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] <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
> 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] <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

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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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 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] 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] 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] 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] 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] 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] 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 
> 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 
> 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] 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] 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] 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 module
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] 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] 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 aloctavo...@gmail.com 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 mar...@chemie.uni-kl.de 
 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

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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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] 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 a.soler...@leeds.ac.uk 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

--
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   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,

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] 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] 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 shane.caldwel...@gmail.com 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] 
 cschu...@its.jnj.com 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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[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 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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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 renderer 

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 
bondurant...@gmail.commailto: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] 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] 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] 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 
sunyep...@aliyun.commailto: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] 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.


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Sudharsan (Sid) Sridharan, Ph.D.
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Engineering

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P: +44(0)1223 898195F: +44(0)1223 471472


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Granta Park, Cambridge, CB21 6GH.

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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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[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] 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] 
cschu...@its.jnj.commailto: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] 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] 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.netmailto: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] 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 = rD:\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: pymol-users@lists.sourceforge.net
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:

PyMOLrun 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 module
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: pymol.CmdException instance at 0x06FF1580
Can anyone help please.

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

On Thu, Jan 9, 2014 at 12:03 AM, Sampson, Jared 
jared.samp...@nyumc.orgmailto: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 
jared.samp...@nyumc.orgmailto: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 

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] 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 
path-to-script - four lines between these coordinates I got by using print 
cmd.get_model('selection-name', 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] 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] 
cschu...@its.jnj.commailto: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.commailto:m...@timo-stein.com] Sent: Friday, July 12, 
20...
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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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[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] 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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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 rsengu...@wisc.edu

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 PyMOL-users@lists.sourceforge.net
rsengu...@wisc.edu') target=1rsengu...@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#39;m using spheres
instead, but wondering if there#39;s a way to work around the problem
and still view the ligands as sticks/lines.

 
 
  Thanks,
  Ritu
 
 

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Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol?

[Schubert, Carsten [PRDUS]]

Thanks to all who replied, 'create' did the trick of combining multiple 
objects/molecules into one object quite painless. I was not  thinking out of 
the box, been using create too long to slice and dice my molecules.

But it turns out that I have TLS-ANISO records in my original file I'd like to 
retain, the save command does not carry them over into the combined file, 
neither are CRYST/SCALE records retained. Any flags I need to set?

Cheers,

Carsten

 -Original Message-
 From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
 Sent: Thursday, June 16, 2011 6:14 PM
 To: Schubert, Carsten [PRDUS]
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] How to merge molecules in Pymol?
 
 Hi Carsten,
 
  Is there an (un)documented way of merging multiple molecular objects
 in
  Pymol into one molecule, which then can be written in a nicely
 formatted PDB
  file? I cobbled something cludgy together with 'multisave' and a
 couple
  read-sort-save cycles, but this is ugly and probably quite fragile.
 An API
  function might be much more robust. Is there a provision like this in
  ChemPy? I've already taken care of adjusting each molecule to be
 unique with
  respect to chain IDs and IDs, so that would not be an issue.
 
 It's documented:
  * help create
  * http://www.pymolwiki.org/index.php/Create
 
 Create can be used to create a single single-state object or a single
 multi-state object. The former will just 'do what you say' but may
 create biologically unrealistic molecules (it just combines the
 objects).  The latter is better as it saves to biologically realistic
 multi-state pdbs.  Try these examples:
 
 # method 1
 # create a single state (possibly biologically infeasible) molecule
 # from two objects
 frag ala
 frag cys
 save test.pdb, ala or cys
 
 Now load test.pdb.
 
 # method 2
 # create a single multi-state object from two molecules
 
 frag ala
 frag cys
 create test, ala, 1, 1
 create test, cys, 1, 2
 save test.pdb, test, state=0
 
 Cheers,
 
 -- Jason
 
 
 On Thu, Jun 16, 2011 at 3:58 PM, Schubert, Carsten [PRDUS]
 cschu...@its.jnj.com wrote:
  Hi,
 
  Is there an (un)documented way of merging multiple molecular objects
 in
  Pymol into one molecule, which then can be written in a nicely
 formatted PDB
  file? I cobbled something cludgy together with 'multisave' and a
 couple
  read-sort-save cycles, but this is ugly and probably quite fragile.
 An API
  function might be much more robust. Is there a provision like this in
  ChemPy? I've already taken care of adjusting each molecule to be
 unique with
  respect to chain IDs and IDs, so that would not be an issue.
 
  Any pointers would be appreciated.
 
  Cheers,
 
      Carsten
 
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Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol?

[Schubert, Carsten [PRDUS]]

Hi Jason,

Good to know. Could we then add this a feature request? I know Pymol is more a 
'consumer' and not a 'producer' but in certain instances 
this would be a nice feature to have.

Cheers,

Carsten

 -Original Message-
 From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
 Sent: Friday, June 17, 2011 11:57 AM
 To: Schubert, Carsten [PRDUS]
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Retention of ANISO Records was How to merge
 molecules in Pymol?
 
 Hi Carsten,
 
 PyMOL doesn't write non-coordinate records to disk.  You'll need to
 write a script to prepend those records.
 
 Cheers,
 
 -- Jason
 
 On Fri, Jun 17, 2011 at 8:15 AM, Schubert, Carsten [PRDUS]
 cschu...@its.jnj.com wrote:
  Thanks to all who replied, 'create' did the trick of combining
 multiple objects/molecules into one object quite painless. I was not
  thinking out of the box, been using create too long to slice and dice
 my molecules.
 
  But it turns out that I have TLS-ANISO records in my original file
 I'd like to retain, the save command does not carry them over into the
 combined file, neither are CRYST/SCALE records retained. Any flags I
 need to set?
 
  Cheers,
 
         Carsten
 
  -Original Message-
  From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
  Sent: Thursday, June 16, 2011 6:14 PM
  To: Schubert, Carsten [PRDUS]
  Cc: pymol-users@lists.sourceforge.net
  Subject: Re: [PyMOL] How to merge molecules in Pymol?
 
  Hi Carsten,
 
   Is there an (un)documented way of merging multiple molecular
 objects
  in
   Pymol into one molecule, which then can be written in a nicely
  formatted PDB
   file? I cobbled something cludgy together with 'multisave' and a
  couple
   read-sort-save cycles, but this is ugly and probably quite
 fragile.
  An API
   function might be much more robust. Is there a provision like this
 in
   ChemPy? I've already taken care of adjusting each molecule to be
  unique with
   respect to chain IDs and IDs, so that would not be an issue.
 
  It's documented:
   * help create
   * http://www.pymolwiki.org/index.php/Create
 
  Create can be used to create a single single-state object or a
 single
  multi-state object. The former will just 'do what you say' but may
  create biologically unrealistic molecules (it just combines the
  objects).  The latter is better as it saves to biologically
 realistic
  multi-state pdbs.  Try these examples:
 
  # method 1
  # create a single state (possibly biologically infeasible) molecule
  # from two objects
  frag ala
  frag cys
  save test.pdb, ala or cys
 
  Now load test.pdb.
 
  # method 2
  # create a single multi-state object from two molecules
 
  frag ala
  frag cys
  create test, ala, 1, 1
  create test, cys, 1, 2
  save test.pdb, test, state=0
 
  Cheers,
 
  -- Jason
 
 
  On Thu, Jun 16, 2011 at 3:58 PM, Schubert, Carsten [PRDUS]
  cschu...@its.jnj.com wrote:
   Hi,
  
   Is there an (un)documented way of merging multiple molecular
 objects
  in
   Pymol into one molecule, which then can be written in a nicely
  formatted PDB
   file? I cobbled something cludgy together with 'multisave' and a
  couple
   read-sort-save cycles, but this is ugly and probably quite
 fragile.
  An API
   function might be much more robust. Is there a provision like this
 in
   ChemPy? I've already taken care of adjusting each molecule to be
  unique with
   respect to chain IDs and IDs, so that would not be an issue.
  
   Any pointers would be appreciated.
  
   Cheers,
  
       Carsten
  
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  Schrodinger, LLC
 
  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 
 
 
 
 
 --
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[PyMOL] How to merge molecules in Pymol?

[Schubert, Carsten [PRDUS]]

Hi,

Is there an (un)documented way of merging multiple molecular objects in
Pymol into one molecule, which then can be written in a nicely formatted
PDB file? I cobbled something cludgy together with 'multisave' and a
couple read-sort-save cycles, but this is ugly and probably quite
fragile. An API function might be much more robust. Is there a provision
like this in ChemPy? I've already taken care of adjusting each molecule
to be unique with respect to chain IDs and IDs, so that would not be an
issue.

Any pointers would be appreciated.

Cheers,

Carsten


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[PyMOL] New 16 char length restriction of object names in menu?

[Schubert, Carsten [PRDUS]]

Has the length of the object name entry in the right hand menu been
restricted to 16 characters in v1.4.x? Prior to 1.4.x there seemed to
have been no limit on the length of the entry. For instance
cmd.load(reallylongmapnamehere,
format=ccp4,object=reallylongmapnamehere) would truncate the display
of the object to reallylongmapna. I suppose that would be fine for
some applications, but in my case I am distributing sessions, which
contain fairly long object names to be self-explanatory, so I am
dependent on this feature to work. Could this be reverted back to
unlimited or at least implement a setting controlling the length of the
entry?

Thanks

Carsten


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Re: [PyMOL] New 16 char length restriction of object names in menu?

[Schubert, Carsten [PRDUS]]

Hi Jason,

thanks for the follow-up. Let us know when the issue is fixed.

Cheers,

Carsten

 -Original Message-
 From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
 Sent: Thursday, May 19, 2011 12:11 PM
 To: Schubert, Carsten [PRDUS]
 Cc: pymol-users@lists.sourceforge.net; h...@schrodinger.com
 Subject: Re: [PyMOL] New 16 char length restriction of object names in
 menu?
 
 Hi Carsten,
 
 I'd like to follow up on this.  There is no character limit, but there
 is a bug.  PyMOL is inappropriately clipping names in groups if the
 internal GUI cuts off the end of the name.  The current workaround for
 your sessions is to expand the internal_gui to show the names, and
 then save your session.
 
 I'll look into fixing this ASAP.
 
 Cheers,
 
 -- Jason
 
 On Thu, May 19, 2011 at 11:33 AM, Jason Vertrees
 jason.vertr...@schrodinger.com wrote:
  Hi Carsten,
 
  Has the length of the object name entry in the right hand menu been
  restricted to 16 characters in v1.4.x? Prior to 1.4.x there seemed
 to have
  been no limit on the length of the entry.
 
