[PyMOL] Pymol and Matlab
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] Ball & Stick representation
Hello to all, I have a protein that contains a substrate and for which I want to create a picture. For the substrate I would like to use a ball and stick representation such that the spheres are colored by atom type and the sticks are on a single color. My problem is that I have not been able to give different color schemes to the sticks and spheres. How do I do that? Any help is greatly appreciated. Thanks, Zach
[PyMOL] Re: Pymol debian package
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
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
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
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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Re: [PyMOL] cmd.translate
Ah! taqeven is a list and I am cycling through the list to translate
each member. I incorrectly thought the problem was in the vector
format, not the variable.
The final working version is:
cmd.translate("[3.3,0,0]", "%s"%taqeven[y]) where y is the position in
the list i am cycling through.
thank you Andreas.
thank you Warren.
best
zach cp
On 06/29/2009 01:26 PM, Andreas Förster wrote:
> Assuming taqeven is the name of the object you want to translate, use
>
> cmd.translate("[3.3,0,0]", "taqeven")
>
>
> Andreas
>
>
>
> zach powers wrote:
>> 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
>> 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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>>
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[PyMOL] Scene/Mview question
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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