pymol-users Mailing List for PyMOL Molecular Graphics System

Hi all,

This is neat enough that I bet it gets implemented (relatively) soon.
If someone would like to, please file this on the open-source tracker.
I'll update the case when it's done.

Cheers,

-- Jason

On Wed, Aug 31, 2011 at 11:11 AM, Arne Dieckmann
<adi...@go...> wrote:
> Hi Shiven,
>
> thanks a lot, but this is not really what I was looking for. I would like to have a new representation or a script that I can load from within python. Anyway, for some special cases I might have a look at the Blender option.
>
>
> Best,
> Arne
>
>
> On Aug 31, 2011, at 7:01 AM, Shivender Shandilya wrote:
>
>> Hi Arne,
>>
>> If you are familiar with Blender, you could setup a bump-map or other texture(s) and apply it to any/all atoms.
>>
>> Here's how you can get your structure into Blender:
>> http://pymolwiki.org/index.php/Blender
>>
>> Good luck!
>>
>> Best,
>> Shiven
>>
>>
>> On Aug 30, 2011, at 5:37 PM, Arne Dieckmann wrote:
>>
>>> Hi all,
>>>
>>> I would be interested in creating custom textures for spheres in pymol. More explicitely, I would like to draw two curved lines onto every sphere. Is there any way I can that except placing CGO-objects on every atom?
>>>
>>>
>>> Thanks a lot,
>>> Arne
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Special Offer -- Download ArcSight Logger for FREE!
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>>
>>
>
>
> ------------------------------------------------------------------------------
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> Finally, a world-class log management solution at an even better
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>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

Hi Shiven, 

thanks a lot, but this is not really what I was looking for. I would like to have a new representation or a script that I can load from within python. Anyway, for some special cases I might have a look at the Blender option. 


Best, 
Arne


On Aug 31, 2011, at 7:01 AM, Shivender Shandilya wrote:

> Hi Arne,
> 
> If you are familiar with Blender, you could setup a bump-map or other texture(s) and apply it to any/all atoms.
> 
> Here's how you can get your structure into Blender:
> http://pymolwiki.org/index.php/Blender
> 
> Good luck!
> 
> Best,
> Shiven
> 
> 
> On Aug 30, 2011, at 5:37 PM, Arne Dieckmann wrote:
> 
>> Hi all, 
>> 
>> I would be interested in creating custom textures for spheres in pymol. More explicitely, I would like to draw two curved lines onto every sphere. Is there any way I can that except placing CGO-objects on every atom? 
>> 
>> 
>> Thanks a lot, 
>> Arne
>> 
>> 
>> ------------------------------------------------------------------------------
>> Special Offer -- Download ArcSight Logger for FREE!
>> Finally, a world-class log management solution at an even better 
>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>> download Logger. Secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsisghtdev2dev
>> _______________________________________________
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> 
> 

Hello Shiven,

thanks for the Blender tip!

Cheers!


 


---
 Ricardo O. S. Soares , PhD Student.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.






>________________________________
>De: Shivender Shandilya <shi...@gm...>
>Para: Arne Dieckmann <adi...@go...>
>Cc: pym...@li...
>Enviadas: Quarta-feira, 31 de Agosto de 2011 11:01
>Assunto: Re: [PyMOL] custom textures
>
>Hi Arne,
>
>If you are familiar with Blender, you could setup a bump-map or other texture(s) and apply it to any/all atoms.
>
>Here's how you can get your structure into Blender:
>http://pymolwiki.org/index.php/Blender
>
>Good luck!
>
>Best,
>Shiven
>
>
>On Aug 30, 2011, at 5:37 PM, Arne Dieckmann wrote:
>
>> Hi all, 
>> 
>> I would be interested in creating custom textures for spheres in pymol. More explicitely, I would like to draw two curved lines onto every sphere. Is there any way I can that except placing CGO-objects on every atom? 
>> 
>> 
>> Thanks a lot, 
>> Arne
>> 
>> 
>> ------------------------------------------------------------------------------
>> Special Offer -- Download ArcSight Logger for FREE!
>> Finally, a world-class log management solution at an even better 
>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>> download Logger. Secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsisghtdev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
>------------------------------------------------------------------------------
>Special Offer -- Download ArcSight Logger for FREE!
>Finally, a world-class log management solution at an even better 
>price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>download Logger. Secure your free ArcSight Logger TODAY!
>http://p.sf.net/sfu/arcsisghtdev2dev
>_______________________________________________
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>Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>Archives: http://www.mail-archive.com/pym...@li...
>
>
>

Hi Arne,

If you are familiar with Blender, you could setup a bump-map or other texture(s) and apply it to any/all atoms.

Here's how you can get your structure into Blender:
http://pymolwiki.org/index.php/Blender

Good luck!

Best,
Shiven


On Aug 30, 2011, at 5:37 PM, Arne Dieckmann wrote:

> Hi all, 
> 
> I would be interested in creating custom textures for spheres in pymol. More explicitely, I would like to draw two curved lines onto every sphere. Is there any way I can that except placing CGO-objects on every atom? 
> 
> 
> Thanks a lot, 
> Arne
> 
> 
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better 
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> 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 Arne,

Unfortunately that is not possible. You could export the scene to
POV-Ray format and make the modifications there.

Cheers,

Tsjerk

On Tue, Aug 30, 2011 at 11:37 PM, Arne Dieckmann
<adi...@go...> wrote:
> Hi all,
>
> I would be interested in creating custom textures for spheres in pymol. More explicitely, I would like to draw two curved lines onto every sphere. Is there any way I can that except placing CGO-objects on every atom?
>
>
> Thanks a lot,
> Arne
>
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> 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
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hi all, 

I would be interested in creating custom textures for spheres in pymol. More explicitely, I would like to draw two curved lines onto every sphere. Is there any way I can that except placing CGO-objects on every atom? 


Thanks a lot, 
Arne

Hi PyMOLers.

I was tired, not to be able to load a dye molecule, and put it next to my
protein with full control.
Especially, I needed to be able to rotate my dye molecule around a line,
which is not supported in PyMOL.
So I investigated the PyMOL TTT matrixes, and made some handy scripts.

Check the scripts kit out: rotkit.py <" rel="nofollow">http://pymolwiki.org/index.php/Rotkit>

I have made there a little tutorial to take one through the functions.

*Available in PyMOL*

   - rotateline(Pos1,Pos2,degangle,molecule): "Pos1->Pos2" define a line
   whereabout "molecule" will be rotated "degangle" degrees *rotateline
   Pos1=P513C_CA, Pos2=P513C_CB, degangle=5, molecule=Atto590* *rotateline
   Pos1=dyeatom87, Pos2=dyeatom85, degangle=10, molecule=Atto590*
   - mutate(molecule,chain,resi,target="CYS",mutframe="1"): Mutate a
   /molecule//chain/resi into a target, and selecting most probable frame 1
   *mutate 1HP1, chain=A, resi=515, target=CYS, mutframe=1*
   - toline(Pos1,Pos2,atom,molecule,dist=1): Translate molecule atom, 1
   angstrom away in the same direction Pos1->Pos2 specify *toline
   Pos1=P513C_CA, Pos2=P513C_CB, atom=dyeatom87, molecule=Atto590, dist=3*

*Available through PyMOL mini shell*

   - printMat(matrix): prints the TTT matrix in a readable format. (4X4)
   - getxyz(Sel): output is a list [x,y,z] in float. The input can be a
   list, a string(list) or a selection.
   - vector(Sel1,Sel2): Finds the vector between points. Gets the xyz list
   from getxyz, so input can be anything.
   - vectorstr(vector): turn a vector in list format into string. No real
   function actually.
   - transmat(vector,dist=1): Makes a TTT translation matrix for according
   to the input vector. The vector is multiplied with dist.
   - unitvector(vector): Make a vector a unitvector.
   - radangle(angle): Convert degree to radians. Not that all input are
   assumed to be in degrees, and are converted automatically.
   - rotmat(angle,vectornorm,pointcoord): This function is the most
   important. That makes the TTT matrix that rotates a molecule around a
   normalized vector, which goes through a coordinate point.
   - crossprod(Vector1, Vector2): Makes a crossproduct between two vectors
   - crosspoint(Pos1, crossprod): Returns the endpoint for the Position plus
   the crossproduct vector. Suitable if one would like to rotate around a
   crossvector.