  There is no such limit on the length of names.
 
  For instance
  cmd.load(reallylongmapnamehere,
  format=ccp4,object=reallylongmapnamehere) would truncate the
 display of
  the object to reallylongmapna. I suppose that would be fine for
 some
  applications, but in my case I am distributing sessions, which
 contain
  fairly long object names to be self-explanatory, so I am dependent
 on this
  feature to work. Could this be reverted back to unlimited or at
 least
  implement a setting controlling the length of the entry?
 
  You have a few options.
 
  If you want to hide the state-counter to get a few more characters on
  the line just set state_counter_mode, 0.  Alternatively, you could
  just increase the internal_gui_width--eg
 
  set internal_gui_width, 300
 
  Cheers,
 
  -- Jason
 
  --
  Jason Vertrees, PhD
  PyMOL Product Manager
  Schrodinger, LLC
 
  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 
 
 
 
 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC
 
 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120


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Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore -- fixed

[Schubert, Carsten [PRDUS]]

Sorry Guys, my bad. I had a Homer Simpson moment while writing a wrapper to 
integrate 32bit and 64bit environments and forgot to pass along arguments to 
the actual pymol startup script. 

Apologies...

Carsten



 -Original Message-
 From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
 Sent: Wednesday, May 11, 2011 6:37 PM
 To: Schubert, Carsten [PRDUS]
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line
 anymore
 
 Hi Carsten,
 
 That's pretty odd.  Can you please show us exactly what you're typing?
  Also, please provide the PyMOL and OS versions.
 
 Cheers,
 
 -- Jason
 
 On Wed, May 11, 2011 at 1:33 PM, Schubert, Carsten [PRDUS]
 cschu...@its.jnj.com wrote:
  Hi,
 
  The latest PyMol (1.4.1, 32bit Linux version) does not load PDB files
 from
  the command line anymore. Does anybody have the same problem? What am
 I
  missing?
 
  Cheers,
 
      Carsten
 
  -
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[PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore

[Schubert, Carsten [PRDUS]]

Hi,


The latest PyMol (1.4.1, 32bit Linux version) does not load PDB files
from the command line anymore. Does anybody have the same problem? What
am I missing?

Cheers,

Carsten


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Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore

[Schubert, Carsten [PRDUS]]

Hi Alvin, 

thanks for the reply. Sorry, but I was not clear in describing the
problem. What I meant was that loading pdb files as arguments to pymol
does not seem to work anymore, i.e. 'shell_prompt # pymol x.pdb y.pdb'
does not load x.pdb and y.pdb on startup. At least in 1.3 that mechanism
worked.

Cheers,

Carsten


 -Original Message-
 From: Alvin Oga [mailto:pymol.l...@mail.linux-1u.net]
 Sent: Wednesday, May 11, 2011 5:49 PM
 To: Schubert, Carsten [PRDUS]
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line
 anymore
 
 
 hi carsten
 
 on freebsd, command line works for me  ( pymol load pept.pdb ),
 works as in the molecule changes to the new loaded one
 
 i downloaded pymol-1.4.1 from svn and compiled the sources on freebsd-
 7.4, 8.2, 6.4
 
 ---
 
 downloading/compiling pymol-1.4.1 on debian-sid has problems tho
 and it doesn't execute properly
 ( probably because i tend to change pesky/unreasonable system default
 files )
 
 i can try to download/compile/test on other linux's ..
 i have centos-5.4, 5.5, 5.6, fedora-core14, opensuse-11.3, 11.4,
 slackware-12.3 )
 
 centos/fedora supposed to be identical to redhat
 
 which linux versions do you have ??
 
 have fun
 alvin
 http://Linux-1U.net/BioChem
 
  The latest PyMol (1.4.1, 32bit Linux version) does not load PDB
files
  from the command line anymore. Does anybody have the same problem?
 What
  am I missing?


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Re: [PyMOL] openGL/GLEW problems when embedding a PyMOL instance in aPyQt4 widget

[Schubert, Carsten [PRDUS]]

Kasper, not sure if this will help you, but I think the GLEW stuff was
added recently in V1.4.x and it seems to be still somewhat experimental.
May be to get you started you could switch to v1.3r1 from the repository
and try to embedd that version. V1.3.x should not contain the new GL
stuff.

 

Good luck

 

Carsten

 

 

 

From: Kasper Thofte [mailto:kasper.tho...@gmail.com] 
Sent: Tuesday, April 26, 2011 10:34 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] openGL/GLEW problems when embedding a PyMOL instance in
aPyQt4 widget

 

Dear pymol user and developer community

I am trying to embed a pymol2.PyMOL instance in a PyQt4 widget.

I am using the latest beta v1.4.1 (although it still says v1.4.0 in
layer0/Version.h, I assume you just forgot to update?). I use ubuntu on
a macbook.

I got it to display a black window inside a PyQt4 app, and I was even
able to produce som ugly little white square H atoms one time, plus som
menus only half visible. Yes, kind of strange.

The problem is openGL related. When typing pymol -v at the command line,
it tells me that my openGL version is pre 2.0, which is not true. 

(Well, actually I wasn't entirely sure what precisely to look for in the
synaptic package manager, but libqt4-opengl is v4:4.7.0, python-opengl
is v3.0.1, python-qt4-gl is v4.7.4, freeglut3-dev is v2.6.0,
libglew1.5-dev is, well v1.5.2 glutg3-dev is 3.7-25)

Anyway, when I runt the following code (which may also contain the
source of the problem, I don't know):

class PymolQWidget(QGLWidget):

def __init__(self, parent=None):
QGLWidget.__init__(self, parent=parent)

self.pymolInstance = pymol2.PyMOL()
self.pymolInstance.start()
 
self.pymolInstance.cmd.load('home-directory/GUI/H2.pdb')'

self.pymolInstance.cmd.draw()
self.pymolInstance.cmd.show_as(sticks)

app = QtGui.QApplication(sys.argv)
pymolWidget = PymolQWidget()
pymolWidget.show()
sys.exit(app.exec_())

I get the following error message:

ShaderMgrInit-Error: Could not initialize GLEW:Missing GL version

which means that GLEW_OK!=err at line 145 in layer0/ShaderMgr.c, which
means the glew hasn't been initialized, which is as far as I was able to
get.

Needless to say, help would be greatly appreaciated.

Best,
Kasper Thofte
University of Copenhagent

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Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

[Schubert, Carsten [PRDUS]]

Joachim,

I'm running into the same issue on a SuSe SLED10 box. The 32bit binary
(on the 64bit OS) displays the same behavior, i.e. only the MESA libs
were used. The 64bit version actually core dumps during startup. I
opened up a bug report with Schrodinger and they were already working on
it (I suppose the crash), but wouldn't hurt to reinforce the fact that
the 32bit version only uses the MESA libs (under SuSe?). Good that your
tried the more recent drivers, I was planning to do that but haven't got
around to do this yet.

Cheers,

Carsten


 -Original Message-
 From: greipel.joac...@mh-hannover.de [mailto:Greipel.Joachim@mh-
 hannover.de]
 Sent: Tuesday, March 29, 2011 7:16 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4
 
 Dear pymol users,
 
 pymol 1.4 on openSuSE with NVIDIA Quadro FX 3700/3800 and new NVIDIA
 drivers (260.xxx and 270.xxx) does not recognize the OpenGL Version
 correctly. As a result there is a kind of software OpenGL used.
 The NVIDIA drivers provide OpenGL 3.3.0 but pymol 1.4 complains:
 
 
 Detected OpenGL version prior to 2.0.  Shaders unavailable.
 OpenGL graphics engine:
 GL_VENDOR: Brian Paul
 GL_RENDERER: Mesa X11
 GL_VERSION: 1.5 Mesa 6.4.2
 
 
 
 This leads to a malfunctioning hardware stereo and renders pymol 1.4
 unusable for us. Earlier pymol versions do not show that strange
 behavior.
 Other programs use the NVIDIA drivers perfectly well and allow
 displaying
 structures in hardware stereo. I tried this thing on several machines
 with
 the same result. Does anyone have a hint?
 
 Regards,
 
 --
 Dr. rer. nat. Joachim Greipel
 Med. Hochschule Hannover
 Biophys. Chem. OE 4350
 Carl-Neuberg-Str. 1
 30625 Hannover
 Germany
 
 Fon: +49-511-532-3718
 Fax: +49-511-532-8924
 
 

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Re: [PyMOL] slab mode fine-tuning

[Schubert, Carsten [PRDUS]]

Nadine,

Probably the command line is your best friend here. Look into the 'clip
near,x' and 'clip far,x' command, which allows to move the front and
back clipping planes in x increments. Positive values move towards you,
negative values of x away from you.
If that does not provide enough fine grained control you may want to
think about making a composite picture to 'fake' clipping planes per
object.

Cheers,

Carsten

 -Original Message-
 From: Nadine Utz [mailto:nad...@mmb.pcb.ub.es]
 Sent: Tuesday, March 29, 2011 6:12 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] slab mode fine-tuning
 
 Dear pymol users,
 
 I am looking for a way to zoom in a molecule, like the slab mode
when
 you are rolling the scroll wheel. The reason why rolling the scroll
 wheel does not work in my case is that the resulting change is too
 coarse grained, i.e. either I cannot see all the atoms I want to or
 there are some atoms in front of the part I am interested in. I tried
 as
 well clip slab, x, but then not just atoms in front of the
 interesting
 part are not shown but as well behind it.
 
 So, what I need is a cross-sectional view of my system, in which only
 everything in front of the cut is not shown (but everything behind).
 
 Thank's a lot for any help,
 
 Nadine
 
 
 Dr. Nadine Utz
 MMB - IRB Barcelona
 
 
 

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Re: [PyMOL] write a script from pse file

[Schubert, Carsten [PRDUS]]

Maia,

as far as I know a .pse is just a dump of the internal data structure of
Pymol. You can save the molecules contained in the session, but the
graphical representation and any modifications would need to be
recreated. 
Hopefully Jason proves me wrong ...

Cheers,

Carsten

 -Original Message-
 From: Maia Cherney [mailto:ch...@ualberta.ca]
 Sent: Sunday, March 13, 2011 7:07 AM
 To: Jason Vertrees
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] write a script from pse file
 
 Hello,
 
 I have an old saved session as a pse file. How can I save a script
that
 produced that pse file. It may be easier just to get information about
 each object in that pse file.
 
 Maia
 
 

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Re: [PyMOL] Different color on each side of strand

[Schubert, Carsten [PRDUS]]

Not sure if this is possible but it would be a nice feature to have. Since it 
mimics the way helices are drawn, when cartoon_highlight_color is set.

