29 Thread zach powers
Hi,

I have been having some trouble with teh cmd.translate syntax/


I have tried variations on the following:

 cmd.translate([3.3,0,0], %s%taqeven)

including
 cmd.translate('[3.3,0,0]', %s%taqeven)

and

cmd.translate(3.3,0,0, %s%taqeven)


I still always get the following error message:
Error: bad vector.
Traceback (most recent call last):
   File /usr/lib/python2.6/site-packages/pymol/parsing.py, line 455, 
in run_file
 execfile(file,global_ns,local_ns)
   File ../Desktop/02_test.py, line 66, in module
 cmd.translate(3.3,0,0, %s%taqeven)
   File /usr/lib/python2.6/site-packages/pymol/editing.py, line 1464, 
in translate
 raise pymol.CmdException


I am sure this is a simple syntax issue but I am unsure of how to write 
the vector into the cmd.tranlate format.

any help would be appreciated.

thanks
zach cp

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[PyMOL] Scene/Mview question

2010-02-24 Thread Zach Charlop-Powers
Hello Pymol-ers,

I am trying to script pymol to make some movies. I would like to:
1) move the molecules around and save their states somehow (as a state or
scene or something to that effect). After that, I would like to be able to
2) move the camera around independently of the molecules to give a nice
effect.

You can see below that I am able to do the first part of this. However when
i use either scene command (in use) or the mview command (commented out)
I run into the same problems: My camera  position seems to be locked so i
can no longer use the positioning and interpolation  functions that Warren
and others worked so hard to put together. I have been playing with this for
a while and can't figure out a solution. I am hoping someone may have some
hints on how to proceed.


thanks,
zach cp

grad student
mount sinai school of medicine.


# setup PyMOL for movies
reinitialize
set movie_auto_interpolate, off
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
config_mouse three_button_motions, 1

# download the complex and set it up
fetch 1yfg.pdb, trna
orient
rotate z,60, trna

# make an array of the molecules
python
s = range(1,7)
for x in s:
cmd.copy(trna%s %x, trna)
cmd.hide(lines, trna)
cmd.translate([0,-60,0], trna)
cmd.origin(trna)
s = range(1,7)
for x in s:
cmd.rotate(z, %d %(60*x), trna%s %x)
cmd.hide(lines ,trna%s %x)
cmd.show(cartoon ,trna%s %x)
cmd.origin(trna)
cmd.zoom()
python end


# overview of the scene
frame 1
mview store
orient


python
for x in range(360):
  cmd.madd(1 x1); cmd.frame(1000);
  cmd.rotate(y, 1.0, object=trna1)
  cmd.rotate([-1.4,1,0], 1.0, object=trna2)
  cmd.rotate([-1.4,-1,0], 1.0, object=trna3)
  cmd.rotate(y, 1.0, object=trna4)
  cmd.rotate([1.4,-1,0], 1.0, object=trna5)
  cmd.rotate([1.4,1,0], 1.0, object=trna6)
  #cmd.mview(store, object=trna1)
  #cmd.mview(store, object=trna2)
  #cmd.mview(store, object=trna3)
  #cmd.mview(store, object=trna4)
  #cmd.mview(store, object=trna5)
  #cmd.mview(store, object=trna6)
  #cmd.mview(reinterpolate)
  cmd.scene(new,store)
python end

frame 180
set_view (\
 0.769429266,   -0.001453266,0.638730288,\
-0.483805567,0.651568949,0.584285855,\
-0.417025983,   -0.758588016,0.500633180,\
 0.0,0.0, -635.205078125,\
   -42.521865845,   33.457977295,   19.863151550,\
   530.689270020,  739.720764160,  -20.0 )
mview store

mview interpolate
mview reinterpolate

mplay
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