Re: [PyMOL] PyMol Question

[Spencer Bliven]

Mohsen–

set transparency , .5, sele

Cheers,
Spencer

On Tue, Nov 3, 2015 at 3:18 AM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:

> Hi there,
>
>
>
> I was wondering how I can make the surface of a selected part of a protein
> transparent? I tried transparency command, but, I came up with a message
> that “transparency” was not found.
>
>
>
> Thank you
>
>
> --
>
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Re: [PyMOL] pymol question

[Tsjerk Wassenaar]

Hi,

You can draw a CGO circle in the yz plane using:

x1,y1,z1 = -0.1, 0, 0 # start point
r1,g1,b1 = 1,0,0 # color (red)
x2,y2,z2 = 0.1, 0, 0 # end point
r2,g2,b2 = 1,1,0 # color (yellow)
radius = 10
cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2,
g2, b2 ], cylinder1 )

To make it transparent, change it to

cmd.load_cgo( [ 25.0, 0.25, 9.0, x1, y1, z1, x2, y2, z2, radius, r1,
g1, b1, r2, g2, b2 ], cylinder1 )

The 9.0 stands for CYLINDER, but you'd need to 'from pymol.cgo import
*' to be able to use the keywords. Likewise, 25.0 stands for ALPHA,
controlling the transparency. Note that the cylinder may not look
quite round. It will do when you raytrace it. I couldn't find a
setting for cgo display quality...

Anyway, it may be that Micheals suggestion is better, but since the
question was for a cylinder... And with a bit of Python scripting such
a circle could be drawn with a given center and normal axis.

Hope it helps,

Tsjerk

On Tue, Jul 7, 2009 at 12:54 AM, Michael
Lernermglerner+sourcefo...@gmail.com wrote:
 I'm sure there's a way to actually draw a circle, but for your particular
 use it might be better to use a sphere. If you're comfortable with python
 scripting, you can use CGO objects. If not, you might do something like
 this:

 fetch 1hhp
 create thing, resi 24 and name ca # create a new object from some single
 atom selection
 alter thing, vdw=10.0 # set desired radius
 rebuild # necessary if spheres have already been shown
 show spheres, thing
 alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords
 set sphere_transparency, 0.5, thing # make it transparent
 zoom
 ray

 you can also use something like select + within to select all residues
 within a cutoff, but I got the impression you wanted a nice visualization.


 Hope that helps,

 -michael

 On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen owe...@marshall.edu
 wrote:

 Does anyone know how to draw a circle with a given radius in pymol? I have
 a distance that I want to use to see what residues lie on the end of that
 radius, but I have no idea how to write the command to draw the circle.
 Could someone help me please?


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Re: [PyMOL] pymol question

[Michael Lerner]

I'm sure there's a way to actually draw a circle, but for your particular
use it might be better to use a sphere. If you're comfortable with python
scripting, you can use CGO objects. If not, you might do something like
this:

fetch 1hhp
create thing, resi 24 and name ca # create a new object from some single
atom selection
alter thing, vdw=10.0 # set desired radius
rebuild # necessary if spheres have already been shown
show spheres, thing
alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords
set sphere_transparency, 0.5, thing # make it transparent
zoom
ray

you can also use something like select + within to select all residues
within a cutoff, but I got the impression you wanted a nice visualization.


Hope that helps,

-michael

On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen
owe...@marshall.eduwrote:

 Does anyone know how to draw a circle with a given radius in pymol? I have
 a distance that I want to use to see what residues lie on the end of that
 radius, but I have no idea how to write the command to draw the circle.
 Could someone help me please?


 --

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IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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Re: [PyMOL] PyMol question?

[Tsjerk Wassenaar]

Hi,

You can do this using alter_state:

alter_state 1,selection,(x,y,z) =
  (a11*x+a12*y+a13*z+d1, a21*x+a22*y+a23*z+d2,
a31*x+a32*y+a33*z+d3)

where a11-a33 are the matrix elements (check whether they have to be
transposed) and d1-d3 are the elements of the shift vector.