Cheers,

Carsten


 -Original Message-
 From: Keitaro Yamashita [mailto:yamash...@castor.sci.hokudai.ac.jp]
 Sent: Sunday, March 06, 2011 7:32 PM
 To: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Different color on each side of strand
 
 Dear all,
 
 Sorry for my unclear explanation.
 
 I made a picture explaining what I'd like to do.
 I want to color the front and back of sheets separately.
 
 Jason said it should be possible, could anyone tell me how to do it?
 
 Cheers,
 
 Keitaro
 
 
 
 2011/3/7 Jason Vertrees jason.vertr...@schrodinger.com:
  Hi Keitaro,
 
  Use the cartoon_highlight_color setting.  For example:
 
  set cartoon_highlight_color, red
 
  Cheers,
 
  -- Jason
 
  On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita
  yamash...@castor.sci.hokudai.ac.jp wrote:
  Dear all,
 
  Can PyMOL set different colors on each side of cartoon strand?
 
  I tried cartoon_discrete_colors but it was not for this purpose.
  (I mean the sides from which sidechains are protruded.)
 
  Thanks in advance,
 
  Keitaro
 
  
 -
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  (o) +1 (603) 374-7120
 

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Re: [PyMOL] labeling by a pseudoatom

[Schubert, Carsten [PRDUS]]

Roberto, 

partial answer to point 3. Adding a _ before an object name hides it
from the panel.

For points 1 or 2. Could you please expand on your question? Is this for
interactive
or scripted mode? 
For scripted mode you could modify the coordinates of the pseudoatom to
be closer to the target atom or not? Otherwise look up the commands in
Edit mode. BTW in Edit mode you can actually mode regular labels with
the mouse as well (Edit Mode: CTRL Middle click)

Hope it helps somewhat

Carsten

 -Original Message-
 From: rv...@libero.it [mailto:rv...@libero.it]
 Sent: Friday, February 25, 2011 5:00 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] labeling by a pseudoatom
 
 Hello everyone,
 
 trying to use a pseudoatom as label I met several problems:
 
 1) How to move the label (pseudoatom) to a target residue?
 Is there a simple command to do?
 
 2) How to change the label without messaging the user?
 The 'label' command appears not have a 'quiet' option.
 
 3)  (less important) How to hide the pseudoatom?
 I wish not have the pseudoatom listed among models in the GUI
 panel.
 
 4)  (less important)  I need to execute all these operations by script
 (mdo
 commands during a movie)
 To simplify the movie I wish use only one mdo command
 
 def doAll()
 .. all my script here ..
 
 extending the cmd just before the movie start
 
 cmd.extend('doAll',  doAll)
 
 and clearing the cmd just at the end of the movie but I don't
 know
 how.
 Is there a way to clear a command?
 
 
 Thanks,
 Roberto
 
 

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Re: [PyMOL] Color scale changed in APBS?

[Schubert, Carsten [PRDUS]]

Hi Wataru, 

in addition to what Jason mentioned: Have you tried to look at the
potential mapped on the solvent accessible surface and display the
molecular surface? If you display the potential like this the colors
will be much more muted, on the other hand this is the setting you will
find most often displayed in the literature.
Another option is to have a look at the charge distribution of your
molecule in the actual PQR file. The potential distribution is dependent
on the charging algorithm used. I would recommend using/looking into
PDQ2PQR, which is available from the APBS website and compare this to
the homegrown charging algorithm from PyMol or GRASP for that matter.

Hope I did not muddle the water too much

Carsten

 -Original Message-
 From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp]
 Sent: Monday, February 21, 2011 10:04 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Color scale changed in APBS?
 
 Dear PyMOL users:
 
 I recently used the APBS plugin (v1.3) to display the surface
potential
 of a protein. I noticed that the charged surfaces were much more
 lightly colored, compared with the surface colors I have calculated in
 the past (maybe a year ago?) on the same protein, using the same
 softwares. The default settings and the same range (-10 kT to 10 kT)
 were used in both cases. Has anyone experienced this?
 
 I would appreciate any help.
 
 Wataru
 
 

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Re: [PyMOL] pymol movie scripting for beginners questions

[Schubert, Carsten [PRDUS]]

Aiko,

I can't directly comment on your problem, but I had good experience with
the eMovie plugin. May be give that a try.
http://www.weizmann.ac.il/ISPC/eMovie.html

HTH

Carsten


 -Original Message-
 From: Aiko Matsumoto [mailto:aikomatsumoto1...@googlemail.com]
 Sent: Friday, February 11, 2011 5:52 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] pymol movie scripting for beginners questions
 
 Dear Mailing list!
 
 I have just started using pymol to make a molecular movie of a protein
 ligand system.
 
 What I came up with is:
 

###
 
 
 reinitialize
 set matrix_mode, 1
 set movie_panel, 1
 set scene_buttons, 1
 set cache_frames, 1
 set static_singletons, off
 set movie_auto_interpolate, off
 set movie_loop, off
 
 config_mouse three_button_motions, 1
 set movie_fps, 30
 bg_color white
 
 load 2fpt-complex-aligned.pdb
 hide everything, all
 
 create ligand, resn ILB and resi 405
 create cofactor, resn FMN and resi 398
 create substrate, resn ORO and resi 399
 create site2, (cofactor substrate)
 create Nterm, (not resn HOH and resi 30-77)
 create Cterm, (not resn HOH and resi 78-396)
 create water1, byres resn HOH within 8 of ligand
 create water2, byres resn HOH within 8 of site2
 create pocket1, byres all within 7 of ligand and not resn HOH
 create pocket2, byres all within 7 of site2 and not resn HOH
 create TOP, Cterm site2
 create BOTTOM, Nterm
 create BOTH, TOP BOTTOM
 
 show cartoon, TOP BOTTOM
 show sticks, ligand
 show sticks, (TOP and (resn FMN or resn ORO))
 #show nb_spheres, water1
 #show nb_spheres, water2
 
 color meitnerium, ss h
 color titanium, ss l
 color thorium, ss s
 util.cbay ligand
 util.cbay (TOP and (resn FMN or resn ORO))
 
 #spectrum b, blue_white_red, water1
 #spectrum b, blue_white_red, water2
 
 set_view (\
   0.296377361,0.815219104,0.497568905,\
  -0.806614339,   -0.065306552,0.587461531,\
   0.511405945,   -0.575454950,0.638211489,\
   0.0,0.0, -235.838287354,\
  48.424118042,   41.582153320,   30.356651306,\
 185.936691284,  285.739868164,  -20.0 )
 
 mset 1 x433
 
 frame 1
 mview store, object=TOP
 mview store, object=BOTTOM
 mview store
 
 frame 180
 translate [0,10,0], object=TOP
 translate [0,-10,0], object=BOTTOM
 mview store, object=TOP
 mview store, object=BOTTOM
 mview store
 mview interpolate, object=TOP
 mview interpolate, object=BOTTOM
 
 frame 282
 util.mroll(180,282,360)
 mview store, object=TOP
 mview store, object=BOTTOM
 mview store
 
 frame 382
 translate [0,-10,0], object=TOP
 translate [0,10,0], object=BOTTOM
 util.mroll(282,382,360)
 mview store, object=TOP
 mview store, object=BOTTOM
 mview store
 mview interpolate, object=TOP
 mview interpolate, object=BOTTOM
 
 frame 432
 
 set_view (\
   0.264227241,0.815219104,0.515365601,\
  -0.842250228,   -0.065306552,0.535127521,\
   0.469904959,   -0.575454950,0.669362724,\
   0.0,0.0, -152.198883057,\
  47.851242065,   41.281734467,   31.806066513,\
 112.558006287,  191.839767456,  -20.0 )
 
 mview store, object=TOP
 mview store, object=BOTTOM
 mview store
 mview interpolate, object=TOP
 mview interpolate, object=BOTTOM
 
 frame 433
 mplay
 

###
 ###
 
 
 I am just beginning to gain familiarity with this but probably someone
 can point me into the right direction?
 My problem is that if I use the script in exactly the way I posted
 above
 then I  don't get the change view (frame 382 to 432).
 At the end the 'set view' just shows up without any interpolation.
 However, when I use a mview reinterpolate statement at the end of
the
 script,
 then frame 382 to 432 essentially zoom into the binding pocket, which
 is
 what I want BUT suddenly all attempts to rotate the system (frames 180
 to 280 and 280 to 380) have somehow been disabled, apart from 2 little
 rocking motions at exactly 2 frames, though I do get the translation
 right.
 
 After day one in using pymol I might not be the expert but even
 following several examples online (pymol-wiki and such) don't really
 give me any indication
 as to what is going on as there doesn't seem to be a really complex
 movie that allows the study on frames/states plus scenes plus proper
 complex use of mdo in one and the same example movie.
 
 Please please help, I am getting desperate here!
 
 Thanks
 
 Aiko
 
 PhD student
 Uni Bristol
 
 
 

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Re: [PyMOL] Independent Zooming in Grid Mode

[Schubert, Carsten [PRDUS]]

Sean,

Just a thought, but the translate command looks like as if it should be 
possible to selectively modify the viewmatrix on a per object basis:
   translate translates the atomic coordinates of atoms in a
selection.  Alternatively, is modifies the matrix associated with
a particular object or object-state.

May be if you create two objects of interest, split states by object and then 
play around with the translate command you could achieve that effect.

 -Original Message-
 From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
 Sent: Thursday, January 27, 2011 11:03 PM
 To: Sean Law
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Independent Zooming in Grid Mode
 
 Hi Sean,
 
 PyMOL is currently not capable of providing and inset-like image or
 grid-mode with independent motions.  Programming this at the Python
 level wouldn't be very easy.
 
 Cheers,
 
 -- Jason
 
 On Wed, Jan 26, 2011 at 9:39 AM, Sean Law magic...@hotmail.com wrote:
  Hi PyMOLers,
 
  I was wondering if anybody had a solution for independent when using
  grid_mode=on.  I want to be able to show, side-by-side, the same
 structure
  where one structure is zoomed in on a specific part on the
 biomolecule and
  the other object is zoomed out (viewing the entire molecule).  And
 as I
  turn one of the two structures, the other one turns accordingly.  I
 think
  this would be useful when trying to keep track of the orientation of
 the
  biomolecule or for docking.
 
  Any suggestions would be greatly appreciated.
 
