pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Yeping,

Searching for "pymol biomt" gives this page on the pymol wiki:

http://www.pymolwiki.org/index.php/BiologicalUnit

Should have all the information you need.

Best regards,
Folmer



2013/2/28 yp sun <sun...@ya...>

> Dear pymol users:
>
> Usually pymol can show only one chain when you open a pdb file of virus
> particles (such as 2buk,1sva, etc.). I am trying to create the whole virus
> particle and I know it may need applying symmetry operations. And these
> symmetry operation has been given in the pdb files. For example, the follow
> is the symmetry operation of 2buk:
>
> REMARK
> 350
> REMARK 350 GENERATING THE
> BIOMOLECULE
> REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE
> KNOWN
> REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF
> THE
> REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT
> TRANSFORMATIONS
> REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC
> AND
> REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE
> GIVEN.
> REMARK
> 350
>
> But I don't understand how to do symmetry operations. Can pymol do these
> or other software is needed? Please help.
>
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Folmer Fredslund

You are probably looking for this:

http://pymolwiki.org/index.php/Symexp

Or else you can do it in CCP4.
Coordinate utilities -> Edit PDB file ->Use pdbset -> generate chains via
symmetry operations

Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234


2013/2/28 yp sun <sun...@ya...>

> Dear pymol users:
>
> Usually pymol can show only one chain when you open a pdb file of virus
> particles (such as 2buk,1sva, etc.). I am trying to create the whole virus
> particle and I know it may need applying symmetry operations. And these
> symmetry operation has been given in the pdb files. For example, the follow
> is the symmetry operation of 2buk:
>
> REMARK
> 350
> REMARK 350 GENERATING THE
> BIOMOLECULE
> REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE
> KNOWN
> REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF
> THE
> REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT
> TRANSFORMATIONS
> REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC
> AND
> REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE
> GIVEN.
> REMARK
> 350
>
> But I don't understand how to do symmetry operations. Can pymol do these
> or other software is needed? Please help.
>
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear pymol users:
 
Usually pymol can show only one chain when you open a pdb file of virus particles (such as 2buk,1sva, etc.). I am trying to create the whole virus particle and I know it may need applying symmetry operations. And these symmetry operation has been given in the pdb files. For example, the follow is the symmetry operation of 2buk:
 
REMARK 350                                                                      
REMARK 350 GENERATING THE BIOMOLECULE                                           
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
 
But I don't understand how to do symmetry operations. Can pymol do these or other software is needed? Please help.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

Hi Matthias, I can at least try and answer some of your questions:


1.       You can simply click on the command button (rhs side grey window... "Command" "Builder" "Volume") to get back to the command info you want. Alternatively type in your commands into the viewer window and use escape to see the details

2.       At this stage I'm not sure you can generate the volume around your protein. The way to get around this is to generate symmetry related molecules and look at one of those in the unit cell. (Jason will know more)

3.       Best to generate 2fofc and fofc maps in say ccp4 and display these (but not sure if you can use the volume or just the classical mesh)

I too would like to be able to do this to use the great graphics output from  pymol

Hope this helps

Joel

From: Matthias Haffke [mailto:mat...@ho...]
Sent: Wednesday, 27 February 2013 9:17 a.m.
To: pym...@li...
Subject: [PyMOL] How to display .mtz files and work with them

Dear all,

I am having some trouble working with PyMOL and the new feature of loading and displaying .mtz files.
Sorry for the number of questions (and sorry if most seem trivial...), but I couldn't find the answers in the PyMOLWiki and not in the Schrodinger documentations.

PyMOL Version is 1.5.0.5 and it's running on Win7 Prof 64 bit.