It may be convenient to make this a function which you can load at
startup time (especially if you have to do this many times). For
example, paste the following in a file mtransform.py:

from pymol import cmd

def mtransform( selection=all, matrix=[[1,0,0],[0,1,0],[0,0,1],[0,0,0]] ):
   if ( len(matrix) == 3 ): # In this way it is also valid to give a
3x3 matrix for rotation only
   matrix.append( [0,0,0] )
   a11, a12, a13 = matrix[0][0], matrix[0][1], matrix[0][2]
   a21, a22, a23 = matrix[1][0], matrix[1][1], matrix[1][2]
   a31, a32, a33 = matrix[2][0], matrix[2][1], matrix[2][2]
   d1,  d2,  d3  = matrix[0][0], matrix[0][1], matrix[0][2]
   cmd.alter_state( 1, selection, (x,y,z) = (%f*x+%f*y+%f*z+%f,
%f*x+%f*y+%f*z+%f, %f*x+%f*y+%f*z+%f ) %
(a11,a12,a13,d1,a21,a22,a23,d2,a31,a32,a33,d3)

#

Of course it could be done more efficiently, better looking, but that
is left as an exercise for the reader ;) (Think of changing
coordinates directly, adding an option to make a copy of the selection
first, and parse a string for the matrix, such that you can use
cmd.extend and can run the command using:

mtransform all, [[0,1,0],[-1,0,0],[0,0,1],[3,1,2]]

rather than:

mtransform(all, [[0,1,0],[-1,0,0],[0,0,1],[3,1,2]])

which is the way to invoke the command with the given code.

Hope this helps,

Tsjerk

On 6/30/06, Peter Adrian Meyer pa...@cornell.edu wrote:

The easiest way I'm aware of to do this would be to use the ccp4 program
pdbset, but there are numerous other ways/programs that will do this (if
pymol has this capacity, I'm not aware of it; but someone else will
correct me).

Pete

snip

 I've been looking through the PyMol reference and wiki page and I can't
find a command for moving a molecule through a matrix, I
 would like to move one pdb onto the other using the info below. Is
there such a command?
 ## MATRICES: UX+T is the least-squares superimposition of STRID2 (X)
onto STRID1
   NR. STRID1 STRID2   U(.,1)U(.,2)U(.,
 3) T(.)
1: 9506-A 1risU(1,.)  -0.230692 -0.010007
 -0.972975   50.701385
1: 9506-A 1risU(2,.)   0.443459  0.888979
 -0.114287   31.716473
1: 9506-A 1risU(3,.)   0.866098 -0.457839
 -0.200643   26.479412



Pete Meyer
Fu Lab
BMCB grad student
Cornell University





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University of Groningen
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9747AG Groningen, The Netherlands
+31 50 363 4336

Re: [PyMOL] PyMol question?

[William Scott]

Hi Mark:

Most likely there is, but I don't know the answer to your question.  
I'm posting this to the pymol users list (via cc) so hopefully  
someone else will know the answer.


I trust all is going well for you.

Bill


On Jun 30, 2006, at 8:19 AM, Mark Collins wrote:


Hi Bill,

I've been looking through the PyMol reference and wiki page and I  
can't find a command for moving a molecule through a matrix, I  
would like to move one pdb onto the other using the info below. Is  
there such a command?


## MATRICES: UX+T is the least-squares superimposition of STRID2  
(X) onto STRID1
  NR. STRID1 STRID2   U(.,1)U(.,2)U(., 
3) T(.)
   1: 9506-A 1risU(1,.)  -0.230692 -0.010007  
-0.972975   50.701385
   1: 9506-A 1risU(2,.)   0.443459  0.888979  
-0.114287   31.716473
   1: 9506-A 1risU(3,.)   0.866098 -0.457839  
-0.200643   26.479412


Thanks Mark

Re: [PyMOL] PyMol question?

[Peter Adrian Meyer]

The easiest way I'm aware of to do this would be to use the ccp4 program
pdbset, but there are numerous other ways/programs that will do this (if
pymol has this capacity, I'm not aware of it; but someone else will
correct me).

Pete

snip

 I've been looking through the PyMol reference and wiki page and I can't
find a command for moving a molecule through a matrix, I
 would like to move one pdb onto the other using the info below. Is
there such a command?
 ## MATRICES: UX+T is the least-squares superimposition of STRID2 (X)
onto STRID1
   NR. STRID1 STRID2   U(.,1)U(.,2)U(.,
 3) T(.)
1: 9506-A 1risU(1,.)  -0.230692 -0.010007
 -0.972975   50.701385
1: 9506-A 1risU(2,.)   0.443459  0.888979
 -0.114287   31.716473
1: 9506-A 1risU(3,.)   0.866098 -0.457839
 -0.200643   26.479412



Pete Meyer
Fu Lab
BMCB grad student
Cornell University