Re: [PyMOL] Visualise molecules to scale?

[Schubert, Carsten [JRDUS]]

Daniel, camera operations are done with move. To zoom out try 'move z, -10'

Carsten

-Original Message-
From: Daniel Lundin [mailto:daniel.lun...@scilifelab.se] 
Sent: Thursday, October 20, 2011 8:20 AM
To: Jason Vertrees
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Visualise molecules to scale?

Thanks Jason,

2011-10-20 14:01, Jason Vertrees skrev:
> Hi Daniel,
>
> If you need a scripted solution but not using grid mode, how about
> something like this from a freshly loaded PyMOL:
>
> # get the view matrix for the origin
> o = cmd.get_view()
>
> # fetch a protein
> fetch 1rx1, async=0
>
> # get the position
> x = cmd.get_position()
>
> # restore the camera to the original coordinates
> cmd.set_view(o)
>
> # move the loaded protein to the origin
> cmd.translate( [-x[0], -x[1], -x[2]], "1rx1")
>
>
> You could easily make this into a loop over your set of structures.
> This is nice because you can still rotate the camera and it will not
> change how far away (and thus change the scale) of the view.
>
The above looks promising. What I'm missing, because of my lack of 
experience with Pymol, is how to move the camera away (i.e. zoom out) a 
defined distance. From the documentation of set_view it appears I should 
fiddle with the 15th and/or 16th floating point number, while keeping 
the other but 18 parameters is a bit dauting.

> Cheers,
>
> -- Jason
>
/Daniel
> On Thu, Oct 20, 2011 at 10:51 AM, Daniel Lundin
>   wrote:
>> Hi,
>>
>> I'm quite new to Pymol, but have searched and found nothing on how to
>> visualise and draw a molecule to a certain scale. The reason I want to
>> do this is to be able to output figures of several molecules separately
>> in a format that displays their relative sizes. I can of course do this
>> manually but it's error prone and laborious, so I'd prefer to be able to
>> say I want a certain number of angstroms per pixel or so. I will ray
>> trace the images.
>>
>> /Daniel
>>
>> --
>> Daniel Lundin, Postdoc
>> SciLifeLab, School of biotechnology,
>> KTH Royal institute of technology,
>> Stockholm, Sweden
>>
>> Postal address:
>> Box 1031
>> 171 21 Solna
>> Sweden
>>
>> Visiting address:
>> Tomtebodavägen 23 A
>>
>> Mobile: +46 (0)708 123 922
>> Email: daniel.lun...@scilifelab.se
>>
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>
>


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Re: [PyMOL] Messed up structures in movie

[Schubert, Carsten [JRDUS]]

Ritu,

 

just an idea. It could be that your PDB files contains CONECT records
for your ligands. Those bonds are defined by atom number or atom index I
believe. There could be a conflict between the different files you are
loading. Try stripping the CONECT records and see if that helps.

 

HTH 

 

Carsten 

 

From: Folmer Fredslund [mailto:folm...@gmail.com] 
Sent: Wednesday, May 23, 2012 1:53 PM
To: Rituparna Sengupta
Cc: PyMol Users Mailing List
Subject: Re: [PyMOL] Messed up structures in movie

 

Hi again Ritu,

This does seem odd. I have no idea what might be wrong, but could you
provide an example pdb, or a png of the output you see?

I would personally try to strip all extra information from the ligand
pdb (so only ATOM and HETATM records is included) and then try loading
that pdb.

Best regards,
Folmer

2012/5/23 Rituparna Sengupta 

Hi,

Sorry about the lack of description in the previous post.
The chemicals show incorrect bond connections. Some of the rings go
missing. In all, the structure changes and just by looking at it, its
possible to tell that the structure is not right. I didn't see much
details though, except that the atom connections seem to be wrong.


Thanks,
Ritu

On 05/23/12, Folmer Fredslund

 wrote:
> Hi Ritu,
>
> Could you elaborate on "some of the ligand structures get completely
messed up when viewed as sticks or lines"?
>
> To get the best possible answer a few more details would help.
>
> Best regards,
> Folmer
>

> 2012/5/23 Rituparna Sengupta rsengu...@wisc.edu>
>
> > Hi,
> >
> > Just observed something weird. When I try loading protein -ligand
complexes as frames of a movie (same protein but different ligands for
different frames), some of the ligand structures get completely messed
up when viewed as sticks or lines. Right now I'm using spheres
instead, but wondering if there's a way to work around the problem
and still view the ligands as sticks/lines.

> >
> >
> > Thanks,
> > Ritu
> >
> >

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Re: [PyMOL] clipping planes

[Schubert, Carsten [JRDUS]]

Christian,

you should be able to get the values from the tuple returned by
get_view(). Looking into this would be a good starting point.

from my old notes (origin unknown...):

0-8 is the 3x3 rotation matrix
9-11 is the camera location (I think -- been a while...)
12-14 is the origin of rotation
15-16 are the clipping distances
and 17 is the orthoscopic flag.

Cheers,

Carsten



-Original Message-
From: Christian Roth [mailto:christian.r...@bbz.uni-leipzig.de] 
Sent: Friday, June 15, 2012 12:57 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] clipping planes

Dear all,

it is nice to set via mouse wheel the clipping. Is it possible to get
this 
values somewhere out of pymol that one could use the actual values in a 
script? I find it a bit complicated and time consuming to play always a
few 
times with the values in a script, to find values which looks fine. 

Best Regards

Christian




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[PyMOL] Syntax for cmd.auto_arg.update

[Schubert, Carsten [JRDUS]]

Hi,

can someone please shed some light on the syntax for
'cmd.auto_arg.update'. I've seen this in a couple of scripts and it
appears to be related to the command line completion feature, but the
details are murky. I'd like to make better use of this for the tools I'm
developing.

Thanks

Carsten



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Re: [PyMOL] Syntax for cmd.auto_arg.update

[Schubert, Carsten [JRDUS]]

Hi Takanori,

thanks for the detailed analysis. Very helpful

Cheers,

Carsten

-Original Message-
From: Takanori Nakane [mailto:t.nak...@mail.mfour.med.kyoto-u.ac.jp] 
Sent: Tuesday, August 21, 2012 5:18 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Syntax for cmd.auto_arg.update

Hi Carsten,

Below is what I learned by reading codes and experimenting.
The relevant code is in parser.py, cmd.py and shortcut.py.
Please correct me if I am wrong.

+

When Pymol's console attempts to auto-complete the n-th argument
of command 'abc', it will look at cmd.auto_arg[n]['abc']
(n starts from 0). This is a list with three elements.

The first element is a lambda function which returns an Shortcut object.
Shortcut object wraps the list of candidate strings, given to
its constructor.

The second element is a string, which describs the argument.

The third element is a string, which will be added after autocompletion 
(postfix).

Example:

cmd.auto_arg[0]['test']=[lambda: cmd.Shortcut(['abc','bcd']), '1st 
argument', ', ']

will setup the autocompletion list of the first argument of command
'test'. When you type 'test ' and press TAB, PyMOL will show you
two candidates as:

  parser: matching 1st argument:
abc  bcd

If you type 'a' and press TAB again, PyMOL will complete it to
"test abc, ". Please note that ', ' is added.

Pre-defined lambdas:

In most cases, you just want to complete from object names or
setting lists. Then you don't have to write your own lambda
function. Just use cmd.object_sc for choosing from objects.

cmd.auto_arg[0]['test'] = [ cmd.object_sc, 'object', '']

Use cmd.selection_sc for setting names (like 'line_width'),
cmd.map_sc for maps, cmd,repres_sc for representations
(sticks, lines, etc).

By the way, update is another way to set values to Python's Dict.
auto_arg[0]['test'] = [some, thing, s] is same as
auto_arg[0].update([('test', [some, thing, s])]).

Best regards,

Takanori Nakane



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Re: [PyMOL] Viewing PyMol in 3D

[Schubert, Carsten [JRDUS]]

Hi Max,

you are already pretty much spot on. Pymol stereo works under XP, Vista, W7 and 
as far as I know any Linux flavor,  as long as you purchase a compatible NVIDIA 
quadro card and Nvidia 3D kit. The only caveat is that under Linux you need to 
have a card which supports the external 3 pin stereo connector, you don't need 
that under any of the windows flavors. Check the Nivida website for compatible 
cards,  machines and monitors.

I'm sure you can also find some structural biology groups at Scripps who are 
already setup with this equipment.

HTH

Carsten



From: Max Ferretti [mailto:mferr...@scripps.edu]
Sent: Monday, December 10, 2012 11:22 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Viewing PyMol in 3D

Hey everyone,

Does anyone have experience setting up pymol to be viewed in 3D with glasses? 
I'm hoping to build a system for this purpose.

>From what I have read, I will need a recent NVidia Quadro card and a 
>3D-capable LCD monitor with a resolution of at least 120Hz. I'm not sure if I 
>need to be more specific than that (if there are particular cards/monitors 
>that are known to work/not work). I'm also not quite sure if this is possible 
>on Windows 7. I've seen reports of people doing this with Windows XP and 
>Vista, but I would prefer to avoid those operating systems.

Any suggestions or advice would be greatly appreciated.

-Max F
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Re: [PyMOL] Shrinking the sidebar

[Schubert, Carsten [JRDUS]]

Alex, there is a little rectangle under the S of "State" in the lower left of 
the sidebar or to the left of the |< button. You can use that as a slider for 
the sidebar



From: Alex Truong [mailto:atru...@bu.edu]
Sent: Monday, December 10, 2012 3:03 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Shrinking the sidebar

Hi All,

I was just wondering if it was possible to shrink the sidebar width so I have 
more viewing space? I regularly work with multiple windows open, usually 
splitscreen (vertically split). Since I do most of my work on a laptop with a 
14-inch screen, that doesn't afford me much space to investigate my models 
with. I've tried dragging; it hasn't worked. Is there a a way to do it, or 
would the actual GUI source code have to be edited?

Thanks,
Alex
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Re: [PyMOL] Viewing PyMol in 3D

[Schubert, Carsten [JRDUS]]

Thanks Sabuj,

useful info indeed.

-Original Message-
From: Sabuj Pattanayek [mailto:sab...@gmail.com] 
Sent: Monday, December 10, 2012 4:18 PM
To: Schubert, Carsten [JRDUS]
Cc: Max Ferretti; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Viewing PyMol in 3D

You don't need a quadro with a 3 pin port to do stereo in linux
anymore, but you do need a "new" model quadro, e.g. a quadro 600. The
tradeoff is that you'll pay more for the 120hz monitors with the
built-in 3d vision v2 emitters, see here :

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008177.html

I haven't' tested a standalone 3d vision v2 emitter with linux, it may
behave the same way as the lcd's with the built-in v2 emitter.

> NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux
> you need to have a card which supports the external 3 pin stereo connector,
> you don't need that under any of the windows flavors. Check the Nivida


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Re: [PyMOL] Creating coloured and transparent polyhedra

[Schubert, Carsten [JRDUS]]

Hi Timo,

That is best approached with CGO objects. You can find some examples in 
\PyMOL\PyMOL\modules\pymol\cgo.py

Here is a bit of a write-up I attempted a while ago. BTW transparency of CGO 
objects can be controlled via the "setting cgo_transparency"

HTH 

Carsten


Lines
=

The LINES command draws a lines between a set of coordinates defined by the
VERTEX command. The colour of the lines can be changed at any time even
between vertices, so that the start and end line color can be different. The
color of the line will be interpolated between the start and end color. The
thickness of the line is set by LINEWIDTH. However there is a bug in the
implementation. The GL renderer accepts the LINEWIDTH statement only before a
BEGIN statement. The internal renderer honors the change of the linewidth
before every VERTEX pair. Note: Tapered lines are not supported by either
implementation. LINEWIDTH and COLOR are optional commands.

LINEWIDTH, w,
BEGIN, LINES,
COLOR, r, g, b,
VERTEX, x1,y1,z1,
VERTEX, x2,y2,z2,
END

Line Strips


The LINE_STRIP command draws a continuous line between sets of coordinates
defined by the VERTEX command. The main difference to the LINES command is
that the endpoint of the first line is automatically the start of the next
line, but the first and last point are NOT connected, see LINE_LOOP instead.
The colour of the lines can be changed at any time even between vertices, so
that the start and end line color can be different. The color of the line
will be interpolated between the start and end color. The thickness of the
line is set by LINEWIDTH. However there is a bug in the implementation. The
GL renderer accepts the LINEWIDTH statement only before a BEGIN statement.
The internal renderer honors the change of the linewidth before every VERTEX
pair. Note: Tapered lines are not supported by either implementation.
LINEWIDTH and COLOR are optional commands.

LINEWIDTH, w,
BEGIN, LINE_STRIP,
COLOR, r, g, b,
VERTEX, x1,y1,z1,
VERTEX, x2,y2,z2, ...
VERTEX, xn,yn,zn
END

-Original Message-
From: Timo Stein [mailto:m...@timo-stein.com] 
Sent: Friday, July 12, 2013 4:39 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Creating coloured and transparent polyhedra

Hello PyMOL users,

I'm using PyMOL to create fancy images of Metal-Organic Framework structural 
units. They feature metal ions of different coordination spheres. The 
structural features of these units can be clarified by showing the 
corresponding coordination polyhedron (for example of the metal ions colour) 
with the coordinating atoms sitting on the polyhedron's corners. The polyhedron 
should be quite transparent. How can you draw such polyhedrons with PyMOL? The 
Google image search for
MOF-5 gives some examples of structures showing these coordination polyhedra.

Thank you very much!

Timo Stein

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Re: [PyMOL] Creating coloured and transparent polyhedra

[Schubert, Carsten [JRDUS]]

Hey Tsjerk,

Good to know, I missed that feature. Wonder what else is hidden…

Cheers,

Carsten

From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: Monday, July 15, 2013 11:42 AM
To: Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net; Timo Stein
Subject: Re: [PyMOL] Creating coloured and transparent polyhedra


Hey :)

Nice summary...
There is also the keyword ALPHA for setting the cgo transparency, allowing per 
element control. Just set

ALPHA, value,

before the element.

Cheers,

Tsjerk
On Jul 14, 2013 10:28 PM, "Schubert, Carsten [JRDUS]" 
mailto:cschu...@its.jnj.com>> wrote:

Hi Timo,

That is best approached with CGO objects. You can find some examples in 
\PyMOL\PyMOL\modules\pymol\cgo.py

Here is a bit of a write-up I attempted a while ago. BTW transparency of CGO 
objects can be controlled via the "setting cgo_transparency"

HTH

Carsten


Lines
=

The LINES command draws a lines between a set of coordinates defined by the
VERTEX command. The colour of the lines can be changed at any time even
between vertices, so that the start and end line color can be different. The
color of the line will be interpolated between the start and end color. The
thickness of the line is set by LINEWIDTH. However there is a bug in the
implementation. The GL renderer accepts the LINEWIDTH statement only before a
BEGIN statement. The internal renderer honors the change of the linewidth
before every VERTEX pair. Note: Tapered lines are not supported by either
implementation. LINEWIDTH and COLOR are optional commands.

LINEWIDTH, w,
BEGIN, LINES,
COLOR, r, g, b,
VERTEX, x1,y1,z1,
VERTEX, x2,y2,z2,
END

Line Strips


The LINE_STRIP command draws a continuous line between sets of coordinates
defined by the VERTEX command. The main difference to the LINES command is
that the endpoint of the first line is automatically the start of the next
line, but the first and last point are NOT connected, see LINE_LOOP instead.
The colour of the lines can be changed at any time even between vertices, so
that the start and end line color can be different. The color of the line
will be interpolated between the start and end color. The thickness of the
line is set by LINEWIDTH. However there is a bug in the implementation. The
GL renderer accepts the LINEWIDTH statement only before a BEGIN statement.
The internal renderer honors the change of the linewidth before every VERTEX
pair. Note: Tapered lines are not supported by either implementation.
LINEWIDTH and COLOR are optional commands.

LINEWIDTH, w,
BEGIN, LINE_STRIP,
COLOR, r, g, b,
VERTEX, x1,y1,z1,
VERTEX, x2,y2,z2, ...
VERTEX, xn,yn,zn
END

-Original Message- From: Timo Stein 
[mailto:m...@timo-stein.com<mailto:m...@timo-stein.com>] Sent: Friday, July 12, 
20...
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Re: [PyMOL] Creating coloured and transparent polyhedra

[Schubert, Carsten [JRDUS]]

Hi Timo,

I think you may have to switch to a different drawing primitive like TRIANGLES 
or TRIANGLE_STRIP. Since these are closed objects I assume that the enclosing 
area  should be fillable with a color of choice. Unfortunately I have not 
actually had a chance to play with these primitives, so I can't provide any 
docs. Check out \PyMOL\PyMOL\examples\devel\cgo08.py and/or cgo07.py for 
examples of TRIANGLE_STRIPS.

HTH

Carsten

From: Timo Stein [mailto:m...@timo-stein.com]
Sent: Wednesday, July 17, 2013 7:21 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Creating coloured and transparent polyhedra

Hi PyMOL users,

thank you for your help. I tried to apply Carsten's suggestions using the 
LINE_STRIP approach. This is what I tested:
from pymol.cgo import *# get constants
from pymol import cmd

obj = [
LINEWIDTH, 50,
BEGIN, LINE_STRIP,
COLOR, 255, 0, 0,
VERTEX, 11.335700035095215, 7.798659801483154, 7.798659801483154,
VERTEX, 11.335700035095215, 5.352089881896973, 5.352089881896973,
VERTEX, 14.965800285339355, 5.352089881896973, 5.352089881896973,
VERTEX, 14.965800285339355, 7.798659801483154, 7.798659801483154,
VERTEX, 11.335700035095215, 7.798659801483154, 7.798659801483154,
END
   ]

cmd.load_cgo(obj,'cgo01')
where four atoms make up a square. This snippet creates - when called by "run 
" - four lines between these coordinates I got by using "print 
cmd.get_model('', 1).get_coord_list()". How can I have the the 
area between those four points filled with a colour of my choice and have it be 
partly transparent? The next step would be to create polyhedra with 
corresponding surfaces with atoms spanning a three dimensional object.

Thanks in advance
Timo
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Re: [PyMOL] Selection algebra issue

[Schubert, Carsten [JRDUS]]

Katherine,

not sure if that is what you are looking for but you can select for non-polymer 
residues with:

select lig, prot and organic

That will select any non polymer (protein and R(D)NA) residues present in the 
pdb. You then would need to break the selection further into the individual 
constituents, by either chain Id and resid.

Hope this helps a bit.

Carsten

From: Katherine Sippel [mailto:katherine.sip...@gmail.com]
Sent: Friday, December 13, 2013 10:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selection algebra issue

Hi all,
I'm trying to write a script to data mine the pdb. I'm want to look at the 
ligands in a pdb file and fish out those that meet a certain criteria. I've got 
a script that can look at the ligands all at once but I need to assess each 
ligand individually. Since I'm looking at 40,000+ pdbs I need a way to define 
them individually. I've tried variations on "%s' % (resi)" and "bymolec" but I 
can't seem to figure out how to get them parsed separately without specifying a 
number. I've also tried using index to create a tuples list and iterating from 
that but I keep hitting the same issue. I've attached a couple of the attempted 
scripts so you can laugh at my google derived python skills.
I've been trying to figure this out for a week now and I'm completely stumped. 
If anyone could nudge me in the right direction, even if it's some Pymolwiki 
article I missed, I would appreciate it immensely.
Thanks for your time,
Katherine

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Re: [PyMOL] How to automate RMSD calculation for large no of structures

[Schubert, Carsten [JRDUS]]

Hi Om,

asides from the usual list of suspects like access permissions try double 
backslashes or  a raw string in your path-filenames. Python on Windows is a bit 
peculiar in that respect. Read up on raw strings in the Python docs.

Try

wt_file = "D:\\STUDY\\STRUCTURE_PPT\\RMSD\\Pymol\\Original\\1APS.pdb"
or
wt_file = r"D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb"

note the 'r' at the beginning of the string indicating a raw string.

HTH

Carsten

From: Om Shiv [mailto:harhaalmekhu...@gmail.com]
Sent: Thursday, January 09, 2014 6:26 AM
To: Sampson, Jared
Cc: 
Subject: Re: [PyMOL] How to automate RMSD calculation for large no of structures

Hello
I am using the following script file:
### begin script ###

from pymol import cmd
from glob import glob

# Edit these two variables with the paths to your files
wt_file = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb"
mut_glob = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\models\1APS\1APS_*.pdb"

# load the wild-type pdb
cmd.load(wt_file,"wt")

# loop through the mutants
for file in glob(mut_glob):

print file
cmd.load(file,"mut")
rms = cmd.align("wt","mut")[0]
print " %s rmsd: %s" % (file,rms)
cmd.delete("mut")

### end script ###
I ran the above script using Pymol. But I am receiving the following error:

PyMOL>run D:/STUDY/STRUCTURE_PPT/RMSD/Pymol/mut_rmsd.py

ExecutiveProcessPDBFile-Error: Unable to open file 
'D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\OriginalAPS.pdb'.
Traceback (most recent call last):

File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py", line 455, 
in run_file
execfile(file,global_ns,local_ns)

File "D:/STUDY/STRUCTURE_PPT/RMSD/Pymol/mut_rmsd.py", line 11, in 
cmd.load(wt_file,"wt")

File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\importing.py", line 878, 
in load
if _self._raising(r,_self): raise pymol.CmdException

CmdException: 
Can anyone help please.

On Thu, Jan 9, 2014 at 4:48 PM, Om Shiv 
mailto:harhaalmekhu...@gmail.com>> wrote:
Thanks Jared

On Thu, Jan 9, 2014 at 12:03 AM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:
Hi Om -

I hope you don't mind me posting your questions back to the list.  (When 
replying to this list, you have to use Reply All, otherwise it just goes to the 
sender.)

Also, a quick disclaimer: I haven't used PyMOL on Windows in over 5 years, so 
what I'm saying may not be entirely accurate.  (Others, please correct me if 
there's anything incorrect here.)