1.) When loading a .mtz file, you start with the new volume representation. Options for color gradients, sigma levels, etc. are displayed in a nice graph in the command line window - but the command line is gone and I don't get any feedback about commands I write in PyMOL. How do I turn this graphical representation of the sigma levels & color gradients on and off?
2.) The volume is represented for one unit cell - and for one unit cell only. I would like to display the density just around one molecule in the unit cell or around a symmetry mate OUTSIDE the unit cell - which is the command to do so? Things like "map_trim" don't work (which is not a surprise - I am obviously not displaying a map as one used to do in the older PyMOL versions). You can't align the "group", which is created by loading a .mtz file to a selection or molecule by using the drop down menus or I couldn't find any other way to limit the map to one molecule or one chain in of my .pdb file. Any help on this is greatly appreciated.

3.) What I basically want to do (in other words): Open a .pdb file. Open a .mtz file. Display the electron density at 2.0 sigma around one specific chain or around one specific symmetry mate of my molecule. Can't be that difficult, can it? ;-)

Many thanks for any help!

Matthias

Dear all,

I am having some trouble working with PyMOL and the new feature of loading and displaying .mtz files.
Sorry for the number of questions (and sorry if most seem trivial...), but I couldn't find the answers in the PyMOLWiki and not in the Schrodinger documentations.

PyMOL Version is 1.5.0.5 and it's running on Win7 Prof 64 bit.

1.) When loading a .mtz file, you start with the new volume representation. Options for color gradients, sigma levels, etc. are displayed in a nice graph in the command line window - but the command line is gone and I don't get any feedback about commands I write in PyMOL. How do I turn this graphical representation of the sigma levels & color gradients on and off?
2.) The volume is represented for one unit cell - and for one unit cell only. I would like to display the density just around one molecule in the unit cell or around a symmetry mate OUTSIDE the unit cell - which is the command to do so? Things like "map_trim" don't work (which is not a surprise - I am obviously not displaying a map as one used to do in the older PyMOL versions). You can't align the "group", which is created by loading a .mtz file to a selection or molecule by using the drop down menus or I couldn't find any other way to limit the map to one molecule or one chain in of my .pdb file. Any help on this is greatly appreciated.

3.) What I basically want to do (in other words): Open a .pdb file. Open a .mtz file. Display the electron density at 2.0 sigma around one specific chain or around one specific symmetry mate of my molecule. Can't be that difficult, can it? ;-)

Many thanks for any help!

Matthias


 		 	   		  

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

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

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

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

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
>
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

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

in the most recent version of PyMOL, which can render measurement objects with shaders, you can also use the distance command to get a similar result:

set use_shaders
set dash_gap, 0
distance sele and n. CA, sele and n. CA

Cheers,
  Thomas

On Feb 21, 2013, at 10:11 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi,
> 
> If you want to draw all bonds for all pairs between two selections,
> you can just use bond:
> 
> bond sele and n. ca, sele and n. ca
> 
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Thu, Feb 21, 2013 at 9:19 PM, Robert Campbell
> <rob...@qu...> wrote:
>> Hi Anasuya,
>> 
>> On Thu, 21 Feb 2013 17:10:40 +0530
>> Anasuya Dighe <an...@mb...> wrote:
>> 
>>> 
>>> Hi,
>>> 
>>> I have been trying to use the script draw_links.py at
>>> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links
>>> between each pair of c-alpha atoms present in an atom selection.
>>> Once I load a PDB (1q16.pdb) and make an atom selection, lets say :
>>> PyMOL>select pk1, name CA in resi 5+10+15+12+16 and chain C , on the
>>> PyMOL>command-line in pymol, I
>>> do : PyMOL>run draw_links.py
>>> 
>>> I wanted to visualise links between all pairs of calpha atoms present in
>>> the atom selection, pk1.
>>> However I am unable to do that using draw_links.py
>>> I am doing: PyMOL> draw_links pk1
>>> 
>>> How can I do this using draw_links.py?
>>> Where am I going wrong?
>> 
>> Perhaps the instructions are not clear enough, but the script is not
>> designed to automatically draw links between all pairs of C-alphas in a
>> selection. It expects two different selections and it will draw links
>> between the first residue of each selection and then the second and so on.
>> It doesn't therefore make sense to give it the same selection for both
>> because, in your example, it draws a zero-length link between residue 5 and
>> residue 5, and another between residue 10 and residue 10 and so on.
>> 
>> You will have to run the script multiple times to get the links you want:
>> 
>> draw_links name CA & resi 5 and chain C, name CA  resi 10 and chain C
>> draw_links name CA & resi 5 and chain C, name CA  resi 15 and chain C
>> draw_links name CA & resi 5 and chain C, name CA  resi 12 and chain C
>> 
>> Sorry that it doesn't quite do what you were expecting!  I designed it for
>> the situation where I have two structures that exhibit a conformational
>> change and I wanted to show how the C-alphas were moving so then it made
>> sense to have the two selections be the same atoms, but in different
>> molecules.
>> 
>> Cheers,
>> Rob