  Sean
 
  From: pymol-users-requ...@lists.sourceforge.net
  Subject: PyMOL-users Digest, Vol 56, Issue 9
  To: pymol-users@lists.sourceforge.net
  Date: Mon, 24 Jan 2011 22:11:17 +
 
  Send PyMOL-users mailing list submissions to
  pymol-users@lists.sourceforge.net
 
  To subscribe or unsubscribe via the World Wide Web, visit
  https://lists.sourceforge.net/lists/listinfo/pymol-users
  or, via email, send a message with subject or body 'help' to
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  You can reach the person managing the list at
  pymol-users-ow...@lists.sourceforge.net
 
  When replying, please edit your Subject line so it is more specific
  than Re: Contents of PyMOL-users digest...
 
 
  Today's Topics:
 
  1. Re: Faster way to find polymer chains? (Tsjerk Wassenaar)
  2. Re: Faster way to find polymer chains? (Thomas Holder)
  3. unable to open the file (wang_qi)
  4. Re: unable to open the file (Christoph Gohlke)
  5. Re: Faster way to find polymer chains? (Seth Harris)
  6. dialogs in pyMOL (rv...@libero.it)
 
 
  
 --
 
  Message: 1
  Date: Sun, 23 Jan 2011 10:48:20 +0100
  From: Tsjerk Wassenaar tsje...@gmail.com
  Subject: Re: [PyMOL] Faster way to find polymer chains?
  To: Seth Harris set...@gmail.com
  Cc: pymol-users@lists.sourceforge.net
  Message-ID:
  AANLkTi=jdcwaci5n2jav_vqjybffatyb8cw5q0egq...@mail.gmail.com
  Content-Type: text/plain; charset=ISO-8859-1
 
  Oops... That should've been:
 
  polychains = set([i.chain for i in cmd.get_model('polymer').atom])
 
  Sorry for that. :p
 
  Tsjerk
 
  On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar
 tsje...@gmail.com
  wrote:
   Hi Seth,
  
   So you just want to have all unique chain identifiers for the
   'polymer' selection? Does the following give what you want?:
  
   polychains = set([i.chain for i in cmd.get_model('polymer')])
  
   Hope it helps,
  
   Tsjerk
  
   On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris set...@gmail.com
 wrote:
   Hi All,
   I am script-plowing through PDB files and extracting unique chain
   identifiers only for polymers using PyMOL's polymer selection.
 Right
   now
   my code is a kind of brute force thing like this:
   code
   ??cmd.create (justpolys,polymer)
   ??polymer_chains=[]
   ??for a in cmd.index(justpolys):
   ?? ?q_sel = %s`%d%a
   ?? ?#print q_sel+:,
   ?? ?cmd.iterate(q_sel, stored.qry_info =
 (chain,resn,resi,name))
   ?? ?#cmd.iterate_state(1,q_sel, stored.qry_xyz = (x,y,z))
   ?? ?#print
  
  
 stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_inf
 o[3]
   ?? ?# Track any unique chains by adding to polymer_chains list if
 not
   already there
   ?? ?# first reformat to get rid of flanking ' marks
   ?? ?thischain=`stored.qry_info[0]`
   ?? ?thischain=thischain.replace(',)
   ?? ?if thischain not in polymer_chains:
   ?? ? ?polymer_chains.append(thischain)
   /code
   This works, but is quite slow as it iterates over every atom in
 every
   pdb
   just to get out the chain so it is quite redundant.
   Is there any way to iterate in a 'chain by chain' fashion? This
 q_sel
   stuff
   is recycled from something Warren suggested for a different
 purpose
   years
   ago, and I only have a loose idea of how that is interacting with
 the
   cmd.index part. Maybe there's a way to get just the chain from
 the
   get-go
   instead of all the individual atoms? Any reminders on that one or

[PyMOL] Wiki down?

[Schubert, Carsten [PRDUS]]

I am just getting a blank page when I try to access the Pymol Wiki. Do
other people see the same problem?

Carsten

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Re: [PyMOL] Wiki down?

[Schubert, Carsten [PRDUS]]

OK, works here again as well. Main Page was somehow screwy or I had a
dirty cache in my browser

 

From: Nat Echols [mailto:nathaniel.ech...@gmail.com] 
Sent: Thursday, January 27, 2011 1:09 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Wiki down?

 

On Thu, Jan 27, 2011 at 9:54 AM, Schubert, Carsten [PRDUS]
cschu...@its.jnj.com wrote:

I am just getting a blank page when I try to access the Pymol Wiki. Do
other people see the same problem?

Working fine for me (using Safari on a Mac). 

 

-Nat

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Re: [PyMOL] colors and font size while ray tracing

[Schubert, Carsten [PRDUS]]

Hi Madhavi,

with regards to your first question:
I usually add text after rendering the stereo figures. That gives much
better control and has the advantage that label come out cleaner. Look
into Canvas, Photoshop or GIMP to do this. As an additional tip you can
control the depth of the labels this way as well. Lets say you want to
label Leu76 in the back of the figure, create one label, copy it to the
other panel and place the same part of the text on the same atom or
point of the residue you want to label. Group the labels and move them
to an unobstructive position. Repeat for the other labels. 
Spheres: Tough to tell, may be you inadvertently changed the depth queue
settings and the spheres got lighter. Did the the rest of the figure
change as well?

HTH

Carsten


 -Original Message-
 From: Nalam, Madhavi [mailto:madhavi.na...@umassmed.edu]
 Sent: Thursday, January 20, 2011 2:36 PM
 To: 'pymol-users@lists.sourceforge.net'
 Subject: [PyMOL] colors and font size while ray tracing
 
 Hello:
 I am trying to generate stereo figures for my manuscript. When I try
to
 ray trace at higher resolution, the font size (I use label_font_id=4)
 is becoming very small. If I use any fonts from the settings tab, the
 font size doesn't change with ray tracing. If I am correct, many
 journals prefer Helvitica/Arial fonts for the publication quality
 figures. So my question is are the fonts found in the settings
 preferred by the journals? If not, can anyone please tell me what can
 be done to keep the font size from decreasing during ray tracing?
 
 Also, I have vdW spheres shown as dots in the figure. The color of the
 dots for the vdW spheres is very light after I ray trace the figure.
 Last week when I ray traced the figure from the same PyMOL session,
the
 colors are much darker!! As far as I know, I haven't changed anything
 in the session file. So can anyone please tell me how to increase the
 darkness of the vdW spheres?
 
 I use PyMOL version 1.3.x on Windows.
 
 Thanks in advance,
 Madhavi
 
 

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[PyMOL] 3D TVs experience with PyMOL?

[Schubert, Carsten [PRDUS]]

Hello List:

Has anyone been able to put together a workable system where they can
run PyMOL from a 3D HDTV using a regular workstation (Linux or Windoze)
and the NVIDIA 3D Kit for presentation purposes? I did some preliminary
research and while there is a wide range of 3D TVs out there I am not
sure about compatibility. For instance a quick look at the Samsung 3D
LCD TVs revealed that they don't even have a dual DVI interface, only 15
pin analog, doesn't look as if that is going to work...
I'll keep looking, but if anyone is willing to share their experience it
would be greatly appreciated.

Thanks

Carsten


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Re: [PyMOL] Force of pure white background when ray tracing with fog

[Schubert, Carsten [PRDUS]]

Hi Jason,

sorry but it looks as if I've sent you on a wild goose chase. I did some more 
research and recreated the actual images using some of the original scripts and 
they look fine. Turns out that the culprit is the RGB to CMYK conversion in 
Canvas, which I am using to make the panels for publication. Unfortunately the 
publisher only accepts CMYK figures, so it looks as if I need to tackle this 
from another angle.

Thanks for your help, glad Pymol is not at fault... (-:

Cheers,

Carsten

 -Original Message-
 From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
 Sent: Tuesday, January 04, 2011 4:31 PM
 To: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Force of pure white background when ray tracing
 with fog
 
 Hi Carsten,
 
 What version of PyMOL are you using?  ray_trace_mode, 3 used to burn
 the background but doesn't any longer.  I just set my background to
 white and tested all ray_trace_mode settings (with fog on) and the
 background is pure white.  Can you please provide a snippet of code
 that produces the effect?
 
 Cheers,
 
 -- Jason
 
 On Tue, Jan 4, 2011 at 8:22 AM, Schubert, Carsten [PRDUS]
 cschu...@its.jnj.com wrote:
  Hi Pymolers,
 
  I just noticed that Pymol produces an off-whitish background when ray
  tracing a figure with fog enabled. The RGB values are (252,253,254)
 with my
  standard settings and are devilishly hard to spot on a monitor, but
 show up
  on some printers as a grayish background. Is there a setting or a
 trick to
  get rid of this effect and force a pure white background during
 rendering? I
  suppose rending with transparent background and pasting in pure white
 box
  should do as a post-production workaround, but that is not very
 convenient
  especially if the figures are already all made.
 
  Cheers,
 
      Carsten
 
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[PyMOL] Force of pure white background when ray tracing with fog

[Schubert, Carsten [PRDUS]]

Hi Pymolers,

I just noticed that Pymol produces an off-whitish background when ray
tracing a figure with fog enabled. The RGB values are (252,253,254) with
my standard settings and are devilishly hard to spot on a monitor, but
show up on some printers as a grayish background. Is there a setting or
a trick to get rid of this effect and force a pure white background
during rendering? I suppose rending with transparent background and
pasting in pure white box should do as a post-production workaround, but
that is not very convenient especially if the figures are already all
made.

Cheers,

Carsten


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Re: [PyMOL] Start PyMOL session in web browser

[Schubert, Carsten [PRDUS]]

Hi Martin,

not directly applicable to your question, but may be it directs your
thinking into a different direction. If I remember correctly Warren
pointed out a couple of year ago the p1m file format was supposed to
support downloading of structural information from the web with some
limited scripting options. Hope this helps.

Cheers,

Carsten



 -Original Message-
 From: Martin Hediger [mailto:ma@bluewin.ch]
 Sent: Sunday, December 19, 2010 7:38 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Start PyMOL session in web browser
 
 Dear all
 Is it possible to start a PyMOL viewer through a web browser? What I
 mean by this is, is it possible to view a protein over the internet
 where the viewing features are provided by some limited PyMOL
server?
 The only thing able to do that right now is Jmol, but i think its very
 inconvenient to use when viewing large structures such as proteins.
 
 Thanks for your answers
 Martin
 

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Re: [PyMOL] Charged Surface Calculation at different pHs?

[Schubert, Carsten [PRDUS]]

Steve,

 

you need to use PDB2PQR to generate your pqr file, with choice of pH and
then run APBS on that file. I pulled reasonable defaults for APBS from
the APBS plugin tool. PDB2PQR is accessible through the APBS website. 