Best
Troels Emtekær Linnet

Dear All,

Thanks a lot for your help. I am able to do now :-)

Cheers,

-Suda

Try this.

import subprocess
# propkaprocess
# shell=False controls that the process remains in the same thread.
propkap = Popen(['propka'],
                  stdin=open('1pdb.pdb', 'r')
                  stdout=subprocess.PIPE
                  stderr=subprocess.PIPE
                  shell=False)
propkap.stdout.read()


Martin Hediger





On 28.08.11 19:24, Troels Emtekær Linnet wrote:
> Thanks Jason. But still no luck...
>
> So, I changed it to a python script. It was important that the ending 
> of the file is .py :-)
> But, I can see from the list of objects, that PyMOL fetches the next 
> protein before it has finished propka first.
> Does pymol run external script in some kind of asynchron mode as default?
>
> ---------------------------------
> import pymol
> from pymol import cmd
> import os
> os.chdir("/homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/predict_reactivity/Comparison/Match")
>
> cmd.cartoon("auto")
> cmd.set("cartoon_fancy_helices","1")
> cmd.bg_color("white")
> cmd.set("fog","0")
> cmd.set("cartoon_transparency","0.7")
> cmd.set("auto_zoom","off")
>
> import propka
> #resis = 
> [["1bj6","36"],["1bj6","39"],["1bj6","49"],["1ag1","14"],["1gu9","133"],["1gu9","130"],["1omu","56"],["1khg","273"],["2trx","35"],
> #["1tde","32"],["1tde","35"],["2ovo","56"],["1m8b","56"],["1hic","39"],["1m8c","56"],["1ppo","25"],["1qlp","232"]]
> resis = [["1ppo","25"],["1qlp","232"]]
> i = 0
> results = []
> for p,r in resis:
>     cmd.fetch(p,async="0")
>     cmd.refresh()
>     # When we import a module in python, the namespace is normally: 
> module.function
>     # And we see, that propka expect resi to be in "str" format.
>     # And we don't want the logtime function
>     pkavalues = propka.propka(molecule=p,resi=r,resn="CYS",logtime=i)
>     results.append(pkavalues)
>     cmd.refresh()
>     i = i + 1
> cmd.zoom("all")
> print results[0]
> print results[1]
>
>
>
> 2011/8/28 Jason Vertrees <jas...@sc... 
> <mailto:jas...@sc...>>
>
>     Hi Troels,
>
>     In PyMOL, it you try the following, what happens for you?
>
>     # make this a file called chill.py
>     import time
>     def chill():
>        rightThisSecond = time.time()
>        i = 0
>        while time.time() < rightThisSecond + 3.0:
>            i+=1
>        print "The farthest I could count in 3 seconds was %d." % i
>
>     # make this a file called troels.py
>     import pymol
>     from pymol import cmd
>     import chill
>     resis = [ ["1bj6","36"], ["1bj6","39"], ["1bj6","49"],
>              ["1ag1","14"],
>              ["1gu9","133"], ["1gu9","130"], ]
>     for p,r in resis:
>        # fetch a protein
>        cmd.fetch(p,async=0)
>        print "-- Fetched %s" % p
>        # do something slow
>        chill.chill()
>        # some post processing
>        print "%s has %d atoms" % (p, cmd.count_atoms(p))
>        print "%s/%s has %d atoms" % (p, r, cmd.count_atoms("%s and i.
>     %s" % (p,r)))
>        cmd.delete(p)
>        print "-- Deleted protien"
>
>
>     Now load PyMOL and try,
>
>     run ~/troels.py
>
>     Does PyMOL wait for the chill calls to finish? The idea is, wrap your
>     call in a module/file and import it. Then, call through that function.
>
>     It's about 3 AM my time and I'm sure there's a better solution--but
>     this might work for now.
>
>     Cheers,
>
>     -- Jason
>
>
>
>
>     2011/8/26 Troels Emtekær Linnet <tl...@gm...
>     <mailto:tl...@gm...>>:
>     > Well, I cant get it to work.
>     > Pymol speeds ahead of calling propka.propka
>     >
>     > Can you give an example of subprocess?
>     > ---------------------------
>     >
>     > import propka
>     >
>     > python
>     > resis = [["1bj6","36"],["1bj6","39"]]
>     > #resis =
>     >
>     [["1bj6","36"],["1bj6","39"],["1bj6","49"],["1ag1","14"],["1gu9","133"],["1gu9","130"],["1omu","56"],["1khg","273"],["2trx","35"],
>     >
>     #["1tde","32"],["1tde","35"],["2ovo","56"],["1m8b","56"],["1hic","39"],["1m8c","56"]]
>     > i = 0
>     > for resi in resis:
>     >     cmd.fetch(resi[0],async="0")
>     >     cmd.refresh()
>     >     # When we import a module in python, the namespace is normally:
>     > module.function
>     >     # And we see, that propka expect resi to be in "str" format.
>     >     # And we don't want the logtime function
>     >     propka.propka(molecule=resi[0],resi=resi[1],logtime=i)
>     >     cmd.refresh()
>     >     i = i + 1
>     > python end
>     > zoom all
>     >
>     >
>     >> hth
>     >> Martin
>     >>
>     >> On 23.08.11 10:48, Troels Emtekær Linnet wrote:
>     >>
>     >> Hi.
>     >>
>     >> If one writes a pymol script, and calls an external function,
>     the pymol
>     >> script continues its operation before waiting for the "success"
>     of the
>     >> external function.
>     >>
>     >> Is it possible to give a keyword, so it "waits" for the
>     external function
>     >> before preceding?
>     >>
>     >> Kind of the same function with:
>     >> fetch 1hp1, async=0
>     >>
>     >> Best
>     >> Troels
>     >>
>     >>
>     >>
>     ------------------------------------------------------------------------------
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>     >>
>     >>
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>     >>
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>     <mailto:PyM...@li...>)
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>     http://www.mail-archive.com/pym...@li...
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > EMC VNX: the world's simplest storage, starting under $10K
>     > The only unified storage solution that offers unified management
>     > Up to 160% more powerful than alternatives and 25% more efficient.
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>     http://www.mail-archive.com/pym...@li...
>     >
>
>
>
>     --
>     Jason Vertrees, PhD
>     PyMOL Product Manager
>     Schrodinger, LLC
>
>     (e) Jas...@sc...
>     <mailto:Jas...@sc...>
>     (o) +1 (603) 374-7120 <tel:%2B1%20%28603%29%20374-7120>
>
>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
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> Archives: http://www.mail-archive.com/pym...@li...

Dear Suda,
cealign can be used to do structure based superposition
PyMOL> cealign target, mobile
However, it's a pair-wise based alignment. You have to align two 
structures each time.
Hope this helps.

Zhijian Xu

Suda Ravindran wrote:
> Hi,
>
> I would like to know how to do structure based superposition using 
> PyMol for 3 or more structures. Please help me out.
>
> Thanks,
>
> -Suda
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management 
> Up to 160% more powerful than alternatives and 25% more efficient. 
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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 Suda and Tsjerk,

there is "alignto" which used cealign. There is also in the menu "Action 
 > align > all to this" which uses cmd.util.mass_align (and that uses 
cmd.align).

On Robert Campbell's site there is the "align_all.py" script: 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

On my PyMOLWiki user page there is a "extra_fit" script.
http://pymolwiki.org/index.php/User:Speleo3

All those align to a reference object (or state, in case of intra_fit) 
instead of an all-against-all best fit.

