date:20111219

Re: [PyMOL] Color states as rainbow

2011-12-19 Thread Thomas Holder

Hi Jacob,

I fixed the color_obj script in the wiki, it had a bug.

Btw. I like Tsjerk's suggestion best, using b-factors.

Cheers,
   Thomas

Jacob Keller wrote, On 12/19/11 03:38:
 Dear Pymol list,
 
 I have been trying to color the states in a morph by spectrum to try
 to show the motion in still form, using the following method:
 
 split_states foo, # after which I get the states as new objects as 
 expected
 color_obj(rainbow=1) # after which I get the following error message:
 
 Error: unknown type: 'models'
 
 Can someone help me out here--what's the error about? Or, still
 better, can you tell me the most efficient way to color the states by
 some color pattern (presumably I will just use the spectrum). This
 kind of thing should have been used in NMR or MD figures all the time,
 no?
 
 Thanks very much,
 
 Jacob Keller

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

--
Learn Windows Azure Live!  Tuesday, Dec 13, 2011
Microsoft is holding a special Learn Windows Azure training event for 
developers. It will provide a great way to learn Windows Azure and what it 
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[PyMOL] Annual CCP4 summer school in USA, at APS, June 19-26

2011-12-19 Thread Sanishvili, Ruslan

Dear Colleagues,

We are pleased to announce the fifth annual CCP4 summer school at Advanced 
Photon Source (APS), Argonne National Laboratory (ANL). All details can be 
found at http://www.ccp4.ac.uk/schools/APS-2012/

Title:
CCP4 school: From data collection to structure refinement and beyond
Dates: June 19 to 26.
Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 
(Near Chicago), USA

The school content:
Data collection workshop the first two days: beamline training and data 
collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only 
the participants' crystals will be used.
Software workshop: The rest of the time after data collection will feature many 
modern crystallographic software packages taught by authors and other experts. 
It will be organized in three
Sections - lectures, tutorials and hands-on trouble-shooting.
There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

Applicants:
Graduate students, postdoctoral researchers and young scientists at the 
assistant professor level are encouraged to apply. Only 20 applicants will be 
selected for participation. Participants of the workshop are strongly 
encouraged to bring their own problem data sets or crystals so the problems can 
be addressed during data collection workshop and/or hands-on sessions.

Application:
Application deadline is April 17. The application form, the program, contact 
info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2012/

Fees: There is no fee for the workshop. The students will be responsible for 
their transportation and lodging. The workshop organizers will arrange 
economical lodging at the Argonne Guest House. The workshop will also cover the 
expenses for all meals and refreshments.

Garib, Ronan and Nukri


Ruslan Sanishvili (Nukri), Ph.D.

GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov

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Microsoft is holding a special Learn Windows Azure training event for 
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[PyMOL] Problem with open source pymol

2011-12-19 Thread Lauren Porter

Hi Everyone,

   I've compiled and installed pymol 1.3 on my Mac (OS 10.6 running Snow
Leopard), but pymol keeps crashing.  The compilation looks clean, so I have
no idea why it's giving me trouble.  I have pasted the details below.  Any
help would be much appreciated.  Thanks!

