[PyMOL] Run pymol from source or compile?

[Martin Hediger]

Can one run PyMOL from source (in order to see effects of changes to the 
source code whenever restarting) or can one only run a compiled version 
of PyMOL?


Are there instructions for running from source?

Best regards
Martin




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[PyMOL] Current and up to date manual

[Martin Hediger]

I found this manual page:

http://pymol.sourceforge.net/newman/user/toc.html 



It says, its ancient and obsolete.

Is the wiki the current and up to date manual?

Is there a PDF manual anywhere?

Many thanks
Martin

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[PyMOL] What does do_library do?

[Martin Hediger]

Hi all

I'm trying to understand wizarding better (PyMOL Source code - i think -
around 1.7).

What does the 'do_library' function do?

It seems to be called from every wizard at one point.

Thanks, Martin

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Re: [PyMOL] Dynamic reloading of plugin

[Martin Hediger]

Thats great input.

Thanks alot, will check.

Martin

On 27.04.16 20:36, Sampson, Jared M. wrote:

Hi Martin -

I've also experienced this kind of tedium.  Depending on the type of extension 
it is, you could also consider writing tests for your function that can be run 
by either:

a) importing PyMOL commands into a python (.py) script and running e.g. 
`nosetests` or other unit testing software

```extension_tests.pml
import pymol
from pymol import cmd
pymol.finish_launching()
...do stuff here...
```

or,

b) run PyMOL (.pml) scripts in command line only mode.

For example, I've used approach (b) before with a setup something like this:

```test1.pml
from pymol import cmd
frag ala
python
if 'ala' in cmd.get_names():
print 'OK'
else:
print 'Not OK'
python end
```

Then run each test from the shell:

```
pymol -cq test1.pml
```

For running many tests automatically, I've also used a "run_tests.sh" that 
looks something like this:

```run_tests.sh
#!/bin/bash
function run_test() {
  PML="test${1}.pml"
  if [ -f "$PML" ]; then
echo ""
echo 
""
echo "Running Test ${1}: $PML"
echo ""
pymol -ckq $PML
echo ""
  fi
}

# call `./run_tests.sh` with no args to run all the tests (up to 100)
if [ $# -lt 1 ]; then
  for i in {1..100}  # increase if you have more than 100 tests
  do
run_test $i
  done

# call with args, e.g. `./run_tests.sh 1 2 4 7` to run specific test(s)
else
  for i in $@
  do
run_test $i
  done
fi
```

Hope this is helpful.  Good luck!

Cheers,
Jared





On Apr 25, 2016, at 11:06 AM, Thomas Holder <thomas.hol...@schrodinger.com> 
wrote:

Hi Martin,

how about:

set_key F1, run script.py; function_from_script()

Reduces step 3) and 4) to hitting "F1" on the keyboard.

Cheers,
Thomas

On 24 Apr 2016, at 06:36, Martin Hediger <ma@bluewin.ch> wrote:


Hi all

When working on a PyMOL extension script, my workflow is currently something 
like this:

1) Start PyMOL
2) Work on script
3) PyMOL> run script.py
4) PyMOL> function_from_script()
5) See if function works, go back to 2)

Is it possible to have PyMOL automatically re-run the script everytime i save 
it?

Thanks and best regards
Martin

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[PyMOL] ccmutate

[Martin Hediger]

I found the ccmutate script on the pymol wiki

I tried it but I receive a weird error:

PyMOL>ccmutate "ALA", resi 112
Traceback (most recent call last):
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/parser.py", 
line 254, in parse

self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "021_scripts/ccmutate.py", line 47, in ccmutate
cmd.fetch(code, tmp_frag, type='cc', zoom=0)
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py", 
line 1417, in fetch

r = _multifetch(*args)
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py", 
line 1352, in _multifetch

discrete, multiplex, zoom, type, path, file, quiet, _self)
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py", 
line 1263, in _fetch

raise ValueError('type')
ValueError: type


What could be going on? The PyMOL mutagenesis wizard in any case works 
when I do the mutation by hand.


Thanks for hints
Martin



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Re: [PyMOL] Function signature

[Martin Hediger]

Hi Robert

Thanks, in principle yes it's doing it now the way i was hoping. As I 
wrote, the point was to be able to enter the command at the pymol prompt 
like:


zoom_custom resi 117

and not

zoom_custom(117)

--> So to avoid the parenthesis (user friendliness and stuff...)

Thanks again
Martin


On 18.04.16 03:17, Robert Campbell wrote:

Hi Martin,

If you simply want to be able to have the function operate on any
selection, simply do this:


def zoom_custom(position):
   cmd.zoom(position)

cmd.extend("zoom_custom", zoom_custom)

This allows you to type:

zoom_custom resi 117

or any other more complicated selection syntax without any parentheses.
Perhaps I am missing something in your specific requirements?

Cheers,
Rob

  On Sun, 2016-04-17 20:18  +0200,  Martin
Hediger <ma@bluewin.ch> wrote:


Dear all

In PyMOL, the syntax for eg. zooming in on residue 110 of a protein
would be

zoom resi 117

I have a pymol script where I define a function that also zooms in on
a residue (it's simple, only to illustrate the point):

def zoom_custom(position):
  cmd.zoom("resi" + " " + str(position))
cmd.extend("zoom_custom", zoom_custom)

However, when I want to call it from the PyMOL promt, i have to use

zoom_custom(117)

i.e. using parenthesis. How do i need to design the function such
that I can enter it as above?

Thanks and best regards
Martin

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[PyMOL] What does do_library() do?

[Martin Hediger]

Hi all

I'm trying to understand wizarding better (PyMOL Source code - i think -
around 1.7).

What does the 'do_library' function do?

It seems to be called from every wizard at one point.

Thanks, Martin

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[PyMOL] Function signature

[Martin Hediger]

Dear all

In PyMOL, the syntax for eg. zooming in on residue 110 of a protein would be

zoom resi 117

I have a pymol script where I define a function that also zooms in on a 
residue (it's simple, only to illustrate the point):

def zoom_custom(position):
 cmd.zoom("resi" + " " + str(position))
cmd.extend("zoom_custom", zoom_custom)

However, when I want to call it from the PyMOL promt, i have to use

zoom_custom(117)

i.e. using parenthesis. How do i need to design the function such that I 
can enter it as above?

Thanks and best regards
Martin

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[PyMOL] What does do_library() do?

[Martin Hediger]

Hi all

I'm trying to understand wizarding better (PyMOL Source code - i think - 
around 1.7).

What does the 'do_library' function do?

It seems to be called from every wizard at one point.

Thanks, Martin

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[PyMOL] setting fetch_path fails

[Martin Hediger]

Hi all

I tried to adjust the 'fetch_path' property such that downloaded PDB 
files would be saved in

os.path.abspath(os.path.join(os.path.curdir, pdbfiles))

where 'curdir' is $HOME and 'pdbfiles' is within $HOME.

However, I get 'fetch-error'.

What am I doing wrong?

Thanks for help.

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[PyMOL] Real-time black and white view possible?

[Martin Hediger]

Hi all

I wonder if it's possible to have something like ray_trace_mode, 2 (i.e. 
black and white with outlines) but in the interactive view. Also, is it 
possible to have part of the structure in color (say some active site 
amino acids) and the rest in black and white?

Thanks for help
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Re: [PyMOL] Real-time black and white view possible?

[Martin Hediger]

Impressive, how did you figure this out?

Martin




On 12.06.14 23:18, Shiven Shandilya wrote:

Hi Martin,

I guess you can do this using modified GLSL shaders …

Two examples I posted on the PyMOL wiki a while ago:
http://www.pymolwiki.org:/index.php/GLSL_Shaders

Best,
Shiven


On Jun 12, 2014, at 5:10 PM, Martin Hediger ma@bluewin.ch
mailto:ma@bluewin.ch wrote:


Hi all

I wonder if it's possible to have something like ray_trace_mode, 2 (i.e.
black and white with outlines) but in the interactive view. Also, is it
possible to have part of the structure in color (say some active site
amino acids) and the rest in black and white?

Thanks for help
Martin

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[PyMOL] Ray trace mode 1 outline thickness

[Martin Hediger]

Hi guys

I wonder if you could help, I'm rendering this image:

http://qmviews.blogspot.ch/2014/05/illustrating-protein-structures.html

and I wonder if and how I could increase the thickness of the black 
outlines?

Thanks for help
Martin

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Re: [PyMOL] pymol does not free-up the RAM when objects are deleted

[Martin Hediger]

It's been a problem for a while, check the thread
[PyMOL] Memory not released after load and delete of structure froom 2012.

Martin





On 04.04.14 21:54, Thomas Holder wrote:
 Hi Osvaldo,

 you are right, I can reproduce this. We'll look into it and let you know when 
 it has been fixed.

 Cheers,
Thomas

 On 02 Apr 2014, at 20:30, Osvaldo Martin aloctavo...@gmail.com wrote:
 Hi,

 I need to run an script based on PyMOL  for a thousands of proteins. The 
 problem is that even when I delete all object the RAM usage keeps 
 increasing. I am using PyMOL 1.7 on ubuntu 14.04 (beta 2).


 my script looks like this.

 import __main__
 __main__.pymol_argv = ['pymol','-qc']
 import pymol
 from pymol import cmd, stored
 import glob

 pdb_files = glob.glob('*.pdb')
 for protein in pdb_files:
  cmd.load(protein)
  some code here
  cmd.delete('all')


 I tried the following.

 1) removing the  some code here
 2) adding cmd.reinitialize()
 3) adding cmd.set('suspend_undo', 1) 
 (https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11126.html)

 Cheers and thanks in advance.

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Re: [PyMOL] sculpt settings

[Martin Hediger]

I describe this in a blog post. Maybe it helps you.

http://qmviews.blogspot.ch/2012/01/pymol-005-optimizing-only-part-of.html






On 24.04.13 19:21, Osvaldo Martin wrote:
Where I can find documentation about the exact meaning of all the 
settings related to the sculpt function? In particular what the 
sculpt_field_mask setting does?


I am trying to sculpt the sidechaiin of a particular residue while 
protecting the rest of the structure. Which are the bet parameters to 
try to move the sidechain while avoiding clashes/bumps?


Thanks.


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[PyMOL] Show and hide different sets of measurements

[Martin Hediger]

Dear PyMOL users

Assume I have two objects loaded in a PyMOL session and in each I'm 
interested in a specific distance. So in both objects I measure this 
distance and see it displayed in the viewer. Can I somehow configure the 
measurement such that when I disable the object, also the corresponding 
measurement hides? So every measurement is always only visible when 
its object is visible?

Thanks for hints
Martin

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[PyMOL] Increase sphere size for heavy element

[Martin Hediger]

Hi PyMOL users

If I display these coordinates

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

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

Thanks
Martin

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Re: [PyMOL] Write vector graphics of session

[Martin Hediger]

I'm no expert but I guess my favorite would be EPS. Converting to PDF, 
if required, is easy on the Mac.

Best regards
Martin



On 14.01.13 23:53, Jason Vertrees wrote:
 Martin,

 That would be a nice feature. Which format would you and the others
 prefer: SVG, PDF, or EPS?

 Cheers,

 -- Jason

 On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger ma@bluewin.ch wrote:
 Hi PyMOL users
 Can PyMOL write a vector based picture of a session? Does not require to
 be very fancy, but vector based would be cool. Something like in the
 old days with molscript.

 Best regards
 Martin

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[PyMOL] Write vector graphics of session

[Martin Hediger]

Hi PyMOL users
Can PyMOL write a vector based picture of a session? Does not require to 
be very fancy, but vector based would be cool. Something like in the 
old days with molscript.

Best regards
Martin

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Re: [PyMOL] Pymol visualization problem

[Martin Hediger]

Hi Abida
Is it possible that you have multiple states in your PDB file? Try 
clicking the  arrow in the bottom right corner of PyMOL and see if 
you can display the other protein. If so, you probably need to delete 
the MODEL and END from your PDB file. Then all should appear at once.


Martin





On 08.01.13 06:12, Abida Siddiqa wrote:

Hello,

I have docked one protein named 'L1'( 450 amino acid)  with another protein
named 'E2'(68 amino acid, Chain A) and used  pymol-v1.3r1-edu-Win32.msi to 
visualize
the complex. my system is  windows 7 , 64 bit. The problem is, i am unable
to see the sequence of 'E2' protein and so as its structure. In order to
confirm, if it is docking problem or visualization problem, i have used
  swiss pdb viewer. it has shown me sequence and structure of both proteins. i
wonder why can not i see it in pymol.
secondly, i docked L1 and E2 ( this time used chain A and B of it), and
visualized the complex in pymol. i was only able to see L1, and chain A of
E2 (both chain A and B are alike).  Then in order to see if it is docking
error or visualization error, i rendered the complex in swiss pdb viwer and
  saw the L1 and E2 (both chain A and B).
Thirdly, i changed the docking software and generated a complex using
another software, this time i still was unable to visualize complete complex
in pymol.
Any help will be much appreciated.
Kind regards
Abida


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[PyMOL] unittest for get_coordinate function

[Martin Hediger]

Hi PyMOL users
I wonder, what is a most meaningful way of programmatically determining 
that a line of text in an arbitrary file contains atomic coordinates? 
The context of this question is that I plan to write a program that 
reads two files containing coordinates and has to perform operations on 
pairs of coordinates r1 and r2, where ri is the coordinate value from 
file i.