Cheers,
   Thomas

On 08/29/2011 08:52 AM, Tsjerk Wassenaar wrote:
> Hi Suda,
>
> Do you mean different structures of the same molecule or different
> molecules? For a multistate object, there is intra_fit. for selections
> comprising multiple objects it's not currently possible. But it's
> being worked on.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Aug 29, 2011 at 8:43 AM, Suda Ravindran<bio...@gm...>  wrote:
>> Hi,
>>
>> I would like to know how to do structure based superposition using PyMol for
>> 3 or more structures. Please help me out.
>>
>> Thanks,
>>
>> -Suda

-- 
Thomas Holder
MPI for Developmental Biology

Hi Suda,

Do you mean different structures of the same molecule or different
molecules? For a multistate object, there is intra_fit. for selections
comprising multiple objects it's not currently possible. But it's
being worked on.

Cheers,

Tsjerk

On Mon, Aug 29, 2011 at 8:43 AM, Suda Ravindran <bio...@gm...> wrote:
> Hi,
>
> I would like to know how to do structure based superposition using PyMol for
> 3 or more structures. Please help me out.
>
> Thanks,
>
> -Suda
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> 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
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hi,

I would like to know how to do structure based superposition using PyMol for
3 or more structures. Please help me out.

Thanks,

-Suda

Thanks Jason. But still no luck...

So, I changed it to a python script. It was important that the ending of the
file is .py :-)
But, I can see from the list of objects, that PyMOL fetches the next protein
before it has finished propka first.
Does pymol run external script in some kind of asynchron mode as default?

---------------------------------
import pymol
from pymol import cmd
import os
os.chdir("/homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/predict_reactivity/Comparison/Match")

cmd.cartoon("auto")
cmd.set("cartoon_fancy_helices","1")
cmd.bg_color("white")
cmd.set("fog","0")
cmd.set("cartoon_transparency","0.7")
cmd.set("auto_zoom","off")

import propka
#resis =
[["1bj6","36"],["1bj6","39"],["1bj6","49"],["1ag1","14"],["1gu9","133"],["1gu9","130"],["1omu","56"],["1khg","273"],["2trx","35"],
#["1tde","32"],["1tde","35"],["2ovo","56"],["1m8b","56"],["1hic","39"],["1m8c","56"],["1ppo","25"],["1qlp","232"]]
resis = [["1ppo","25"],["1qlp","232"]]
i = 0
results = []
for p,r in resis:
    cmd.fetch(p,async="0")
    cmd.refresh()
    # When we import a module in python, the namespace is normally:
module.function
    # And we see, that propka expect resi to be in "str" format.
    # And we don't want the logtime function
    pkavalues = propka.propka(molecule=p,resi=r,resn="CYS",logtime=i)
    results.append(pkavalues)
    cmd.refresh()
    i = i + 1
cmd.zoom("all")
print results[0]
print results[1]



2011/8/28 Jason Vertrees <jas...@sc...>

> Hi Troels,
>
> In PyMOL, it you try the following, what happens for you?
>
> # make this a file called chill.py
> import time
> def chill():
>    rightThisSecond = time.time()
>    i = 0
>    while time.time() < rightThisSecond + 3.0:
>        i+=1
>    print "The farthest I could count in 3 seconds was %d." % i
>
> # make this a file called troels.py
> import pymol
> from pymol import cmd
> import chill
> resis = [ ["1bj6","36"], ["1bj6","39"], ["1bj6","49"],
>          ["1ag1","14"],
>           ["1gu9","133"], ["1gu9","130"], ]
> for p,r in resis:
>    # fetch a protein
>    cmd.fetch(p,async=0)
>    print "-- Fetched %s" % p
>    # do something slow
>    chill.chill()
>    # some post processing
>    print "%s has %d atoms" % (p, cmd.count_atoms(p))
>    print "%s/%s has %d atoms" % (p, r, cmd.count_atoms("%s and i. %s" %
> (p,r)))
>    cmd.delete(p)
>    print "-- Deleted protien"
>
>
> Now load PyMOL and try,
>
> run ~/troels.py
>
> Does PyMOL wait for the chill calls to finish? The idea is, wrap your
> call in a module/file and import it. Then, call through that function.
>
> It's about 3 AM my time and I'm sure there's a better solution--but
> this might work for now.
>
> Cheers,
>
> -- Jason
>
>
>
>
> 2011/8/26 Troels Emtekær Linnet <tl...@gm...>:
> > Well, I cant get it to work.
> > Pymol speeds ahead of calling propka.propka
> >
> > Can you give an example of subprocess?
> > ---------------------------
> >
> > import propka
> >
> > python
> > resis = [["1bj6","36"],["1bj6","39"]]
> > #resis =
> >
> [["1bj6","36"],["1bj6","39"],["1bj6","49"],["1ag1","14"],["1gu9","133"],["1gu9","130"],["1omu","56"],["1khg","273"],["2trx","35"],
> >
> #["1tde","32"],["1tde","35"],["2ovo","56"],["1m8b","56"],["1hic","39"],["1m8c","56"]]
> > i = 0
> > for resi in resis:
> >     cmd.fetch(resi[0],async="0")
> >     cmd.refresh()
> >     # When we import a module in python, the namespace is normally:
> > module.function
> >     # And we see, that propka expect resi to be in "str" format.
> >     # And we don't want the logtime function
> >     propka.propka(molecule=resi[0],resi=resi[1],logtime=i)
> >     cmd.refresh()
> >     i = i + 1
> > python end
> > zoom all
> >
> >
> >> hth
> >> Martin
> >>
> >> On 23.08.11 10:48, Troels Emtekær Linnet wrote:
> >>
> >> Hi.
> >>
> >> If one writes a pymol script, and calls an external function, the pymol
> >> script continues its operation before waiting for the "success" of the
> >> external function.
> >>
> >> Is it possible to give a keyword, so it "waits" for the external
> function
> >> before preceding?
> >>
> >> Kind of the same function with:
> >> fetch 1hp1, async=0
> >>
> >> Best
> >> Troels
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> >> user administration capabilities and model configuration. Take
> >> the hassle out of deploying and managing Subversion and the
> >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> >> user administration capabilities and model configuration. Take
> >> the hassle out of deploying and managing Subversion and the
> >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >
> >
> >
> ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > 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
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>

Hi all,

I will be demoing PyMOL at the Schrödinger booth at the Denver ACS.
Please feel free to dop ini, check out the new features, and get help
if needed.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

Well, I cant get it to work.
Pymol speeds ahead of calling propka.propka

Can you give an example of subprocess?
---------------------------

import propka

python
resis = [["1bj6","36"],["1bj6","39"]]
#resis =
[["1bj6","36"],["1bj6","39"],["1bj6","49"],["1ag1","14"],["1gu9","133"],["1gu9","130"],["1omu","56"],["1khg","273"],["2trx","35"],
#["1tde","32"],["1tde","35"],["2ovo","56"],["1m8b","56"],["1hic","39"],["1m8c","56"]]
i = 0
for resi in resis:
    cmd.fetch(resi[0],async="0")
    cmd.refresh()
    # When we import a module in python, the namespace is normally:
module.function
    # And we see, that propka expect resi to be in "str" format.
    # And we don't want the logtime function
    propka.propka(molecule=resi[0],resi=resi[1],logtime=i)
    cmd.refresh()
    i = i + 1
python end
zoom all


hth
> Martin
>
>
> On 23.08.11 10:48, Troels Emtekær Linnet wrote:
>
> Hi.
>
> If one writes a pymol script, and calls an external function, the pymol
> script continues its operation before waiting for the "success" of the
> external function.
>
> Is it possible to give a keyword, so it "waits" for the external function
> before preceding?
>
> Kind of the same function with:
> fetch 1hp1, async=0
>
> Best
> Troels
>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Thanks Tsjerk,

When I run this script, I see:

PyMOL>pplanes selection, (sele)
Selector-Error: Invalid Selection Name.
( selection and n. ca )<-- 

I have tried selecting just one "n and ca" in the pdb, tried selecting multiple "n and ca", tried a bunch of other selections, but it's not working. What am I supposed to be selecting in the pdb to make the script work?