~Lauren

Python 2.5.4 (r254:67916, Aug  1 2011, 15:52:49)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type help, copyright, credits or license for more information.
 import pymol
 pymol.finish_launching()
 2011-12-19 12:32:21.895 Python[243:5d03] -[GLUTApplication _setup:]:
unrecognized selector sent to instance 0x1805490
2011-12-19 12:32:21.898 Python[243:5d03] An uncaught exception was raised
2011-12-19 12:32:21.899 Python[243:5d03] -[GLUTApplication _setup:]:
unrecognized selector sent to instance 0x1805490
2011-12-19 12:32:21.901 Python[243:5d03] *** Terminating app due to
uncaught exception 'NSInvalidArgumentException', reason: '-[GLUTApplication
_setup:]: unrecognized selector sent to instance 0x1805490'
*** Call stack at first throw:
(
0   CoreFoundation  0x906e36ca __raiseError + 410
1   libobjc.A.dylib 0x990c15a9 objc_exception_throw
+ 56
2   CoreFoundation  0x9073090b -[NSObject(NSObject)
doesNotRecognizeSelector:] + 187
3   CoreFoundation  0x90689c06 ___forwarding___ +
950
4   CoreFoundation  0x906897d2
_CF_forwarding_prep_0 + 50
5   Tk  0x17e11ea8 TkpInit + 601
6   Tk  0x17d7d60a Tk_PkgInitStubsCheck
+ 2489
7   _tkinter.so 0x01d9afe8 Tcl_AppInit + 130
8   _tkinter.so 0x01d9af09 var_perform + 2295
9   Python  0x0007ad4d PyEval_EvalFrameEx +
16241
10  Python  0x0007cac6 PyEval_EvalCodeEx +
1734
11  Python  0x000274ce PyClassMethod_New +
2213
12  Python  0xc2a8 PyObject_Call + 50
13  Python  0x00015db7 PyClass_New + 1710
14  Python  0xc2a8 PyObject_Call + 50
15  Python  0x00076130
PyEval_CallObjectWithKeywords + 211
16  Python  0x0001566f PyInstance_New + 330
17  Python  0xc2a8 PyObject_Call + 50
18  Python  0x0007c332 PyEval_EvalFrameEx +
21846
19  Python  0x0007cac6 PyEval_EvalCodeEx +
1734
20  Python  0x000274ce PyClassMethod_New +
2213
21  Python  0xc2a8 PyObject_Call + 50
22  Python  0x00015db7 PyClass_New + 1710
23  Python  0xc2a8 PyObject_Call + 50
24  Python  0x00076130
PyEval_CallObjectWithKeywords + 211
25  Python  0x0001566f PyInstance_New + 330
26  Python  0xc2a8 PyObject_Call + 50
27  Python  0x0007c332 PyEval_EvalFrameEx +
21846
28  Python  0x0007cac6 PyEval_EvalCodeEx +
1734
29  Python  0x00027461 PyClassMethod_New +
2104
30  Python  0xc2a8 PyObject_Call + 50
31  Python  0x0007c363 PyEval_EvalFrameEx +
21895
32  Python  0x0007aedc PyEval_EvalFrameEx +
16640
33  Python  0x0007aedc PyEval_EvalFrameEx +
16640
34  Python  0x0007cac6 PyEval_EvalCodeEx +
1734
35  Python  0x000274ce PyClassMethod_New +
2213
36  Python  0xc2a8 PyObject_Call + 50
37  Python  0x00015db7 PyClass_New + 1710
38  Python  0xc2a8 PyObject_Call + 50
39  Python  0x00076130
PyEval_CallObjectWithKeywords + 211
40  Python  0x000a3edf initthread + 1756
41  libSystem.B.dylib   0x91446259 _pthread_start + 345
42  libSystem.B.dylib   0x914460de thread_start + 34
)
Trace/BPT trap
--
Learn Windows Azure Live!  Tuesday, Dec 13, 2011
Microsoft is holding a special Learn Windows Azure training event for 
developers. It will provide a great way to learn Windows Azure and what it 
provides. You can attend the event by watching it streamed LIVE online.  
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Info Page:

Re: [PyMOL] Problem with open source pymol

2011-12-19 Thread Troels Emtekær Linnet

2011-12-19 12:32:21.901 Python[243:5d03] *** Terminating app due to
uncaught exception 'NSInvalidArgumentException', reason*:
'-[GLUTApplication _setup:]:* unrecognized
--


Do you have glut installed ?

http://www.pymolwiki.org/index.php/Linux_Install#Requirements


freeglut3-dev


Best
Troels



2011/12/19 Lauren Porter lauren.pers...@gmail.com

 Hi Everyone,

I've compiled and installed pymol 1.3 on my Mac (OS 10.6 running Snow
 Leopard), but pymol keeps crashing.  The compilation looks clean, so I have
 no idea why it's giving me trouble.  I have pasted the details below.  Any
 help would be much appreciated.  Thanks!