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi,

If you want to draw all bonds for all pairs between two selections,
you can just use bond:

bond sele and n. ca, sele and n. ca


Hope it helps,

Tsjerk

On Thu, Feb 21, 2013 at 9:19 PM, Robert Campbell
<rob...@qu...> wrote:
> Hi Anasuya,
>
> On Thu, 21 Feb 2013 17:10:40 +0530
> Anasuya Dighe <an...@mb...> wrote:
>
>>
>> Hi,
>>
>> I have been trying to use the script draw_links.py at
>> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links
>> between each pair of c-alpha atoms present in an atom selection.
>> Once I load a PDB (1q16.pdb) and make an atom selection, lets say :
>> PyMOL>select pk1, name CA in resi 5+10+15+12+16 and chain C , on the
>> PyMOL>command-line in pymol, I
>> do : PyMOL>run draw_links.py
>>
>> I wanted to visualise links between all pairs of calpha atoms present in
>> the atom selection, pk1.
>> However I am unable to do that using draw_links.py
>> I am doing: PyMOL> draw_links pk1
>>
>> How can I do this using draw_links.py?
>> Where am I going wrong?
>
> Perhaps the instructions are not clear enough, but the script is not
> designed to automatically draw links between all pairs of C-alphas in a
> selection. It expects two different selections and it will draw links
> between the first residue of each selection and then the second and so on.
> It doesn't therefore make sense to give it the same selection for both
> because, in your example, it draws a zero-length link between residue 5 and
> residue 5, and another between residue 10 and residue 10 and so on.
>
> You will have to run the script multiple times to get the links you want:
>
> draw_links name CA & resi 5 and chain C, name CA  resi 10 and chain C
> draw_links name CA & resi 5 and chain C, name CA  resi 15 and chain C
> draw_links name CA & resi 5 and chain C, name CA  resi 12 and chain C
>
> Sorry that it doesn't quite do what you were expecting!  I designed it for
> the situation where I have two structures that exhibit a conformational
> change and I wanted to show how the C-alphas were moving so then it made
> sense to have the two selections be the same atoms, but in different
> molecules.
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
> Queen's University,
> Kingston, ON K7L 3N6  Canada
> Tel: 613-533-6821
> <rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada

Hi Anasuya,

On Thu, 21 Feb 2013 17:10:40 +0530
Anasuya Dighe <an...@mb...> wrote:

> 
> Hi,
> 
> I have been trying to use the script draw_links.py at 
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links
> between each pair of c-alpha atoms present in an atom selection.
> Once I load a PDB (1q16.pdb) and make an atom selection, lets say :
> PyMOL>select pk1, name CA in resi 5+10+15+12+16 and chain C , on the
> PyMOL>command-line in pymol, I
> do : PyMOL>run draw_links.py
> 
> I wanted to visualise links between all pairs of calpha atoms present in
> the atom selection, pk1.
> However I am unable to do that using draw_links.py
> I am doing: PyMOL> draw_links pk1
> 
> How can I do this using draw_links.py?
> Where am I going wrong?

Perhaps the instructions are not clear enough, but the script is not
designed to automatically draw links between all pairs of C-alphas in a
selection. It expects two different selections and it will draw links
between the first residue of each selection and then the second and so on.
It doesn't therefore make sense to give it the same selection for both
because, in your example, it draws a zero-length link between residue 5 and
residue 5, and another between residue 10 and residue 10 and so on.