On Aug 25, 2011, at 11:28 AM, Tsjerk Wassenaar wrote:

> Hi Adam,
> 
> Here's an alternative script... The command is pplanes (peptide-planes):
> 
> run triangles.py
> pplanes selection[, color[, alpha[, state[, name]]]]
> 
> Hope it helps,
> 
> Tsjerk
> 
> 
> On Thu, Aug 25, 2011 at 5:34 PM, H. Adam Steinberg <ad...@st...> wrote:
>> Hi all,
>> Can anyone help me with a problem that I am having trying to run a python
>> script?
>> I am trying to run the bbPlane script from the PyMOLWiki
>> <" rel="nofollow">http://www.pymolwiki.org/index.php/BbPlane>
>> I have copied the script from the web page, to a plain text document, saved
>> it as "bbPlane.py" but when I run it I get:
>> ------------
>> PyMOL>run bbPlane.py
>> Traceback (most recent call last):
>>   File "/Volumes/Port
>> 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
>>   File "/Volumes/Port
>> 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in
>> run_file
>>   File "bbPlane.py", line 14
>> 
>>      ^
>>  SyntaxError: invalid syntax
>> -------------
>> script is here:
>> 
>> #
>> # -- bbPlane.py - draws a CGO plane across the backbone atoms of
>> #                 neighboring amino acids
>> #
>> # Author: Jason Vertrees, 06/2010
>> #   Modified by Thomas Holder, 06/2010
>> #   Modified by Blaine Bell, 08/2011
>> # Copyright (C) Schrodinger
>> # Open Source License: MIT
>> #
>> from pymol.cgo import *    # get constants
>> from pymol import cmd, stored
>> from chempy import cpv
>> 
>> def bbPlane(objSel='(all)', color='white', transp=0.0):
>>    """
>> DESCRIPTION
>> 
>>    Draws a plane across the backbone for a selection
>> 
>> ARGUMENTS
>> 
>>    objSel = string: protein object or selection {default: (all)}
>> 
>>    color = string: color name or number {default: white}
>> 
>>    transp = float: transparency component (0.0--1.0) {default: 0.0}
>> 
>> NOTES
>> 
>>    You need to pass in an object or selection with at least two
>>    amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
>>    """
>>    # format input
>>    transp = float(transp)
>>    stored.AAs = []
>>    coords = dict()
>> 
>>    # need hydrogens on peptide nitrogen
>>    cmd.h_add('(%s) and n. N' % objSel)
>> 
>>    # get the list of residue ids
>>    for obj in cmd.get_object_list(objSel):
>>        sel = obj + " and (" + objSel + ")"
>>        for a in cmd.get_model(sel + " and n. CA").atom:
>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>            stored.AAs.append(key)
>>            coords[key] = [a.coord,None,None]
>>        for a in cmd.get_model(sel + " and n. O").atom:
>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>            if key in coords:
>>                coords[key][1] = a.coord
>>        for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and
>> n. N)").atom:
>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>            if key in coords:
>>                coords[key][2] = a.coord
>> 
>>    # need at least two amino acids
>>    if len(stored.AAs) <= 1:
>>        print "ERROR: Please provide at least two amino acids, the
>> alpha-carbon on the 2nd is needed."
>>        return
>> 
>>    # prepare the cgo
>>    obj = [
>>        BEGIN, TRIANGLES,
>>        COLOR,
>>        ]
>>    obj.extend(cmd.get_color_tuple(color))
>> 
>>    for res in range(0, len(stored.AAs)-1):
>>        curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
>> 
>>        # populate the position array
>>        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2],
>> coords[nextIdx][0]]
>> 
>>        # if the data are incomplete for any residues, ignore
>>        if None in pos:
>>            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
>>            continue
>> 
>>        if cpv.distance(pos[0], pos[3]) > 4.0:
>>            print '%s and %s not adjacent' % (curIdx, nextIdx)
>>            continue
>> 
>>        # need to order vertices to generate correct triangles for plane
>>        #      modified/added by B.Bell 8/18/2011
>>        sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
>>        centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
>>        angles = [ [ 0., 0 ] ]
>>        s00 = cpv.sub(pos[0], centerpos)
>>        for i in range(1,4):
>>            s = cpv.sub(pos[i], centerpos)
>>            ang = cpv.get_angle(s00, s)
>>            angles.append( [ ang, i] )
>>        def sortfirst(a, b):
>>            return cmp(a[0], b[0])
>>        angles.sort(sortfirst)
>>        verts = map(lambda x: x[1], angles)
>>        vorder = [ verts[0], verts[1], verts[2],
>>                   verts[1], verts[3], verts[2] ]
>>        # fill in the vertex data for the triangles;
>>        for i in vorder:
>>            obj.append(VERTEX)
>>            obj.extend(pos[i])
>> 
>>    # finish the CGO
>>    obj.append(END)
>> 
>>    # update the UI
>>    newName =  cmd.get_unused_name("backbonePlane")
>>    cmd.load_cgo(obj, newName)
>>    cmd.set("cgo_transparency", transp, newName)
>> 
>> 
>> cmd.extend("bbPlane", bbPlane)
>> 
>> artforscience
>> H. Adam Steinberg
>> Artist, Scientist, Developmental Editor
>> www.artforscience.com
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/729-5944
>> 
>> ------------------------------------------------------------------------------
>> EMC VNX: the world's simplest storage, starting under $10K
>> The only unified storage solution that offers unified management
>> Up to 160% more powerful than alternatives and 25% more efficient.
>> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>> _______________________________________________
>> 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
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> <triangles.py>

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Hi Adam,

I updated the wiki page to remove the spurious spaces--good idea.

> I am trying to follow the example in the Wiki to make sure it works before I try it on my pdb. However, when I run the command "bbPlane i. 4-10" I get a new error:
>
> PyMOL>bbPlane i. 4-10
> Traceback (most recent call last):
>  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 250, in parse
>  File "bbPlane.py", line 110, in bbPlane
>    newName =  cmd.get_unused_name("backbonePlane")
> AttributeError: 'module' object has no attribute 'get_unused_name'

This sounds like you need to update your version of PyMOL. What
version are you using?