Hi I have installed Pymol in windows 7 platform. Why does it not allow me to 
save the script in the Pymol folder ?
 Is there any way to save it in Pymol working directory ?

I don't think you really want to save it to the folder where PyMOL is installed 
(if that's what you mean by "the Pymol folder").  The working directory is the 
directory from which PyMOL is launched.  You can see where this is by typing 
`pwd` at the PyMOL command prompt.  Some other shell commands work as well, 
such as `cd` and `ls`.


Thanks for your guidance.

I have modified your script as follows:
### begin script ###

from pymol import cmd
from glob import glob

# Edit these two variables with the paths to your files
wt_file = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb"
mut_glob = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\models\1APS\1APS_*.pdb"

# load the wild-type pdb
cmd.load(wt_file,"wt")

# loop through the mutants
for file in glob(mut_glob):
print file
cmd.load(file,"mut")
rms = cmd.align("wt","mut")[0]
print " %s rmsd: %s" % (file,rms)
cmd.delete("mut")

### end script ###
Used the following command from the command line:  run 
D:\STUDY\STRUCTURE_PPT\RMSD\mut-rmsd.py
But I am receiving the following error:

IOError: [Errno 2] No such file or directory: 
'D:\\STUDY\\STRUCTURE_PPT\\RMSD\\mut-rmsd.py'

Please help.
thanks

Maybe try using the GUI:

1. File > Log... - create a log file (I usually call mine "log.pml"), which 
will be useful later.
2. File > Run... - navigate to your mut-rmsd.py file and run it.
3. Go back and open your log file to see what the command looked like when you 
ran the script.

PyMOL log files are very widely useful for finding out how to translate GUI 
actions into scriptable commands.

Hope that helps!

Cheers,
Jared




On Wed, Jan 8, 2014 at 1:13 AM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:
Hi Om -

Here is another option that loads only one mutant at a time.  You can save the 
following as a Python script (e.g., "mut-rmsd.py") and run it from the PyMOL 
command line by typing `run mut-rmsd.py` (with a full or relative path if it's 
not in PyMOL's working directory).

For more information about these functions, you can also check out a few things 
on the PyMOL Wiki:

http://pymolwiki.org/index.php/Process_All_Files_In_Directory
http://pymolwiki.org/index.php/Align

### begin script ###

from pymol import cmd
from glob import glob

# Edit these two variables with the paths to your files
wt_file = "wt.pdb"
mut_glob = "mut/*.pdb"

# load the wil

Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

[Schubert, Carsten [JRDUS]]

Hi Seth,

I had problems with the underlying APBS version (1.4 I believe) under Windows 
in Pymol 1.7. It croaked with an memory allocation error, which I only found 
after I ran the .in file manually in APBS. Try that. You can either install an 
upgraded version of APBS or switch to Pymol 1.8, which has a "working" APBS 
version.

HTH

Carsten

From: Seth Harris [mailto:set...@gmail.com]
Sent: Wednesday, January 22, 2014 4:16 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

Hi all,

I was trying to use the APBS plug in with PyMOL version 1.7 and I'm getting 
this error with pymol generated files not being found in the tmp directory:

Could not find 
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated.dx so 
searching for 
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 
'/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx' 
exist?
It is true that neither of these files exist there, though pymol-generated.pqr, 
.in and .pdb are there.
I was attempting this with a PDB file that worked in earlier versions, so I 
don't think the problem is with the input. Is it working for others?
Cheers,
Seth

Also, BTW, in the visualization GUI for several versions I've had misbehaving 
buttons where some of the update field lines end up actually controlling the 
isosurfaces and not doing what they are advertised to do.

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Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

[Schubert, Carsten [JRDUS]]

Sorry, I got my versions crossed. I had the same issues with 1.6, it worked 
again with 1.7. Nevertheless I'd try running the .in file separately to debug 
what is going on behind the scenes.

-C.

From: Schubert, Carsten [JRDUS]
Sent: Wednesday, January 22, 2014 4:57 PM
To: Seth Harris; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

Hi Seth,

I had problems with the underlying APBS version (1.4 I believe) under Windows 
in Pymol 1.7. It croaked with an memory allocation error, which I only found 
after I ran the .in file manually in APBS. Try that. You can either install an 
upgraded version of APBS or switch to Pymol 1.8, which has a "working" APBS 
version.

HTH

Carsten

From: Seth Harris [mailto:set...@gmail.com]
Sent: Wednesday, January 22, 2014 4:16 PM
To: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

Hi all,

I was trying to use the APBS plug in with PyMOL version 1.7 and I'm getting 
this error with pymol generated files not being found in the tmp directory:

Could not find 
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated.dx so 
searching for 
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 
'/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx' 
exist?
It is true that neither of these files exist there, though pymol-generated.pqr, 
.in and .pdb are there.
I was attempting this with a PDB file that worked in earlier versions, so I 
don't think the problem is with the input. Is it working for others?
Cheers,
Seth
Also, BTW, in the visualization GUI for several versions I've had misbehaving 
buttons where some of the update field lines end up actually controlling the 
isosurfaces and not doing what they are advertised to do.

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[PyMOL] Roving maps from scripting level?

[Schubert, Carsten [JRDUS]]

Dear All,

I am trying to get the roving density features to work from a scripting level 
w/o invoking the Density Wizard. Setting up the following script loads fine, 
but does not enable roving. Is there anything else I need to define in the 
settings or am I stuck with using the Density  Wizard?

Many thanks for any pointers

Carsten


# Roving_test.py

cmd.load("test.pdb","MyProt")
cmd.zoom("polymer and chain A and resi 1")

cmd.load("2fofc.ccp4",object="2FoFc_map")
cmd.load("fofc.ccp4",object="FoFc_map")

cmd.isomesh(name="2fofc",map="2FoFc_map",level="1.0", selection="polymer and 
chain A and resi 1")
cmd.color("skyblue","2fofc")
cmd.isomesh(name="fofc", map="FoFc_map", level="3.0", selection="polymer and 
chain A and resi 1")
cmd.color("green","fofc")
cmd.isomesh(name="neg-fofc", map="FoFc_map", level="-3.0", selection="polymer 
and chain A and resi 1")
cmd.color("red","neg-fofc")

cmd.set("roving_map1_name","2fofc")
cmd.set("roving_map2_name","fofc")
cmd.set("roving_map3_name","neg-fofc")

cmd.set("roving_map1_level",1.0)
cmd.set("roving_map2_level",3.0)
cmd.set("roving_map3_level",-3.0)

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Re: [PyMOL] Error while starting Pymol 1.7

[Schubert, Carsten [JRDUS]]

Hi Roy,

I ran into the same issue last week. I am running Pymol of a laptop with an 
Intel chip driving the internal monitor and a Nvidia chip for the external 
monitor. The same error pops up when I ran Pymol using the intel graphics chip, 
but not when I run Pymol of the Nvidia head. According to Schrodinger support 
the issue has to do with the poor implementation of GL on the Intel chips. From 
what I gather from their information only the shader and volume support is 
affected/disabled even though the error message sounds rather scary.

The only solution to the problem seems to be to switch to a Nvidia based 
system, which supports the advanced GL commands.

Cheers,

Carsten

From: Roy Eylenstein [mailto:roy.eylenst...@morphosys.com]
Sent: Monday, January 27, 2014 7:45 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Error while starting Pymol 1.7

Dear all,

I see following error message when starting pymol 1.7 incentive on Win 7 
enterprise SP1 32 bit (i3 M370)

This Executable Build integrates and extends Open-Source PyMOL 1.7.0.1.
Detected OpenGL version 2.0 or greater. Shaders available.
CShaderPrg_New-Error: geometry shader compilation failed name='connector'; log 
follows.
infoLog=ERROR: 0:2: '' :  extension 'GL_EXT_geometry_shader4' is not supported
ERROR: 0:3: '' :  extension 'GL_EXT_gpu_shader4' is not supported
ERROR: 0:5: 'vec3' : syntax error parse error


Any suggestions?

Best,


Roy



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Re: [PyMOL] Roving maps from scripting level?

[Schubert, Carsten [JRDUS]]

Thanks Nat,

that example worked nicely.

Cheers,

Carsten

From: Nat Echols [mailto:nathaniel.ech...@gmail.com]
Sent: Friday, January 24, 2014 3:13 PM
To: Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Roving maps from scripting level?

On Fri, Jan 24, 2014 at 11:55 AM, Schubert, Carsten [JRDUS] 
mailto:cschu...@its.jnj.com>> wrote:
I am trying to get the roving density features to work from a scripting level 
w/o invoking the Density Wizard. Setting up the following script loads fine, 
but does not enable roving. Is there anything else I need to define in the 
settings or am I stuck with using the Density  Wizard?

Try this:

cmd.load("test.pdb","MyProt")
cmd.zoom("polymer and chain A and resi 1")

cmd.load("2fofc.ccp4",object="2FoFc_map")
cmd.load("fofc.ccp4",object="FoFc_map")

cmd.set("suspend_updates", 1)
cmd.set("roving_detail", 10)
cmd.set("roving_origin", 1)
cmd.set("roving_map1_name","2FoFc_map")
cmd.set("roving_map2_name","FoFc_map")
cmd.set("roving_map3_name","FoFc_map")

cmd.set("roving_map1_level",1.0)
cmd.set("roving_map2_level",3.0)
cmd.set("roving_map3_level",-3.0)

cmd.isomesh(name="rov_m1",map="2FoFc_map",level="1.0", selection="polymer and 
chain A and resi 1")
cmd.color("skyblue","rov_m1")
cmd.isomesh(name="rov_m2", map="FoFc_map", level="3.0", selection="polymer and 
chain A and resi 1")
cmd.color("green","rov_m2")
cmd.isomesh(name="rov_m3", map="FoFc_map", level="-3.0", selection="polymer and 
chain A and resi 1")
cmd.color("red","rov_m3")
cmd.set("suspend_updates", 0)
-Nat
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[PyMOL] List residues functionality ?

[Schubert, Carsten [JRDUS]]

Hi All,

probably a question for the developers, but may not hurt to ask publicly: Is 
there a functionality in Pymol to list the residues in a given selection? I am 
looking for the equivalent to the get_chains() function. I have scripted 
something up, but the code is not 100% clean and not flexible enough. For large 
molecules the performance is not great either.


 start script
def list_resi(obj=""):
"""
DESCRIPTION

"list_resi" prints and returns the unique residue IDs from the input
object. The object must be present in the object list
on the GUI. Selections are currently not implemented.
Chain or Segments are also not taken into account
USAGE

list_resi obj

EXAMPLES

list_resi my_prot

l = list_resi(my_prot)
"""

if ( obj == "" ):
obj="(all)"

ol = cmd.get_object_list()
if (obj in ol):
pass
else:
print "Error: Object (%s) not found" % obj
return

stored.resi_list = []
cmd.iterate(obj,"stored.resi_list.append(int(resi))")
stored.resi_list=list(set(stored.resi_list))  # make list unique
stored.resi_list.sort()

for i in range(0,len(stored.resi_list)):
print "%s," % stored.resi_list[i],
if ((i+1) % 10 == 0):
print ""

return stored.resi_list

# End Script

Thanks for any input


Carsten
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Re: [PyMOL] apbs plugin

[Schubert, Carsten [JRDUS]]

Hi jpd,

try running APBS directly just using the .in file generated from a failed run. 
That may provide a clue as to where the problem is, i.e. within APBS itself or 
within the plugin. If it is APBS, which is throwing the error you may want to 
try to grab an updated version or the source code to compile yourself.

HTH

Carsten

From: jp d [mailto:yo...@yahoo.com]
Sent: Tuesday, February 11, 2014 2:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] apbs plugin

hi,
anyone else having trouble with the apbs plugin?
i keep crashing as soon as i try to do anything.
if i select 'Choose externally generated PQR'
or 'run APBS' i get this
In show error 1
alloc: invalid block: 0x2c29fb78: 0 0
Abort

this is with pymol 1.7
ubuntu 12.04
using 1FAS fetched from the pdb

thanks
jpd
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Re: [PyMOL] boundaries/outlines of overlapping regions on surface

[Schubert, Carsten [JRDUS]]

Sid,

I'm guessing here, but may be coloring by properties (new in 1.7) may be the 
way to go. Usually I would color the residues and if you want to show the 
underlying residues I would just make another object for those.

HTH,

Carsten

From: Sridharan, Sudharsan [mailto:sridhar...@medimmune.com]
Sent: Tuesday, April 08, 2014 9:48 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] boundaries/outlines of overlapping regions on surface

Hi all,

I'd like to colour different regions on the same protein surface but also draw 
the outlines/boundaries of these regions as well to show where they overlap (I 
guess I could colour the common residues in a different colour but I don't want 
to do that!). Can someone please let me know how to do this in Pymol (v 1.7)?

Many thanks.

Kind regards,
Sid.


[MedI Logo Sig]

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Scientist I, Protein Sciences, Department of Antibody Discovery and Protein 
Engineering

Aaron Klug Building, Granta Park,
Cambridge, CB21 6GH, UK.
P: +44(0)1223 898195F: +44(0)1223 471472


sridhar...@medimmune.com
www.medimmune.com


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Re: [PyMOL] animation showing conformational change

[Schubert, Carsten [JRDUS]]

Alternatively you could try the Morph server in Gerstein's lab and then load 
each intermediate structure into a separate state for animation purposes.

http://morph2.molmovdb.org/

HTH

Carsten

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Wednesday, April 09, 2014 12:34 PM
To: sunyeping
Cc: pymol-users
Subject: Re: [PyMOL] animation showing conformational change

Hi Yeping -

With incentive PyMOL version 1.6 or later, you can use `morph`.  >From what I 
read at http://pymolwiki.org/index.php/Morph, you'll need to put both 
conformations of the protein into one object, as different states.  See 
http://pymolwiki.org/index.php/Load for more info on that.

Cheers,
Jared

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On Apr 9, 2014, at 11:58 AM, sunyeping 
mailto:sunyep...@aliyun.com>> wrote:


Dear all,

If I have the structures representing two conformations of one protein, then 
could I make a animation movie that shows how the protein transforms from one 
conformation to the other conformation using pymol? Thanks.



Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

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Re: [PyMOL] regarding APBS tools in PyMOL

[Schubert, Carsten [JRDUS]]

Hi Vaheh,

my recollection is a bit hazy, but I remember having some issues with the 
distributed APBS version earlier this year. Try downloading the latest APBS and 
run the plug-in generated input file using the latest version from the 
commandline. If that works you may have to swap the APBs binary or adjust the 
path to APBS accordingly.

HTH

Carsten

From: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
Sent: Tuesday, April 22, 2014 9:45 AM
To: pymol-users
Subject: [PyMOL] regarding APBS tools in PyMOL

Colleagues,

The latest PyMOL version 1.7.0.3 looks like having issues with molecule size 
when APBS is being used. I’m loading whole molecule consisting of ~500 aa and 
APBS plugin after setting up the grid and after starting APBS run few seconds 
later opens a window with message: APBS stopped working. Close Program. If I 
load a portion of the molecule (and it doesn’t matter which, but should be less 
than 200 aa) then it works fine.
It is being run on Intel Core i7, 64-bit with 8 GB RAM.
Did anyone see such behavior?

Regards,

Vaheh
8-5851

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Re: [PyMOL] Other coloring strategies based on user-provided properties

[Schubert, Carsten [JRDUS]]

Chen,

not sure if this has made it yet into the open source version, but to quote the 
incentive version documentation “Beginning with incentive PyMOL 1.6, arbitrary 
object level and atom level properties are supported. Now, for each object and 
each atom you can possibly have an arbitrary dictionary associated with each.” 
So if you are a subscriber you could make use of that feature, which could be 
more powerful than relying either on the B-factor or Occupancy fields.

HTH

Carsten

From: Chen Zhao [mailto:chenzhaoh...@gmail.com]
Sent: Friday, August 29, 2014 12:25 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Other coloring strategies based on user-provided properties

Dear all,
I am thinking whether it is possible to color a molecule by a specific property 
residue-wise or atom-wise like generally be done on B-factor? This property 
could be provided as numbers in a column. An obvious way might just be to 
change the B-factor column to the user-provided column and "color by B-factor". 
But I am wondering whether there are some direct ways of doing this.
Best,
Chen
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Re: [PyMOL] How to draw clashes in pymol -> integration/plug-in of Molprobity in PyMol???

[Schubert, Carsten [JRDUS]]

Tim: Good suggestion, I would second this effort. Thanks for raising the issue

Cheers,

Carsten

From: Tim Schulte [mailto:tim.schu...@ki.se]
Sent: Wednesday, October 22, 2014 2:11 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to draw clashes in pymol -> integration/plug-in of 
Molprobity in PyMol???

Hej everybody,
my question is related to this post.
I am just analyzing a structure and really like the way Molprobity puts out 
information about hydrogen bonds and vdW contacts and so on.

It is also possible to take advantage of this analysis in phenix during/after 
refinement, because Coot provides a graphical interface for visualization of 
the Molprobity output - however, Coot is not my favorite program for making 
nice figures.

So I just wonder whether it might be of general interest to the pymol community 
if someone would write a plug-in to integrate the Molprobity output in PyMol?

I can definitely not do it, but maybe this could be an interesting feature 
request to the PyMol developers?

All the best,
Tim



Am 30/08/14 01:53, schrieb Robert Immormino:
Hi Bondurant,

I really like the merging of the graphic beauty of pymol with the detailed 
depictions of reduce and probe.  I have a method that is a bit clunky for doing 
what you ask, but I don't know if it ever made it to the mainstream in 
MolProbity.  The caveat of wanting to work with a ligand makes it a bit harder 
to explain so my apologies in advance if things aren't 100% clear but here 
goes

1. Make sure you have a reduce definition file for your ligand.  If the ligand 
had been deposited in the PDB before ~2012 then the reduce_wwPDB_het_dict file 
found (http://kinemage.biochem.duke.edu/software/reduce.php)  should have it, 
otherwise here's an example:

RESIDUE   ACP  11
CONECT  P  4 O1   O2   O3   O4
CONECT  O1 1 P
CONECT  O2 1 P
CONECT  O3 1 P
CONECT  O4 2 PC1
CONECT  C1 3 O4   O5   C2
CONECT  O5 1 C1
CONECT  C2 4 C1  HC1  HC2  HC3
CONECT HCH11 C2
CONECT HCH21 C2
CONECT HCH31 C2
END
HETACP  8
HETNAM ACP ACETYL PHOSPHATE
FORMUL  ACPC2 H3 O5 P1 2-

2. download the reduce and probe executables also from 
http://kinemage.biochem.duke.edu/

3.  run reduce make sure to use the -DB flag to input your ligand dictionary

4. run probe with a command something like:
probe -both "chaina 88 (ATOM_OG1 | ATOM_HG1)" "chainx 1" CheY_A88T_AcP_H.pdb
Where chain A in this case is the protein and the hydroxyl of Thr 88 is the 
only relevant interacting group with chain X the ligand.

5. convert the probe output to a python script to render the cgo objects in 
pymol using the attached perl script.  ./probe_to_cgo [input probe dots] 
[output pymol cgo]

6. use the run command in pymol to execute the python script and draw the cgo 
output.

If this all works the first go then amazing!  If not I can try to help get 
things working, but it's been a few years since I last used these tools.

Best of Luck!
-bob


On Fri, Aug 29, 2014 at 10:30 AM, Bondurant 
mailto:bondurant...@gmail.com>> wrote:
Hello community,
I would like to draw a figure similar to this one
http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg
showing the clashes between a potential ligand and the protein. The only way i 
know how to do this in pymol is using the show_bumps plugin, but i don't really 
like the "red disks" format.
Could anyone tell me how i could easily draw something similar to those red 
spikes from the example to represent the clashes in pymol or any other program? 
I'm able to do it using molprobity and kinemage, but there's no much 
possibilities for editing and to get it in printing quality.
Thanks

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Re: [PyMOL] CGOs

[Schubert, Carsten [JRDUS]]

Hi Bob,

a while back I attempted to document the CGO capabilities, but never finished 
it. Attached is a bit of a write-up from that attempt.

Hope it helps somewhat.

Carsten

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Monday, December 22, 2014 12:27 PM
To: David Hall
Cc: pymol-users
Subject: Re: [PyMOL] CGOs

OK, that explains it. I think I made that one up. It was a while ago that I 
worked on this. :)
I see the list at 
https://github.com/speleo3/pymol/blob/master/modules/pymol/cgo.py
Thanks​, David.
Bob
# CGO documentation
This documentation will attempt to shed some light on the syntax and provide
usage examples for each of the individual CGO primitives and if possible the
drawing directives

The module PyMOL\modules\pymol\cgo.py defines the following symbols,
which seem to be the current supported primitives in PyMOL. 

POINTS = 0.0
LINES  = 1.0
LINE_LOOP  = 2.0
LINE_STRIP = 3.0
TRIANGLES  = 4.0
TRIANGLE_STRIP = 5.0
TRIANGLE_FAN   = 6.0
#QUADS  = 7.0
#QUAD_STRIP = 8.0
#POLYGON= 9.0   
 

STOP   =  0.0
NULL   =  1.0
BEGIN  =  2.0
END=  3.0
VERTEX =  4.0
NORMAL =  5.0
COLOR  =  6.0
SPHERE =  7.0
TRIANGLE   =  8.0
CYLINDER   =  9.0
LINEWIDTH  = 10.0
WIDTHSCALE = 11.0
ENABLE = 12.0
DISABLE= 13.0
SAUSAGE= 14.0
CUSTOM_CYLINDER= 15.0
DOTWIDTH   = 16.0
ALPHA_TRIANGLE = 17.0
ELLIPSOID  = 18.0

#SHAPE_VERTEX   = 16.0
#SHAPE_COLOR= 17.0
#SHAPE_NORMAL   = 18.0

FONT   = 19.0
FONT_SCALE = 20.0
FONT_VERTEX= 21.0
FONT_AXES  = 22.0

CHAR   = 23.0

ALPHA  = 25.0
QUADRIC= 26.0 # NOTE: Only works with ellipsoids and disks
CONE   = 27.0 

LIGHTING   = float(0x0B50)

Header 
== 

The following header lines must be defined to import the required symbols
into the internal python interpreter:

from pymol.cgo import *
from pymol import cmd

Syntax
==

The syntax for most of the primitives seems to be of the form
PRIMITIVE ARG1 ARG2 ... ARGn

were ARG1-ARGn are the required arguments. In reality these primitives are
nothing but numbers, which represent drawing directives for the internal
OpenGL renderer and the interal raycaster. Usually they are assembled in a
list, also called a CGO object. This list can either be assembled by hand or
generated by code. In the case of "hand-assembly" into a python list the
primitives and individual arguments are comma separated. In the case of code
generated primitives the usual python list manipulation methods can be used
as well.

Example (cgo01.py from PyMOL\examples\devel)

 cgo01.py ##
from pymol.cgo import *
from pymol import cmd

# this is a trivial example of creating a cgo object consisting of a
# a single state 

# first we create a list of floats containing a GL rendering stream

obj = [
   BEGIN, LINES,# inline comments are allowed
   COLOR, 1.0, 1.0, 1.0,# white color
   
   VERTEX, 0.0, 0.0, 0.0,   # origin at (0,0,0)
   VERTEX, 1.0, 0.0, 0.0,   # extend line one unit in x
   
   VERTEX, 0.0, 0.0, 0.0,   # origin at (0,0,0)
   VERTEX, 0.0, 2.0, 0.0,   # extend line two units in y
   
   VERTEX, 0.0, 0.0, 0.0,   # origin at (0,0,0)
   VERTEX, 0.0, 0.0, 3.0,   # extend line three units in z

   END
   ]

# then we load it into PyMOL ads the object 'cgo01'

cmd.load_cgo(obj,'cgo01')

# move the read clipping plane back a bit to that that is it brighter

cmd.clip('far',-5)
 END cgo01.py ##

The whole object could have also been defined as:

obj =[2.0, 1.0, 6.0, 1.0, 1.0, 1.0, 4.0, 0.0, 0.0, 0.0, 4.0, 1.0, 0.0, 0.0,
4.0, 0.0, 0.0, 0.0, 4.0, 0.0, 2.0, 0.0, 4.0, 0.0, 0.0, 0.0, 4.0, 0.0, 0.0,
3.0, 3.0]

but much less readable.

Color
=
The color of CGO objects is set by the COLOR command and it has the form

COLOR, r,g,b,

where r g and b are floating point numbers ranging from 0.0 to 1.0 for each
of the red, green and blue channels of a colour. You may be familiar with RGB
colourspace expressed in different ways for example as integers 0 to 255
(RGB-255) or percentages (RGB-100). So you may have to do a simple numeric
conversion to get your favourite colours.


Lines
=

The LINES command draws a lines between a set of coordinates defined by the
VERTEX command. The colour of the lines can be changed at any time even
between vertices, so that the start and end line color can be different. The
color of the line will be interpolated between the start and end color. The
thickness of the line is set by LINEWIDTH. However there is a bug in the
implementation. The GL rendere

Re: [PyMOL] How do I undo my last command I executed in the PyMOL command line and viewer?

[Schubert, Carsten [JRDUS]]

As far as I you cannot undo commands issued on the command line. This feature 
seems to be mostly targeted towards the builder interface or some other 
interactive features. For 'newbies' I would recommend opening up a session, 
starting to work on your presentation and saving frequently. That way you have 
a fallback. However it is much easier in the long run to invest some time and 
building the presentation with a script. A good way to do that would be to have 
a clear picture in mind what kind of presentation to make, then enable logging 
and work your way through your presentation, can be combined with sessions as 
well. You can use the log file as a starting point for a pml (not python based) 
script. 

-Original Message-
From: Brenton Horne [mailto:brentonho...@ymail.com] 
Sent: Tuesday, January 06, 2015 10:44 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] How do I undo my last command I executed in the PyMOL command 
line and viewer?

Hi,

I thought that running "undo" from the PyMOL command line would do this but it 
didn't do anything that I could see visually in the viewer. I've also tried 
going to Edit->Undo and it didn't do anything visually apparent in the viewer.

Thanks for your time,
Brenton

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[PyMOL] How to determine distance of matching atoms in aligned nonidentical structures?

[Schubert, Carsten [JRDUS]]

Hi,

How can I best determine the distance between matching pairs of atoms in two or 
more aligned structures? Fairly easy to do when the two aligned structures are 
the same, but how does one go about when the structures are not the same? The 
problem is that I cannot figure out how to dependably match structurally 
superimposed CA's besides a distance criterion, which does not seem to be to 
reliable in the case of large deviations. I tried to snoop around in the 
alignment object created by the align command, but did not make much inroads.

Anyone have any experience with this?

Thanks

Carsten

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Re: [PyMOL] How to determine distance of matching atoms in aligned nonidentical structures?

[Schubert, Carsten [JRDUS]]

Yep, that was it and will take care of most of the issues I encountered. Just 
stumbled upon colorbyrmsd.py, which contained that function a couple of minutes 
ago as well. 

Thanks for all the suggestions and pointers!

Cheers,

Carsten

-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Monday, January 19, 2015 3:33 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to determine distance of matching atoms in aligned 
nonidentical structures?

Hi Carsten & Shane,

I assume Carsten is looking for cmd.get_raw_alignment(). Recent versions of 
PyMOL can create an alignment object with all alignment commands (align, super, 
cealign). get_raw_alignment returns the (model, index) keys for all pairs.

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

Example:

fetch 1ubq 2lgd, async=0
super 1ubq & guide, 2lgd & guide, object=aln

python
pairs = cmd.get_raw_alignment('aln')
for pair in pairs:
  print pair, cmd.get_distance(pair[0], pair[1]) python end

Hope that helps.

Cheers,
  Thomas

On 19 Jan 2015, at 14:47, Shane Caldwell  wrote:

> Hi Carsten,
> 
> This sounds like a non-trivial problem, my understanding is that it's still 
> an ongoing challenge to best align dissimilar structures. Other ways of 
> aligning structures involves using the vectors from secondary structure 
> elements, or feeding in (multiple) sequence alignments. All have their 
> benefits and drawbacks. Which you use will depend on what you are trying to 
> do.
> 
> Depending on what information you have, the strategy will change and CA-CA 
> distances may or may not be reasonable to compare. The underlying challenge 
> is the question of how to know which parts of structures are functionally 
> equivalent, and the answer gets philosophical once the sequences diverge a 
> lot. With drift of sequence, geometry and function can drift as well. 
> 
> I'd have a look into the various algorithms detailed at 
> http://www.rbvi.ucsf.edu/home/meng/grpmt/structalign.html and see if one fits 
> your situation. Of course, if you're just looking for a few values, PyMol's 
> Measurement Wizard is a low-tech way to get a few distances.
> 
> Sorry if this isn't too helpful, but without knowing more about your 
> situation it's difficult to make recommendations.
> 
> Cheers,
> 
> Shane Caldwell
> McGill University
> 
> On Sun, Jan 18, 2015 at 9:12 PM, Schubert, Carsten [JRDUS] 
>  wrote:
> Hi,
> 
> How can I best determine the distance between matching pairs of atoms in two 
> or more aligned structures? Fairly easy to do when the two aligned structures 
> are the same, but how does one go about when the structures are not the same? 
> The problem is that I cannot figure out how to dependably match structurally 
> superimposed CA's besides a distance criterion, which does not seem to be to 
> reliable in the case of large deviations. I tried to snoop around in the 
> alignment object created by the align command, but did not make much inroads.
> 
> Anyone have any experience with this?
> 
> Thanks
> Carsten

--
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PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] when number of atoms changes, colors change in an uncontrolled manner

[Schubert, Carsten [JRDUS]]

Hi Efrem,

do you still see the same behavior if you disable automatic change of colors 
when loading your PDBs? The relevant setting would be auto_color set to off.
Does not quite answer your question, but could be a work-around.

HTH

Carsten


From: Efrem Braun [mailto:efrem.br...@gmail.com]
Sent: Friday, March 27, 2015 3:19 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] when number of atoms changes, colors change in an uncontrolled 
manner

Hello,

I'm running a Monte Carlo simulations in which the number of atoms in my 
simulation box changes over the course of the simulation. I print all atoms as 
Hydrogen, so the colors of them should all be white. When I load the resulting 
pdb file into PyMOL, the first frame has all atoms colored white, but by frame 
3 some of the atoms have turned black, by frame 9 some atoms have turned orange 
or blue, and by frame 15 lots of purple atoms show up (the purple atoms 
disappear in frame 16 and reappear in frame 17 along with a whole bunch of 
other colors).

I tried to troubleshoot this by typing "iterate all, print color." It printed 
"29" for the 219 atoms it iterated over (at no frame does my simulation box 
contain 219 atoms; the first 10 frames contain 200, 206, 209, 213, 206, 209, 
221, 238, 235, and 253 atoms, and the last 10 all contain more than 253 atoms). 
Since it doesn't appear to be iterating over all atoms, I suspect this 
indicates what the problem is, but I can't figure it out.

I put frame 20 into its own pdb file and displayed it in pymol, and it 
displayed all 428 atoms as white. So the problem definitely appears to be 
coming from the fact that the number of atoms in the box is changing. With 
simulations in which the number of atoms remains constant, I've never had this 
problem.

This occurs both when I run on Linux (Version 1.7.0.0) or on a Mac (Version 
1.7.2.1).

Any help would be greatly appreciated. Both pdb files are attached.

Efrem Braun
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Re: [PyMOL] RMS over a MD trajectory.

[Schubert, Carsten [JRDUS]]

Hi Al,

you would need to go through the Python API:

python
rms=cmd.align("mobCA","tarCA", quiet=0)
print rms
python end

rms contains a tuple with various parameters related to the superposition. The 
first value in the tuple i.e. rms[0] should be the RMS value.

HTH 

Carsten

-Original Message-
From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] 
Sent: Wednesday, May 06, 2015 8:32 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RMS over a MD trajectory.

Hi,
I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I 
can see that "align" does things correctly when:
  align trj, pdb1, mobile_state=1
i. e., when I align the first snapshot of the trajectory with the PDB file. I 
also understand that PyMOL does compute the RMS along the trajectory if I 
simply:
  align trj, pdb1
as it is told in:
  http://www.pymolwiki.org/index.php/Align
However, I am unable to get the list of RMS values printed out. How could I do 
that?

Thanks,
Albert

--
-
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451


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Re: [PyMOL] RMS over a MD trajectory.

[Schubert, Carsten [JRDUS]]

Hi Al,

based on my experience running align or super with "cycles=0" has the tendency 
to produce inferior alignment results. So depending on how similar the 
conformation of your structures are you may end up with skewed statistics. What 
I've done in the past and for a paper I'm working on now is to run the 
alignment with default parameters to get the best superposition and then 
calculate the statistics by hand from the superposed structures. Not sure if 
cmd.rms() would do this for all residues w/o outlier rejection, so I ended up 
writing code for myself. The colorbyrmsd.py 
(http://pymolwiki.org/index.php/ColorByRMSD) script gives a nice illustration 
on how to approach this this.

Carsten

-Original Message-
From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] 
Sent: Friday, May 08, 2015 10:04 AM
To: Thomas Holder
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] RMS over a MD trajectory.

Thanks Thomas,
I was already printing k[i][3] (RMSD before refinement) instead of k[i][0] 
(RMSD after refinement) but your "cycles=0" looks cleaner.

Cheers,
Albert

On 05/06/2015 05:14 PM, Thomas Holder wrote:
> Hi Albert,
>
> Please pay attention to the difference between all-atom RMSD and RMSD after 
> outlier rejection.
> http://pymolwiki.org/index.php/Align#RMSD
>
> If your "trj" and "pdb1" have identical topology and matching atom 
> identifiers, then you can also use cmd.rms().
> http://pymolwiki.org/index.php/Rms
>
> Cheers,
>Thomas
>
> On 06 May 2015, at 11:56, Albert Solernou  wrote:
>
>> Terribly useful Carsten!
>>
>> I could easily do a loop and get the RMS along the trajectory:
>>   k = []
>>   for i in range(1,101): k.append(cmd.align("trj","pdb1",mobile_state=i))
>>   for i in range(100): print k[i][0]
>>
>> Cheers,
>> Albert
>>
>>
>> On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
>>> Hi Al,
>>>
>>> you would need to go through the Python API:
>>>
>>> python
>>> rms=cmd.align("mobCA","tarCA", quiet=0) print rms python end
>>>
>>> rms contains a tuple with various parameters related to the superposition. 
>>> The first value in the tuple i.e. rms[0] should be the RMS value.
>>>
>>> HTH
>>>
>>> Carsten
>>>
>>> -Original Message-
>>> From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
>>> Sent: Wednesday, May 06, 2015 8:32 AM
>>> To: pymol-users@lists.sourceforge.net
>>> Subject: [PyMOL] RMS over a MD trajectory.
>>>
>>> Hi,
>>> I am trying to compute the RMS between a PDB file and a Gromacs trajectory. 
>>> I can see that "align" does things correctly when:
>>>align trj, pdb1, mobile_state=1
>>> i. e., when I align the first snapshot of the trajectory with the PDB file. 
>>> I also understand that PyMOL does compute the RMS along the trajectory if I 
>>> simply:
>>>align trj, pdb1
>>> as it is told in:
>>>http://www.pymolwiki.org/index.php/Align
>>> However, I am unable to get the list of RMS values printed out. How could I 
>>> do that?
>>>
>>> Thanks,
>>> Albert
>>>
>>> --
>>> -
>>> Dr Albert Solernou
>>> EPSRC Research Fellow,
>>> Department of Physics and Astronomy,
>>> University of Leeds
>>> Tel: +44 (0)1133 431451

--
-
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451


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[PyMOL] Handling of scene specific global settings?

[Schubert, Carsten [JRDUS]]

Hi,

with the current refactoring of the scene code was there any consideration 
given to the handling of scene specific global settings? For instance "cartoon 
putty" vs. "cartoon automatic" or settings like "sphere_scale" are only applied 
once on a global scope and carry over to all scenes, even though in my script 
they have been defined individually for different scenes.
Right now I am using 1.7.3, but was wondering if anything has changed in 1.7.6 
in that regard? The issue is not new, but it would be nice if there would be a 
feature like this implemented.

Cheers,

Carsten

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Re: [PyMOL] create bonds between selections within cutoff radius

[Schubert, Carsten [JRDUS]]

Shamelessly hijacking this thread... 

...but the index page for the Wiki 
http://www.pymolwiki.org/index.php/Category:Commands has not been updated for 
the last 10 year, according to the footer. In other words the "find_pairs" 
function is not on the index. Makes me wonder, what else is missing?!

What is the current status with regards to updates on the Wiki? Is there anyone 
from the community with time and capability willing to take this up and 
maintain this resource or are we just letting this wither away?

Cheers,

Carsten

-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Thursday, May 28, 2015 9:17 AM
To: Osvaldo Martin
Cc: Tobias Martin; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] create bonds between selections within cutoff radius

Hi Osvaldo,

your solution can be simplified if you use cmd.find_pairs:

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

Cheers,
  Thomas

On 28 May 2015, at 09:06, Osvaldo Martin  wrote:

> Hi Tobias,
> 
> One possible solution will be to run the following code.
> 
> import pymol
> from pymol import cmd, stored
> 
> stored.pd = []
> stored.pairs = []
> 
> cmd.iterate('name pd', 'stored.pd.append(index)')
> 
> for i in stored.pd: 
> cmd.iterate('name si within 2.5 of index %s' % i, 
> 'stored.pairs.append((%s, index))' % i)
> 
> print stored.pairs
> 
> 
> If you run the above code you will obtain a list of tuples, each tuple 
> contains the indexes of the pairs Pd-Si atoms (fulfilling the "within 2.5 A" 
> criteria).  Then you should iterate over "stored.pairs"  to create the bonds 
> between the atoms in each pair. Something like this:
> 
> for pair in stored.pairs:
> cmd.bond('index %s' % pair[0], 'index %s' % pair[1])
> 
> 
> Cheers,
> Osvaldo.
> 
> On Thu, May 28, 2015 at 7:37 AM, Tobias Martin  
> wrote:
> I want to create bonds between e.g. all Pd atoms and all Si atoms, but 
> only within a specified cutoff radius.
> 
>  bond (n. pd), (n. si) within 2.5 of (n. pd)
> 
> creates all possible bonds between all Pd atoms and all Si atoms near 
> enough to any Pd atom. This yields a weired structure with very long, 
> unwanted bonds.
> I tried to iterate over the first selection, to draw only bonds 
> between an Pd atom and Si atoms which are within range to that Pd atom 
> like
> 
>iterate (n. pd), bond id ID, (n. si) within 2.5 of (id
> ID)
> 
> but get an syntax error. Is it possible to create bonds within an 
> iteration?
> 
> Best regards,
> tmartin

--
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PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] How to forbid merging of files?

[Schubert, Carsten [JRDUS]]

AE, 

you need to delete the loaded file before loading another. cmd.save will save 
ALL objects in the buffer by default as you have experienced yourself. Also 
your handling of the filename is slightly off, since pymol strips the extender 
upon loading, i.e. "test01.pdb" becomes "test01" object. You have two choices 
here, either you can retain all files in the buffer (not sure if this is your 
intention) or use Pymol as a file converter (you could use BABEL for that as 
well, might work better ?!). This is how I would write the code (untested 
however):

cmd.reinitialize()
myDir = ‘/dirWithFiles'

for filename in os.listdir(myDir):
cmd.load (filename)
obj_name = os.path.splitext(filename)[0]
filenameN = obj_name + '.mol'
cmd.save(filename, obj_name)
cmd.delete(obj_name)# comment out this line of you want to keep all 
files in the buffer


-Original Message-
From: AE [mailto:alsalisb...@yahoo.com] 
Sent: Saturday, June 06, 2015 5:54 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to forbid merging of files?

Good day,

I have several thousands of files, which I upload using the loop:

myDir = ‘/dirWithFiles'
for filename in os.listdir(myDir):
cmd.load (filename)
filenameN = os.path.splitext(filename)[0]
cmd.save(filenameN + '.mol')
cmd.disable(filename)

I am trying to save them one by one in a different (.mol) format. However, the 
files are saved together, i.e.: first file opened contains only molecule from 
the first file; second: first + second; third: first + second + third etc. But 
I want firstFile.readableFormat to be converted into firstFile.mol, 
secondFile.readableFormat - secondFile.mol etc, without any addition of other 
files. How can I do that?

Thank you,

Best Regards,

Alsa

Sorry I have sent it already, accidentally forgot to finish the question in 
subject(
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Re: [PyMOL] A strange mistake when working with files. KeyError: 'atomName' Selector-Error: Invalid selection name myFile

[Schubert, Carsten [JRDUS]]

Alsa,

it looks as if the error does not originate from within the script itself, but 
it caused in the chempy module, which reads the sdf files. It looks to me as if 
one of your SDF files is either corrupted or PyMol does not like it. Since you 
are logging, which file is read, why don’t you load that particular SDF file in 
by hand and see what happens. You may have to exclude that file from your 
script.

Cheers,

Carsten

-Original Message-
From: AE [mailto:alsalisb...@yahoo.com] 
Sent: Tuesday, June 09, 2015 7:23 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] A strange mistake when working with files. KeyError: 
'atomName' Selector-Error: Invalid selection name myFile

Hello pyMol Users,

I have recently started working with pyMol. Here is my script, which one of the 
users (I am not sure whether it is right or not to write the name) has helped 
me to fix:

import os
from pymol import cmd
cmd.reinitialize()
myDir = '/Users/User/myFolder'
#print(myDir)
for filename in os.listdir(myDir):
print('HERE FILENAME is' , filename)
if os.access(filename, os.R_OK):
#check whether file exists and readable
if ‘cif' in filename:
#only cif format is needed
cmd.load (filename)
obj_name = os.path.splitext(filename)[0]
filenameN = obj_name + '.mol'
cmd.save(filenameN, obj_name)
cmd.delete(obj_name)


Here is the mistake log:

File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/importing.py",
 line 819, in load
_processCIF(cif,oname,state,quiet,discrete,_self)
  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/importing.py",
 line 409, in _processCIF
for i, rec in enumerate(cif):
  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py",
 line 671, in next
rec = CIFRec(self.datablocks_it.next())
  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py",
 line 226, in __init__
self.read_chem_comp_bond()
  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py",
 line 575, in read_chem_comp_bond
if self.read_chem_comp_bond_atom_ids(None, loop.keys, loop.rows):
  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py",
 line 557, in read_chem_comp_bond_atom_ids
name_dict[self.index_to_str(label_2,value)]]

KeyError: ‘AtomName’

#atom name, e.g. ‘O’, ‘H2'


Selector-Error: Invalid selection name «obj_name".
(obj_name)<--
Traceback (most recent call last):
  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/parsing.py",
 line 452, in run_file
execfile(file,global_ns,local_ns)
  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/parsing.py",
 line 447, in execfile
b.execfile(filename, global_ns, local_ns)
  File "/Users/User/pyMolScript.py", line 13, in 
cmd.save(filenameN, obj_name)
  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/exporting.py",
 line 626, in save
io.mol.toFile(_self.get_model(selection,state,ref,ref_state),filename)

  File 
"/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/querying.py",
 line 1064, in get_model
if _raising(r,_self): raise pymol.CmdException

CmdException:  Error: None

Can you, please, tell how to fix this? And, if possible, what caused the 
mistake?

Thank you,

Best Regards,

Alsa


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Re: [PyMOL] Phosphorylation

[Schubert, Carsten [JRDUS]]

Hi Melanie,

funny you ask. Just did this myself a week ago...