Example format 1 (MOPAC):
C( LABEL TEXT ) 1.0 +0 1.0 +0 1.0 +0

Example format 2 (PDB):
ATOM  1  N   ALA A   1  32.517  42.012  20.144  1.00 0.00  
PROT N

(some whitespace omitted).

In example 1, the coordinates are 1.0, 1.0 and 1.0, the +0 are 
program specific labels to identify the coordinate as fixed or relaxed.
Can this really only be done by hardcoding the positions of the coordinates?

Can this be unittested? I mean, if it indeed is only possible to read 
the coordinate by collecting, say

[python]
s=ATOM  1  N   ALA A   1  32.517  42.012  20.144  1.00 
0.00  PROT N
def get_x(s):
 x=s[32:38]
 return x
[/python]

what would a unittest for get_x look like? Would it even make sense to 
write such a test?

Looking forward to discussions.
Martin

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Re: [PyMOL] Memory not released after load and delete of structure

[Martin Hediger]

Hi Thomas, thanks for the feedback.
I would like to point out that I observe this with version PyMOL 1.3 
(also Hybrid), where, correct me if I'm wrong, there is no undo feature 
available (at least I have never used or seen it here). To me this would 
mean, the problem has to be with something else (possibly in addition to 
undo).
To perfectly reproduce my situation, you can run the script that I 
posted on pastebin (http://pastebin.com/mC6Rs6wk). Let me know if you 
need some guidance with all the variables, I'm sorry for the terrible 
code. I can also send you the PDB file I used when I got into this 
problem, then you dont need to adjust any variables.

Best regards
Martin



On 21.12.12 17:31, Thomas Holder wrote:
 Hi Gianluigi and Martin,

 thanks for reporting, this is a serious issue and we are looking into it.

 As far as we can reproduce, it's related to the undo feature. Adding this to 
 your scripts should help:

 cmd.set(suspend_undo, 1)

 Cheers,
Thomas

 On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano chimic...@yahoo.it wrote:

 I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 
 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and 
 pymol version 1.5.0.3.
 I had to renounce working with Hybrid unless I really need some plug-in.

 Gianluigi


 Da: Jason Vertrees jason.vertr...@schrodinger.com
 A: Martin Hediger ma@bluewin.ch
 Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net
 Inviato: Giovedì 20 Dicembre 2012 17:05
 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure

 Martin,

 That sounds like a memory leak in v1.3. Can you try a newer version of
 PyMOL and let us know if it still happens? We've fixed lots of bugs
 since v1.3.

 Also, is your script simply iterating over structures and deleting
 them when done? You sure you're not missing a cleanup step somewhere?
 (Any chance we can see the script or a stub of it?)

 Cheers,

 -- Jason

 On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote:
 Hi Jason,
 I'm using PyMOL 1.3.

 Best regards
 Martin



 On 20.12.12 15:53, Jason Vertrees wrote:
 Hi Martin,

 Which version of PyMOL are you using?

 Cheers,

 -- Jason

 On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote:
 Dear PyMOL users
 In a directory are PDB files of combined size equal to around 3MB. When
 I load all files into PyMOL, I observe that the required RAM of PyMOL
 (MacOS X 10.6) increases by roughly this amount.
 When I delete all objects, the RAM requirement remains the same and when
 I then reload all structures, the RAM requirement increases even further.
 I'm currently using PyMOL to batch process a number of files where a
 structure is loaded, modified and then deleted again from the objects
 list. This then results in RAM requirements of over 1GB and together
 with other applications, I run out of memory.
 Is there a way I can prevent PyMOL from behaving this way?

 Best regards and thanks for any help
 Martin
 -- 
 Jason Vertrees, PhD
 Director of Core Modeling Product Management
 Schrödinger, Inc.

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120


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[PyMOL] Memory not released after load and delete of structure

[Martin Hediger]

Dear PyMOL users
In a directory are PDB files of combined size equal to around 3MB. When 
I load all files into PyMOL, I observe that the required RAM of PyMOL 
(MacOS X 10.6) increases by roughly this amount.
When I delete all objects, the RAM requirement remains the same and when 
I then reload all structures, the RAM requirement increases even further.
I'm currently using PyMOL to batch process a number of files where a 
structure is loaded, modified and then deleted again from the objects 
list. This then results in RAM requirements of over 1GB and together 
with other applications, I run out of memory.
Is there a way I can prevent PyMOL from behaving this way?

Best regards and thanks for any help
Martin

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Re: [PyMOL] Memory not released after load and delete of structure

[Martin Hediger]

Hi Jason,
I'm using PyMOL 1.3.

Best regards
Martin




On 20.12.12 15:53, Jason Vertrees wrote:
 Hi Martin,

 Which version of PyMOL are you using?

 Cheers,

 -- Jason

 On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote:
 Dear PyMOL users
 In a directory are PDB files of combined size equal to around 3MB. When
 I load all files into PyMOL, I observe that the required RAM of PyMOL
 (MacOS X 10.6) increases by roughly this amount.
 When I delete all objects, the RAM requirement remains the same and when
 I then reload all structures, the RAM requirement increases even further.
 I'm currently using PyMOL to batch process a number of files where a
 structure is loaded, modified and then deleted again from the objects
 list. This then results in RAM requirements of over 1GB and together
 with other applications, I run out of memory.
 Is there a way I can prevent PyMOL from behaving this way?

 Best regards and thanks for any help
 Martin

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Re: [PyMOL] Memory not released after load and delete of structure

[Martin Hediger]

I'll give it a try with the newer versions.
I just checked, and I believe I'm doing some cleaning up.

Sure, I posted the scripte on this pastebin:

http://pastebin.com/mC6Rs6wk

Sorry for the layout (all pretty in development). In production, the 
script is invoked from the frag function.

Martin







On 20.12.12 17:05, Jason Vertrees wrote:
 Martin,

 That sounds like a memory leak in v1.3. Can you try a newer version of
 PyMOL and let us know if it still happens? We've fixed lots of bugs
 since v1.3.

 Also, is your script simply iterating over structures and deleting
 them when done? You sure you're not missing a cleanup step somewhere?
 (Any chance we can see the script or a stub of it?)

 Cheers,

 -- Jason

 On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote:
 Hi Jason,
 I'm using PyMOL 1.3.

 Best regards
 Martin





 On 20.12.12 15:53, Jason Vertrees wrote:
 Hi Martin,

 Which version of PyMOL are you using?

 Cheers,

 -- Jason

 On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote:
 Dear PyMOL users
 In a directory are PDB files of combined size equal to around 3MB. When
 I load all files into PyMOL, I observe that the required RAM of PyMOL
 (MacOS X 10.6) increases by roughly this amount.
 When I delete all objects, the RAM requirement remains the same and when
 I then reload all structures, the RAM requirement increases even further.
 I'm currently using PyMOL to batch process a number of files where a
 structure is loaded, modified and then deleted again from the objects
 list. This then results in RAM requirements of over 1GB and together
 with other applications, I run out of memory.
 Is there a way I can prevent PyMOL from behaving this way?

 Best regards and thanks for any help
 Martin


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Re: [PyMOL] problems with mutagenesis wizard II

[Martin Hediger]

Hi Carola
For future reference, good to know it seems to be a version issue.

Best regards
Martin


Am 07.11.12 18:38, schrieb Carola Sophie Hengstenberg:
 Hi Martin,

 thanks for your reply. Yes, I played with these settings, but it did not
 work for me. I ended up with installing the pymol version 1.5 now. Here
 the problem did not appear anymore, but the real cause of the problem I
 could not find out...

 Carola

 Am Mittwoch, den 07.11.2012, 11:24 +0100 schrieb Martin Hediger:
 Hi Carola
 What did you try? Does it work when you use these commands right after
 starting up PyMOL and before you do any of the steps you take:

 set retain_order, 0
 set pdb_retain_ids

 Martin







 On 31.10.12 14:03, Carola Sophie Hengstenberg wrote:
 Dear all,

 I recently upgraded to Ubuntu 12.04 (pymol version 1.4.1-3). Since I did
 the upgrade, mutations done with the mutagenesis wizard lead to
 incorrect atom numbering in the saved pdb file. Before, the problem
 definitely did not exist. I read the recent post in this forum
 concerning this, but the pymol version 1.4 seems to lead to this
 problem, too.

 Here an example:

 ATOM  1  N   MET A   7  72.739 -17.539   8.852  1.00 36.46
 N
 TER   2  MET A   7
 ATOM  0  N   ALA A  12  77.920  -8.244  14.624  1.00  0.00
 N
 TER   1  ALA A  12
 ATOM  2  CA  MET A   7  73.836 -17.058   9.739  1.00 35.87
 C
 TER   3  MET A   7
 ATOM  1  CA  ALA A  12  77.603  -6.935  15.187  1.00  0.00
 C
 TER   2  ALA A  12
 ATOM  3  C   MET A   7  74.382 -18.171  10.623  1.00 36.04
 C
 TER   4  MET A   7
 ATOM  2  CB  ALA A  12  78.933  -6.222  15.489  1.00  0.00
 C
 TER   3  ALA A  12
 ATOM  4  O   MET A   7  73.676 -18.689  11.489  1.00 36.57
 O
 TER   5  MET A   7
 ATOM  3  C   ALA A  12  76.716  -6.146  14.255  1.00  0.00
 C
 TER   4  ALA A  12
 ATOM  5  CB  MET A   7  73.338 -15.921  10.634  1.00 34.58
 C
 TER   6  MET A   7
 ATOM  4  O   ALA A  12  77.070  -6.025  13.073  1.00  0.00
 O
 TER   5  ALA A  12
 ATOM  6  CG  MET A   7  72.989 -14.645   9.899  1.00 33.55
 C
 ATOM  7  SD  MET A   7  72.558 -13.328  11.053  1.00 30.82
 S
 ATOM  8  CE  MET A   7  74.184 -12.785  11.572  1.00 31.08
 C
 ATOM  9  N   THR A   8  75.645 -18.528  10.413  1.00 36.23
 N
 ATOM 10  CA  THR A   8  76.278 -19.573  11.207  1.00 35.81
 C
 ATOM 11  C   THR A   8  76.461 -19.071  12.633  1.00 34.75
 C
 ATOM 12  O   THR A   8  76.529 -19.861  13.578  1.00 35.68
 O
 ATOM 13  CB  THR A   8  77.662 -19.947  10.646  1.00 37.30
 C
 ATOM 14  OG1 THR A   8  78.530 -18.810  10.723  1.00 38.49
 O
 ATOM 15  CG2 THR A   8  77.544 -20.390   9.196  1.00 38.06
 C
 ATOM 16  N   GLY A   9  76.539 -17.750  12.779  1.00 32.20
 N
 ATOM 17  CA  GLY A   9  76.713 -17.161  14.096  1.00 27.95
 C
 ATOM 18  C   GLY A   9  76.334 -15.690  14.126  1.00 24.78
 C
 ATOM 19  O   GLY A   9  76.080 -15.092  13.083  1.00 24.20
 O

 [...]

 Can somebody help me out?

 Thanks in advance,

 Caro


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Re: [PyMOL] problems with mutagenesis wizard II

[Martin Hediger]

Hi Carola
What did you try? Does it work when you use these commands right after 
starting up PyMOL and before you do any of the steps you take:

set retain_order, 0
set pdb_retain_ids

Martin







On 31.10.12 14:03, Carola Sophie Hengstenberg wrote:
 Dear all,

 I recently upgraded to Ubuntu 12.04 (pymol version 1.4.1-3). Since I did
 the upgrade, mutations done with the mutagenesis wizard lead to
 incorrect atom numbering in the saved pdb file. Before, the problem
 definitely did not exist. I read the recent post in this forum
 concerning this, but the pymol version 1.4 seems to lead to this
 problem, too.

 Here an example:

 ATOM  1  N   MET A   7  72.739 -17.539   8.852  1.00 36.46
 N
 TER   2  MET A   7
 ATOM  0  N   ALA A  12  77.920  -8.244  14.624  1.00  0.00
 N
 TER   1  ALA A  12
 ATOM  2  CA  MET A   7  73.836 -17.058   9.739  1.00 35.87
 C
 TER   3  MET A   7
 ATOM  1  CA  ALA A  12  77.603  -6.935  15.187  1.00  0.00
 C
 TER   2  ALA A  12
 ATOM  3  C   MET A   7  74.382 -18.171  10.623  1.00 36.04
 C
 TER   4  MET A   7
 ATOM  2  CB  ALA A  12  78.933  -6.222  15.489  1.00  0.00
 C
 TER   3  ALA A  12
 ATOM  4  O   MET A   7  73.676 -18.689  11.489  1.00 36.57
 O
 TER   5  MET A   7
 ATOM  3  C   ALA A  12  76.716  -6.146  14.255  1.00  0.00
 C
 TER   4  ALA A  12
 ATOM  5  CB  MET A   7  73.338 -15.921  10.634  1.00 34.58
 C
 TER   6  MET A   7
 ATOM  4  O   ALA A  12  77.070  -6.025  13.073  1.00  0.00
 O
 TER   5  ALA A  12
 ATOM  6  CG  MET A   7  72.989 -14.645   9.899  1.00 33.55
 C
 ATOM  7  SD  MET A   7  72.558 -13.328  11.053  1.00 30.82
 S
 ATOM  8  CE  MET A   7  74.184 -12.785  11.572  1.00 31.08
 C
 ATOM  9  N   THR A   8  75.645 -18.528  10.413  1.00 36.23
 N
 ATOM 10  CA  THR A   8  76.278 -19.573  11.207  1.00 35.81
 C
 ATOM 11  C   THR A   8  76.461 -19.071  12.633  1.00 34.75
 C
 ATOM 12  O   THR A   8  76.529 -19.861  13.578  1.00 35.68
 O
 ATOM 13  CB  THR A   8  77.662 -19.947  10.646  1.00 37.30
 C
 ATOM 14  OG1 THR A   8  78.530 -18.810  10.723  1.00 38.49
 O
 ATOM 15  CG2 THR A   8  77.544 -20.390   9.196  1.00 38.06
 C
 ATOM 16  N   GLY A   9  76.539 -17.750  12.779  1.00 32.20
 N
 ATOM 17  CA  GLY A   9  76.713 -17.161  14.096  1.00 27.95
 C
 ATOM 18  C   GLY A   9  76.334 -15.690  14.126  1.00 24.78
 C
 ATOM 19  O   GLY A   9  76.080 -15.092  13.083  1.00 24.20
 O

 [...]