 ~Lauren

 Python 2.5.4 (r254:67916, Aug  1 2011, 15:52:49)
 [GCC 4.2.1 (Apple Inc. build 5646)] on darwin
 Type help, copyright, credits or license for more information.
  import pymol
  pymol.finish_launching()
  2011-12-19 12:32:21.895 Python[243:5d03] -[GLUTApplication _setup:]:
 unrecognized selector sent to instance 0x1805490
 2011-12-19 12:32:21.898 Python[243:5d03] An uncaught exception was raised
 2011-12-19 12:32:21.899 Python[243:5d03] -[GLUTApplication _setup:]:
 unrecognized selector sent to instance 0x1805490
  selector sent to instance 0x1805490'
 *** Call stack at first throw:
 (
 0   CoreFoundation  0x906e36ca __raiseError + 410
 1   libobjc.A.dylib 0x990c15a9
 objc_exception_throw + 56
 2   CoreFoundation  0x9073090b
 -[NSObject(NSObject) doesNotRecognizeSelector:] + 187
 3   CoreFoundation  0x90689c06 ___forwarding___ +
 950
 4   CoreFoundation  0x906897d2
 _CF_forwarding_prep_0 + 50
 5   Tk  0x17e11ea8 TkpInit + 601
 6   Tk  0x17d7d60a
 Tk_PkgInitStubsCheck + 2489
 7   _tkinter.so 0x01d9afe8 Tcl_AppInit + 130
 8   _tkinter.so 0x01d9af09 var_perform + 2295
 9   Python  0x0007ad4d PyEval_EvalFrameEx
 + 16241
 10  Python  0x0007cac6 PyEval_EvalCodeEx +
 1734
 11  Python  0x000274ce PyClassMethod_New +
 2213
 12  Python  0xc2a8 PyObject_Call + 50
 13  Python  0x00015db7 PyClass_New + 1710
 14  Python  0xc2a8 PyObject_Call + 50
 15  Python  0x00076130
 PyEval_CallObjectWithKeywords + 211
 16  Python  0x0001566f PyInstance_New + 330
 17  Python  0xc2a8 PyObject_Call + 50
 18  Python  0x0007c332 PyEval_EvalFrameEx
 + 21846
 19  Python  0x0007cac6 PyEval_EvalCodeEx +
 1734
 20  Python  0x000274ce PyClassMethod_New +
 2213
 21  Python  0xc2a8 PyObject_Call + 50
 22  Python  0x00015db7 PyClass_New + 1710
 23  Python  0xc2a8 PyObject_Call + 50
 24  Python  0x00076130
 PyEval_CallObjectWithKeywords + 211
 25  Python  0x0001566f PyInstance_New + 330
 26  Python  0xc2a8 PyObject_Call + 50
 27  Python  0x0007c332 PyEval_EvalFrameEx
 + 21846
 28  Python  0x0007cac6 PyEval_EvalCodeEx +
 1734
 29  Python  0x00027461 PyClassMethod_New +
 2104
 30  Python  0xc2a8 PyObject_Call + 50
 31  Python  0x0007c363 PyEval_EvalFrameEx
 + 21895
 32  Python  0x0007aedc PyEval_EvalFrameEx
 + 16640
 33  Python  0x0007aedc PyEval_EvalFrameEx
 + 16640
 34  Python  0x0007cac6 PyEval_EvalCodeEx +
 1734
 35  Python  0x000274ce PyClassMethod_New +
 2213
 36  Python  0xc2a8 PyObject_Call + 50
 37  Python  0x00015db7 PyClass_New + 1710
 38  Python  0xc2a8 PyObject_Call + 50
 39  Python  0x00076130
 PyEval_CallObjectWithKeywords + 211
 40  Python  0x000a3edf initthread + 1756
 41  libSystem.B.dylib   0x91446259 _pthread_start + 345
 42  libSystem.B.dylib   0x914460de thread_start + 34
 )
 Trace/BPT trap



 --
 Learn Windows Azure Live!  Tuesday, Dec 13, 2011
 Microsoft is holding a special Learn Windows Azure training event for
 developers. It will provide a great way to

[PyMOL] Center of screen?

2011-12-19 Thread Francis E Reyes

Hi  all

Is it possible to put a crosshairs at the center of the viewing area that 
always shows where the center is?

Thanks!
F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder






--
Learn Windows Azure Live!  Tuesday, Dec 13, 2011
Microsoft is holding a special Learn Windows Azure training event for 
developers. It will provide a great way to learn Windows Azure and what it 
provides. You can attend the event by watching it streamed LIVE online.  
Learn more at http://p.sf.net/sfu/ms-windowsazure
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Re: [PyMOL] Center of screen?