Cheers,

-- Jason


On Thu, Aug 25, 2011 at 12:41 PM, H. Adam Steinberg <ad...@st...> wrote:
> I erased all of the spaces in the "blank" lines and now the script works. When I erased them in line 14 then it found them in kine 38, etc. You may want to update the script on the WIki to one without spaces.
>
> I am trying to follow the example in the Wiki to make sure it works before I try it on my pdb. However, when I run the command "bbPlane i. 4-10" I get a new error:
>
> PyMOL>bbPlane i. 4-10
> Traceback (most recent call last):
>  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 250, in parse
>  File "bbPlane.py", line 110, in bbPlane
>    newName =  cmd.get_unused_name("backbonePlane")
> AttributeError: 'module' object has no attribute 'get_unused_name'
>
> On Aug 25, 2011, at 11:09 AM, Jason Vertrees wrote:
>
>> Hi Adam,
>>
>> I just copy/pasted the script you attached in your email and it worked
>> fine. There are, however two spaces on line 14--maybe the parser
>> thinks it found a block indent? Try erasing line 14 (the line
>> following "from chempy import cpv") and re-running the script.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Thu, Aug 25, 2011 at 11:34 AM, H. Adam Steinberg <ad...@st...> wrote:
>>> Hi all,
>>> Can anyone help me with a problem that I am having trying to run a python
>>> script?
>>> I am trying to run the bbPlane script from the PyMOLWiki
>>> <" rel="nofollow">http://www.pymolwiki.org/index.php/BbPlane>
>>> I have copied the script from the web page, to a plain text document, saved
>>> it as "bbPlane.py" but when I run it I get:
>>> ------------
>>> PyMOL>run bbPlane.py
>>> Traceback (most recent call last):
>>>   File "/Volumes/Port
>>> 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
>>>   File "/Volumes/Port
>>> 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in
>>> run_file
>>>   File "bbPlane.py", line 14
>>>
>>>      ^
>>>  SyntaxError: invalid syntax
>>> -------------
>>> script is here:
>>>
>>> #
>>> # -- bbPlane.py - draws a CGO plane across the backbone atoms of
>>> #                 neighboring amino acids
>>> #
>>> # Author: Jason Vertrees, 06/2010
>>> #   Modified by Thomas Holder, 06/2010
>>> #   Modified by Blaine Bell, 08/2011
>>> # Copyright (C) Schrodinger
>>> # Open Source License: MIT
>>> #
>>> from pymol.cgo import *    # get constants
>>> from pymol import cmd, stored
>>> from chempy import cpv
>>>
>>> def bbPlane(objSel='(all)', color='white', transp=0.0):
>>>    """
>>> DESCRIPTION
>>>
>>>    Draws a plane across the backbone for a selection
>>>
>>> ARGUMENTS
>>>
>>>    objSel = string: protein object or selection {default: (all)}
>>>
>>>    color = string: color name or number {default: white}
>>>
>>>    transp = float: transparency component (0.0--1.0) {default: 0.0}
>>>
>>> NOTES
>>>
>>>    You need to pass in an object or selection with at least two
>>>    amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
>>>    """
>>>    # format input
>>>    transp = float(transp)
>>>    stored.AAs = []
>>>    coords = dict()
>>>
>>>    # need hydrogens on peptide nitrogen
>>>    cmd.h_add('(%s) and n. N' % objSel)
>>>
>>>    # get the list of residue ids
>>>    for obj in cmd.get_object_list(objSel):
>>>        sel = obj + " and (" + objSel + ")"
>>>        for a in cmd.get_model(sel + " and n. CA").atom:
>>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>>            stored.AAs.append(key)
>>>            coords[key] = [a.coord,None,None]
>>>        for a in cmd.get_model(sel + " and n. O").atom:
>>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>>            if key in coords:
>>>                coords[key][1] = a.coord
>>>        for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and
>>> n. N)").atom:
>>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>>            if key in coords:
>>>                coords[key][2] = a.coord
>>>
>>>    # need at least two amino acids
>>>    if len(stored.AAs) <= 1:
>>>        print "ERROR: Please provide at least two amino acids, the
>>> alpha-carbon on the 2nd is needed."
>>>        return
>>>
>>>    # prepare the cgo
>>>    obj = [
>>>        BEGIN, TRIANGLES,
>>>        COLOR,
>>>        ]
>>>    obj.extend(cmd.get_color_tuple(color))
>>>
>>>    for res in range(0, len(stored.AAs)-1):
>>>        curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
>>>
>>>        # populate the position array
>>>        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2],
>>> coords[nextIdx][0]]
>>>
>>>        # if the data are incomplete for any residues, ignore
>>>        if None in pos:
>>>            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
>>>            continue
>>>
>>>        if cpv.distance(pos[0], pos[3]) > 4.0:
>>>            print '%s and %s not adjacent' % (curIdx, nextIdx)
>>>            continue
>>>
>>>        # need to order vertices to generate correct triangles for plane
>>>        #      modified/added by B.Bell 8/18/2011
>>>        sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
>>>        centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
>>>        angles = [ [ 0., 0 ] ]
>>>        s00 = cpv.sub(pos[0], centerpos)
>>>        for i in range(1,4):
>>>            s = cpv.sub(pos[i], centerpos)
>>>            ang = cpv.get_angle(s00, s)
>>>            angles.append( [ ang, i] )
>>>        def sortfirst(a, b):
>>>            return cmp(a[0], b[0])
>>>        angles.sort(sortfirst)
>>>        verts = map(lambda x: x[1], angles)
>>>        vorder = [ verts[0], verts[1], verts[2],
>>>                   verts[1], verts[3], verts[2] ]
>>>        # fill in the vertex data for the triangles;
>>>        for i in vorder:
>>>            obj.append(VERTEX)
>>>            obj.extend(pos[i])
>>>
>>>    # finish the CGO
>>>    obj.append(END)
>>>
>>>    # update the UI
>>>    newName =  cmd.get_unused_name("backbonePlane")
>>>    cmd.load_cgo(obj, newName)
>>>    cmd.set("cgo_transparency", transp, newName)
>>>
>>>
>>> cmd.extend("bbPlane", bbPlane)
>>>
>>> artforscience
>>> H. Adam Steinberg
>>> Artist, Scientist, Developmental Editor
>>> www.artforscience.com
>>> 7904 Bowman Rd
>>> Lodi, WI 53555
>>> 608/729-5944
>>>
>>> ------------------------------------------------------------------------------
>>> EMC VNX: the world's simplest storage, starting under $10K
>>> The only unified storage solution that offers unified management
>>> Up to 160% more powerful than alternatives and 25% more efficient.
>>> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>>> _______________________________________________
>>> 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
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

I erased all of the spaces in the "blank" lines and now the script works. When I erased them in line 14 then it found them in kine 38, etc. You may want to update the script on the WIki to one without spaces.

I am trying to follow the example in the Wiki to make sure it works before I try it on my pdb. However, when I run the command "bbPlane i. 4-10" I get a new error:

PyMOL>bbPlane i. 4-10
Traceback (most recent call last):
  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 250, in parse
  File "bbPlane.py", line 110, in bbPlane
    newName =  cmd.get_unused_name("backbonePlane")
AttributeError: 'module' object has no attribute 'get_unused_name'

On Aug 25, 2011, at 11:09 AM, Jason Vertrees wrote:

> Hi Adam,
> 
> I just copy/pasted the script you attached in your email and it worked
> fine. There are, however two spaces on line 14--maybe the parser
> thinks it found a block indent? Try erasing line 14 (the line
> following "from chempy import cpv") and re-running the script.
> 
> Cheers,
> 
> -- Jason
> 
> On Thu, Aug 25, 2011 at 11:34 AM, H. Adam Steinberg <ad...@st...> wrote:
>> Hi all,
>> Can anyone help me with a problem that I am having trying to run a python
>> script?
>> I am trying to run the bbPlane script from the PyMOLWiki
>> <" rel="nofollow">http://www.pymolwiki.org/index.php/BbPlane>
>> I have copied the script from the web page, to a plain text document, saved
>> it as "bbPlane.py" but when I run it I get:
>> ------------
>> PyMOL>run bbPlane.py
>> Traceback (most recent call last):
>>   File "/Volumes/Port
>> 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
>>   File "/Volumes/Port
>> 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in
>> run_file
>>   File "bbPlane.py", line 14
>> 
>>      ^
>>  SyntaxError: invalid syntax
>> -------------
>> script is here:
>> 
>> #
>> # -- bbPlane.py - draws a CGO plane across the backbone atoms of
>> #                 neighboring amino acids
>> #
>> # Author: Jason Vertrees, 06/2010
>> #   Modified by Thomas Holder, 06/2010
>> #   Modified by Blaine Bell, 08/2011
>> # Copyright (C) Schrodinger
>> # Open Source License: MIT
>> #
>> from pymol.cgo import *    # get constants
>> from pymol import cmd, stored
>> from chempy import cpv
>> 
>> def bbPlane(objSel='(all)', color='white', transp=0.0):
>>    """
>> DESCRIPTION
>> 
>>    Draws a plane across the backbone for a selection
>> 
>> ARGUMENTS
>> 
>>    objSel = string: protein object or selection {default: (all)}
>> 
>>    color = string: color name or number {default: white}
>> 
>>    transp = float: transparency component (0.0--1.0) {default: 0.0}
>> 
>> NOTES
>> 
>>    You need to pass in an object or selection with at least two
>>    amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
>>    """
>>    # format input
>>    transp = float(transp)
>>    stored.AAs = []
>>    coords = dict()
>> 
>>    # need hydrogens on peptide nitrogen
>>    cmd.h_add('(%s) and n. N' % objSel)
>> 
>>    # get the list of residue ids
>>    for obj in cmd.get_object_list(objSel):
>>        sel = obj + " and (" + objSel + ")"
>>        for a in cmd.get_model(sel + " and n. CA").atom:
>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>            stored.AAs.append(key)
>>            coords[key] = [a.coord,None,None]
>>        for a in cmd.get_model(sel + " and n. O").atom:
>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>            if key in coords:
>>                coords[key][1] = a.coord
>>        for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and
>> n. N)").atom:
>>            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>>            if key in coords:
>>                coords[key][2] = a.coord
>> 
>>    # need at least two amino acids
>>    if len(stored.AAs) <= 1:
>>        print "ERROR: Please provide at least two amino acids, the
>> alpha-carbon on the 2nd is needed."
>>        return
>> 
>>    # prepare the cgo
>>    obj = [
>>        BEGIN, TRIANGLES,
>>        COLOR,
>>        ]
>>    obj.extend(cmd.get_color_tuple(color))
>> 
>>    for res in range(0, len(stored.AAs)-1):
>>        curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
>> 
>>        # populate the position array
>>        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2],
>> coords[nextIdx][0]]
>> 
>>        # if the data are incomplete for any residues, ignore
>>        if None in pos:
>>            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
>>            continue
>> 
>>        if cpv.distance(pos[0], pos[3]) > 4.0:
>>            print '%s and %s not adjacent' % (curIdx, nextIdx)
>>            continue
>> 
>>        # need to order vertices to generate correct triangles for plane
>>        #      modified/added by B.Bell 8/18/2011
>>        sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
>>        centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
>>        angles = [ [ 0., 0 ] ]
>>        s00 = cpv.sub(pos[0], centerpos)
>>        for i in range(1,4):
>>            s = cpv.sub(pos[i], centerpos)
>>            ang = cpv.get_angle(s00, s)
>>            angles.append( [ ang, i] )
>>        def sortfirst(a, b):
>>            return cmp(a[0], b[0])
>>        angles.sort(sortfirst)
>>        verts = map(lambda x: x[1], angles)
>>        vorder = [ verts[0], verts[1], verts[2],
>>                   verts[1], verts[3], verts[2] ]
>>        # fill in the vertex data for the triangles;
>>        for i in vorder:
>>            obj.append(VERTEX)
>>            obj.extend(pos[i])
>> 
>>    # finish the CGO
>>    obj.append(END)
>> 
>>    # update the UI
>>    newName =  cmd.get_unused_name("backbonePlane")
>>    cmd.load_cgo(obj, newName)
>>    cmd.set("cgo_transparency", transp, newName)
>> 
>> 
>> cmd.extend("bbPlane", bbPlane)
>> 
>> artforscience
>> H. Adam Steinberg
>> Artist, Scientist, Developmental Editor
>> www.artforscience.com
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/729-5944
>> 
>> ------------------------------------------------------------------------------
>> EMC VNX: the world's simplest storage, starting under $10K
>> The only unified storage solution that offers unified management
>> Up to 160% more powerful than alternatives and 25% more efficient.
>> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>> _______________________________________________
>> 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
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Hi Andrew,

On Thu, Aug 25, 2011 at 8:51 AM, Malaby, Andrew
<And...@um...> wrote:
> I am working on a figure showing the sticks of one molecule interacting with the surface of another.  I am trying to keep my normal coloring in a figure, but make background portions of the molecule lighter.  I have tried "set fog" followed by chain and residue numbers, to no avail.  The program responds, but no visible change occurs.  I feel that I am missing something inherent in the program.  Any help here would be greatly appreciated.

The fog setting is really a numerical parameter in an equation---not
just on and off. So try,

set fog, 5

set fog, 10

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

Hi Adam,

Here's an alternative script... The command is pplanes (peptide-planes):

run triangles.py
pplanes selection[, color[, alpha[, state[, name]]]]

Hope it helps,

Tsjerk


On Thu, Aug 25, 2011 at 5:34 PM, H. Adam Steinberg <ad...@st...> wrote:
> Hi all,
> Can anyone help me with a problem that I am having trying to run a python
> script?
> I am trying to run the bbPlane script from the PyMOLWiki
> <" rel="nofollow">http://www.pymolwiki.org/index.php/BbPlane>
> I have copied the script from the web page, to a plain text document, saved
> it as "bbPlane.py" but when I run it I get:
> ------------
> PyMOL>run bbPlane.py
> Traceback (most recent call last):
>   File "/Volumes/Port
> 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
>   File "/Volumes/Port
> 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in
> run_file
>   File "bbPlane.py", line 14
>
>      ^
>  SyntaxError: invalid syntax
> -------------
> script is here:
>
> #
> # -- bbPlane.py - draws a CGO plane across the backbone atoms of
> #                 neighboring amino acids
> #
> # Author: Jason Vertrees, 06/2010
> #   Modified by Thomas Holder, 06/2010
> #   Modified by Blaine Bell, 08/2011
> # Copyright (C) Schrodinger
> # Open Source License: MIT
> #
> from pymol.cgo import *    # get constants
> from pymol import cmd, stored
> from chempy import cpv
>
> def bbPlane(objSel='(all)', color='white', transp=0.0):
>     """
> DESCRIPTION
>
>     Draws a plane across the backbone for a selection
>
> ARGUMENTS
>
>     objSel = string: protein object or selection {default: (all)}
>
>     color = string: color name or number {default: white}
>
>     transp = float: transparency component (0.0--1.0) {default: 0.0}
>
> NOTES
>
>     You need to pass in an object or selection with at least two
>     amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
>     """
>     # format input
>     transp = float(transp)
>     stored.AAs = []
>     coords = dict()
>
>     # need hydrogens on peptide nitrogen
>     cmd.h_add('(%s) and n. N' % objSel)
>
>     # get the list of residue ids
>     for obj in cmd.get_object_list(objSel):
>         sel = obj + " and (" + objSel + ")"
>         for a in cmd.get_model(sel + " and n. CA").atom:
>             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>             stored.AAs.append(key)
>             coords[key] = [a.coord,None,None]
>         for a in cmd.get_model(sel + " and n. O").atom:
>             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>             if key in coords:
>                 coords[key][1] = a.coord
>         for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and
> n. N)").atom:
>             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>             if key in coords:
>                 coords[key][2] = a.coord
>
>     # need at least two amino acids
>     if len(stored.AAs) <= 1:
>         print "ERROR: Please provide at least two amino acids, the
> alpha-carbon on the 2nd is needed."
>         return
>
>     # prepare the cgo
>     obj = [
>         BEGIN, TRIANGLES,
>         COLOR,
>         ]
>     obj.extend(cmd.get_color_tuple(color))
>
>     for res in range(0, len(stored.AAs)-1):
>         curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
>
>         # populate the position array
>         pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2],
> coords[nextIdx][0]]
>
>         # if the data are incomplete for any residues, ignore
>         if None in pos:
>             print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
>             continue
>
>         if cpv.distance(pos[0], pos[3]) > 4.0:
>             print '%s and %s not adjacent' % (curIdx, nextIdx)
>             continue
>
>         # need to order vertices to generate correct triangles for plane
>         #      modified/added by B.Bell 8/18/2011
>         sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
>         centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
>         angles = [ [ 0., 0 ] ]
>         s00 = cpv.sub(pos[0], centerpos)
>         for i in range(1,4):
>             s = cpv.sub(pos[i], centerpos)
>             ang = cpv.get_angle(s00, s)
>             angles.append( [ ang, i] )
>         def sortfirst(a, b):
>             return cmp(a[0], b[0])
>         angles.sort(sortfirst)
>         verts = map(lambda x: x[1], angles)
>         vorder = [ verts[0], verts[1], verts[2],
>                    verts[1], verts[3], verts[2] ]
>         # fill in the vertex data for the triangles;
>         for i in vorder:
>             obj.append(VERTEX)
>             obj.extend(pos[i])
>
>     # finish the CGO
>     obj.append(END)
>
>     # update the UI
>     newName =  cmd.get_unused_name("backbonePlane")
>     cmd.load_cgo(obj, newName)
>     cmd.set("cgo_transparency", transp, newName)
>
>
> cmd.extend("bbPlane", bbPlane)
>
> artforscience
> H. Adam Steinberg
> Artist, Scientist, Developmental Editor
> www.artforscience.com
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/729-5944
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> 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
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hi Adam,

I just copy/pasted the script you attached in your email and it worked
fine. There are, however two spaces on line 14--maybe the parser
thinks it found a block indent? Try erasing line 14 (the line
following "from chempy import cpv") and re-running the script.