 

 

HTH

 

Carsten

 

 

From: Soisson, Stephen M [mailto:stephen_sois...@merck.com] 
Sent: Wednesday, April 07, 2010 12:49 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Charged Surface Calculation at different pHs?

 

Hi- 

Does anyone know if it is possible to calculate the charged surface
using apbs at different pHs?  I am assuming the default pH is 7.

Thanks in advance- 

Steve 

 

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Re: [PyMOL] stereo rotation lost with draw command

[Schubert, Carsten [PRDUS]]

Norbert,

Try something like this for a side-by-side stereo image:

turn y,3
draw
png left_image.png
turn y, -6
draw
png right_image.png
turn y,3


Caveat is that potential shadows may not be rendered correctly in stereo. 
That's why the angle option was implemented in ray.

HTH

 Carsten



-Original Message-
From: Norbert Straeter [mailto:stra...@bbz.uni-leipzig.de]
Sent: Fri 2/5/2010 4:42 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] stereo rotation lost with draw command
 

I want to render a stereo image using the draw command instead of ray
tracing. Unfortunately, the stereo rotation is lost with the command and
the image is flat. If this is not a bug, is there a way to change this
behaviour?

Norbert Straeter



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Re: [PyMOL] Whitespacing?

[Schubert, Carsten [PRDUS]]

Not much of a help, but WingIDE Professional Edition has a very good 
indentation manager, which takes care of the mixed/space tab issues. If you are 
working in python frequently it is a worthwhile investment.

Cheers,

Carsten


 -Original Message-
 From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
 Sent: Tuesday, January 26, 2010 10:10 AM
 To: David Hall
 Cc: pymol-users
 Subject: Re: [PyMOL] Whitespacing?
 
 David,
 
 Oh, the joys of open-source.  Here's my solution for you:
  (1) load your file in your favorite editor
  (2) determine user-desired tab stop setting
  (3) convert all tabs to spaces in your editor (or search replace tabs
 with X-spaces)
  (4) save your file
 
 One warning though, I have seen some interpreters crash when they
 encounter spaces over tabs.
 
 -- Jason
 
 On Tue, Jan 26, 2010 at 9:12 AM, David Hall li...@cowsandmilk.net
 wrote:
  During my editing of dynoplot.py, I noticed that there were some
  whitespace issues.  Normally I consider whitespace a bikeshedding
  topic, but in python, it is significant, so it matters.  When tabs
 and
  spaces are mixed, our own personal settings for how tabs are
 displayed
  in an editor makes a huge difference in whether the script is
  understandable.
 
  I checked out the git repo of pymol scripts (
  http://github.com/jlec/Pymol-script-repo/ ) and did some analysis
 
  First, these files switch between some lines where all indenting is
  tabs to lines where all indenting is spaces:
  Objects_and_Selections/color_objects.py has 8 tab lines and 34 space
 lines
  ThirdParty_Scripts/WFMesh.py has 52 tab lines and 21 space lines
  biochemical_scripts/pucker.py has 167 tab lines and 5 space lines
  math_geo_cgo/modevectors.py has 160 tab lines and 2 space lines
  structural_biology_scripts/DynoPlot.py has 82 tab lines and 27 space
 lines
  structural_biology_scripts/Rotamers.py has 86 tab lines and 22 space
 lines
  structural_biology_scripts/kabsch.py has 51 tab lines and 4 space
 lines
 
  Second, there are files where the indenting inside a line switches
  back and forth (numbers are the counts of lines that have both tabs
  and spaces in indenting):
  Objects_and_Selections/color_objects.py: 19
  ThirdParty_Scripts/WFMesh.py: 29
  ThirdParty_Scripts/transform_odb.py: 6
  math_geo_cgo/modevectors.py: 12
  structural_biology_scripts/DynoPlot.py: 83
  structural_biology_scripts/Rotamers.py: 86
  structural_biology_scripts/kabsch.py: 1
 
  I've tried using pindent.py (
  http://svn.python.org/projects/python/trunk/Tools/scripts/pindent.py
 )
  and PythonTidy ( http://pypi.python.org/pypi/PythonTidy/ ) to
  generally fix these, but they both run into problems.  Is there a
  general solution out in the python world to automatically fix this?
  I
  don't care whether it produces tabs or spaces.  I just want one or
 the
  other.  If someone points me to something, I'm more than willing to
  run it on these scripts, push them back to github and copy them back
  onto the wiki.
 
  -David
 
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[PyMOL] New Feature Ideas

[Schubert, Carsten [PRDUS]]

Jason,

here are my feature requests, only slightly biased by the fact that some
of them would be useful for my paper now (-:

1) arbitrary clipping planes bound to an object with an intelligent gui
to place them. Something akin to be found in Maestro or semi-transparent
CGO objects which can be manipulated freely in space and then used to
define clipping planes

2) Implementation of bounding planes in raytracing to avoid showing the
inside of clipped surfaces, raster3D has this option. I know one can
fumble around in Povray to get the same effect, but I'd rather spend my
time on something more productive.

3) If 2) is not an easy option, how about raster3D output in addition to
povray? Pymol can read raster3d, why not have the output as well. 

4) A better density wizard, let's just copy coot and be done with it.
Ability to dynamically bind density levels or some other properties to
the scroll-wheel for that matter.

5) Updated documentation. One thing that always irritated me as a paying
subscriber was the fact that the documentation never kept up with
development and the search capabilities were not that great. Don't get
me wrong the Wiki and BB are great resources, but I'd expect a bit more
of the docs. Also having the internal help functionality for functions
and the API up to date would be great. Some functions don't seem to have
a doc-string.

6) Integration/bundling of wxPython as an alternative to TCL/Tk??

7) Internal FFT routines to be able to read map-coefficients

8) A CGO library for commonly used objects like arrows and such

Cheers,

Carsten

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[PyMOL] Preserving sec. structure in states for animation

[Schubert, Carsten [PRDUS]]

Hi,

I am trying to make a movie form a set of morphed pdb files. Currently
the individual files are loaded into the same object with increasing
states, all pdb files contain the SHEET and HELIX record created by
dssp.  The object is then displayed as a cartoon. When I loop over the
states I noticed that Pymol only seems to take secondary structure
information from the first pdb file into account. For instance I have a
helix which is split into 2 during the morph, but only displayed as one
helix during the animation, albeit a bit stretched. Loading the
individual files produces the right sec. structure. Any idea how I can
convince Pymol to update the cartoon representation with each frame? 

Cheers,

Carsten


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[PyMOL] Viewport dimensions query

[Schubert, Carsten [PRDUS]]

Hi,

Does anyone know how to  get a hold of the viewport dimensions from
within a script? I vaguely remember some posts about this subject, but
could not find anything in my archive.

Thanks

Carsten
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Re: [PyMOL] Viewport dimensions query

[Schubert, Carsten [PRDUS]]

Yep,

thanks Folmer

 -Original Message-
 From: Folmer Fredslund [mailto:folm...@gmail.com]
 Sent: Thursday, September 24, 2009 9:33 AM
 To: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Viewport dimensions query
 
 Hi Carsten,
 
 Is this what you are looking for?
 http://www.mail-archive.com/pymol-
 us...@lists.sourceforge.net/msg05888.html
 
 Best regards,
 Folmer Fredslund
 
 2009/9/24 Schubert, Carsten [PRDUS] cschu...@its.jnj.com:
  Hi,
 
  Does anyone know how to  get a hold of the viewport dimensions from
 within a
  script? I vaguely remember some posts about this subject, but could
 not find
  anything in my archive.
 
  Thanks
 
      Carsten
 
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Re: [PyMOL] label a stereo .png image in pymol

[Schubert, Carsten [PRDUS]]

Peter, 

 

here are some general considerations for stereo images

 

A.  The images should be ~63mm apart with respect to a point which you 
consider to be neutral, i.e. neither lies in front or in the back of the 
zero-plane

B.  The distance of the images also put restrictions on their size, which 
is something you need to consider. Usually it is 1 ½ columns in a journal, if I 
am not mistaken.

C.  For labels I use a program like photoshop or canvas, just because one 
has a wider selection of fonts and they produce antialiased renderings. I 
usually attach labels to landmarks, with which they share the same depth. For 
example if you want to label residue 234 and have the residue drawn in stick, 
you could place both upper left corners of the labels on the CA position, group 
them and move them out of the way so as they do not interfere with the rest of 
the graphic. Using this trick ensures that the labels appear in the correct 
depth.

 

HTH

 

Carsten

 

From: peter hudson [mailto:peter.hudson.pe...@gmail.com] 
Sent: Monday, September 07, 2009 12:30 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] label a stereo .png image in pymol

 

Hello all

I have made  a stereo image in pymol and photoadobeshop. But, i would like to 
label the image file which should like a stereo image label. how that can be 
done in the pymol. I can do it in photoadobeshop .problem lies her that i am 
not sure is the labels are really stereo or not?

can anyone suggest solutions. I would appreciate that.


Thanks in advance 

peter

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Re: [PyMOL] Smooth fading of surface in movie?

[Schubert, Carsten [PRDUS]]

Dirk,

 

you could try playing around with different transparency settings in
subsequent scenes to emulate the effect. 

 

HTH 

 

Carsten

 

From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] 
Sent: Tuesday, September 01, 2009 8:57 AM
To: PyMOLBB
Subject: [PyMOL] Smooth fading of surface in movie?

 

Dear Warren,

 

using PyMOL without any additional plug-ins, like slerpy or eMovie, is
it possible to fade in or out a surface of, say, a ligand, between
scenes?

 

Best regards,

 

Dirk.


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Re: [PyMOL] object-specific Z-clipping

[Schubert, Carsten [PRDUS]]

Warren,

Can PyMol actually write raster3D objects? That's news to me. I did a
couple of the clipped, bounded surfaces in raster3d since it supports it
supports the option and was easier to implement than in PovRay. Again
the biggest drag is always to find the right orientation of the clipping
planes. If we can achieve this in PyMol then the rest is fairly easy.

Cheers,

Carsten

 -Original Message-
 From: Warren DeLano [mailto:war...@delsci.com]
 Sent: Friday, May 01, 2009 8:53 PM
 To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net
 Subject: RE: [PyMOL] object-specific Z-clipping
 
 Carsten,
 
 I think you're on to something.
 
 So long as this rendering problem remains too hard for us to solve
with
 PyMOL alone, probably the next best thing would be for us to figure
out
 at least an interim PovRay or Raster3D-based process for creating such
 figures.  Having an object-selective but non-renderable OpenGL-based
 clipping plane available could certainly help with that!
 