 Can somebody help me out?

 Thanks in advance,

 Caro


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Re: [PyMOL] Select crystal waters inside protein

[Martin Hediger]

Dear PyMOL Users
I'm trying to remove water molecules from a crystal structure which are 
on the crystal surface while preserving the ones within the crystal 
interior.

What I do is:

select waters, resn HOH
# cmd.select(waters, (waters extend 1), enable=1)
get_area waters, load_b=1
remove waters and b20

This only works partially because of some waters, only the oxygen atom 
is removed, while of others only one of the hydrogens is removed (some 
waters are completely removed which is good). It does not make a 
difference if I include the commented command above.
Also, what does load_b=1 mean?

Further feedback would be greatly appreciated.
Martin





On 26.04.12 14:46, Thomas Holder wrote:
 Hi Martin  James,

 is it just a coincident that you both ask almost the same question?

 You could remove all water atoms with few protein contacts or with a 
 small surface area. For example:

 remove solvent beyond 3.5 of polymer
 set dot_solvent
 get_area solvent, load_b=1
 remove solvent and b  20

 Hope that helps.

 Cheers,
   Thomas

 On 04/26/2012 10:55 AM, James Starlight wrote:
 Another question- I have my protein.pdb with some inserted crystall
 waters within protein interiour as well as water surrounded of my
 protein. I want to remove only sorrounding water but prevent internal
 water ( wich could be functional relevant ).

 How I could to select such surrounded water ( e.g via some cutoff
 radius relative my protein etc) wich I'd like to remove further ?

 On 04/25/2012 05:34 PM, Martin Hediger wrote:
 In a crystal structure, there are usually a number of relevant crystal
 waters, as well as water molecules on the surface. In our approach, we
 model the protein structure within a dielectric continuum, so surface
 water molecules are not required (to save computer time). However,
 waters in the interior should remain in our model. How could we discard
 the surface waters while keeping the internal waters?



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[PyMOL] Parallelize mutation script

[Martin Hediger]

Dear PyMOL Users
I use the following script to prepare small side chain fragment PDB 
files of mutants in PyMOL:
http://pastebin.com/nDTZApHP
I use the PyMOL built-in mutagenesis wizard and the sculpting wizard to 
locally optimize the side chains within the environment of the protein.
For large amounts of side chains, the script currently mutates every 
side chain within a selection to every other amino acid, this starts to 
take a long amoutn of time.
Is it possible to parallelize the mutagenesis process? I'm not an expert 
on how to do this, maybe somebody could point me out on something. Where 
in the code would one do that? I know the threading module can be used, 
but I'm still working on that.

Any feedback is appreciated.

Martin

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[PyMOL] PyMOL Model player

[Martin Hediger]

Dear PyMOL Users
Is it possible to let the PyMOL model player go back and forward, 
instead of jumping from the end to the start, once it reached the last 
loaded model of an object?

Thanks for hints.
Martin

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[PyMOL] Adding hydrogens

[Martin Hediger]

Dear PyMOL list
I'm adding hydrogens to a crystal structure. Upon saving, however, I 
realize all hydrogens have been added to the beginning of the PDB file. 
Can PyMOL be configured such that the hydrogens are placed at the 
intuitively appropriate place in the PDB file?

Thanks for any hints.
Martin

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Re: [PyMOL] Use arrows to switch between models

[Martin Hediger]

Sweet:)
I disabled the animate but I can see its applicability in some 
situations though (makes it pretty impressive).

Definitly a must-have from now on, in fact how could I even live without 
it;)

Martin






On 20.09.12 19:38, Tsjerk Wassenaar wrote:
 Hi :)

 You can also add

 cmd.disable('all')
 cmd.enable(cur_obj)

 To have all other objects turned off. This is one I'm definitely going to use 
 :)

 Cheers,

 Tsjerk

 On Thu, Sep 20, 2012 at 6:32 PM, Jason Vertrees
 jason.vertr...@schrodinger.com wrote:
 Hi Martin,

 Is it possible to somehow assign page up or page down keys to switch
 from one loaded model to the next one in the PyMOL models list?
 This would be useful because I often have several similar models listed
 and in doing so it would be easier and convenient to identify changes
 within them.
 How about something like http://pymolwiki.org/index.php/ObjectFocus.
 It's cool what you can do with PyMOL and 8 minutes of coding.

 Two changes to the script you might want:
* replace 'orient' with 'zoom'
* don't animate the change, remote ',animate=1' from the orient command.

 Cheers,

 -- Jason

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[PyMOL] Use arrows to switch between models

[Martin Hediger]

Dear PyMOL users
Is it possible to somehow assign page up or page down keys to switch 
from one loaded model to the next one in the PyMOL models list?
This would be useful because I often have several similar models listed 
and in doing so it would be easier and convenient to identify changes 
within them.

Thanks for any hints
Martin

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[PyMOL] Verify PDB format

[Martin Hediger]

Dear PyMOL users
Does anybody know a script to verify that a file contains valid a valid 
PDB formatted structure?
The file extension alone obviously does not provide sufficient validation.

Thanks for any feedback.
Martin

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Re: [PyMOL] Dont resequence atoms when saving

[Martin Hediger]

Dear Pymol users
We are trying to generate a number of mutated structures using the 
mutagenesis wizard. However, after mutating a position and saving to a 
new PDB file, the mutated residue ends up being mixed into the 
coordinate lines of the first residue. Some two coordinate lines are 
separated by TER statements. At the position, where the residue should 
sit, there is a TER statement, and the residue is skipped (e.g Res ID 
139, TER, Res ID 141).
We also observe this using

set retain_order
set pdb_retain_ids

Is there a fix for this?

Any help is appreciated.

Thanks,
Martin








On 13.12.10 16:52, Jason Vertrees wrote:
 Hi Martin,

 As you've found, the mutagenesis wizard destroys the ordering in some
 cases.  I'll look into it.

 Cheers,

 -- Jason

 On Tue, Dec 7, 2010 at 11:34 AM, Martin Hedigerma@bluewin.ch  wrote:
 Good day
 I use PyMOL to introduce mutations into a structure. It occured to me that
 when saving the modified structure, atom sequence was not preserved. Using

 set retain_order
 set pdb_retain_ids

 is supposed to control this. It seems now, as if mutating a structure does a
 really weired thing:
 Once the mutation is introduced, the sequence becomes completely disordered
 in a sense that the atoms of the new residue are placed in between the
 atoms of the very first residue, in terms of sequence (not geometry).
 This results in a PDB file like this (PRO is the first residue, PHE is the
 residue to which the mutation is being carried out):

 ATOM  1  N   PRO A   1  53.611  -4.470  40.679  1.00  0.00  PROT
 N
 TER   2  PRO A   1
 ATOM  0  N   PHE D  14  55.428  -5.717  38.365  1.00  0.00  PROT
 N
 TER   1  PHE D  14
 ATOM  2  CA  PRO A   1  52.399  -3.722  40.197  1.00  0.00  PROT
 C
 TER   3  PRO A   1
 ATOM  1  CA  PHE D  14  55.821  -4.897  37.223  1.00  0.00  PROT
 C
 TER   2  PHE D  14
 ATOM  3  C   PRO A   1  52.805  -2.296  39.783  1.00  0.00  PROT
 C
 TER   4  PRO A   1
 ATOM  2  CB  PHE D  14  54.681  -4.879  36.160  1.00  0.00  PROT
 C
 TER   3  PHE D  14
 ATOM  4  O   PRO A   1  53.381  -1.530  40.550  1.00  0.00  PROT
 O
 TER   5  PRO A   1
 ATOM  3  CG  PHE D  14  54.928  -4.027  34.905  1.00  0.00  PROT
 C
 TER   4  PHE D  14
 ATOM  5  CB  PRO A   1  51.360  -3.675  41.342  1.00  0.00  PROT
 C
 TER   6  PRO A   1
 ATOM  4  CD1 PHE D  14  56.116  -4.189  34.183  1.00  0.00  PROT
 C
 TER   5  PHE D  14
 ATOM  6  CG  PRO A   1  52.019  -4.362  42.549  1.00  0.00  PROT
 C
 TER   7  PRO A   1
 ATOM  5  CD2 PHE D  14  54.011  -3.049  34.512  1.00  0.00  PROT
 C
 TER   6  PHE D  14
 ATOM  7  CD  PRO A   1  53.253  -5.096  41.996  1.00  0.00  PROT
 C
 TER   8  PRO A   1
 ATOM  6  CE1 PHE D  14  56.391  -3.370  33.093  1.00  0.00  PROT
 C
 TER   7  PHE D  14
 ATOM  8  HA  PRO A   1  51.990  -4.297  39.323  1.00  0.00  PROT
 H
 TER   9  PRO A   1
 ATOM  7  CE2 PHE D  14  54.282  -2.238  33.413  1.00  0.00  PROT
 C
 TER   8  PHE D  14
 ATOM  9 1HB  PRO A   1  50.434  -4.192  41.043  1.00  0.00  PROT
 H
 TER  10  PRO A   1
 ATOM  8  CZ  PHE D  14  55.473  -2.397  32.707  1.00  0.00  PROT
 C
 TER   9  PHE D  14
 ATOM 10 2HB  PRO A   1  51.070  -2.637  41.594  1.00  0.00  PROT
 H
 TER  11  PRO A   1
 ATOM  9  C   PHE D  14  56.113  -3.478  37.649  1.00  0.00  PROT
 C
 TER  10  PHE D  14
 ATOM 11 1HG  PRO A   1  51.327  -5.056  43.052  1.00  0.00  PROT
 H
 TER  12  PRO A   1
 ATOM 10  O   PHE D  14  55.357  -2.867  38.421  1.00  0.00  PROT
 O
 TER  11  PHE D  14
 ATOM 12 2HG  PRO A   1  52.313  -3.615  43.311  1.00  0.00  PROT
 H
 TER  13  PRO A   1
 ATOM 11 1HD  PHE D  14  56.847  -4.922  34.497  1.00  0.00  PROT
 H
 TER  12  PHE D  14
 ATOM 13 1HD  PRO A   1  54.110  -5.062  42.704  1.00  0.00  PROT
 H


 Can this be explained somehow?

 Thanks for your answers.
 Martin








 On 09.11.10 13:26, Jason Vertrees wrote:
 Hi Martin,

 set retain_order
 set pdb_retain_ids

 Cheers,

 -- Jason

 On Tue, Nov 9, 2010 at 4:30 AM, Martin Hedigerma@bluewin.chwrote:
 Dear all
 It occured to me that PyMOL is resequencing a structure when saving. I
 am trying to interpolate between two structures where it is critical to
 have identical sequence in both structures. Is it possible submit a
 DO_NOT_RESEQUENCE-option to the save command?

 Thanks for your help
 Martin


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[PyMOL] Select crystal waters inside protein

[Martin Hediger]

Dear List
In a crystal structure, there are usually a number of relevant crystal 
waters, as well as water molecules on the surface. In our approach, we 
model the protein structure within a dielectric continuum, so surface 
water molecules are not required (to save computer time). However, 
waters in the interior should remain in our model. How could we discard 
the surface waters while keeping the internal waters?

Thanks for any feedback.
Martin

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[PyMOL] PyMOL Selector

[Martin Hediger]

Dear PyMOL List
What is the segi-identifier?

Thanks for your answer.

Martin

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Re: [PyMOL] Display technical info about objects

[Martin Hediger]

Most helpful, thats exactly the solution I was looking for.
Thanks a lot
Martin






On 17.01.12 16:01, Jason Vertrees wrote:
 Hi Martin,

 PyMOL does not keep track of which files the objects were loaded from.
 If you wanted, you could wrap the load command in with your own load
 command that keeps track of such information, for example in a
 dictionary. That could look something like this:

 def load_with_props(fileName, objName):

# store whatever info you want, like the filename

obj_info[objName] = fileName

# ... do more recording of properties you choose

# ask PyMOL to now load the file

cmd.load(fileName,objName)

 Then you could just query obj_info based on object name:

 for obj in cmd.get_names():
print obj_info[obj]

 Cheers,

 -- Jason



 On Tue, Jan 17, 2012 at 3:44 AM, Martin Hedigerma@bluewin.ch  wrote:
 Dear List
 I'm frequently loading a number of objects into PyMOL which formally
 have the same name, but are different in structure. Sometimes it can
 become a bit difficult to keep track of which object is what.
 Is there a way to display technical information about a loaded object?
 Say, the file path to the loaded PDB file? That would be great.