You will have to run the script multiple times to get the links you want:

draw_links name CA & resi 5 and chain C, name CA  resi 10 and chain C
draw_links name CA & resi 5 and chain C, name CA  resi 15 and chain C
draw_links name CA & resi 5 and chain C, name CA  resi 12 and chain C

Sorry that it doesn't quite do what you were expecting!  I designed it for
the situation where I have two structures that exhibit a conformational
change and I wanted to show how the C-alphas were moving so then it made
sense to have the two selections be the same atoms, but in different
molecules.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hi,

I have been trying to use the script draw_links.py at 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links between each
pair of c-alpha atoms present in an atom selection.
Once I load a PDB (1q16.pdb) and make an atom selection, lets say : PyMOL>select
pk1, name CA in resi 5+10+15+12+16 and chain C , on the command-line in pymol, I
do : PyMOL>run draw_links.py

I wanted to visualise links between all pairs of calpha atoms present in the
atom selection, pk1.
However I am unable to do that using draw_links.py
I am doing: PyMOL> draw_links pk1

How can I do this using draw_links.py?
Where am I going wrong?

 - Anasuya Dighe


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Hi Yamei,

There's nothing wrong with your approach. If you like the results, and
they illustrate the point your trying to make, it's good.

Cheers,

Tsjerk

On Thu, Feb 21, 2013 at 9:22 AM, Yamei Yu <ymy...@gm...> wrote:
> Hi All,
>
> I want to generate a stereo image for a structure. I use
> pymol-diaplay-Stereo mode cross-eye stereo and then I ray the figure and
> save the figure.
>
> But previously I notice the others manually rotate the model and manually
> generate the figure. Is there something wrong for the first method?
>
> Thanks !
>
> yamei
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada

Hi All,

I want to generate a stereo image for a structure. I use
pymol-diaplay-Stereo mode cross-eye stereo and then I ray the figure and
save the figure.

But previously I notice the others manually rotate the model and manually
generate the figure. Is there something wrong for the first method?

Thanks !

yamei

Hi Jordan,

distance measurements actually should be multistate by default. Do you
create those with a script and provide the state argument?

# create multi-state measurement (default)
distance test, pk1, pk2, state=0

# create only for state 1
distance test, pk1, pk2, state=1

Cheers,
  Thomas

Jordan Willis wrote, On 02/21/13 06:46:
> Hi everyone,
> 
> I was wondering if there is an easy way to show distances as a
> function of state. As you show each state (using the play button or
> mplay), can you show the distance measurement changing? For now it
> just keeps the distance of the first state shown.  I could script
> this but first would like to ask the users group if there is an
> easier alternative.
> 
> Jordan

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi everyone,

I was wondering if there is an easy way to show distances as a function of state. As you show each state (using the play button or mplay), can you show the distance measurement changing? For now it just keeps the distance of the first state shown.  I could script this but first would like to ask the users group if there is an easier alternative.

Jordan

Unless the values have changed since I last checked the documentations, 
by default pymol contours maps at 1.0 sigma and coot defaults to 1.5 
sigma (for non-difference maps).

Pete

Yarrow Madrona wrote:
> Hi,
> 
> When I display ccp4 maps in pymol they look a bit larger than I am used to
> seeing in coot for a given sigma setting. Is it common for users to
> increase the sigma setting when displaying maps in pymol?
> 
> 
> 

On Wed, Feb 20, 2013 at 2:21 PM, Yarrow Madrona <ama...@uc...> wrote:
> When I display ccp4 maps in pymol they look a bit larger than I am used to
> seeing in coot for a given sigma setting. Is it common for users to
> increase the sigma setting when displaying maps in pymol?

Have you tried:

set normalize_ccp4_maps = 0

?

-Nat

Hi,

When I display ccp4 maps in pymol they look a bit larger than I am used to
seeing in coot for a given sigma setting. Is it common for users to
increase the sigma setting when displaying maps in pymol?