Cheers,

-- Jason

On Thu, Aug 25, 2011 at 11:34 AM, H. Adam Steinberg <ad...@st...> wrote:
> Hi all,
> Can anyone help me with a problem that I am having trying to run a python
> script?
> I am trying to run the bbPlane script from the PyMOLWiki
> <" rel="nofollow">http://www.pymolwiki.org/index.php/BbPlane>
> I have copied the script from the web page, to a plain text document, saved
> it as "bbPlane.py" but when I run it I get:
> ------------
> PyMOL>run bbPlane.py
> Traceback (most recent call last):
>   File "/Volumes/Port
> 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
>   File "/Volumes/Port
> 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in
> run_file
>   File "bbPlane.py", line 14
>
>      ^
>  SyntaxError: invalid syntax
> -------------
> script is here:
>
> #
> # -- bbPlane.py - draws a CGO plane across the backbone atoms of
> #                 neighboring amino acids
> #
> # Author: Jason Vertrees, 06/2010
> #   Modified by Thomas Holder, 06/2010
> #   Modified by Blaine Bell, 08/2011
> # Copyright (C) Schrodinger
> # Open Source License: MIT
> #
> from pymol.cgo import *    # get constants
> from pymol import cmd, stored
> from chempy import cpv
>
> def bbPlane(objSel='(all)', color='white', transp=0.0):
>     """
> DESCRIPTION
>
>     Draws a plane across the backbone for a selection
>
> ARGUMENTS
>
>     objSel = string: protein object or selection {default: (all)}
>
>     color = string: color name or number {default: white}
>
>     transp = float: transparency component (0.0--1.0) {default: 0.0}
>
> NOTES
>
>     You need to pass in an object or selection with at least two
>     amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
>     """
>     # format input
>     transp = float(transp)
>     stored.AAs = []
>     coords = dict()
>
>     # need hydrogens on peptide nitrogen
>     cmd.h_add('(%s) and n. N' % objSel)
>
>     # get the list of residue ids
>     for obj in cmd.get_object_list(objSel):
>         sel = obj + " and (" + objSel + ")"
>         for a in cmd.get_model(sel + " and n. CA").atom:
>             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>             stored.AAs.append(key)
>             coords[key] = [a.coord,None,None]
>         for a in cmd.get_model(sel + " and n. O").atom:
>             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>             if key in coords:
>                 coords[key][1] = a.coord
>         for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and
> n. N)").atom:
>             key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
>             if key in coords:
>                 coords[key][2] = a.coord
>
>     # need at least two amino acids
>     if len(stored.AAs) <= 1:
>         print "ERROR: Please provide at least two amino acids, the
> alpha-carbon on the 2nd is needed."
>         return
>
>     # prepare the cgo
>     obj = [
>         BEGIN, TRIANGLES,
>         COLOR,
>         ]
>     obj.extend(cmd.get_color_tuple(color))
>
>     for res in range(0, len(stored.AAs)-1):
>         curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
>
>         # populate the position array
>         pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2],
> coords[nextIdx][0]]
>
>         # if the data are incomplete for any residues, ignore
>         if None in pos:
>             print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
>             continue
>
>         if cpv.distance(pos[0], pos[3]) > 4.0:
>             print '%s and %s not adjacent' % (curIdx, nextIdx)
>             continue
>
>         # need to order vertices to generate correct triangles for plane
>         #      modified/added by B.Bell 8/18/2011
>         sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
>         centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
>         angles = [ [ 0., 0 ] ]
>         s00 = cpv.sub(pos[0], centerpos)
>         for i in range(1,4):
>             s = cpv.sub(pos[i], centerpos)
>             ang = cpv.get_angle(s00, s)
>             angles.append( [ ang, i] )
>         def sortfirst(a, b):
>             return cmp(a[0], b[0])
>         angles.sort(sortfirst)
>         verts = map(lambda x: x[1], angles)
>         vorder = [ verts[0], verts[1], verts[2],
>                    verts[1], verts[3], verts[2] ]
>         # fill in the vertex data for the triangles;
>         for i in vorder:
>             obj.append(VERTEX)
>             obj.extend(pos[i])
>
>     # finish the CGO
>     obj.append(END)
>
>     # update the UI
>     newName =  cmd.get_unused_name("backbonePlane")
>     cmd.load_cgo(obj, newName)
>     cmd.set("cgo_transparency", transp, newName)
>
>
> cmd.extend("bbPlane", bbPlane)
>
> artforscience
> H. Adam Steinberg
> Artist, Scientist, Developmental Editor
> www.artforscience.com
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/729-5944
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> 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
PyMOL Product Manager
Schrodinger, LLC

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

Hi all,

Can anyone help me with a problem that I am having trying to run a python script?
I am trying to run the bbPlane script from the PyMOLWiki <" rel="nofollow">http://www.pymolwiki.org/index.php/BbPlane>
I have copied the script from the web page, to a plain text document, saved it as "bbPlane.py" but when I run it I get:

------------
PyMOL>run bbPlane.py
Traceback (most recent call last):
  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse
  File "/Volumes/Port 3/software/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in run_file
  File "bbPlane.py", line 14
     
     ^
 SyntaxError: invalid syntax 
-------------

script is here:
#
# -- bbPlane.py - draws a CGO plane across the backbone atoms of
#                 neighboring amino acids
# 
# Author: Jason Vertrees, 06/2010
#   Modified by Thomas Holder, 06/2010
#   Modified by Blaine Bell, 08/2011
# Copyright (C) Schrodinger
# Open Source License: MIT
#
from pymol.cgo import *    # get constants
from pymol import cmd, stored
from chempy import cpv
 
def bbPlane(objSel='(all)', color='white', transp=0.0):
    """
DESCRIPTION
 
    Draws a plane across the backbone for a selection
 
ARGUMENTS
 
    objSel = string: protein object or selection {default: (all)}
 
    color = string: color name or number {default: white}
 
    transp = float: transparency component (0.0--1.0) {default: 0.0}
 
NOTES
 
    You need to pass in an object or selection with at least two
    amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
    """
    # format input
    transp = float(transp)
    stored.AAs = []
    coords = dict()
 
    # need hydrogens on peptide nitrogen
    cmd.h_add('(%s) and n. N' % objSel)
 
    # get the list of residue ids
    for obj in cmd.get_object_list(objSel):
        sel = obj + " and (" + objSel + ")"
        for a in cmd.get_model(sel + " and n. CA").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            stored.AAs.append(key)
            coords[key] = [a.coord,None,None]
        for a in cmd.get_model(sel + " and n. O").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            if key in coords:
                coords[key][1] = a.coord
        for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and n. N)").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            if key in coords:
                coords[key][2] = a.coord
 
    # need at least two amino acids
    if len(stored.AAs) <= 1:
        print "ERROR: Please provide at least two amino acids, the alpha-carbon on the 2nd is needed."
        return
 
    # prepare the cgo
    obj = [
        BEGIN, TRIANGLES,
        COLOR,
        ]
    obj.extend(cmd.get_color_tuple(color))
 
    for res in range(0, len(stored.AAs)-1):
        curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
 
        # populate the position array
        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
 
        # if the data are incomplete for any residues, ignore
        if None in pos:
            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
            continue
 
        if cpv.distance(pos[0], pos[3]) > 4.0:
            print '%s and %s not adjacent' % (curIdx, nextIdx)
            continue
 