 Cheers,
 Warren
 
  -Original Message-
  From: Schubert, Carsten [PRDUS] [mailto:cschu...@its.jnj.com]
  Sent: Thursday, April 30, 2009 1:40 PM
  To: Warren DeLano; pymol-users@lists.sourceforge.net
  Subject: Re: [PyMOL] object-specific Z-clipping
 
  Hi Warren,
 
  I would be interested to see the OpenGL version implemented,
  despite the lack of raytracing support. In a pinch the draw
  command could just be sufficient to produce a good picture.
 
  As for the implementation in a raytracer context I second
  Tsjerk's and Harry's thoughts on the subject. Probably some
  sort of PovRay based implementation would help in the
  interim. What I find most challenging with that approach is
  the fact that the placement of the clipping objects is
  difficult to achieve in PovRay since it lacks the
  interactivity of a graphics program. I.e. finding the right
  cut through a protein surface when depicting a ligand in a
  cut-away surface is tough. Although there are other ways to
  achieve this they require some cheating or creative use of
  Photoshop/PowerPoint to phrase it differently.
  I am thinking that if it would be possible to write out the
  orientation of the clipping planes/slabs as PovRay objects,
  they could be used as bounding objects in PovRay. Since the
  placement of the clipping planes is easily achieved in Pymol
  this could be done interactively. All the user has to do is
  to associate clipping plane(s) with a graphics object, place
  the planes and write out the corresponding PovRay code of the
  object and the planes. Of course the code of the clipping
  objects needs to be separate from the other stuff, so
  expanding the PovRay tuple
  into (matrix,clipping,data) parts would help.
  Getting it all together requires some knowledge of PovRay but
  examples in the Wiki should help to get over the initial pain.
 
  Any thoughts on this approach?
 
  Carsten
 
 
   -Original Message-
   From: Warren DeLano [mailto:war...@delsci.com]
   Sent: Wednesday, April 29, 2009 10:36 PM
   To: Mankin Alexander; pymol-users@lists.sourceforge.net
   Subject: Re: [PyMOL] object-specific Z-clipping
  
   Sorry, still not done (I have made two attempts, but both failed).
  
   While OpenGL supports arbitrary clipping planes, accomplishing
this
   correctly in the ray tracer is a much harder problem that one
might
   think...
  
   Cheers,
   Warren
  
-Original Message-
From: Mankin Alexander [mailto:sh...@uic.edu]
Sent: Wednesday, April 29, 2009 6:18 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] object-specific Z-clipping
   
Dear all,
Does anyone know whether object-selective z-clipping has been
implemented in the newer Pymol version(s)? If not, has
  anyone found
any solution around (since 2002 no new threads on the matter)?
Thanks,
Shura Mankin
   
  
  
  
  
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Re: [PyMOL] object-specific Z-clipping

[Schubert, Carsten [PRDUS]]

Hi Warren,

I would be interested to see the OpenGL version implemented, despite the
lack of raytracing support. In a pinch the draw command could just be
sufficient to produce a good picture.

As for the implementation in a raytracer context I second Tsjerk's and
Harry's thoughts on the subject. Probably some sort of PovRay based
implementation would help in the interim. What I find most challenging
with that approach is the fact that the placement of the clipping
objects is difficult to achieve in PovRay since it lacks the
interactivity of a graphics program. I.e. finding the right cut through
a protein surface when depicting a ligand in a cut-away surface is
tough. Although there are other ways to achieve this they require some
cheating or creative use of Photoshop/PowerPoint to phrase it
differently. 
I am thinking that if it would be possible to write out the orientation
of the clipping planes/slabs as PovRay objects, they could be used as
bounding objects in PovRay. Since the placement of the clipping planes
is easily achieved in Pymol this could be done interactively. All the
user has to do is to associate clipping plane(s) with a graphics object,
place the planes and write out the corresponding PovRay code of the
object and the planes. Of course the code of the clipping objects needs
to be separate from the other stuff, so expanding the PovRay tuple
into (matrix,clipping,data) parts would help. 
Getting it all together requires some knowledge of PovRay but examples
in the Wiki should help to get over the initial pain. 

Any thoughts on this approach?

Carsten


 -Original Message-
 From: Warren DeLano [mailto:war...@delsci.com]
 Sent: Wednesday, April 29, 2009 10:36 PM
 To: Mankin Alexander; pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] object-specific Z-clipping
 
 Sorry, still not done (I have made two attempts, but both failed).
 
 While OpenGL supports arbitrary clipping planes, accomplishing this
 correctly in the ray tracer is a much harder problem that one might
 think...
 
 Cheers,
 Warren
 
  -Original Message-
  From: Mankin Alexander [mailto:sh...@uic.edu]
  Sent: Wednesday, April 29, 2009 6:18 AM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] object-specific Z-clipping
 
  Dear all,
  Does anyone know whether object-selective z-clipping has been
  implemented in the newer Pymol version(s)? If not, has anyone found
  any solution around (since 2002 no new threads on the matter)?
  Thanks,
  Shura Mankin
 
 
 
 

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Re: [PyMOL] pymol and bonds to symmetry related molecules

[Schubert, Carsten [PRDUS]]

Christian,
 
as far as I know, PyMol is only able to draw bonds between atoms within the 
same object. The easiest way would be to combine the pdb files, probably a good 
idea to give the symm-mate a different chain or segid and then issue the bond 
command to draw the bond.
 
HTH
 
Carsten

-Original Message-
From: Christian Roth [mailto:christian.r...@bbz.uni-leipzig.de]
Sent: Monday, April 06, 2009 7:21 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] pymol and bonds to symmetry related molecules



Dear all,



I have incorporated a bond to a symmetry related molecule in my structure and I 
want see this bond in my picture. Is it possible to visualize this bond in 
pymol?

Thansk in advance for your help.



Christian

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Re: [PyMOL] Showing only part of a surface around a ligand

[Schubert, Carsten [PRDUS]]

Wulf,

suppose you have this scenario:
Protein in chain A
Ligand in chain I

Then 

create b-site, byres chain A within 5 of chain I
show sticks, chain I
show surface, b-site

should get you close.

HTH

Carsten

BTW If you replace the create command with select your surface will be 
scribed i.e. with frizzled ends. If this is what you want then you should use 
select.

-Original Message-
From: Wulf Blankenfeldt [mailto:wulf.blankenfe...@mpi-dortmund.mpg.de]
Sent: Wednesday, March 25, 2009 1:31 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Showing only part of a surface around a ligand


Hi all,

this question may be resolvable by sufficient RTFMing, but maybe there 
is someone out there to help me...

I am trying to generate a figure in which I want to show only a part of 
the protein surface around a ligand - pretty much like

preset -- ligand sites -- solid surface

I have already tried some amateur solutions like splitting the ligand 
into parts, placing waters to generate pseudo-ligand atoms and the like. 
Somewhat unsatisfying. I have also realized that I can click on every 
atom of the protein and do a show surface, but this will drive me insane 
sooner than later.

I guess it must be doable through some magic selection commands - if I 
could only see how the preset command works, I could probably work it 
out from there.

Can somebody please point me in the right direction?

Thanks in advance,


Wulf


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[PyMOL] Procedure for adding packages to pymol site-packages?

[Schubert, Carsten [PRDUS]]

Hi,

how would I go about adding a package to the $PYMOL_PATH/ext/.../site-packages 
w/o screwing up the install?

For most packages the mechanism is python setup.py install. Would this work 
to run this from within pymol?

Thanks

Carsten

Re: [PyMOL] selenomethionine

[Schubert, Carsten [PRDUS]]

Scott,

the MSEs are probably HETATM records instead of ATOM records. You can either 
replace the HETATM records to ATOM records or set surface_mode to 1 which 
allows rendering of surfaces with HETATM records (I think, am a bit fuzzy on 
that)

HTH

Carsten

-Original Message-
From: Scott Lefurgy [mailto:slefu...@aecom.yu.edu]
Sent: Wednesday, January 21, 2009 12:20 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] selenomethionine



I am looking at a structure that contains selenomethionine (rendered MSE
in the sequence).  When I Show Surface, Se-Met is not displayed with a
surface, but all the other residues are.  Is there any way to make a
surface over Se-Met as well?

Scott

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Re: [PyMOL] PyMOL crashes under Vista Home Premium Ubuntu 8.04 LTS

[Schubert, Carsten [PRDUS]]

Michael, play around with the hash_max value, which seem to partially control 
how much memory is used during rendering. You can also reduce the quality of 
the rendering Display-Quality, that should reduce memory requirements too. I 
know you don't want that, but do you really need max quality? Finally on Unix 
or even Windoze you can look at how much memory is consumed during rendering 
using top (on Unix) and the task manager on windows. That should give you some 
clue if you are really exceeding the physical memory or not. Finally you could 
split the rendering into smaller pieces, export to Povray, combine the files 
under a common header and render there, alternatively try if the Draw command 
gives you what you want, albeit not quite as fancy as the raytracer.

HTH 

Carsten



-Original Message-
From: Michael Weber [mailto:web...@staff.uni-marburg.de]
Sent: Friday, January 16, 2009 7:24 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] PyMOL crashes under Vista Home Premium  Ubuntu 8.04
LTS


Hi,
I have a problem when trying to ray 750,750 a quite large ribosome file 
with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or 
31 MB after reducing objects I do not need for the figure production). 
PyMOL simply crashes under Windows Vista Home Premium as well as under 
Ubuntu Linux v8.04 LTS without error report. My dual OS system is a 
Samsung Aura Seven Notebook (Core2Duo @2.4 GHz each, 3 GB of RAM, NVIDIA 
GeForce 9200M GS graphics board with 256 MB of RAM, 12 TFT @1280x800 
resolution settings). I first thought the RAM under Vista is still 
insufficient (Vista alone takes 900 MB of the 3 GB of memory) but then  
I realized that this crash occurs as well under Linux. However, since 
both OS are 32 bit and therefore to my (limited) knowledge cannot handle 
more than 2 GB in a single task, RAM limitation might still be an issue 
to think about, right?
I have experienced (and occasionally reported) this type of serious 
crashes with PyMOL on a broad variety of machines over some years now - 
usually occurring when trying to render final files - but, sadly, none 
of these has ever been diagnosed and fixed properly. Maybe this time I 
am lucky and someone knows what to do?
Best regards,
Michael.

