pymol-users

[PyMOL] PyMOL script with a parameter ?

[Someone E. <tn...@gm...>]

Hi everyone,

I would like my PyMOL script take a command line parameters, e.g:

pymol get_neighbors.py ALA

How to extract "ALA" from inside my neighbors.py?

Best regards,
Tim

Re: [PyMOL] PyMOL script with a parameter ?

[Matthew B. <mp...@pi...>]

Hi Tim,

You can use two dashes on the command line, like:
pymol -r get_neighbors.py -- ALA

And then access them using sys.argv in your script.

For example: save the following as tmp_pymol.py and run: 'pymol -r 
tmp_pymol.py -- ALA' ( without quotes)

 >>>>
from pymol import cmd
import sys


def foo(string):
         print string
         return

cmd.extend('foo',foo)


if __name__ == '__main__':
         foo(sys.argv[1])

 >>>
Hope this helps,
Matt

On 02/22/2013 10:50 AM, Someone Else wrote:
> Hi everyone,
>
> I would like my PyMOL script take a command line parameters, e.g:
>
> pymol get_neighbors.py ALA
>
> How to extract "ALA" from inside my neighbors.py?
>
> Best regards,
> Tim
>
>
>
>
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[PyMOL] Increase sphere size for heavy element

[Martin H. <ma...@bl...>]

Hi PyMOL users

If I display these coordinates

HETATM   38  C   LIG     2       1.535   2.288  -4.156  1.00  0.00           C
HETATM   39  C   LIG     2       2.284   1.535  -3.066  1.00  0.00           C
HETATM   40  O   LIG     2       3.406   2.362  -2.714  1.00  0.00           O
HETATM   41  C   LIG     2       1.426   1.234  -1.850  1.00  0.00           C
HETATM   42  S   LIG     2      -0.260   0.689  -2.100  1.00  0.00           S
HETATM   43  C   LIG     2       1.886   1.450  -0.593  1.00  0.00           C
HETATM   44  S   LIG     2       0.838   1.262   0.813  1.00  0.00           S
HETATM   45  C   LIG     2       3.318   1.872  -0.336  1.00  0.00           C
HETATM   46  C   LIG     2       4.139   1.803  -1.624  1.00  0.00           C
HETATM   47  W   LIG     2      -1.132  -0.004   0.041  1.00  0.00           W
HETATM   48  O   LIG     2       0.155  -1.665   0.118  1.00  0.00           O
HETATM   49  C   LIG     2       0.721  -3.870  -0.567  1.00  0.00           C
HETATM   50  C   LIG     2       0.384  -2.594  -0.826  1.00  0.00           C
HETATM   51  C   LIG     2      -5.606  -3.611  -1.000  1.00  0.00           C
HETATM   52  O   LIG     2      -6.664  -4.080  -0.564  1.00  0.00           O
HETATM   53  N   LIG     2      -4.607  -4.417  -1.426  1.00  0.00           N

using "Preset/Ball-and-stick", the tungsten atom is drawn with a very 
small radius. Can this radius be increased?

Thanks
Martin

Re: [PyMOL] Increase sphere size for heavy element

[Thomas H. <tho...@sc...>]

Hi Martin,

PyMOL> alter elem W, vdw=2.0
PyMOL> rebuild

Cheers,
  Thomas

Martin Hediger wrote, On 02/26/13 08:38:
> Hi PyMOL users
> 
> If I display these coordinates
> 
> HETATM   38  C   LIG     2       1.535   2.288  -4.156  1.00  0.00           C
> HETATM   39  C   LIG     2       2.284   1.535  -3.066  1.00  0.00           C
> HETATM   40  O   LIG     2       3.406   2.362  -2.714  1.00  0.00           O
> HETATM   41  C   LIG     2       1.426   1.234  -1.850  1.00  0.00           C
> HETATM   42  S   LIG     2      -0.260   0.689  -2.100  1.00  0.00           S
> HETATM   43  C   LIG     2       1.886   1.450  -0.593  1.00  0.00           C
> HETATM   44  S   LIG     2       0.838   1.262   0.813  1.00  0.00           S
> HETATM   45  C   LIG     2       3.318   1.872  -0.336  1.00  0.00           C
> HETATM   46  C   LIG     2       4.139   1.803  -1.624  1.00  0.00           C
> HETATM   47  W   LIG     2      -1.132  -0.004   0.041  1.00  0.00           W
> HETATM   48  O   LIG     2       0.155  -1.665   0.118  1.00  0.00           O
> HETATM   49  C   LIG     2       0.721  -3.870  -0.567  1.00  0.00           C
> HETATM   50  C   LIG     2       0.384  -2.594  -0.826  1.00  0.00           C
> HETATM   51  C   LIG     2      -5.606  -3.611  -1.000  1.00  0.00           C
> HETATM   52  O   LIG     2      -6.664  -4.080  -0.564  1.00  0.00           O
> HETATM   53  N   LIG     2      -4.607  -4.417  -1.426  1.00  0.00           N
> 
> using "Preset/Ball-and-stick", the tungsten atom is drawn with a very 
> small radius. Can this radius be increased?
> 
> Thanks
> Martin

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

[PyMOL] Display style for partial bond

[Martin H. <ma...@bl...>]

Dear PyMOL Users

If you load these coordinates in PyMOL

HETATM    1  W   LIG     1      -1.357  -0.079   0.052  1.00  0.00           W
HETATM    2  C   LIG     1      -0.713  -1.686   1.008  1.00  0.00           C
HETATM    3  C   LIG     1      -0.323  -1.855  -0.270  1.00  0.00           C
HETATM    4  H   LIG     1      -0.664  -2.180   1.970  1.00  0.00           H
HETATM    5  H   LIG     1      -0.441  -2.597  -1.043  1.00  0.00           H

you'll see that a bond between W and C is drawn. However, this is 
supposed to be a transition state, so a dashed bond would be more 
appropriate. Can this somehow be drawn?

Thanks,
Martin

Re: [PyMOL] Display style for partial bond

[Thomas H. <tho...@sc...>]

Hi Martin,

only distance measures can draw dashed lines in PyMOL, so try this:

unbond elem W, elem C
show sticks
show sphere, elem W
distance transbonds, elem W, elem C
hide label
set dash_round_ends, off
set dash_radius, 0.2
set dash_length, 0.4
set dash_gap, 0.15
ray

The dashes will display as nice cylinders when ray traced and also with
the new shader rendering in PyMOL 1.5 (set use_shaders).

Cheers,
  Thomas

Martin Hediger wrote, On 02/26/13 09:57:
> Dear PyMOL Users
> 
> If you load these coordinates in PyMOL
> 
> HETATM    1  W   LIG     1      -1.357  -0.079   0.052  1.00  0.00           W
> HETATM    2  C   LIG     1      -0.713  -1.686   1.008  1.00  0.00           C
> HETATM    3  C   LIG     1      -0.323  -1.855  -0.270  1.00  0.00           C
> HETATM    4  H   LIG     1      -0.664  -2.180   1.970  1.00  0.00           H
> HETATM    5  H   LIG     1      -0.441  -2.597  -1.043  1.00  0.00           H
> 
> you'll see that a bond between W and C is drawn. However, this is 
> supposed to be a transition state, so a dashed bond would be more 
> appropriate. Can this somehow be drawn?
> 
> Thanks,
> Martin

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor