Re: [PyMOL] 3d plotting in pymol

Hi Amit (and other users),

Here's a script which can be used to put marks on the positions of every 
atom in a selection. There are several types of marks included now, e.g. 
cube, rhombic dodecahedron, tetrahedron, plus and star. Using a matrix 
operator these can be extended a bit, to 2D counterparts for example, or 
to elongated or rotated shapes. I should still include some 
documentation but in brief the usage is as follows:

graph selection = '(all)', shape = 'plus' | 'sphere' | 'star' | 
'tetrahedron' | 'dodecahedron', size = 1, r = 0.10, rgb1 = [1,0,0], rgb2 
= [0,0,1], mtx = [[1,0,0],[0,1,0],[0,0,1]], name = "graph"

Selection should be obvious, as is shape. Size is a relative indicator 
for the size, though at present I haven't fixed things such that a size 
1 tetrahedron matches a size 1 dodecahedron. r is the radius of the 
lines. rgb1 and rgb2 are the start and end color for each line. mtx is 
the matrix operator, which works on the original shape centered around 
the origin (before translation to the point of the atom from the selection).

Hope this already works a bit as wanted. I'll be trying to make it a bit 
better in the future ;)

Cheers,

Tsjerk

Amit Chourasia wrote:

>Tsjerk,
>
>Great I'll look forward to see your script.
>By that time I'll also gain some familiarity with Python.
>
>For spline related stuff I found this in archive.
>set ribbon_trace,1
>This will create ribbons for arbitrary atoms, but they should be seperate
>objects if we dont want them connected by one ribbon.
>
>Have a nice time in Rome. I wish to travel to Venice sometime.
>
>Thanks and Regards
>--Amit
>
>
>
>-----Original Message-----
>From: Tsjerk Wassenaar [mailto:t.a...@ch...]
>Sent: Thursday, May 13, 2004 3:04 AM
>To: am...@sd...
>Subject: Re: [PyMOL] 3d plotting in pymol
>
>
>
>Hi Amit,
>
>This isn't too difficult actually, and I have done something alike
>recently. What it comes down to is to write some python extensions and
>have definitions for the CGO shapes you want to use. Then you can read
>the coordinates for the atoms ( sel =
>cmd.get_selection("selection_string")  and reading coordinates from
>sel.atom[i].coord ) and add these coordinates to your CGO object. Doing
>this for all atoms and loading it back into pymol would give you what
>you want. I'm not completely sure where I have the script I wrote. But I
>can have a look in about a week (when I get back from Rome) and write
>the script if it hasn't been done already (the feature sounds cool
>enough ;) ).
>
>Wouldn't have ideas on the spline at this moment.
>
>Cheers,
>
>Tsjerk
>
>Amit Chourasia wrote:
>
>  
>
>>Hi,
>>I am trying to use pymol as a 3d plotting tool.
>>
>>I have few questions
>>
>>1)Is there a way to add represenation in pymol. ?
>>For instance I would like to see the atom as a triangle or nhedron.
>>I was going through CGO objects that looks promising to what I want to
>>accomplish. What I am looking for is to add represenation module and
>>use them.
>>
>>2)Is there a method to represent a group of atoms connected by cartoon
>>even if the chains are not biologically feasable. What I am looking
>>for is you have bunch of points(atoms) through which the ribbon should
>>pass like a spline curve.
>>
>>Any inputs and pointers would be most appreciated.
>>
>>Thanks
>>--Amit
>>
>>
>>
>>
>>    
>>
>
>
>
>--
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>-- :)
>-- :) 	Tsjerk A. Wassenaar, M.Sc.
>-- :) 	Molecular Dynamics Group
>-- :) 	Dept. of Biophysical Chemistry
>-- :) 	University of Groningen
>-- :) 	Nijenborgh 4
>-- :) 	9747 AG Groningen
>-- :) 	The Netherlands
>-- :)
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>  
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~