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Re: [PyMOL] Making Stereo Pair Graphics

[Schubert, Carsten [PRDUS]]

Buz your image size will automatically be limited by the separation of two 
equal points in the respective images, which should be ~62 mm apart. Let me 
know if you need more details.

Carsten

-Original Message-
From: Buz Barstow [mailto:b...@mac.com]
Sent: Monday, November 24, 2008 3:01 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Making Stereo Pair Graphics


Dear All,

I'd like to make a stereo pair graphic using pymol.

I'd like to know what is an appropriate size for each image in the  
pair, and what their separation should be.

Thanks! and all the best,

--Buz



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Re: [PyMOL] remove cartesian coordinate from w/in transparent metal ions

[Schubert, Carsten [PRDUS]]

Tom,
 
you need to hide the 'nonbonded' representation of your ion, which shows up as 
a little coordinate system i.e.
 
hide nonbonded, chain I#if your ion is in chain I
show spheres, chain I
set sphere_transparency=0.5, chain I
 
Cheers,
 
Carsten

-Original Message-
From: Thomas S. Leyh, Ph. D. [mailto:l...@aecom.yu.edu]
Sent: Wednesday, October 29, 2008 2:39 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] remove cartesian coordinate from w/in transparent metal ions


Every once in a while, I try to show a metal ion as a tranparent sphere and 
inevetiably get stuck trying to make the tiny cartesian coordinate system that 
appears at the center of the sphere disappear so it doesn't show through.  
Suggestions?
 
Tom Leyh  

Re: [PyMOL] Electron density map in pymol

[Schubert, Carsten [PRDUS]]

Jhon,

all the newer builds of PyMol are able to read ccp4 maps, no need to convert to 
xplor format. 
As far as your commands are concerned, you are almost there. 
Try this:
load mymap.ccp4, format=ccp4, mymap
isomesh map, mymap, 2.0, site, carve=1.6

were map is the name of the map graphical object you want to create, mymap is 
the name of the object that holds the actual map as defined by the load 
command. 

HTH

Carsten


-Original Message-
From: Jhon Thomas [mailto:jhon1.tho...@gmail.com]
Sent: Friday, September 26, 2008 7:15 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Electron density map in pymol


Hello all pymol users

I am new to pymol and trying to open a .xplor map file in pymol to get the 
electron density map of publication grade. 
The command i write for pymol to open the file and show electron density map  
is -

1) I convert ccp4 .map file into the .xplor file through mapman.

# mymap.xplor loaded as  mymap loaded as state 0.
2) Then i load the .xplor map file into pymol and write the following commands-

isomesh map, mymap.xplor, 2.0, site, carve=1.6
isomesh: map or brick object mymap.xplor not found.


What could be the problem? can any one give suggestion to solve it?

Thanks in advance

Jhon 

Re: [PyMOL] hydrogen naming

[Schubert, Carsten [PRDUS]]

phenix.reduce is an option

-Original Message-
From: pymol-users-boun...@lists.sourceforge.net 
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of David A. Horita
Sent: Thursday, August 21, 2008 3:32 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] hydrogen naming


Hi,
How do I get proper (HN,HA, HE1, etc) hydrogen naming when using h_add (instead 
of H01, H02, ...)?  
 
Worst case I can build them in Xplor/CNS; second worst would be if there is a 
uniform rule per residue that I could write a script to convert on a residue 
type basis.
 
Thanks,
Dave
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm 
http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ 
 

Re: [PyMOL] How to disable automatic atom connection?

[Schubert, Carsten [PRDUS]]

I believe show valence=on,your_selection will do the trick. Where 
your_selection is the ligand or whatever you want to display. 
 
Good luck
 
Carsten

-Original Message-
From: pymol-users-boun...@lists.sourceforge.net 
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Piter_
Sent: Monday, July 14, 2008 3:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] How to disable automatic atom connection?


Hi all.
How can I disable automatic atom connection in pymol.
I want Pymol to make bonds only using connect field in pdb file.
Thanks.
Petro.

Re: [PyMOL] different transparency surfaces proteins

[Schubert, Carsten [PRDUS]]

Joris,
 
you should be able to apply different transparency settings if your proteins 
are part of different objects i.e.
 
set transparency=0.8, sel1
set transparency=0.5, sel2
 
HTH
 
Carsten

-Original Message-
From: pymol-users-boun...@lists.sourceforge.net 
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Beld, Joris
Sent: Wednesday, July 09, 2008 1:02 PM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] different transparency surfaces proteins



Dear all,

 

Two questions which I haven't been able to find on the web: 

 

Is there a way to set different surface transparency levels for a couple of 
different proteins compiled in one pymol session, all displayed as surface?! 

 

Is there a nice way to give pymol more priority/RAM to do difficult (big 
protein particle surfaces) ray tracing? Or would  POVray do a better job at 
that?

 

Thanks a lot.

Best,

 

Joris Beld

 

ETH Zürich 

Switzerland

 

Re: [PyMOL] drawing axes

[Schubert, Carsten [PRDUS]]

Just to add onto what Tsjerk had to say about running python snippets in a .pml 
script. You can also encapsulate the python code in blocks like this:

python
your python code here
python end

This works with all newer version of pymol (1.0) and enhances readability of 
the code quite a bit.

HTH

Carsten


 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Tsjerk
 Wassenaar
 Sent: Wednesday, June 11, 2008 3:25 AM
 To: David Goldenberg
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] drawing axes
 
 
 Hi David,
 
 Regarding the first part of your question, the way to load a python
 (not a PyMol) script is:
 
 run axes.py
 
 .. and not @axes.py. The latter is used for loading PyMol scripts
 (.pml). You _can_ use python code in a .pml script, but then you
 better, or in some cases have to, start with a slash (/) to let the
 command parser know that there's python code coming.
 
 Hope it helps,
 
 Tsjerk
 
 On Wed, Jun 11, 2008 at 12:10 AM, David Goldenberg
 goldenb...@biology.utah.edu wrote:
  Hi,
 I would like to make a figure that shows a set of coordinate axes
  aligned in a particular way with respect to a molecule.  I 
 have found
  the axes.py script (copied at the bottom of this message) 
 on the PyMol
  Wiki, but have run into the following problems:
 
  1. I can't get the script to load and run properly in 
 MacPymol.  I get a
  long string of error messages beginning with:
 
  PyMOL@axes.py
  PyMOLfrom pymol.cgo import *
  PyMOLfrom pymol import cmd
  PyMOLfrom pymol.vfont import plain
  PyMOLobj = [
  Traceback (most recent call last):
File /Applications/Molecular
  Graphics/MacPyMOL.app/pymol/modules/pymol/parser.py, line 
 208, in parse
  exec(layer.com2+\n,self.pymol_names,self.pymol_names)
File string, line 1
   obj = [
  ^
   SyntaxError: unexpected EOF while parsing
 
  I can get the script to run with an old version (0.98) of 
 the Mac-X11
  hybrid.  I can live with this, if necessary.
 
  2. Once I have the axes and the molecule loaded, I would 
 like to place a
  particular atom at the origin and then rotate the molecule into a
  particular orientation.  I thought that I could do the first part by
  using the translate command, by moving the molecule by amounts that
  correspond to the negative of the initial coordinates of the atom of
  interest.  That is, if the initial coordinates (from the 
 pdb file) are,
  1,-2,2, it seems that if I do
  translate [-1,2,-2]
  I should move the molecule so that the atom is at the 
 origin.  But, this
  doesn't happen; The molecule moves, but not along the expected axes.
  There is clearly something about the coordinate system and 
 the translate
  command that I don't understand.
 
  Any suggestions for how to go about this would be greatly 
 appreciated!
 
  David
 
 
  
 
  The script:
 
  # axes.py
  from pymol.cgo import *
  from pymol import cmd
  from pymol.vfont import plain
 
  # create the axes object, draw axes with cylinders coloured 
 red, green,
  #blue for X, Y and Z
 
  obj = [
 CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 
 1.0, 0.0, 0.,
 CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 
 0., 1.0, 0.,
 CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 
 0., 0.0, 1.0,
 ]
 
  # add labels to axes object (requires pymol version 0.8 or 
 greater, I
  # believe
 
  
 cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0
 ,3,0],[0,0,3]])
  
 cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],
 [0,0,3]])
  
 cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],
 [0,0,3]])
  
 cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],
 [0,0,3]])
 
  # then we load it into PyMOL
  cmd.load_cgo(obj,'axes')
 
  --
  Department of Biology
  University of Utah
  257 South 1400 East
  Salt Lake City, UT  84112-0840
 
  Telephone: (801) 581-3885
  Fax:  (801) 581-2174
 
  E-mail: goldenb...@biology.utah.edu
  Lab web page: http://www.biology.utah.edu/goldenberg
 
  
 --
 ---
  Check out the new SourceForge.net Marketplace.
  It's the best place to buy or sell services for
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 -- 
 Tsjerk A. Wassenaar, Ph.D.
 Junior UD (post-doc)
 Biomolecular NMR, Bijvoet Center
 Utrecht University
 Padualaan 8
 3584 CH Utrecht
 The Netherlands
 P: +31-30-2539931
 F: +31-30-2537623
 
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 just about anything Open Source.
 

[PyMOL] Embeding commands in PyMol session?

[Schubert, Carsten [PRDUS]]

Hi,

is it possible to embed commands or scripts into a pymol session? I am 
routinely creating PyMol sessions for users who for the most part have no clue 
how to use PyMol. So I'd like to include a dialog or message, which gets 
displayed after the session has loaded and clues the user in how to start or at 
least what he is looking at.

Cheers,

Carsten

Re: [PyMOL] Embeding commands in PyMol session?

[Schubert, Carsten [PRDUS]]

Hi Warren,

I got all that covered already. I think I have a way of doing what I want. I 
just define the help on the first scene and predisplay it upon loading. That 
should do the trick. 

Cheers,

Carsten


 -Original Message-
 From: DeLano Scientific [mailto:del...@delsci.info]
 Sent: Friday, April 25, 2008 3:28 PM
 To: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net
 Subject: RE: [PyMOL] Embeding commands in PyMol session?
 
 
 Hi Carsten,
 
 The best way to share PyMOL content with novice users is via 
 pre-defined
 scenes stored in a session file.  Users can then simply open 
 the session
 file and use Page Down to iterate through the scenes.  Each 
 scene can be
 annotated with text, for example:
 
 scene 001, store, The target structure (press the Page Down key).
 ...
 scene 002, store, Surface of the binding site.
 ...
 scene 003, store, Our lead compound ABC-12346.
 ...
 