 Thanks for hints.
 Martin

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[PyMOL] Display technical info about objects

[Martin Hediger]

Dear List
I'm frequently loading a number of objects into PyMOL which formally 
have the same name, but are different in structure. Sometimes it can 
become a bit difficult to keep track of which object is what.
Is there a way to display technical information about a loaded object? 
Say, the file path to the loaded PDB file? That would be great.

Thanks for hints.
Martin

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[PyMOL] Context sensitive mutation wizard

[Martin Hediger]

Dear PyMOL List
I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation 
of tryptophan to phenylalanin. If the sidechain is mutated from W to F, 
its reasonable to assume that the plane of the phenyl moiety of F 
would/should/could/might lie in the same plane as the indol part of the 
W if there was such a protein.
Would it be possible to scriptically adjust the F side chain, after 
mutation, such that it lies in the W plane?
Of course, this becomes ambiguous when, say, a A is mutated to a D, 
because what would then be the reference for the D side chain? However, 
N to D would be another case, where it would be desired to have the D 
end group be in as much overlay with the former N end group as possible.

Any ideas on how this might be afforded? Probably not a one-liner though.

Kind regards
Martin

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Re: [PyMOL] RMSD between two structures

[Martin Hediger]

Is the RMS the same as RMSD? PyMOL writes RMS when using align.
Martin





Am 11.11.11 14:59, schrieb Thomas Holder:
 Hi Martin,

 is it the transform=0 argument what you are looking for?

 http://pymolwiki.org/index.php/Align#PYMOL_API

 x = cmd.align('foo', 'bar', transform=0)
 print 'RMSD:', x[0]

 About the some kind of refinement: There are arguments cutoff and 
 cycles that control this behaviour.

 Cheers,
   Thomas

 On 11/11/2011 02:46 PM, Martin Hediger wrote:
 Dear List.
 When aligning two structures using the PyMOL align command, one gets a
 final RMS value indicating some kind of convergence i would say. Can I
 somehow access the function for calculating this value directly from the
 pymol prompt without aligning?

 Thanks for hints
 Martin



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[PyMOL] Get number of residues in model

[Martin Hediger]

Dear List
How can I compute the numbers of residues in a model?

Martin

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[PyMOL] Question Iterate

[Martin Hediger]

In this example below (from Thomas), the method 'iterate' is used. The 
function saves every amino acid of a structure to a separate file. First 
of all, I'm not sure of how to understand the docs:

 iterate iterates over an expression within a temporary namespace for 
each atom.

What does temporary namespace for each atom mean? Also, since 'iterate' 
is used within the while-loop, are we only iterating over the single 
amino acid? Its confusing me because I constantly think of iterate as 
somekind of short hand notation of a for-loop, but I guess thats not it. 
It would be great if somebody could explain the iterate function a bit 
more to me.

Thanks for your feedback.
Martin

# *
# import statements
def seq(state, selection=name ca or resn hoh or resn lig):
  cmd.select(prot, selection)
  while cmd.pop(_tmp, prot):
  cmd.iterate(_tmp, stored.x=(resn,resv))
  # Special case 1: Waters.
  if stored.x[0] == 'HOH':
  filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
  # Special case 2: Substrate.
  elif stored.x[0] == 'LIG':
  filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
  # Other: protein back-bone.
  else:
  filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(), 
stored.x[1], state)
  cmd.save(filename, byres _tmp)
  cmd.delete('_tmp prot')

cmd.extend('seq', seq)
# -



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Re: [PyMOL] creating PDB structure

[Martin Hediger]

If you are in the PyMOL Viewer and in Edit mode, you can hit 
ALT+{a,g,d,e,...} to build up a linear polypeptide, where the single 
letters correspond to the amino acide identifiers.

Is this useful to you?









Am 23.11.11 11:43, schrieb James Starlight:

Dear PyMol Users!

I wounder to know about possible ways of creation of the peptide 
structures via PyMol Builder module. In particular I need create a 
linear structure of my protein ( with fixed phi and psi angles) for 
futher folding molecular dynamics simulation of that peptide. But in 
builder module I found only helix and sheet conformations for each aa. 
residue. How I can specify desired values for both torsion angles ?


Also I'd like to know is there any module for pymol wich could be used 
for obtaining linear unfolded structure for the defined sequence or 
folded protein ( in pdb) ?


Thanks,


James


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[PyMOL] Expose PyMOL API

[Martin Hediger]

Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features from 
outside of PyMOL? An example, the below is a script (inspired by Thomas 
Holder) which saves down to disk all amino acids of a protein structure 
into separate PDB files.

# *
from pymol import cmd
from pymol import stored
from pymol.exporting import _resn_to_aa as one_letter
# *
def seq(state, selection=name ca or resn hoh or resn lig):
 print Generating seqs.
 cmd.select(prot, selection)
 while cmd.pop(_tmp, prot):
 cmd.iterate(_tmp, stored.x=(resn,resv))
 #print stored.x[0], stored.x[1]

 # Special case 1: Waters.
 if stored.x[0] == 'HOH':
 filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
 # Special case 2: Substrate.
 elif stored.x[0] == 'LIG':
 filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
 # Other: protein back-bone.
 else:
 filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(), 
stored.x[1], state)
 cmd.save(filename, byres _tmp)
 cmd.delete('_tmp prot')

cmd.extend('seq', seq)
# -

Is it possible to somehow include this in a Python script, and running 
it from the command line? If not, why?


Thanks for any feedback.



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Re: [PyMOL] Expose PyMOL API

[Martin Hediger]

Thanks for the answers. I'll be trying to get it compile on a linux box, 
if I could access some of the PyMOL features there, that's fine as well. 
A friend tried to compile PyMOL on Mac and had quite some trouble, so 
I'll be first trying the Linux option.
Martin







Am 22.11.11 15:56, schrieb Jason Vertrees:
 Martin,

 The _cmd module is indeed statically linked into MacPyMOL. But, if you
 built from open-source it's dumped into site-packages/pymol. Also,
 view the files inside pymol/examples/launching. There are plenty of
 examples. If you're using a pre-built package from elsewhere, then
 please contact the package maintainer to see how it's built.

 Last, I prefer the newer pymol2 strategy where you get a handle to a
 PyMOL cmd instance:

 from pymol2 import PyMOL
 cmd=PyMOL().cmd

 Cheers,

 -- Jason

 On Tue, Nov 22, 2011 at 8:19 AM, Thomas Holder
 spel...@users.sourceforge.net  wrote:
 Hi Martin,

 I don't have a Mac so I can't test this, sorry.

 I suspect that the _cmd module is built into the MacPyMOL executable.
 This would imply that you cannot use MacPyMOL like in the
 Launching_From_a_Script examples. Maybe someone of the MacPyMOL users
 knows more?

 Cheers,
Thomas

 Martin Hediger wrote, On 11/22/11 13:14:
 Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.

 me @ ~/PROG_TEST $ python
 Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
 [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
 Type help, copyright, credits or license for more information.
 imported numpy
 from PyQt4.QtGui imported *
 from PyQt4.QtCore imported *
   import os, sys
   import readline
   import rlcompleter
   readline.parse_and_bind('tab: complete')
   moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
   sys.path.insert(0, moddir)
   os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
   import pymol
 Traceback (most recent call last):
File stdin, line 1, inmodule
File
 /Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py, line
 472, inmodule
  import _cmd
 ImportError: No module named _cmd
   import pymol

 What could be the problem? Could it be that the 'pymol/pymol_path' call
 is not exactly right? In the modules/pymol directory, there is a module
 'pymol/launch_pymol', but I have a similar error (No module named
 _cmd) when I try to import it.
 Martin






 Am 22.11.11 09:47, schrieb Thomas Holder:
 Hi Martin,

 the recommended way is to use PyMOL as your python interpreter, so
 instead of:

python file.py

 do this:

pymol -cqr file.py


 However, launching a PyMOL process from a python terminal as you
 suggested is also possible. Have a look at Example 2 of
 http://pymolwiki.org/index.php/Launching_From_a_Script , the important
 lines are those:

 import pymol
 pymol.pymol_argv = ['pymol','-qc']
 pymol.finish_launching()

 Cheers,
Thomas


 Martin Hediger wrote, On 11/22/11 09:26:
 Dear PyMOL List
 It comes up once in a while, is it possible to use PyMOL features
 from outside of PyMOL? An example, the below is a script (inspired by
 Thomas Holder) which saves down to disk all amino acids of a protein
 structure into separate PDB files.

 # *
 from pymol import cmd
 from pymol import stored
 from pymol.exporting import _resn_to_aa as one_letter
 # *
 def seq(state, selection=name ca or resn hoh or resn lig):
   print Generating seqs.
   cmd.select(prot, selection)
   while cmd.pop(_tmp, prot):
   cmd.iterate(_tmp, stored.x=(resn,resv))
   #print stored.x[0], stored.x[1]

   # Special case 1: Waters.
   if stored.x[0] == 'HOH':
   filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
   # Special case 2: Substrate.
   elif stored.x[0] == 'LIG':
   filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
   # Other: protein back-bone.
   else:
   filename = 'seq-%s%d-%s.pdb' %
 (one_letter[stored.x[0]].lower(), stored.x[1], state)
   cmd.save(filename, byres _tmp)
   cmd.delete('_tmp prot')

 cmd.extend('seq', seq)
 # -

 Is it possible to somehow include this in a Python script, and
 running it from the command line? If not, why?


 Thanks for any feedback.
 --
 Thomas Holder
 MPI for Developmental Biology
 Spemannstr. 35
 D-72076 Tübingen

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[PyMOL] RMSD between two structures

[Martin Hediger]

Dear List.
When aligning two structures using the PyMOL align command, one gets a 
final RMS value indicating some kind of convergence i would say. Can I 
somehow access the function for calculating this value directly from the 
pymol prompt without aligning?

Thanks for hints
Martin

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[PyMOL] PQR Display in PyMOL

[Martin Hediger]

Dear List
I have the below model of three charged atoms (as a PQR file).
ATOM  1C ASP A   0.0 0.010.0   -2.0  4.0
ATOM  2C ASP A   0.0 0.0 0.0   -2.0  4.0
ATOM  3C ASP A   0.0 0.0   -10.02.0  4.0

The last two numbers are the charge and the radius, it's supposed to be 
in pqr format.
Can PyMOL display the negative atoms blue and the positive one red (or 
the other way around)?

Thanks for any help.
Martin

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[PyMOL] Saving Issue

[Martin Hediger]

Dear List
When I try to save an object as a PDB (after editing it slightly with 
the PyMOL edit mode, i.e. adjusting a dihedral angle),
the Save Molecule dialog asks to save all, global or objects 
current state. When saving with the last two, I get no coordinates in 
the generated file only an END statement, thats the only thing written 
to the file. Only when using all i get the coordinates in the file, 
but the file is called file_state01.pdb and I need to edit it on the 
command line.
The object I'm trying to save is the following amino acid:

  ATOM  1  N   GLN A 189  61.015   3.522  29.377  1.00  0.00  PROT N
  ATOM  2  CA  GLN A 189  60.796   4.359  30.552  1.00  0.00  PROT C
  ATOM  3  C   GLN A 189  61.841   4.093  31.609  1.00  0.00  PROT C
  ATOM  4  O   GLN A 189  62.557   5.012  32.048  1.00  0.00  PROT O
  ATOM  5  CB  GLN A 189  59.376   4.085  31.097  1.00  0.00  PROT C
  ATOM  6  CG  GLN A 189  59.191   4.225  32.644  1.00  0.00  PROT C
  ATOM  7  CD  GLN A 189  59.212   5.623  33.275  1.00  0.00  PROT C
  ATOM  8  NE2 GLN A 189  60.166   6.464  32.970  1.00  0.00  PROT N
  ATOM  9  OE1 GLN A 189  58.336   5.977  34.048  1.00  0.00  PROT O
  ATOM 10  HA  GLN A 189  60.884   5.420  30.254  1.00  0.00  PROT H
  ATOM 11 2HB  GLN A 189  59.072   3.062  30.790  1.00  0.00  PROT H
  ATOM 12 3HB  GLN A 189  58.662   4.765  30.594  1.00  0.00  PROT H
  ATOM 13 2HG  GLN A 189  59.945   3.612  33.173  1.00  0.00  PROT H
  ATOM 14 3HG  GLN A 189  58.222   3.797  32.956  1.00  0.00  PROT H
  ATOM 15 1HE2 GLN A 189  60.070   7.393  33.383  1.00  0.00  PROT H
  ATOM 16 2HE2 GLN A 189  60.828   6.131  32.266  1.00  0.00  PROT H
  ATOM 17  H01 GLN A 189  61.024   2.517  29.478  1.00  0.00  PROT H



Any hints are welcomed, because its a bit inconvenient having to rename 
all the time..
Martin

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Re: [PyMOL] Script for Torsion angles

[Martin Hediger]

Great page. Good to know.
Thanks all for the feedback.