        # need to order vertices to generate correct triangles for plane
        #      modified/added by B.Bell 8/18/2011
        sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
        centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
        angles = [ [ 0., 0 ] ]
        s00 = cpv.sub(pos[0], centerpos)
        for i in range(1,4):
            s = cpv.sub(pos[i], centerpos)
            ang = cpv.get_angle(s00, s)
            angles.append( [ ang, i] )
        def sortfirst(a, b):
            return cmp(a[0], b[0])
        angles.sort(sortfirst)
        verts = map(lambda x: x[1], angles)
        vorder = [ verts[0], verts[1], verts[2],
                   verts[1], verts[3], verts[2] ]
        # fill in the vertex data for the triangles; 
        for i in vorder:
            obj.append(VERTEX)
            obj.extend(pos[i])
 
    # finish the CGO
    obj.append(END)
 
    # update the UI
    newName =  cmd.get_unused_name("backbonePlane")
    cmd.load_cgo(obj, newName)
    cmd.set("cgo_transparency", transp, newName)
 
 
cmd.extend("bbPlane", bbPlane)


artforscience

H. Adam Steinberg
Artist, Scientist, Developmental Editor

www.artforscience.com
7904 Bowman Rd
Lodi, WI 53555
608/729-5944

I don't know what the current stance on such things is, and Schrodinger's
acquisition of PyMOL might have changed things, but I remember two very
clear messages from Warren relating to Windows compilation. I'd read these
and think about them pretty carefully before you go out of your way to do
the seemingly obvious thing and make Windows compilation easier. The first
is from 2007:

http://www.mail-archive.com/pym...@li.../msg05696.html
> > The goal is
> > to produce a Pymol that uses native Windows graphics, not one
> > that requires X11.
>
> David,
>
> Please note that the goal behind Open-Source PyMOL (as maintained by
DeLano
> Scientific LLC) is to enable compilation under open-source operating
> systems, and primarily, Linux with X11/GLUT.  It not our current intent to
> support, assist, or encourage native compilation of PyMOL open-source code
> on closed-source operating systems, despite the fact that such compilation
> is deliberately permitted under the unrestrictive open-source license
terms.
>
> An open-source version targeting native Windows (via any means) would
> necessarily comprise a fork of the project.  Since such a fork would
provide
> a realistic alternative to DeLano Scientific LLC's precompiled incentive
> builds for Windows, it could jeopardize our ability to continue funding
> development of the open-source code.
>
> If PyMOL revenues were imperiled, then to make ends meet, DeLano
Scientific
> LLC would have no choice but to redirect development efforts into
> proprietary assets, significantly curtailing participation in the
> unrestricted open-source project.  At the very least, our unrestrictive
> open-source license would have to be restricted in future versions, thus
> defeating one of the primary aims of the project.
>
> We don't want that... do you?
>
> If not, then proceed down this path only with due care and consideration
of
> the possible consequences.  Given enough effort, native compilation is
> certainly do-able, but it is not intended to be easy... nor commonplace.
>
> To the extent that you achieve your goal, please do think twice before
> publicly sharing the fruits and/or details of that success.  We would
> naturally prefer that such accomplishments remain private, since the
future
> of PyMOL could well depend upon it.
>
> With great freedom comes great responsibility! ;)
>
> Warren L. DeLano
> DeLano Scientific LLC

The second is from 2009
http://www.mail-archive.com/pym...@li.../msg06761.html

> Bryn & others,
>
> By design, the PyMOL Open-Source Code only targets Linux and other 100%
> open-source operating systems (e.g. FreeBSD).  So to compile Open-Source
> PyMOL on Mac OS X or Microsoft Windows, you need to pretend you are
> running Linux by making use of X11 and the various GNU-compatible
> free-software porting systems (e.g. Fink, GNU-Darwin, Cygwin, etc.).
>
> Also by design, the current precompiled PyMOL builds for proprietary
> operating systems (i.e.  Microsoft Windows & Mac OS X) are themselves
> proprietary products offered by DeLano Scientific LLC.
>
> In other words, if you are willing to pay to use a proprietary operating
> system, then we feel you should be equally willing to support the PyMOL
> project financially via paid subscription access to our current builds
> for proprietary platforms.  That, indeed, is how we make ends meet while
> still keeping the PyMOL code open-source.
>
> For those who are not able to support the project financially, well,
> there are still plenty of older PyMOL builds for Mac & Windows floating
> around the internet.  They just don't include the latest fixes &
> features.  Of course, without a subscription, you don't have access to
> all the documentation -- only the public portion ( http://pymolwiki.org
> ).
>
> Please visit http://pymol.org/funding.html if you wish to purchase a
> subscription.
>
> Cheers,
> Warren
>
> PS. FREE builds for educational-use-only can be had via
> http://pymol.org/educational.html

2011/8/24 Troels Emtekær Linnet <tl...@gm...>

> After some tries, I found that that the .reg file should be changed a
> little.
> Then .pdb files gets icon and gets opened by pymol.cmd
>
> C:\Python2X\PyMOL\PDB_file.reg
>
> REGEDIT4
>
> [-HKEY_CLASSES_ROOT\.pdb]
>
> [HKEY_CLASSES_ROOT\.pdb]
> @="PDB.File"
> "Content Type"="chemical/x-pdb"
>
> [-HKEY_CLASSES_ROOT\PDB.File]
>
> [HKEY_CLASSES_ROOT\PDB.File]
> @="PDB File"
>
> [HKEY_CLASSES_ROOT\PDB.File\DefaultIcon]
> @="C:\\Python27\\PyMOL\\PyMOL.exe"
>
> [HKEY_CLASSES_ROOT\PDB.File\Shell]
> @=""
>
> [HKEY_CLASSES_ROOT\PDB.File\Shell\open]
>
> [HKEY_CLASSES_ROOT\PDB.File\Shell\open\command]
> @="\"C:\\Python27\\PyMOL\\PyMOL.cmd\" %*"
>
> [-HKEY_CLASSES_ROOT\pdb_auto_file]
>
> [HKEY_CLASSES_ROOT\pdb_auto_file]
> @="PDB File"
>
> [HKEY_CLASSES_ROOT\pdb_auto_file\DefaultIcon]
> @="C:\\Python27\\PyMOL\\PyMOL.exe"
>
> [HKEY_CLASSES_ROOT\pdb_auto_file\Shell]
> @=""
>
> [HKEY_CLASSES_ROOT\pdb_auto_file\Shell\open]
>
> [HKEY_CLASSES_ROOT\pdb_auto_file\Shell\open\command]
> @="\"C:\\Python27\\PyMOL\\PyMOL.cmd\" %*"
>
>
>
> 2011/8/24 Troels Emtekær Linnet <tl...@gm...>
>
>> Hi.
>>
>> I was very happy to find a post how to easy install pymol 1.4 from source
>> on windows.
>>
>> 1) Install python, 2.5, or 2.6 or 2.7 for windows.
>> 2) Download appropriate installer from:
>> http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol   Select according to
>> your python version.
>> 3) Run it
>> 4) PyMOL is now installed in: C:\Python2X\PyMOL
>>
>> A) C:\Python2X\PyMOL\PDB_file.reg   should be edited in a text editor, to
>> match your python version. Run it.
>> B) Pymol is started by clicking C:\Python27\PyMOL\pymol.cmd   which
>> executes python on C:\Python27\PyMOL\pymol-launch.py
>>
>> Happy pymoling.
>>
>> Best
>> Troels
>>
>
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
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> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
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)

This is a very basic question, but I have been having trouble with this for a couple of days.  I am working in pymol for Windows, but have access to Mac pymol if the problem is a windows-specific problem.

I am working on a figure showing the sticks of one molecule interacting with the surface of another.  I am trying to keep my normal coloring in a figure, but make background portions of the molecule lighter.  I have tried "set fog" followed by chain and residue numbers, to no avail.  The program responds, but no visible change occurs.  I feel that I am missing something inherent in the program.  Any help here would be greatly appreciated.

Thanks!
Andrew Malaby
University of Massachusetts Medical School.