To reverse the morph  A->B to B->A  to create a continuous loop you need a bit 
of python scripting, the same for gluing stuff together at the end. This 
example needs to be adapted for your needs, but should get you started. For 
coloring between the states look at the script “spectrum_states” from the 
script repository on the wiki.

HTH

Carsten

##

# create objetcs with common residues between the states otherwise rigimol will 
bomb
#non working example adjust according to your needs
create ERK_morph, ERK and (resi 339:466,482:497,508:716) and (alt A or alt '')
create ERKP_morph, ERKP and (resi 339:466,482:497,498:716) and (alt A or alt '')

# Eliminate alternate conformations as they are silently rejected in the 
alignment or morph
alter EKR_morph, alt=''
alter ERKP_morph, alt=''

# Align the starting structures, the alignment object contains
# matching aligned residues to make sure rigimol stays sane
align ERK_morph, ERKP_morph, object=aln, cycles=0

# create the input structure from the aligned structures
# we begin with the start state
create morph_in, ERK_morph in aln, 1, 1
#
# now add the end-state as state 2
create morph_in, ERKP_morph in aln, 1, 2
#
# now we import the epymol module, this is where
# the rigimol code can be found (incentive only)
from epymol import rigimol
#
# call RigiMOL.  Here we ask it to take our 2-state
# object "morph_in", create the morph object,
# use high refinement (10), and not update the PyMOL GUI
# while it thinks (async=0)

rigimol.morph("morph_in", "ERK_2_ERKP", refinement=10, steps=30, async=0)

# Generate the reverse morph by creating a new object and reversing
# the order of states

python

for i in range(1,31):
ts = 31-i
print "Creating state %i" % i
cmd.create("ERKP_2_ERK", "ERK_2_ERKP", source_state=i, target_state=ts)

# add 4 instances of the inital state for final morph
for i in range(1,5):
print "Adding 4 instances of the inital state for final morph: %i" % i
cmd.create("morph", "ERK", source_state=0, target_state=i)

print "Appending all 30 states of ERK->ERKP transition"
cmd.create("morph", "ERK_2_ERKP", source_state=0, target_state=-1)

print "Adding 4 instances of the final state in the middle"
for i in range(1,5):
cmd.create("morph", "ERKP", source_state=0, target_state=-1)

print "Appending all 30 states of ERKP->ERK transition to complete the loop"
cmd.create("morph", "ERKP_2_ERK", source_state=0, target_state=-1)


python end

show cartoon, morph

#show phospotyrosine
show sticks, resn PTR and not (name n,c,o)





From: Melanie Prakash [mailto:melanie.prak...@gmail.com]
Sent: Wednesday, July 29, 2015 8:19 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Phosphorylation

Hi!

Recently, i have been trying to assemble a PyMol video of the phosphorylation 
of the MAP kinase ERK from deactivated to activated to deactivated stages. 
While I have had success showing the conformational change from inactivated to 
activated (using morph mout, 1ERK, 2ERK), not only am I not sure how to 
important a phosphate image to show what causes the change, but I also do not 
know how to fuse the two morph mout scenes between the deactivated to the 
activated and the activated to the deactivated.

Would any of you happen to have any general ideas or some past email 
suggestions as to how to solve this? I know I've tried ImageJ (but the quality 
is always so poor and i have to make multiple images form my videos and then 
fuse them together) as well as a variety of other steps using just the PyMol 
program but I haven't found anything.

-Mel
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Re: [PyMOL] Ray tracing on PBS queue with multiple cores?

[Schubert, Carsten [JRDUS]]

Dan,

pymol has a setting “max_threads” which (AFIK) controls the number of CPUs on a 
multicore machine used during rendering. The program tries to set these to a 
reasonable default value, but if that fails you can try to do this yourself. I 
don’t think it is possible to spread the same job over multiple CPUs when these 
are located on different boxes.

HTH

Carsten

From: Dan Lin [mailto:dh...@caltech.edu]
Sent: Monday, August 31, 2015 8:29 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Ray tracing on PBS queue with multiple cores?

Hello all:

I'm trying to ray trace some large movies and I have access to a cluster that 
uses PBS queues. However, I am having difficulty getting pymol to render with 
more than 1 CPU. Has anybody encountered this problem and found a solution?

Thanks in advance!

-Dan
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Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

[Schubert, Carsten [JRDUS]]

If you have access to the incentive version, I would recommend looking at the 
new properties capabilities in Pymol. The distances can be nicely encoded in a 
property and rendered with spectrum w/o having to resort to messing with other 
properties like B-factors. I believe the docs at Schrodinger contain examples 
to that end.

HTH

Carsten

From: David Hall [mailto:li...@cowsandmilk.net]
Sent: Wednesday, November 18, 2015 8:13 AM
To: Smith Liu
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] on coloring residues based on y values in the x y z 
coordinates

I forgot:
spectrum b

at the end.


On Wed, Nov 18, 2015 at 8:11 AM, David Hall 
mailto:li...@cowsandmilk.net>> wrote:
Assuming you are ok with overwriting the B-factors

stored.y=[]
iterate_state 1, prot, stored.y.append(y) % prot here should be replaced with 
your pymol object name
alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object name



On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu 
mailto:smith_liu...@163.com>> wrote:
Dear All,

Is any way we can colour the molecule by pymol based on the y values in the z y 
z coordinates, so that we can view easily the residues (or atoms) with 
equivalent position in the primary sequence but has a y-axis shift in the 3-D 
structure?

Smith




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Re: [PyMOL] default fetch format

[Schubert, Carsten [JRDUS]]

You may want to form you own opinion and take a look at this thread and others 
in CCP4

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;8e513bea.1308

I hope the link works. There has been extensive and heated debate over the 
merits of mmCIF vs. PDB on the same BB. The wwPDB is pushing mmCIF, which was 
developed as an ARCHIVAL format, but in my opinion the community as a whole is 
rather reluctant to accept mmCIF as a WORKING format. The distinction between a 
working and archiving format is vital in this context. 
As far as I am concerned the PDB format as a working format is unmatched in its 
utility (try to concatenate 2 structures in both formats or prepare a file for 
MR and you see what I mean), but has drawbacks, some of which would be adapted 
by an extended PDB format.
So as long as the current programs support PDB, I really could care less what 
the wwPDB thinks; however if programs drop support for the PDB format, I'll be 
more than happy to look for alternatives... 

Cheers,

Carsten

-Original Message-
From: Albert [mailto:mailmd2...@gmail.com] 
Sent: Sunday, November 22, 2015 2:23 PM
To: Thomas Holder
Cc: pymol-users
Subject: Re: [PyMOL] default fetch format

Hi Thomas:

thanks a lot for helpful advice.

May I ask is there any superior features of mmCIF format against PDB format?

regards

Albert

On 11/22/2015 04:15 PM, Thomas Holder wrote:
> Hi Albert,
>
> Unfortunately the default fetch type can't be configured. But you can 
> override the fetch command. Example which you could place in your ~/.pymolrc 
> file:
>
> python
> from pymol import cmd
>
> def fetchpdb(*args, **kwargs):
>  if 'type' not in kwargs:
>  kwargs['type'] = 'pdb'
>  return cmd.fetch(*args, **kwargs)
>
> cmd.extend('fetch', fetchpdb)
> python end
>
> However, if you don't have a compelling reason to work with PDB instead of 
> mmCIF, then I recommend to give the new mmCIF default a try.
>
> Cheers,


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Re: [PyMOL] light reposition

[Schubert, Carsten [JRDUS]]

Darya,

I have never used that feature, but do you see a difference when raytracing or 
drawing the scene? Could be that the regular display mode does not take these 
feature into account (this is a wild guess though)

Cheers,

Carsten

From: Дарья Николаева [mailto:daranikola...@gmail.com]
Sent: Monday, November 30, 2015 9:58 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] light reposition


Hello,



I want to change the position of my light sources.



First I set the number of light sources:

>set light_count, 3



Then I attempt to reposition the light source, e.g., #2:

>set light2, [x, y, z]



The problem is - I see no changes to the scene.



The question: How to use the "set light(2-8)" command or is there any

other way to reposition light sources?



Thank you,

Darya
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Re: [PyMOL] OBJECT argument in ALIGN command - color

[Schubert, Carsten [JRDUS]]

Hi Tim,

I ran into the same issue a while back as well. I gets complicated very quickly 
when you dive deeper into the subject. Your are right the colors of the CGO 
lines seem to be hardcoded. A  way to get around this is to extract the 
matching residues with cmd.get_raw_alignment(alignment_object). The result is a 
tuple of tuples of matching atoms as determined by the alignment algorithm. You 
could then take these atoms pairs and draw distance lines between them. These 
distance lines can be customized with color, linewidth, etc.

It has been a while since I worked on this, but I believe that the assignment 
of pairs is a non-trivial issue and sometimes fraught with mismatches. So 
manual checking against a sequence alignment is always a good idea especially 
for rather unrelated proteins.

I do have a script which can accomplish this, it is based on “colorbyrmsd.py”. 
However it is not ready for primetime, but I can share this with you if there 
is interest. Contact me offline to arrange something.

Cheers,

Carsten

From: Timothy Umland [mailto:uml...@gmail.com]
Sent: Sunday, January 10, 2016 9:08 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] OBJECT argument in ALIGN command - color




Hi:



I am trying to use the Alignment Objects (i.e., lines between the paired 
aligned atoms) created by using the OBJECT argument of the ALIGN command to 
illustrate domain movement between the superimposed ligand-bound and unbound 
forms of an enzyme.



I successfully made the basic aligned image, and now I want to tweak it.



Is it possible to change the color of the Alignment Object lines between paired 
atoms? For me, they display only in yellow. From what I have read online these 
lines are CGO objects with the color hardwired in upon creation, and so it 
can’t be changed in PyMol latter on. However, I haven’t been able to find a way 
to assign a color upon creation. Is there a way to assign a specific color?



Additionally, I have seen this type of image where the lines between the paired 
aligned atoms are two colors, with half of the line in one color (say blue) and 
the other half another color (say red) to better illustrate which protein is 
the origin of each end of the connecting line. I haven’t discovered a way to 
make these bi-colored lines in ALIGN. Any ideas?



I have tried the open source version 1.8.0, plus several earlier versions from 
various origins (all on Macs) with similar results.





Thanks much for any ideas.



Tim



Tim Umland, Ph.D.

Hauptman-Woodward Institute




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Re: [PyMOL] ColorByRMSD script

[Schubert, Carsten [JRDUS]]

Hi Guilherme,

the script is not a plugin, so you cannot install it since it is missing some 
software infrastructure to work as a plugin. Simply put the script into the 
directory you are working in and run it via ‘run colorbyrmsd.py’ . This will 
add the command to the scripting interface and you can run the command like any 
other pymol command. See the wiki for the details in that regards.

HTH

Carsten

From: Guilherme Souza [mailto:gsouza...@gmail.com]
Sent: Friday, January 29, 2016 7:07 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] ColorByRMSD script

Hi.