Martin





Am 06.09.11 16:17, schrieb Robert Immormino:
 Martin,

 If you end up wanting to do this a lot then it might be worth looking
 into Dangle ( http://kinemage.biochem.duke.edu/software/dangle.php ).
 This is one of the tools from the Richardson Lab which allows quick
 output of various bond length, angle, torsion and plane measurements.

 -bob

 On Fri, Sep 2, 2011 at 5:48 AM, Martin Hedigerma@bluewin.ch  wrote:
 Dear List
 Does anyone have a script to calculate torsion angles lying around?
 Ideally, i would like to be able to enter x1, x2, x3, x4 and get the
 (smaller) angle between the two normals of the planes defined by x1, x2,
 x3 and x2, x3, x4, respectively. For some odd reason the measurment
 wizard in my PyMOL install does not display torsion angles..!?

 Kind regards and thanks for any feedback.
 Martin

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[PyMOL] Configuration of Player

[Martin Hediger]

Dear List
Is it possible to run the PyMOL-Player in a way such that it does not 
skip to the first frame once it reaches the end, but rather that it goes 
back and forward?
I.e. if running over the models/frames in a multi frame file, it goes 
from 1-10 and then from 10-1.

Kind regards.
Martin Hediger

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Re: [PyMOL] Run script synchronized

[Martin Hediger]

Try this.

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


Martin Hediger





On 28.08.11 19:24, Troels Emtekær Linnet wrote:

Thanks Jason. But still no luck...

So, I changed it to a python script. It was important that the ending 
of the file is .py :-)
But, I can see from the list of objects, that PyMOL fetches the next 
protein before it has finished propka first.

Does pymol run external script in some kind of asynchron mode as default?

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

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

import propka
#resis = 
[[1bj6,36],[1bj6,39],[1bj6,49],[1ag1,14],[1gu9,133],[1gu9,130],[1omu,56],[1khg,273],[2trx,35],

#[1tde,32],[1tde,35],[2ovo,56],[1m8b,56],[1hic,39],[1m8c,56],[1ppo,25],[1qlp,232]]
resis = [[1ppo,25],[1qlp,232]]
i = 0
results = []
for p,r in resis:
cmd.fetch(p,async=0)
cmd.refresh()
# When we import a module in python, the namespace is normally: 
module.function

# And we see, that propka expect resi to be in str format.
# And we don't want the logtime function
pkavalues = propka.propka(molecule=p,resi=r,resn=CYS,logtime=i)
results.append(pkavalues)
cmd.refresh()
i = i + 1
cmd.zoom(all)
print results[0]
print results[1]



2011/8/28 Jason Vertrees jason.vertr...@schrodinger.com 
mailto:jason.vertr...@schrodinger.com


Hi Troels,

In PyMOL, it you try the following, what happens for you?

# make this a file called chill.py
import time
def chill():
   rightThisSecond = time.time()
   i = 0
   while time.time()  rightThisSecond + 3.0:
   i+=1
   print The farthest I could count in 3 seconds was %d. % i

# make this a file called troels.py
import pymol
from pymol import cmd
import chill
resis = [ [1bj6,36], [1bj6,39], [1bj6,49],
 [1ag1,14],
 [1gu9,133], [1gu9,130], ]
for p,r in resis:
   # fetch a protein
   cmd.fetch(p,async=0)
   print -- Fetched %s % p
   # do something slow
   chill.chill()
   # some post processing
   print %s has %d atoms % (p, cmd.count_atoms(p))
   print %s/%s has %d atoms % (p, r, cmd.count_atoms(%s and i.
%s % (p,r)))
   cmd.delete(p)
   print -- Deleted protien


Now load PyMOL and try,

run ~/troels.py

Does PyMOL wait for the chill calls to finish? The idea is, wrap your
call in a module/file and import it. Then, call through that function.

It's about 3 AM my time and I'm sure there's a better solution--but
this might work for now.

Cheers,

-- Jason




2011/8/26 Troels Emtekær Linnet tlin...@gmail.com
mailto:tlin...@gmail.com:
 Well, I cant get it to work.
 Pymol speeds ahead of calling propka.propka

 Can you give an example of subprocess?
 ---

 import propka

 python
 resis = [[1bj6,36],[1bj6,39]]
 #resis =


[[1bj6,36],[1bj6,39],[1bj6,49],[1ag1,14],[1gu9,133],[1gu9,130],[1omu,56],[1khg,273],[2trx,35],


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


 hth
 Martin

 On 23.08.11 10:48, Troels Emtekær Linnet wrote:

 Hi.

 If one writes a pymol script, and calls an external function,
the pymol
 script continues its operation before waiting for the success
of the
 external function.

 Is it possible to give a keyword, so it waits for the
external function
 before preceding?

 Kind of the same function with:
 fetch 1hp1, async=0

 Best
 Troels




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Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

[Martin Hediger]

Hi Troels
It's indeed possible.
The wizards are available through the cmd module.

# Initialize
load yourProtein
cmd.wizard(mutagenesis)
cmd.do(refresh_wizard)

# To get an overview over the wizard API:
for i in dir(cmd.get_wizard(): print i

# lets mutate residue 104 to GLN
cmd.get_wizard().set_mode(GLN)
cmd.get_wizard().do_select(104/)

# Select the rotamer
cmd.frame(11)

# Apply the mutation
cmd.get_wizard().apply()

There is alot more you could do inbetween these lines, but this is what 
I use it like.

Martin



On 21.08.11 15:56, Troels Emtekær Linnet wrote:

Hi.

I wonder if it is possible to interact with the mutagenesis wizard 
from the command line?


I am trying to determine best mutants for FRET labelling, by 
predicting the pka value/reactivity for a possible cysteine.


I would like to make a script that loops over the residues in my 
protein, change the residue to a cysteine, save the molecule and then 
initiate propka http://pymolwiki.org/index.php/Propka to get the pka 
for the cysteine.


I have googled myself to:

fetch 4ins, async=0
wizard mutagenesis
cmd.get_wizard().do_select(/4ins//A/ASN`18/CB)
cmd.get_wizard().do_pick(/4ins//A/ASN`18/CB)

But I get:
Error: please select an atom, not a bond.

Can someone help here?

Best
Troels


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Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

[Martin Hediger]

to close the wizard, you can also apply
cmd.set_wizard(done)

and you need to be carefull about the rotamer you're choosing. it 
happens that the first one ends up being in physically non-reasonable 
contact distance to other residues, so atoms become overlayed.
also, the mutagenesis wizard has the funny habit of sometimes not adding 
hydrogens to terminal -C or -N after mutating a residue, just for the 
record.

Martin





On 22.08.11 13:23, Troels Emtekær Linnet wrote:

Absolutely fantastic! :-)

I got this to work with the pymol propka script.

fetch 1ohr, async=0
create 1ohrB3C, 1ohr
hide everything, all
show cartoon, 1ohrB3C

cmd.wizard(mutagenesis)
cmd.do(refresh_wizard)
# To get an overview over the wizard API:
#for i in dir(cmd.get_wizard()): print i

# lets mutate chain B residue 3 to CYS. (1ohrB3C)
cmd.get_wizard().set_mode(CYS)
cmd.get_wizard().do_select(/1ohrB3C//B/3)

# Select the first rotamer, which is most probable
cmd.frame(1)

# Apply the mutation
cmd.get_wizard().apply()
# Close wiard
cmd.wizard(None)
# Find the new pka value
import propka
propka



Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 REhttp://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/8/22 Martin Hediger ma@bluewin.ch mailto:ma@bluewin.ch

Hi Troels
It's indeed possible.
The wizards are available through the cmd module.

# Initialize
load yourProtein
cmd.wizard(mutagenesis)
cmd.do(refresh_wizard)

# To get an overview over the wizard API:
for i in dir(cmd.get_wizard(): print i

# lets mutate residue 104 to GLN
cmd.get_wizard().set_mode(GLN)
cmd.get_wizard().do_select(104/)

# Select the rotamer
cmd.frame(11)

# Apply the mutation
cmd.get_wizard().apply()

There is alot more you could do inbetween these lines, but this is
what I use it like.
Martin




On 21.08.11 15:56, Troels Emtekær Linnet wrote:

Hi.

I wonder if it is possible to interact with the mutagenesis
wizard from the command line?

I am trying to determine best mutants for FRET labelling, by
predicting the pka value/reactivity for a possible cysteine.

I would like to make a script that loops over the residues in my
protein, change the residue to a cysteine, save the molecule and
then initiate propka http://pymolwiki.org/index.php/Propka to
get the pka for the cysteine.

I have googled myself to:

fetch 4ins, async=0
wizard mutagenesis
cmd.get_wizard().do_select(/4ins//A/ASN`18/CB)
cmd.get_wizard().do_pick(/4ins//A/ASN`18/CB)

But I get:
Error: please select an atom, not a bond.

Can someone help here?

Best
Troels



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[PyMOL] Saving each residue to file

[Martin Hediger]

Dear List
I was wondering if there could be a way of having every residue of a 
protein structure being saved to a separate file. How could this be done?
I believe the 'iterate' method might be useful in combination with the 
'byres' identifier, but I havent figured out how to combine them in the 
right way.
It would be great if the residues could be saved by increasing residue 
number, something like
res-a001
res-f002
where 'a' and 'f' where the residue type and the number is the residue 
number in the chain.

Any hints are very welcome.
Martin

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[PyMOL] Generating Image of Periodic System

[Martin Hediger]

Dear List
I am trying to prepare a figure. I have a protein structure, enclosed by 
a rectangular box. Is it possible to copy/translate the enboxed 
structure for a given amount of times? This would end up as something as 
an illustration of a system with periodic boundaries.
I attached a figure on my blog http://qmviews.blogspot.com/. If I cant 
come up with a PyMOL solution, then I guess I'll just try to find a 
Python solution.


Thanks for any hints on this.

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Re: [PyMOL] Downloading the biological assembly from the PDB

[Martin Hediger]

I see, so if i get this right, every protein structure has at least one 
biological unit, sometimes it just conincides with the asymmetric unit. 
So it would be save to write .pdb1 in any case.

Cool, thanks for pointing this out to me.

Martin





On 03.05.11 22:22, li...@cowsandmilk.net wrote:
 http://www.rcsb.org/pdb/files/1avd.pdb1

 The key is adding 1 to the suffix.  Sometimes there is more than one 
 biological unit, in which case, there is a pdb2, pdb3, etc.

 -David

 On May 3, 2011, at 4:00 PM, Martin Hedigerma@bluewin.ch  wrote:

 Dear all
 I would like to ask how it is possible to download the coordinate file
 for the biological assembly of a protein structure from the PDB.
 Naturally, this is not a question directly related to PyMOL, but I
 thought I'll be reaching at least a couple of
 Biochemists/Chrystallographers who know how to do this.
 As an example, when downloading the PDB file of 1AVD, I get a file
 with two chains. The biological assembly would be a tetramer, so I
 wonder what URL I would require to write into a script that does the
 downloading.

 Thanks for help on this.
 Martin

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[PyMOL] Get Protein Dimension

[Martin Hediger]

Dear all

I found that PyMOL offer the cmd.get_extent('protein') function, which 
returns the dimensions of the selection.
Is it complicated to make this function available from within an 
ordinary Pythonscript?

Thanks for hints.
Martin


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Re: [PyMOL] Get Protein Dimension

[Martin Hediger]

Thanks for the feedback. Yes, the idea was to expose the PyMOL function 
to Python. I'll check out the relevant pages mentioned.


On 26.04.11 14:52, Hongbo Zhu wrote:
 you can write your own loop in python to implement the function.

 fh = open(pdbfilename)
 coords =
 numpy.array([[float(line[30:38]),float(line[38:46]),float(line[46:54])]
 for line in fh.readlines() if line.startswith('ATOM  ') or
 line.startswith('HETATM')])
 fh.close()
 extent = (numpy.min(coords,axis=0), numpy.max(coords,axis=0))

 or course the code needs to be tuned if you need only the first MODEL or
 only the first alternate position etc.

 cheers,hongbo

 On 04/26/2011 01:40 PM, Martin Hediger wrote:
 Dear all

 I found that PyMOL offer the cmd.get_extent('protein') function, which
 returns the dimensions of the selection.
 Is it complicated to make this function available from within an
 ordinary Pythonscript?

 Thanks for hints.
 Martin


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[PyMOL] Display coordinate vectors

[Martin Hediger]

Dear all
I'm sure this question was answered before, but I could not find 
anything related to it in neither the mail list nor on the Wiki.
Is it possible to display something like coordinate vectors in PyMOL? 
I.e. arrows in the 3d view space pointing towards [1,0,0], [0,1,0] and 
[0,0,1]?

I would like to illustrate the alignment of the principal axes of a 
protein with the coordinate system.

Kind regards and thank you for answers.
Martin Hediger

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Re: [PyMOL] Display coordinate vectors

[Martin Hediger]

great, thanks.