 NOTE: For multi-line annotations, you need to use the Python 
 form of the
 command:
 
 cmd.scene(003,store,My first line of text\nMy second 
 line of text)
 
 Cheers,
 Warren
 
 --
 DeLano Scientific LLC
 Subscriber Support Services
 mailto:del...@delsci.info
  
 
  -Original Message-
  From: pymol-users-boun...@lists.sourceforge.net 
  [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
  Of Schubert, Carsten [PRDUS]
  Sent: Friday, April 25, 2008 6:38 AM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] Embeding commands in PyMol session?
  
  Hi,
  
  is it possible to embed commands or scripts into a pymol 
  session? I am routinely creating PyMol sessions for users who 
  for the most part have no clue how to use PyMol. So I'd like 
  to include a dialog or message, which gets displayed after 
  the session has loaded and clues the user in how to start or 
  at least what he is looking at.
  
  Cheers,
  
  Carsten
  
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Re: [PyMOL] hardware stereo problem

[Schubert, Carsten [PRDUS]]

Joris,

this is a well known problem with the NVIDIA cards. It gets better with the 
newer highend cards but does not go away completely. You may want to invest in 
such a card and play around with different drivers.

Carsten

 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Joris
 Beld
 Sent: Wednesday, March 12, 2008 4:44 AM
 To: PyMOL-users@lists.sourceforge.net
 Subject: [PyMOL] hardware stereo problem
 
 
 Dear Pymol users,
 
 We have a problem with one of our hardware stereo equipped PCs.
 
 For some reason, hardware stereo works fine for about 30sec but than 
 switches to an inverted 3D image. And it keeps switching back 
 and forth 
 between the 'normal' 3D image and the inverted one, every 
 30sec. This is 
 pretty annoying and even after reinstalling winXP, the right nvidia 
 driver and playing around with all possible nvidia settings, 
 we cannot 
 find the problem. The problem is not Pymol specific, having the same 
 problem in DSviewer. Does anybody recognize this problem?
 
 The PC (AMD X2, 4GB, Nvidia quadro4 980XGL) is running winXP 
 and one of 
 the latest pymol builds (1.0r2).
 The monitor is a high-end 21 (EIZO Flexscan T966) and we are using a 
 stereographics emitter.
 
 Thanks a lot in advance.
 Best,
 
 Joris Beld
 ETH Zürich
 Switzerland
 
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Re: [PyMOL] How to make the dashed line having more dots?

[Schubert, Carsten [PRDUS]]

JunJun

there are a couple of settings which relate to dashes. Go to Setting-Edit 
All... and filter by dash. You need to play around with these settings to get 
the desired effect. Be aware, some of these changes only become visible after 
raytracing. 

Cheers

Carsten

 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of JunJun
 Liu
 Sent: Tuesday, March 04, 2008 1:16 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] How to make the dashed line having more dots?
 
 
 Hello everybody,
 
 I want to make a picture on which two close atoms are connected by a  
 dashed line. I use the distance command to make the dashed line.  
 However, there's only one dot to compose the whole dashed 
 line. Is there a  
 way to make the dashed line having more dots?
 
 ==
 What I want:
 Atom_A  Atom_B
 
 What PyMol gives:
 Atom_A  -   Atom_B
 ===
 
 One more question on the dashed line. Can I modify the dashed line  
 properties, like making it stronger or more compact?
 
 Thanks!
 
 Junjun
 
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Re: [PyMOL] Isotropic thermal ellipsoids

[Schubert, Carsten [PRDUS]]

Warren,

this thread gave me an idea about an enhancement request I had for some time. 
Would it be possible to extend the molecular object module in a way that 2 or 
more general properties per atoms would be available in PyMol in addition to b 
and q. For instance in Grasp 2 properties (Prop1, Prop2) are available, which 
can be used to visualize user defined properties, like distance of an atom from 
other atoms, partial charges or any other computed property. Right now if one 
wants to display these properties they have to be placed into either b and q, 
which actually may contain values one likes to keep around.

This probably requires some serious reworking of the internals, but may be 
worth the effort.

Cheers

Carsten



 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of DeLano
 Scientific
 Sent: Friday, February 22, 2008 2:39 PM
 To: 'Tsjerk Wassenaar'; 'Thomas Stout'
 Cc: PyMOL-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Isotropic thermal ellipsoids
 
 
 Tsjerk,
 
 Close, but the relationship isn't linear.  RMS displacement is
 c*sqrt(temperature-factor), where c is a constant.  The 
 following equation
 can be found in crystallography texts:
 
 B = U * 8 * pi^2.
 
 where U is a mean squared displacement and B is the 
 temperature factor.  If
 I've done the math correctly, then the PyMOL input to show 
 root-mean-squared
 (RMS) displacement would be:
 
 from math import sqrt,pi
 alter all, vdw = sqrt(b/8)/pi
 show spheres
 
 However, given all the fitting performed in the data 
 reduction and structure
 refinement, absolute temperature factors many not be a 
 reliable measure of
 absolute RMS displacement in any sort of modeling or analysis work.  
 
 It is probably safer to stick with relative, qualitative 
 comparisons within
 a single structure, keeping in mind that vdw could be scaled 
 by systematic
 biases.
 
 Cheers,
 Warren
 
 --
 DeLano Scientific LLC
 Subscriber Support Services
 mailto:del...@delsci.info
  
 
  -Original Message-
  From: pymol-users-boun...@lists.sourceforge.net 
  [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
  Of Tsjerk Wassenaar
  Sent: Friday, February 22, 2008 1:11 AM
  To: Thomas Stout
  Cc: PyMOL-users@lists.sourceforge.net
  Subject: Re: [PyMOL] Isotropic thermal ellipsoids
  
  Hi Tom,
  
  Does what you're trying to do come down to:
  
  alter all, vdw=b/100
  show spheres
  
  ?
  
  
  Cheers,
  
  Tsjerk
  
  On Fri, Feb 22, 2008 at 1:42 AM, Thomas Stout 
  tst...@exelixis.com wrote:
  
  
   Hi All --
  
   Yes, I know I want to do something silly here, but does 
  anyone know of 
   a jiffy that will generate anisotropic thermal 
 parameters for an 
   isotropic atom?
  
   My end goal is to create a figure showing a ligand as 
  ball-and-stick 
   where the spheres are scaled by the B-factor.  Since I'm 
  not dealing 
   with ultra-high resolution data, I just have normal 
  isotropic atoms.  
   I'd like to use the new ellipsoids functionality in 
 PyMOL, but it 
   requires anisotropic atom lines.  Obviously, I could 
 write a python 
   script that would scale the vdW radii by some 
 normalization of the 
   B-factor, but I thought I could be lazy and use what Warren 
  has already built into PyMOL.
  
   Thanks!
   -Tom
  
   PS -- I'm thinking of something like the -iso feature of 
  rastep in 
   Ethan Merritt's Raster3D suite..
  
   This email (including any attachments) may contain 
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  --
  Tsjerk A. Wassenaar, Ph.D.
  Junior UD (post-doc)
  Biomolecular NMR, Bijvoet Center
  Utrecht University
  Padualaan 8
  3584 CH Utrecht
  The Netherlands
  P: +31-30-2539931
  F: +31-30-2537623
  
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[PyMOL] Cartoon mode not stored in scene description?

[Schubert, Carsten [PRDUS]]

Hi

I am trying to define 2 scenes, in one the protein is represented in cartoon 
automatic mode in the other with cartoon putty. Pymol (1.0 on Linux or 1.1b 
on Windows) both only draw the recalled scenes in putty mode. Is that expected 
behaviour? I would have thought that the cartoon mode is part of a scene 
description?
The colors do get updated between the scenes. 

Here is a code snipped to make this clearer:


cartoon automatic
refresh

scene F1, store

cartoon putty
spectrum b, palette=rainbow, minimum=0, maximum=60,selection=prot and name CA

scene F2, store


Cheers

Carsten

Re: [PyMOL] displaying unit cell in PyMol

[Schubert, Carsten [PRDUS]]

Satinder,

make sure you have the correct CRYST record in your file, then load it and
in the graphics GUI under S(how) select the Cell menu item. That should do
the trick.

Cheers

Carsten


-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Satinder K.
Singh
Sent: Tuesday, May 08, 2007 10:55 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] displaying unit cell in PyMol


Hello,

I am trying to visualize potential heavy metal sites in PyMol. I can read in
the ha.pdb output from SOLVE, but I would also like to see the boundaries of
the unit cell. In O, I know you can do that with the command sym_cell, but
I haven't been able to figure out how to do it in PyMol nor I have been able
to find a command anywhere on the web. Could someone tell me if this in
indeed possible in PyMol and what the command is? Thanks.

Kind regards,
Satinder

Re: [PyMOL] Suse 10 and PyMOL crashes

[Schubert, Carsten [PRDUS]]

Joris,

just an idea. Check if the /dev entry for your video card has the right
permissions. For the nvidia board I observed that sometimes the entries
(/dev/nvidia0 and/or /dev/nvidiactl) are crw-- instead of crw-rw-rw.
Check if changing the permissions on these entries or changing the owner
makes any difference.

good luck

Carsten



 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Joris
 Beld
 Sent: Wednesday, October 04, 2006 2:15 AM
 To: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Suse 10 and PyMOL crashes
 
 
 Dear all,
 Unfortunately having a similar problem with Suse10 and PyMOL.
 - Freshly installed Suse 10 (KDE3.4) system with binary of 0.99 pymol.
 - the weird thing is: pymol starts fine if logged in as root
 - logged in as a user (pymol was 'installed' as a user, not 
 as root!) pymol crashes on start up with a segmentation fault
 
 /usr/share/pymol/pymol/pymol: line 14: 20717 Segmentation 
 fault  $PYMOL_PATH/pymol.exe $@
 
 - the thing i noticed is that as root the GL_RENDERER is 
 recognized during start up of pymol, as a user the 
 GL_RENDERER says 'unknown board'.
 
 So, although my system doesn't freeze, it seems to be a 
 similar problem.
 Anyone a good idea how to solve this? (I don't want to su to 
 root everytime i want to run pymol)
 
 Thanks a lot in advance.
 Best wishes,
 Joris Beld
 
 
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[PyMOL] Newline character in scene annotation message

[Schubert, Carsten [PRDUS]]

Hi

I am trying to combine a scene with annotations spanning several lines.
So far something like 
 scene new, store, message=Line1\nLine2

would produce some nice coloration effects but not a newline character.

I was able to use the api function to do the trick
mesg=line1\nline2
cmd.scene(new,store,message=mesg)

but I was wondering is there a way to use the non API function in the same
way?

Thanks

Carsten