-- 
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

Hi all,

I am a newbie in Linux, and recently installed Coot, Pymol and VMD on
Ubuntu 12.04. It took me a while to figure out a strange conflict among
them on my machine. If I remove the mesa-swx11 package, Coot becomes
crazily slow. However, if I include that package, which requires the remove
of mesa-glx, the backgrounds of Pymol and VMD becomes transparent, and you
can barely see the molecule.

Does anyone have some suggestions?

Thank you so much!

Best,
Chen

Thank you, Jason. I have completely missed this functionality!

Vitaly

On Mon, Feb 18, 2013 at 12:34 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi Vitaly,
>
> In our later versions of PyMOL there's a setting called "edit_light" that
> controls which light may be moved by the mouse in 3-button Lights Mode. To
> enable 3-button Lights Mode, just click Mouse > 3-Button Lights. Use
> shift+mouse to move the light around.
>
> To control which lights are being manipulated:
>
> # let there be 3 lights
>
> set light_count, 3
>
> # move the second specular light
>
> set edit_light, 2
>
> Now, in 3-button Lights mode, the mouse will move light 2.
>
> The default light is ambient which cannot be moved. If you have 3 lights on
> (ambient and two specular), then you can move the two specular two lights by
> setting edit_light to 1 or 2.
>
> Cheers,
>
> -- Jason
>
>
> On Sun, Feb 17, 2013 at 12:22 AM, V.V. <vv...@gm...> wrote:
>>
>> Occasionally I need to play around with the number of lights and their
>> vectors to get nice rendering. It's not something I do often, so every
>> time I need to scour through the mailing list to recall Pymol
>> definitions of light sources (the page on "light" badly needs
>> updating). So... Can someone write a script that would grab the light
>> data from the settings and present it as a separate object? A reverse
>> action, where dragging the points of the light vector would update the
>> "lightX" values would also be nice.
>>
>> Thank you,
>> Vitaly
>>
>>
>> ------------------------------------------------------------------------------
>> The Go Parallel Website, sponsored by Intel - in partnership with Geeknet,
>> is your hub for all things parallel software development, from weekly
>> thought
>> leadership blogs to news, videos, case studies, tutorials, tech docs,
>> whitepapers, evaluation guides, and opinion stories. Check out the most
>> recent posts - join the conversation now.
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>
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi Vitaly,

In our later versions of PyMOL there's a setting called "edit_light" that
controls which light may be moved by the mouse in 3-button Lights Mode. To
enable 3-button Lights Mode, just click Mouse > 3-Button Lights. Use
shift+mouse to move the light around.

To control which lights are being manipulated:

# let there be 3 lights

set light_count, 3

# move the second specular light

set edit_light, 2

Now, in 3-button Lights mode, the mouse will move light 2.

The default light is ambient which cannot be moved. If you have 3 lights on
(ambient and two specular), then you can move the two specular two lights
by setting edit_light to 1 or 2.

Cheers,

-- Jason


On Sun, Feb 17, 2013 at 12:22 AM, V.V. <vv...@gm...> wrote:

> Occasionally I need to play around with the number of lights and their
> vectors to get nice rendering. It's not something I do often, so every
> time I need to scour through the mailing list to recall Pymol
> definitions of light sources (the page on "light" badly needs
> updating). So... Can someone write a script that would grab the light
> data from the settings and present it as a separate object? A reverse
> action, where dragging the points of the light vector would update the
> "lightX" values would also be nice.
>
> Thank you,
> Vitaly
>
>
> ------------------------------------------------------------------------------
> The Go Parallel Website, sponsored by Intel - in partnership with Geeknet,
> is your hub for all things parallel software development, from weekly
> thought
> leadership blogs to news, videos, case studies, tutorials, tech docs,
> whitepapers, evaluation guides, and opinion stories. Check out the most
> recent posts - join the conversation now.
> http://goparallel.sourceforge.net/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120