On 08.04.11 16:42, Hongbo Zhu wrote:
 Hi, Martin,

 how about this:
 http://www.pymolwiki.org/index.php/Symmetry_Axis

 also check out the script drawing X, Y, and Z reference axes by Robert:
 http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/axes_cyl.py

 hope it helps,
 hongbo

 On 04/08/2011 04:29 PM, Martin Hediger wrote:
 Dear all
 I'm sure this question was answered before, but I could not find
 anything related to it in neither the mail list nor on the Wiki.
 Is it possible to display something like coordinate vectors in PyMOL?
 I.e. arrows in the 3d view space pointing towards [1,0,0], [0,1,0] and
 [0,0,1]?

 I would like to illustrate the alignment of the principal axes of a
 protein with the coordinate system.

 Kind regards and thank you for answers.
 Martin Hediger

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[PyMOL] Logging the sculpt wizard

[Martin Hediger]

Dear List
I'm trying to automate the following sequence of steps in a PyMOL python 
script:
1. Start the mutagenesis wizard
2. Mutate a reside according to an input from the script (some integer 
to specify the id)
3. Apply and close the mutagenesis wizard
4. Start the Sculpt Wizard
5. Fix all coordinates but the residue just mutated
6. Start the sculpt algorithm to get a rough optimization of the side chain
7. End the sculpt algorithm and close the sculpt wizard.
8. Save the structure to a new file.

I have the steps up to 3. ready in a script for generation of variants.
However, when running a log file while performing steps 4. onwards, 
there are no commands written into the log file for the sculpting 
functions. Pressing the Sculpt button in the PyMOLX11Hybrid does not 
lead to a command I can see in the log file.
What would be the Python code to start the sculpt process?

Any hints are welcome.

Thanks a lot.



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Re: [PyMOL] Dont resequence atoms when saving

[Martin Hediger]

hey,
just wanted to ask if you could find something on why the mutagenesis 
wizard is destroying the ordering of atoms?

Is this perhaps fixed in the latest versions? Then a download would make 
sense.

Thanks, Martin




Am 13.12.10 16:52, schrieb Jason Vertrees:
 Hi Martin,

 As you've found, the mutagenesis wizard destroys the ordering in some
 cases.  I'll look into it.

 Cheers,

 -- Jason

 On Tue, Dec 7, 2010 at 11:34 AM, Martin Hedigerma@bluewin.ch  wrote:
 Good day
 I use PyMOL to introduce mutations into a structure. It occured to me that
 when saving the modified structure, atom sequence was not preserved. Using

 set retain_order
 set pdb_retain_ids

 is supposed to control this. It seems now, as if mutating a structure does a
 really weired thing:
 Once the mutation is introduced, the sequence becomes completely disordered
 in a sense that the atoms of the new residue are placed in between the
 atoms of the very first residue, in terms of sequence (not geometry).
 This results in a PDB file like this (PRO is the first residue, PHE is the
 residue to which the mutation is being carried out):

 ATOM  1  N   PRO A   1  53.611  -4.470  40.679  1.00  0.00  PROT
 N
 TER   2  PRO A   1
 ATOM  0  N   PHE D  14  55.428  -5.717  38.365  1.00  0.00  PROT
 N
 TER   1  PHE D  14
 ATOM  2  CA  PRO A   1  52.399  -3.722  40.197  1.00  0.00  PROT
 C
 TER   3  PRO A   1
 ATOM  1  CA  PHE D  14  55.821  -4.897  37.223  1.00  0.00  PROT
 C
 TER   2  PHE D  14
 ATOM  3  C   PRO A   1  52.805  -2.296  39.783  1.00  0.00  PROT
 C
 TER   4  PRO A   1
 ATOM  2  CB  PHE D  14  54.681  -4.879  36.160  1.00  0.00  PROT
 C
 TER   3  PHE D  14
 ATOM  4  O   PRO A   1  53.381  -1.530  40.550  1.00  0.00  PROT
 O
 TER   5  PRO A   1
 ATOM  3  CG  PHE D  14  54.928  -4.027  34.905  1.00  0.00  PROT
 C
 TER   4  PHE D  14
 ATOM  5  CB  PRO A   1  51.360  -3.675  41.342  1.00  0.00  PROT
 C
 TER   6  PRO A   1
 ATOM  4  CD1 PHE D  14  56.116  -4.189  34.183  1.00  0.00  PROT
 C
 TER   5  PHE D  14
 ATOM  6  CG  PRO A   1  52.019  -4.362  42.549  1.00  0.00  PROT
 C
 TER   7  PRO A   1
 ATOM  5  CD2 PHE D  14  54.011  -3.049  34.512  1.00  0.00  PROT
 C
 TER   6  PHE D  14
 ATOM  7  CD  PRO A   1  53.253  -5.096  41.996  1.00  0.00  PROT
 C
 TER   8  PRO A   1
 ATOM  6  CE1 PHE D  14  56.391  -3.370  33.093  1.00  0.00  PROT
 C
 TER   7  PHE D  14
 ATOM  8  HA  PRO A   1  51.990  -4.297  39.323  1.00  0.00  PROT
 H
 TER   9  PRO A   1
 ATOM  7  CE2 PHE D  14  54.282  -2.238  33.413  1.00  0.00  PROT
 C
 TER   8  PHE D  14
 ATOM  9 1HB  PRO A   1  50.434  -4.192  41.043  1.00  0.00  PROT
 H
 TER  10  PRO A   1
 ATOM  8  CZ  PHE D  14  55.473  -2.397  32.707  1.00  0.00  PROT
 C
 TER   9  PHE D  14
 ATOM 10 2HB  PRO A   1  51.070  -2.637  41.594  1.00  0.00  PROT
 H
 TER  11  PRO A   1
 ATOM  9  C   PHE D  14  56.113  -3.478  37.649  1.00  0.00  PROT
 C
 TER  10  PHE D  14
 ATOM 11 1HG  PRO A   1  51.327  -5.056  43.052  1.00  0.00  PROT
 H
 TER  12  PRO A   1
 ATOM 10  O   PHE D  14  55.357  -2.867  38.421  1.00  0.00  PROT
 O
 TER  11  PHE D  14
 ATOM 12 2HG  PRO A   1  52.313  -3.615  43.311  1.00  0.00  PROT
 H
 TER  13  PRO A   1
 ATOM 11 1HD  PHE D  14  56.847  -4.922  34.497  1.00  0.00  PROT
 H
 TER  12  PHE D  14
 ATOM 13 1HD  PRO A   1  54.110  -5.062  42.704  1.00  0.00  PROT
 H


 Can this be explained somehow?

 Thanks for your answers.
 Martin








 On 09.11.10 13:26, Jason Vertrees wrote:
 Hi Martin,

 set retain_order
 set pdb_retain_ids

 Cheers,

 -- Jason

 On Tue, Nov 9, 2010 at 4:30 AM, Martin Hedigerma@bluewin.chwrote:
 Dear all
 It occured to me that PyMOL is resequencing a structure when saving. I
 am trying to interpolate between two structures where it is critical to
 have identical sequence in both structures. Is it possible submit a
 DO_NOT_RESEQUENCE-option to the save command?

 Thanks for your help
 Martin


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Re: [PyMOL] Adding Hydrogens

[Martin Hediger]

Dear all, thanks for the feedback, I'll definitely give it a try.





On 16.03.11 16:50, Michael Lerner wrote:
I've had good results with MolProbity 
(http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15 
http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15) 
in the past.


I had a script that would let me cycle through all of the HIS 
residues, add hydrogens, and cycle between states. It's broken at the 
moment. The trick was that PyMOL doesn't care about the name of the 
residue, so you have to manually cycle the valences.


On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger ma@bluewin.ch 
mailto:ma@bluewin.ch wrote:


Dear All
I would like to ask if the PyMOL function to add hydrogens to an
entire
protein also has options, meaning is it possible to set the
protonation
state of individual residues specifically? Like in a list or
something?
h_add, His202:+1 or so?
And, it can be relevant at what atom a residue gets protonated:
His can
be protonated at Nd, or Ne or both. Is there a way to control this?

On a more general note: what other smart hydrogen adding tools are
there
out there anyway? Does anyone know a really smart tool for this? I
know
OpenBabel has a pH parameter. But on the other hand OpenBabel just
appends the hydrogens to the PDB file, whereas PyMOL really writes
them
within the block of atoms corresponding to one residue.
Also, AutoDock can add hydrogens and it even has an option for the
protonation state of histidine, but it doesn't seem to work in my
case.

Thanks for your answers and input.
martin


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[PyMOL] Adding Hydrogens

[Martin Hediger]

Dear All
I would like to ask if the PyMOL function to add hydrogens to an entire 
protein also has options, meaning is it possible to set the protonation 
state of individual residues specifically? Like in a list or something?
h_add, His202:+1 or so?
And, it can be relevant at what atom a residue gets protonated: His can 
be protonated at Nd, or Ne or both. Is there a way to control this?

On a more general note: what other smart hydrogen adding tools are there 
out there anyway? Does anyone know a really smart tool for this? I know 
OpenBabel has a pH parameter. But on the other hand OpenBabel just 
appends the hydrogens to the PDB file, whereas PyMOL really writes them 
within the block of atoms corresponding to one residue.
Also, AutoDock can add hydrogens and it even has an option for the 
protonation state of histidine, but it doesn't seem to work in my case.

Thanks for your answers and input.
martin

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Re: [PyMOL] R: Re: Re: labeling by a pseudoatom

[Martin Hediger]

Dear all
thanks for the feedback. Indeed, after thinking for a second its totally 
clear why 'select identifyer, (resn asp and resn glu)' returns { }.
So, speaking of syntax, '+' is OR and '' is AND?

Thanks again
Martin







Am 02.03.11 01:35, schrieb rv...@libero.it:
 Hi Jason,
 sorry for last message ..

 To label a residue by an mdo command cmd.mdo(int frame, string command) I can
 pass as command one among these strings:

 1) 'label %s, %s %s' % (..)
   works fine but prints a message (I don't want) to the output window

 1+) 'label %s, %s %s, quiet=1' % (..)
   doesn't work, I get a
   SyntaxError: can't assign to literal

 2) 'cmd.label(%s, \'%s %s\')' % (..)
   works fine and doesn't print a message to the output window (is my 
 choise)

 2+) 'cmd.label(%s, \'%s %s\', quiet=1)' % (..)
   doesn't work, pyMOL crashes

 A similar behaviour I've got about alter_state and cmd.alter_state()

 So the 'label ..' command appears not having a 'quiet' option and appears not
 being the same than 'cmd.label  ..'

 This was strange to me and (hoping I didn't make a mistake in the script) I
 was curious to know the raison of this behaviour if simple to tell. If not,
 please don't care: I solved (thanks to you) my problem and so you can skip my
 request.
 Thanks a lot.

 Cheers
Roberto

 Messaggio originale
 Da: jason.vertr...@schrodinger.com
 Data: 01/03/2011 18.29
 A: rv...@libero.itrv...@libero.it
 Ogg: Re: Re: [PyMOL] labeling by a pseudoatom

 Hi Roberto,

 I'm not sure what you're asking here.  Can you please rephrase this.

 Also, are you trying quite=1 or quiet=1.

 Cheers,

 -- Jason

 On Tue, Mar 1, 2011 at 2:17 AM, rv...@libero.itrv...@libero.it  wrote:
 Hi Jason,
 thanks for your hints.

 I tried. All fine:
 cmd.alter_state doesn't message the user also without a quite=1 option.
 cmd.label makes the same.

 I used (as suggested)
 cmd.alter_state
 cmd.label

 'cmd.alter_state' appears not be the same than 'alter_state'
 and so
 'cmd.label' appears not be the same than 'label'.

 I've got errors when I setted quite=1 options in
 'alter_state' and in 'label'

 So thanks for your hints.

 Cheers
 roberto



 Tjha

 alter_state
 and
 label
 instead message the
 the output window and don't suppor

 If I set a quite=1 option in
 alter_state
 label
 I get errors.

 .. but probably you already know.


 Messaggio originale
 Da: jason.vertr...@schrodinger.com
 Data: 28/02/2011 6.36
 A: rv...@libero.itrv...@libero.it
 Cc:pymol-users@lists.sourceforge.net
 Ogg: Re: [PyMOL] labeling by a pseudoatom

 Hi Roberto,

 It's nice to see people learning how to script and putting PyMOL
 through its paces.

 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?
 The easiest way would be to get the coordinates of the target residue,
 I'd choose the alpha carbon (replace X with your residue number):

 # query residue X's alpha carbon, store the position in targetResPosition

 targetResPosition = cmd.get_atom_coords(resi X and n. CA)

 # next, just assign that position to the pseudoatom:

 cmd.alter_state(1, myPseudoAtom, (x,y,z) = targetResPosition)


 2) How to change the label without messaging the user?
 The 'label' command appears not have a 'quiet' option.
 This is interesting, and not what I'd expect from PyMOL, however it works:

 # make a new text label as a Python string

 newLabel = New Pseudoatom label

 # assign that label

 cmd.label(myPseudoAtom, newLabel)

 Interestingly, PyMOL picks up the 2nd parameter as a variable name.
 Also, label does have a quiet option:

 # assign that label, quietly

 cmd.label(myPseudoAtom, newLabel, quiet=1)



 3)  (less important) How to hide the pseudoatom?
 I wish not have the pseudoatom listed among models in the GUI
 panel.
 To hide a pseudoatom (just the + symbol):

 hide nonbonded, myPseudoAtom

 # or, just hide the labels

 hide labels, myPseudoAtom

 # or, hide all

 hide everything, myPseudoAtom


 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?
 The mdo command takes a frame number and a string.  For that frame it
 stores the string, and then applies it prior to setting the scene.
 PyMOL overwrites the string each time, so you need to cache all your
 commands for one frame and use the mdo command once per fram.  Create
 a small class that stores all the mdo commands as one string.  Then,
 when you want those command executed ask the class to call mdo on the
 given frame, using that long string.  That might look something like:


 

Re: [PyMOL] Selecting ASP and GLU

[Martin Hediger]

yeah, its true.