I'm a starter in PyMOL, and I'm trying to use this script, ColorByRMSD 
(http://www.pymolwiki.org/index.php/ColorByRMSD). However, I'm getting the 
following error message, when I initialize PyMOL after installing the plugin:

Exception in plugin 'colorbyrmsd' -- Traceback follows...
Traceback (most recent call last):
  File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pmg_tk\PMGApp.py", line 313, 
in initializePlugins
__builtin__.__import__(mod_name)
SyntaxError: future feature print_function is not defined (colorbyrmsd.py, line 
10)
Error: unable to initialize plugin 'colorbyrmsd'.

I'm using Python 2.7, and I've already checked '__future__' module, and 
'print_function' is there, so I don't know what could be causing this.

I'd be glad if anyone could give me a help.

Thank you.
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Re: [PyMOL] auto_show_cartoon or similar

[Schubert, Carsten [JRDUS]]

Hi Ivan,

you could either try to overload the “load” function in Pymol (not sure this is 
supported) or write your own custom load function under a different name, which 
loads the protein, assigns the name of the object, hides lines and shows the 
cartoon.

Sorry, this is a rather generic answer but should point you in the right 
direction.

Cheers,

Carsten

From: Ivan Vulovic [mailto:i...@uw.edu]
Sent: Saturday, February 06, 2016 8:18 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] auto_show_cartoon or similar

Hello

Is there a way to make cartoon the default representation, something akin to 
"auto_show_lines", but for cartoon? There was some dicussion of this in 2010 
(link below) but I haven't found anything more recent that does what I'd like.

http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html

Thanks
Ivan
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Re: [PyMOL] how can we make this kind of figure?

[Schubert, Carsten [JRDUS]]

Albert,

looks like it is from 'cutemol'. You can probably achieve a similar effect in 
Pymol

-enable perspective
-play around with occlusion (search in settings for occlusion)
-display protein with 'cartoon loop'
-show sidechains for selected residues
-fog seems to have a tint of grey in there, you could play with that setting
-not knowing the context of the figures it looks like they only displayed 
C-alphas as white spheres maybe with adjusted radii
-There seems to be some light coming from back left, so playing around with 
light positions may also be appropriate

Looks like it would require a lot of tinkering with settings, but you should be 
able to get to a similar figure.

HTH

Carsten

-Original Message-
From: Albert [mailto:mailmd2...@gmail.com] 
Sent: Friday, February 12, 2016 2:39 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] how can we make this kind of figure?



Hello

I found a very nice figure in an article but the author didn't mention which 
software he used for render. I am just wondering is it possible to render in 
the same way in Pymol? I've attached this figure.

thx a lot

Albert



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Re: [PyMOL] how to get an atom coordinates information

[Schubert, Carsten [JRDUS]]

Albert,

there is no command line tool for that purpose per se, however you can use the 
iterate command for that purpose. 
http://pymolwiki.org/index.php/Iterate#Example:_Get_coordinates


There are other ways to do this but this will get you going more quickly.

-Original Message-
From: Albert [mailto:mailmd2...@gmail.com] 
Sent: Thursday, February 25, 2016 12:48 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] how to get an atom coordinates information

Hello:

I would like to know the XYZ information of a specific atom. I am just 
wondering how can we do this? Is there any command line?

thank you very much

Albert

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Re: [PyMOL] how to get an atom coordinates information -- feature request

[Schubert, Carsten [JRDUS]]

Hi Thomas,

for a quick n'dirty look at coordinates would it makes sense to extend the 
label function in the gui and command line to include the coordinates as well. 
Seem like an oversight that this is not available more easily.

Carsten

-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Thursday, February 25, 2016 1:58 PM
To: Albert; Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] how to get an atom coordinates information

Hi Carsten & Albert,

There actually is a function for getting the coordinates of a single atom. 
Example:

PyMOL>print cmd.get_atom_coords('first (elem O)')

Cheers,
  Thomas

On 25 Feb 2016, at 09:54, Schubert, Carsten [JRDUS]  
wrote:

> Albert,
> 
> there is no command line tool for that purpose per se, however you can use 
> the iterate command for that purpose. 
> http://pymolwiki.org/index.php/Iterate#Example:_Get_coordinates
> 
> 
> There are other ways to do this but this will get you going more quickly.
> 
> -Original Message-
> From: Albert [mailto:mailmd2...@gmail.com] 
> Sent: Thursday, February 25, 2016 12:48 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] how to get an atom coordinates information
> 
> Hello:
> 
> I would like to know the XYZ information of a specific atom. I am just 
> wondering how can we do this? Is there any command line?
> 
> thank you very much
> 
> Albert

-- 
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PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] How to store matrix settings for individual scenes?

[Schubert, Carsten [JRDUS]]

Hi,

I am trying to create a session file of a multimeric protein, in which each 
monomer is displayed first using the original  matrix settings broken out into 
individual scenes. After that all monomers are overlayed on top of each other 
and the superposition matrices are copied and applied to the ligands, etc. So 
far so good, however once the matrices are applied this also affects the 
matrices for the scenes created previous to the overlay and matrix_copy. Any 
way I can store the matrices in each scene instead of having them applied 
globally once?

Cheers,

Carsten
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Re: [PyMOL] How to store matrix settings for individual scenes?

[Schubert, Carsten [JRDUS]]

Yeah, but not my preferred choice. Tried to do this the elegant way, but 
bumping up against Pymol's limits unless Thomas has a workaround.

From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Monday, March 07, 2016 12:15 PM
To: Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to store matrix settings for individual scenes?

Hi Carsten -

I'd probably create new objects and use those for superimposition, rather than 
moving the originals.  That would leave your scenes intact.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS] 
mailto:cschu...@its.jnj.com>> wrote:

Hi,

I am trying to create a session file of a multimeric protein, in which each 
monomer is displayed first using the original  matrix settings broken out into 
individual scenes. After that all monomers are overlayed on top of each other 
and the superposition matrices are copied and applied to the ligands, etc. So 
far so good, however once the matrices are applied this also affects the 
matrices for the scenes created previous to the overlay and matrix_copy. Any 
way I can store the matrices in each scene instead of having them applied 
globally once?

Cheers,

Carsten
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Re: [PyMOL] How to store matrix settings for individual scenes?

[Schubert, Carsten [JRDUS]]

Thanks, I’ll give that a shot. Let’s see how well that extends into sessions.

From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Monday, March 07, 2016 1:26 PM
To: Schubert, Carsten [JRDUS]
Cc: pymol-users
Subject: Re: [PyMOL] How to store matrix settings for individual scenes?

Hi Carsten -

Could you wrap the `scene` function and include storing/recalling of the 
matrices as well as the scenes?  I just whipped together the following:

```
from pymol import stored
from pymol import cmd
stored.scene_matrices = {}

def scene_store(scn):
obj_matrices = {}
# only store matrices for enabled objects
for obj in cmd.get_names(enabled_only=1):
print 'storing matrix for %s' % obj
m = cmd.get_object_matrix(obj)
print m
obj_matrices[obj] = m

stored.scene_matrices[scn] = obj_matrices
cmd.scene(scn, 'store')

def scene_recall(scn):
obj_matrices = stored.scene_matrices[scn]
for obj in cmd.get_names():
# don't try to reset objects that aren't in the recalled scene
if obj in obj_matrices.keys():
cmd.matrix_reset(obj)
cmd.transform_selection(obj, obj_matrices[obj])
cmd.scene(scn, 'recall')

cmd.extend('scene_store', scene_store)
cmd.extend('scene_recall', scene_recall)
```

This works for me with, e.g.

```
fetch 1shv, async=0
fetch 3opl, async=0
scene_store F1

super 3opl, 1shv  # changes the 3opl matrix
scene_store F2

scene_recall F1  # restores the original 3opl matrix
```

Not sure if that's closer to what you're looking for...hope it helps!

Cheers,
Jared
--
Jared Sampson
Columbia University

On Mar 7, 2016, at 12:35 PM, Schubert, Carsten [JRDUS] 
mailto:cschu...@its.jnj.com>> wrote:

Yeah, but not my preferred choice. Tried to do this the elegant way, but 
bumping up against Pymol’s limits unless Thomas has a workaround.

From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
Sent: Monday, March 07, 2016 12:15 PM
To: Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] How to store matrix settings for individual scenes?

Hi Carsten -

I'd probably create new objects and use those for superimposition, rather than 
moving the originals.  That would leave your scenes intact.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS] 
mailto:cschu...@its.jnj.com>> wrote:

Hi,

I am trying to create a session file of a multimeric protein, in which each 
monomer is displayed first using the original  matrix settings broken out into 
individual scenes. After that all monomers are overlayed on top of each other 
and the superposition matrices are copied and applied to the ligands, etc. So 
far so good, however once the matrices are applied this also affects the 
matrices for the scenes created previous to the overlay and matrix_copy. Any 
way I can store the matrices in each scene instead of having them applied 
globally once?

Cheers,

Carsten
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Re: [PyMOL] How to store matrix settings for individual scenes?

[Schubert, Carsten [JRDUS]]

Hi Thomas,

Movie won't work since the session files are distributed and need to be 
interactive. I'll try Jared's solution, if that does not work could we treat 
this as an enhancement request?

Cheers,

Carsten

-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Monday, March 07, 2016 2:51 PM
To: Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to store matrix settings for individual scenes?

Hi Carsten,

What's your use case? Since movie frames can store object matrices, would 
creating an actual movie solve your problem? Example of an animated 
superposition:

# get sample data
fetch 1hbb, async=0
split_chains
delete 1hbb

# set up movie frames
mset 1x100

# make "align" modify the motion matrix (but without # instant storing to 
current frame) set matrix_mode, 1 set movie_auto_store, 0

# store object matrices to frame 1
mview store, 1, object=*

# superpose structures and store matrices to frame 100 extra_fit mview store, 
100, object=*

# optional: add scenes
color blue
scene blue, store
color red
scene red, store
mview store, 1, scene=blue
mview store, 100, scene=red


If this doesn't fit your use case, I'd go with Jared's solution of an enhanced 
scene function.

Cheers,
  Thomas

On 07 Mar 2016, at 12:35, Schubert, Carsten [JRDUS]  
wrote:

> Yeah, but not my preferred choice. Tried to do this the elegant way, but 
> bumping up against Pymol's limits unless Thomas has a workaround.
>  
> From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
> Sent: Monday, March 07, 2016 12:15 PM
> To: Schubert, Carsten [JRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] How to store matrix settings for individual scenes?
>  
> Hi Carsten -
>  
> I'd probably create new objects and use those for superimposition, rather 
> than moving the originals.  That would leave your scenes intact.
>  
> Cheers,
> Jared
>  
> --
> Jared Sampson
> Columbia University
>  
> On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS]  
> wrote:
>  
> Hi,
>  
> I am trying to create a session file of a multimeric protein, in which each 
> monomer is displayed first using the original  matrix settings broken out 
> into individual scenes. After that all monomers are overlayed on top of each 
> other and the superposition matrices are copied and applied to the ligands, 
> etc. So far so good, however once the matrices are applied this also affects 
> the matrices for the scenes created previous to the overlay and matrix_copy. 
> Any way I can store the matrices in each scene instead of having them applied 
> globally once?
>  
> Cheers,
>  
> Carsten

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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