We should work out a tutorial for this kind of things. Something where 
there is only one line of instruction and one line of command, like:

1) Download a file
fetch pdb1.pdb

2) Select all ASP or GLU residues:
select acids, resn ASP+GLU

3) Suggestions?






Am 02.03.11 22:36, schrieb Hongbo Zhu:
 On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote:
 Hey :)

 It's good to note that programs are written by programmers, using
 programmer's logic.
 First of all, I was not complaining about the logic of the PyMOL
 programmers. I tried to help find out the reason that might cause
 Martin's script to break based on the similar complains I had received.

 It is true that programs are written by programmers. But I guess many
 users actually hate that fact so much because they see again and again
 that some programmers just presume that all users will think the same
 way as they think. (Of course after these users become programmers they
 start to do the same ;)

 The confusion is not so much caused by the
 simplified expression, but by users with little background in
 mathematics/logic assessing 'and' and 'or' from a linguistic
 background.In computer science and mathematics OR := union, AND :=
 intersection. It's covered quite well in
 http://www.pymolwiki.org/index.php/Selection_Algebra
 I disagree. I think it is caused by the simplified expression to the
 users who think intuitively instead of immediately mathematically when
 they try to write down the first line of selection script, no matter how
 much mathematics/logic they have (the colleague I mentioned is a
 computer scientist). After staring at the unexpected outcome for a
 while, they will try to think mathematically or google-ly ;).

 I can not think of a good way to address this small issue for new users.
 Maybe a more informative hint to the users is helpful rather than just
 print 0 atoms selected. For example, PyMOL can print the selection
 result of each operand, or print the complete selection expression
 translated from the the simplified selection expression.

 Cheers,

 Tsjerk

 On Wed, Mar 2, 2011 at 11:06 AM, Hongbo Zhu
 hongbo@biotec.tu-dresden.de   wrote:
 I believe the confusion is caused by the simplified selection expression
 in PyMOL (and some other visualization tools as well). I remember that
 one of my colleagues once questioned strongly the reason of using OR
 instead of AND in such situation.

 The expression:

 select resn GLU or resn ASP

 actually means

 select (resn == GLU) or (resn == ASP)

 The reason of using Boolean operator *or* is very clean when the two
 operands are stated completely. But when the operands are simplified,
 our first reaction is to use *and* because it is very natural to say

 I want GLU *and* ASP

 if you want both GLU and ASP.

 And it is even more confusing in Jmol :

 select 110 or 112 (select resno==110 or resn==112)

 if want you really want is 110 *and* 112 :)

 hongbo

 On 03/01/2011 05:43 PM, Jason Vertrees wrote:
 Hi Martin,

 To select all ASPs and GLUs just type,

 select resn GLU+ASP

 or

 select resn GLU or resn ASP

 or, if you need parentheses,

 select ((resn GLU) or (resn ASP))


 Maybe this will help:

 # fetch a test protein

 fetch 1rsy, async=0

 # color all ASPs and GLUs red

 color tv_red, (resn ASP or resn GLU)


 While the boolean 'and' works, the following will fail to select and
 color any atoms:

 color tv_red, (resn ASP and resn GLU)

 because there will be no _single atom_ in both an ASP and a GLU.  The
 boolean 'and' in (resn ASP and resn GLU) requests an atom that is in
 any ASP _and_ in any GLU--which is impossible.

 Cheers,

 -- Jason



 On Tue, Mar 1, 2011 at 7:44 AM, Martin Hedigerma@bluewin.ch 
 wrote:
 Dear all
 What is the selection syntax to select all GLU and ASP residues within an
 object?

 I'm trying it the way its written on the wiki:

 remove resn hoh# remove water
 h_add  # add hydrogens

 as surface
 color grey90

 color slate, resn lys   # lysines in light blue
 color paleyellow, resn cys  # cysteines in light yellow
 color tv_red, (resn asp or(resn glu))  # aspartic and glutamic acid in 
 light
 red

 but, the selection kind of does not work for me (I'm assuming the operator
 for the logical AND is 'and').
 What is it that I need to do differently?

 Kind regards
 Martin

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[PyMOL] Selecting ASP and GLU

[Martin Hediger]

Dear all
What is the selection syntax to select all GLU and ASP residues within 
an object?


I'm trying it the way its written on the wiki:

remove resn hoh# remove water
h_add  # add hydrogens

as surface
color grey90

color slate, resn lys   # lysines in light blue
color paleyellow, resn cys  # cysteines in light yellow
*color tv_red, (resn asp or(resn glu))  # aspartic and glutamic acid in light 
red*

but, the selection kind of does not work for me (I'm assuming the 
operator for the logical AND is 'and').

What is it that I need to do differently?

Kind regards
Martin
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[PyMOL] Plugin Tutorial

[Martin Hediger]

Dear all
I was just working through the Plugin tutorial
http://www.pymolwiki.org/index.php/Plugins_Tutorial
Writing the plugin from the tutorial as is shown, I happen to receive a 
gzip error (from the Python Shell):



 zlib.decompress(pdbFile.read()[22:], -zlib.MAX_WBITS)

Traceback (most recent call last):
  File stdin, line 1, inmodule
zlib.error: Error -5 while decompressing data

So I figured, why is the PDB file decompressed in the first place, why 
not just call the PDB file directly from the PDB database:


def remote(pdbCode):
pdbCode = pdbCode.upper()
try:
*pdbFile = urllib2.urlopen('http://www.pdb.org/pdb/files/'
+ pdbCode
+ '.pdb')*
#pdbFile = urllib2.urlopen('http://www.rcsb.org/pdb/cgi/export.cgi/' +
#pdbCode + '.pdb.gz?format=PDBpdbId=' +
#pdbCode + 'compression=gz')
#cmd.read_pdbstr(zlib.decompress(pdbFile.read()[22:], -zlib.MAX_WBITS),
#pdbCode)
*cmd.read_pdbstr(pdbFile.read()[22:], pdbCode)*
except:
print Unexpected Error:, sys.exc_info()[0]
tkMessageBox.showerror('Invalid Code', pdbCode)

This seems to work fine in the sense that the PDB file is correctly 
downloaded and loaded into the PyMOL viewer.


I have two questions now:
1) Are there any problems I could run into using this approach?
2) I was thinking its a bit tedious to reinstall a plugin everytime I 
change a single line of code. Is there an easy and smart way to see how 
new code is working within PyMOL without having to reinstall the plugin 
all the time?


Thanks for any suggestions.



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Re: [PyMOL] Plugin Tutorial

[Martin Hediger]

Ok, good to know.
I was using the code as shown on the tutorials page, and since I have 
only limited experience with the zlib module, I was not exactly sure 
about what it's doing in the first place.
I am still wondering though if it is possible to avoid the reinstallment 
of the plugin whenever a line in the code is changed to see how it 
affects the functionality. Can this be circumvented somehow?

Martin






On 09.02.11 15:57, Tsjerk Wassenaar wrote:
 Hi Martin,

 I have trouble to see how the window buffer size could be negative.
 Probably it should be

 zlib.decompress(pdbFile.read()[22:], zlib.MAX_WBITS)

 Downloading in compressed form is much more efficient. But otherwise I
 don't think it should give you trouble doing it like that.

 Cheers,

 Tsjerk

 On Wed, Feb 9, 2011 at 1:43 PM, Martin Hedigerma@bluewin.ch  wrote:
 Dear all
 I was just working through the Plugin tutorial
 http://www.pymolwiki.org/index.php/Plugins_Tutorial
 Writing the plugin from the tutorial as is shown, I happen to receive a gzip
 error (from the Python Shell):

 zlib.decompress(pdbFile.read()[22:], -zlib.MAX_WBITS)
 Traceback (most recent call last):
File stdin, line 1, inmodule
 zlib.error: Error -5 while decompressing data

 So I figured, why is the PDB file decompressed in the first place, why not
 just call the PDB file directly from the PDB database:

 def remote(pdbCode):
  pdbCode = pdbCode.upper()
  try:
  pdbFile = urllib2.urlopen('http://www.pdb.org/pdb/files/'
  + pdbCode
  + '.pdb')
  #pdbFile = urllib2.urlopen('http://www.rcsb.org/pdb/cgi/export.cgi/'
 +
  #pdbCode + '.pdb.gz?format=PDBpdbId=' +
  #pdbCode + 'compression=gz')
  #cmd.read_pdbstr(zlib.decompress(pdbFile.read()[22:],
 -zlib.MAX_WBITS),
  #pdbCode)
  cmd.read_pdbstr(pdbFile.read()[22:], pdbCode)
  except:
  print Unexpected Error:, sys.exc_info()[0]
  tkMessageBox.showerror('Invalid Code', pdbCode)

 This seems to work fine in the sense that the PDB file is correctly
 downloaded and loaded into the PyMOL viewer.

 I have two questions now:
 1) Are there any problems I could run into using this approach?
 2) I was thinking its a bit tedious to reinstall a plugin everytime I change
 a single line of code. Is there an easy and smart way to see how new code is
 working within PyMOL without having to reinstall the plugin all the time?

 Thanks for any suggestions.




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[PyMOL] Start PyMOL session in web browser

[Martin Hediger]

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] Start PyMOL session in web browser

[Martin Hediger]

Of course, Jmol is very poweful and I am using it as well for many things.
Inconvenient probably is the wrong word, I just find the PyMOL handling 
of large molecules a bit more intuitive. As far as I can see, there are 
more view options in PyMOL (Ribbons, Surfaces, etc), this would be 
particularyl helpful.
Anyway, the questions remains, how one could run a PyMOL session through 
a web browser. I will be looking at the input from the previous postings.






Am 19.12.10 14:11, schrieb Rich:
 On 19-12-2010 7:37, Martin Hediger wrote:
 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.
 Have you tried asking about what you find inconvenient about Jmol on the
 Jmol list? Perhaps the behaviour that you don't like could be addressed?
 I know a of of people seem satisfied to use Jmol for browser-based
 rendering.

 Rich

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[PyMOL] Orienting protein on surface

[Martin Hediger]

Dear all

Let protein P be of C1 symmetry, so no symmetry elements. It can be 
approximated by a cube C, where every face of C has its own value, say 1 
to 6.
Lets assume, the positive x-direction is coming out of the computer 
screen, the plane of the screen is the yz plane, the lower left corner 
is now (0,0,0). Lets say, C lies in first quadrant of the xy plane, and 
face 1 is visible facing towards the reader.
I now want to generate all possible orientations of the protein on the 
xy surface, so 6 in total. Are there any tools built into PyMOL? I went 
through the scripts library and saw a couple of things I might be using 
as a guide line, but so far nothing definitive. Its not a difficult 
thing to do, I just thought maybe there is something I can build on 
(instead of contributing to script inflation).

Thanks for any hints on this.

Martin

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Re: [PyMOL] Fwd: What is the difference between Atom ID and Index

[Martin Hediger]

Thanks Hongbo Zhu. Great summary of the topic.
Rank rules.
Martin



On 01.11.10 11:57, Hongbo Zhu wrote:
 ID is theexternal-index-number, which is parsed from columns 7-11
 of the PDB file (Atom serial number).
 Try pymol command:
 select id 110

 RANK is the order of the atoms as they are listed in the PDB file
 (0-based). Therefore, the nitrogen is at rank 11 (line 12).
 Try pymol command:
 select rank 11

 INDEX is theinternal-index-number  of the atom. Obviously, the atoms
 get their internal indices based on their names as atoms of the same
 name are grouped together.
 Try pymol command:
 select index 1

 PyMOL suggests that
  Atom indices are fragile and will change as atoms are added
 or deleted.  Whenever possible, use integral atom identifiers
 instead of indices. 


 I suppose you should useRANK, if you like to find a way to get the
 'linenumber-dependent' index of an atom.

 cheers,
 Hongbo Zhu


 On 11/01/2010 10:02 AM, Martin Hediger wrote:
 Hi Tsjerk,
 I am still wondering about how the numbering is done.
 Given a PDB file looking like this (some random molecule):

 HETATM 1 C LIG 1 -4.242 2.555 -0.814 1.00 0.00 C
 HETATM 2 C LIG 1 -2.736 2.361 -0.665 1.00 0.00 C
 HETATM 3 H LIG 1 -4.461 3.588 -1.106 1.00 0.00 H
 HETATM 4 C LIG 1 -4.961 2.214 0.487 1.00 0.00 C
 HETATM 5 H LIG 1 -4.615 1.908 -1.617 1.00 0.00 H
 HETATM 6 H LIG 1 -2.333 3.133 0.004 1.00 0.00 H
 HETATM 7 H LIG 1 -2.247 2.493 -1.637 1.00 0.00 H
 HETATM 8 C LIG 1 -2.409 0.977 -0.105 1.00 0.00 C
 HETATM 9 H LIG 1 -4.728 2.975 1.243 1.00 0.00 H
 HETATM 10 C LIG 1 -4.549 0.837 1.003 1.00 0.00 C
 HETATM 11 H LIG 1 -6.045 2.243 0.329 1.00 0.00 H
 HETATM 110 N LIG 1 -3.097 0.727 1.164 1.00 0.00 N
 HETATM 13 H LIG 1 -4.907 0.053 0.324 1.00 0.00 H
 HETATM 14 H LIG 1 -5.027 0.653 1.972 1.00 0.00 H
 HETATM 15 H LIG 1 -1.329 0.896 0.057 1.00 0.00 H
 HETATM 16 H LIG 1 -2.677 0.200 -0.831 1.00 0.00 H
 HETATM 17 H LIG 1 -2.789 1.419 1.847 1.00 0.00 H

 What PyMOL-function returns me the 'physical' index in the array of
 atoms? So for atom '12' (nitrogen), (with label '110') I would like '12'
 displayed in the PyMOL viewer. Right now, 'ID' displayes '110', 'RANK'
 displays '11' and 'INDEX' displayes '1'.

 After deleting row 4, again for atom labeled '110' nitrogen, 'ID'
 displayes '110', 'RANK' displayes '10' and index displayes '1'.

 I'm not sure now if this is in agreement with what we have said so far.
 What I dont like too much about relying on 'ID' is the fact that if the
 labels get changed (or none are present), its not possible to tell
 anymore which atom has which index. Thats why i was hoping to find a way
 to get the 'linenumber-dependent' index of an atom.

 Thanks for your help so far.

 Martin



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[PyMOL] What is the difference between Atom ID and Index

[Martin Hediger]

Dear All
I'm trying to figure out for myself, what the two labels 'Label  Atom 
Identifiers  ID' and 'Label  Atom Identifiers  index' mean, or what 
the respective difference between the two is. For sure, the numerical 
value is very different when I show the labels in a structure. ID seems 
to be the index of the atom in the list of atom-descriptor lines in the 
PDB input file. But I cant figure out what 'index' is referring to.

Any help on this would be very welcome.

Martin

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Re: [PyMOL] Fwd: What is the difference between Atom ID and Index

[Martin Hediger]

Thanks Tsjerk (on both occasions).
As a matter of fact, I'm kind of making a living out of writing a Python 
script once in a while, so thats no worry ;)
What I was trying to get at was that I was trying to understand how 
certain PyMOL scripts work, and naturally from that become able to 
improve my own ones.

In particular, I was trying to understand the following script:
http://pastebin.com/5mkwWJdd

Its is supposed to find hydrogen bonds within a structure and it should 
allow to monitor the change in the HB network throughout a reaction. 
Credit to the person who wrote it.
Especially, lines 61 to 69 make heavy use of iterate, but I cant quite 
follow it. Understanding 'iterate' (and naturally iterate_state, alter 
and alter_state), I believe, would help me alot in writing better scripts.

Anyway, thanks again for the support.

Martin





On 25.10.10 12:49, Tsjerk Wassenaar wrote:
 Never get used to that only-reply-to-sender policy...


 -- Forwarded message --
 From: Tsjerk Wassenaartsje...@gmail.com
 Date: Mon, Oct 25, 2010 at 12:30 PM
 Subject: Re: [PyMOL] What is the difference between Atom ID and Index
 To: Martin Hedigerma@bluewin.ch


 Hi Martin,

 ID is indeed the atom id from the coordinate (PDB) file. Index, AFAIK,
 is the atom index in the model, starting from 1.

 Probably you should get yourself acquainted with the command line and
 with python, as it will help you to solve these and other problems.
 For example, you can access properties from the atoms easily through
 constructions like these:

 x = [ at.id for at in cmd.get_model(selection).atom ]
 y = [ at.index for at in cmd.get_model(selection).atom ]

 That will first build a selection/model object, with a list of atoms
 (.atom), over which you can iterate to extract some properties. To
 check whether the index is indeed a straightforward list of increasing
 numbers, you can then look at the output of

 print y == range(1,len(y)+1)

 Hope it helps :)

 Tsjerk

 On Mon, Oct 25, 2010 at 10:55 AM, Martin Hedigerma@bluewin.ch  wrote:
 Dear All
 I'm trying to figure out for myself, what the two labels 'Label  Atom
 Identifiers  ID' and 'Label  Atom Identifiers  index' mean, or what
 the respective difference between the two is. For sure, the numerical
 value is very different when I show the labels in a structure. ID seems
 to be the index of the atom in the list of atom-descriptor lines in the
 PDB input file. But I cant figure out what 'index' is referring to.

 Any help on this would be very welcome.

 Martin

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[PyMOL] Question about Iterate and Edit-Mode

[Martin Hediger]

Dear All
I am trying to get behind the way 'iterate' works, since I see it quite 
frequently in PyMOL scripts.
The example in the help page is a bit limited in the sense that I cant 
explain to myself what actually is happening.

Say, if I were to write the functionality of 'iterate' using a for-loop, 
how would this for-loop look like?
Something like this maybe?

for i in selection:
 i.expression()

I'm a bit confused about what can go into 'expression'.

The second question is related to the Edit-Mode of PyMOL. When I switch 
to Edit-Mode and click on a atom, a couple of states/objects (?) appear 
in the object list: pk1, pkmol, pkresi, pkchain, pkobject.
What do these objects mean? What are they useful for? I'm sure there is 
a reason for them, but I cant figure it out.

Thanks a lot for your help guys.

Martin

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Re: [PyMOL] Mutagenesis How many rotamers per amino acid

[Martin Hediger]

', if I want to know how
 many
 GLU
 rotamers are in the library.

 Thanks again
 Martin




 Am 12.09.10 22:00, schrieb Jason Vertrees:
 Hi Martin,

 PyMOL first searches the Dunbrack rotamer library for hits based
 upon
 the amino acid type and it's original phi/psi angles.  If it
 cannot
 find a hit, it will then look for backbone independent positions.
   To
 get the number of available rotamers given a residue, you need to
 unpickle the library, create the lookup key into the library and
 then
 count the results.  It might look something like this:

 # unpickle the library
 import pickle
 rot_lib =




 pickle.load(open($PYMOL_HOME/data/chempy/sidechains/sc_bb_dep.pkl,'r'))

 # get residue name, you need to select the residue
 # into my_res
 from pymol import stored
 stored.r = ''
 iterate first my_res, stored.r = resn

 # get residue info; prepare dictionary key
 (phi,psi) = cmd.phi_psi(br. first my_res)

 # warren also does 20 and 60 in place of 10--three possible
 lookups
 key = ( stored.r, int(10*round(phi/10)), int(10*round(psi/10)))

 if key in rot_lib.keys():
print This rotamer has %s possible positions %
 len(rot_lib[key])

 Lookups in the independent library are easier--just provide a
 residue
 name.

 Cheers,

 -- Jason


 On Sun, Sep 12, 2010 at 11:04 AM, Martin
 Hedigerma@bluewin.ch
   wrote:
   Dear all, let me rephrase my question in a less confusing way.
 For a given mutant, I need a PDB file for every available
 rotamer.
 I
 guess thats the simplest way of putting it. How can I achieve
 that?

 Thanks for hints.
 Martin





 Am 12.09.10 00:08, schrieb Martin Hediger:
 Hi all
 I want to do some scripted mutations on a range of residues. Say
 I
 want
 to mutate residue 189 to every rotamer of [Asp, His, Glu, Thr,
 Lys]
 available in the PyMOL internal rotamer library. I'm seeing that
 PyMOL
 issues cmd.get_wizard().do_state(i) to select rotamer 'i' for a
 mutation. Now, if I want to iterate over all available rotamers,
 I
 need
 the limit rotamer number. How can I obtain the maximum number of
 rotamers available for every amino acid?

 Thanks for hints on this

 Martin






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[PyMOL] Mutagenesis How many rotamers per amino acid

[Martin Hediger]

  Hi all
I want to do some scripted mutations on a range of residues. Say I want 
to mutate residue 189 to every rotamer of [Asp, His, Glu, Thr, Lys] 
available in the PyMOL internal rotamer library. I'm seeing that PyMOL 
issues cmd.get_wizard().do_state(i) to select rotamer 'i' for a 
mutation. Now, if I want to iterate over all available rotamers, I need 
the limit rotamer number. How can I obtain the maximum number of 
rotamers available for every amino acid?

Thanks for hints on this

Martin

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[PyMOL] Wizard Measurement

[Martin Hediger]

  Dear All
I'm trying to write a littel function that allows for a short cut to 
invoke the wizard measurement. The idea is, that instead of having to 
open the GUI menueMeasurement or typing wizard measurement, I would 
like to be able to just type mes and have the measurement tool-box 
available.
Observing what happens in the log-file when doing this shows that two 
things happen:

wizard measurement
refresh_wizard


I figured out, that I can write cmd.wizard(measurement) into the 
function definition (called mes, in mes.py), and the measurement box 
appears. What I cant figure out is how to implement the refreshment of 
the wizard using the PyMOL-API.
Can someone point this out to me?

Thanks for any help on this, btw. the same thing would kind of be nice 
for mutagenesis.

Martin

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[PyMOL] Specific Expansion of selection

[Martin Hediger]

  Dear All
I am trying to cut out a subset of a protein structure. I am selecting 
an active site atom and expanding by residue with radius 12 Angstrom 
around that atom. Is there a way of doing the following:
If the edge of the selection ends with a carbonyl of a peptide bond, 
keep it included. If the edge of the selection ends in a peptide 
nitrogen, extend the selection up to the carbonyl group and add it to 
the selection. Since the subset will consist of fragments of the peptide 
chain, a couple of seperate chains are generated. In doing so, every 
chain should start and end with carbonyls.
The point is, this way there is less ambiguity in what direction added 
hydrogens point, than with terminal nitrogens.
I am trying to accomplish this by issuing the 'neighbour' command, but i 
cant get the syntax right.

Thanks for any help on this.

Martin

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[PyMOL] Writing Hbond list

[Martin Hediger]

  Dear all
I am using the script of Robert Campell to collect hydrogen bonds and 
the essential part looks like this:

[collect pairs in hb by cmd.find_pairs]
 for pairs in hb:
 cmd.iterate(%s and index %s % (pairs[0][0], pairs[0][1]),
 'print %1s/%3s`%s/%-4s  % (chain, resn, resi, name),')


 cmd.iterate(%s and index %s % (pairs[1][0],pairs[1][1]),
 'print %1s/%3s`%s/%-4s  % (chain, resn, resi, name),')


 print %.2f % cmd.distance(hb_list_name, %s and index %s %
 (pairs[0][0], pairs[0][1]), %s and index %s % 
(pairs[1][0],
 pairs[1][1]))

This nicely lists three columns, where the interacting pairs are shown 
together with the length of the hydrogen bond.
I have now started various unsuccessfull attempts to direct the output 
of 'cmd.iterate(...)' to a file which I would like to process further 
(sorting for largest change for two different configurations, etc.).

How do I direct the output from iterate to a file?

Suggestions would be appreciated.
Martin

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[PyMOL] as sticks set up

[Martin Hediger]

  Hi all
Is there a way to have the command as sticks show sticks and only 
polar hydrogens? Right now it shows all hydrogens and it would be nice 
if I could set it to leave out non polar hydrogens.

Thanks for any suggestions.

Martin

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Re: [PyMOL] How does PyMol add hydrogen atoms?

[Martin Hediger]

That would be really interesting to know.
If there is no connectivity data provided, then my only guess is that it 
has some really precise bond length data to compare to.

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[PyMOL] PyMol Connectivity Data

[Martin Hediger]

Dear all
I am confused about the requirement of providing connectivity data in a 
pdb file to properly render a protein with PyMol.
Right now, I am displaying a pdb file not containing any connectivity 
data but still the protein seems perfectly valid.

My question is: how does PyMol know how to properly display structures 
when no connectivity is provided (i understand this usually is at the 
end of the file in the 'CONECT...' section. Can it determine 
connectivity from the atom-labels, like the residue and the 
atom-descriptor (e.g ATOM   5   CB  VAL A 1 ...)?
Related to this: I'm not a specialist in protein dynamics, but i 
understand, every reasonable force field (AMBER, CHARMM, ...) will 
require me to provide connectivity, correct? The point is, i see the 
protein displayed correctly in PyMol, but there is no connectivity in 
the PDB file. Does this mean the force field computation will also work?

Thanks for a statement
Martin

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[PyMOL] Align different Structures

[Martin Hediger]

Hi all,
My problem is:
I have two structures, A and B. Both are part of a protein and contain 
residues from the active site. A is a subset of B in a sense that B is 
contains residues even further from the active site (generated by the 
expand command).
I ran a QM calculation on the active site in the minimal set A to obtain 
a transition state for an enzymatic reaction (ester cleavage). So A is 
not in its original configuration anymore, i.e. some of the residues 
have moved.
What I want to do is this: the same calculation on the expanded model B 
would be too expensive. So I want to align B as reasonably as possible 
to A, since I know what the transition state looks like in the simple 
model. How do I do this in the smartest way? By pair-fitting in Pymol? I 
believe to issue the align command is not the best idea, since i dont 
want an overlay, I want the catalytically relevant residues to be 
superimposed.
I would very much appreciate any suggestions.

Martin

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