2011-12-19 Thread Thomas Holder

Hi Francis,

you could use a pseudoatom (or CGO object) and a callback that 
constantly updates the position.

python
from pymol import cmd
cmd.pseudoatom('crosshair', pos=(0,0,0))
cmd.show_as('nonbonded', 'crosshair')
def crosshair_put_center():
 t = cmd.get_position()
 m = [1, 0, 0, t[0], 0, 1, 0, t[1], 0, 0, 1, t[2], 0, 0, 0, 1]
 cmd.set_object_ttt('crosshair', m, homogenous=1)
cmd.load_callback(crosshair_put_center, '_crosshair_cb')
python end

Hope that helps.

Cheers,
   Thomas

Francis E Reyes wrote, On 12/19/11 20:31:
 Hi  all
 
 Is it possible to put a crosshairs at the center of the viewing area
 that always shows where the center is?
 
 Thanks! F
 
 -
 Francis E. Reyes M.Sc. 
 215 UCB University of Colorado at Boulder

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

--
Learn Windows Azure Live!  Tuesday, Dec 13, 2011
Microsoft is holding a special Learn Windows Azure training event for 
developers. It will provide a great way to learn Windows Azure and what it 
provides. You can attend the event by watching it streamed LIVE online.  
Learn more at http://p.sf.net/sfu/ms-windowsazure
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Re: [PyMOL] Color states as rainbow

2011-12-19 Thread Thomas Holder

Jacob Keller wrote, On 12/19/11 19:04:
 Yes, now it works perfectly--thanks very much! Also, did you see some
 advantage of doing the b-factor idea over your script, or just a good
 parallel strategy?

it's just a good parallel strategy. And is done with 2 lines instead of 
loading an extra script.

Cheers,
   Thomas

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

--
Learn Windows Azure Live!  Tuesday, Dec 13, 2011
Microsoft is holding a special Learn Windows Azure training event for 
developers. It will provide a great way to learn Windows Azure and what it 
provides. You can attend the event by watching it streamed LIVE online.  
Learn more at http://p.sf.net/sfu/ms-windowsazure
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Re: [PyMOL] Problem with open source pymol

2011-12-19 Thread Lauren Porter

Yes, I have GLUT installed (I'm using the framework), and I rerouted
everything to make sure it was pointing to the right path.  After doing
that, I rebuilt and got a new error:

Python 2.5.4 (r254:67916, Aug  1 2011, 15:52:49)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type help, copyright, credits or license for more information.
 import pymol
Traceback (most recent call last):
  File stdin, line 1, in module
  File /Library/Python/2.5/site-packages/pymol/__init__.py, line 473, in
module
import _cmd
ImportError: dlopen(/Library/Python/2.5/site-packages/pymol/_cmd.so, 2):
Symbol not found: _FT_Done_Face
  Referenced from: /Library/Python/2.5/site-packages/pymol/_cmd.so
  Expected in: flat namespace
 in /Library/Python/2.5/site-packages/pymol/_cmd.so



I read that this is because of a problem with the freetype 2 library, but I
included the library's path in the setup file, so I have no idea what else
to do.  Any ideas?  Thanks!

~Lauren

2011/12/19 Troels Emtekær Linnet tlin...@gmail.com

 2011-12-19 12:32:21.901 Python[243:5d03] *** Terminating app due to
 uncaught exception 'NSInvalidArgumentException', reason*:
 '-[GLUTApplication _setup:]:* unrecognized
 --


 Do you have glut installed ?

 http://www.pymolwiki.org/index.php/Linux_Install#Requirements

 freeglut3-dev


 Best
 Troels



 2011/12/19 Lauren Porter lauren.pers...@gmail.com

 Hi Everyone,

I've compiled and installed pymol 1.3 on my Mac (OS 10.6 running Snow
 Leopard), but pymol keeps crashing.  The compilation looks clean, so I have
 no idea why it's giving me trouble.  I have pasted the details below.  Any
 help would be much appreciated.  Thanks!

 ~Lauren

 Python 2.5.4 (r254:67916, Aug  1 2011, 15:52:49)
 [GCC 4.2.1 (Apple Inc. build 5646)] on darwin
 Type help, copyright, credits or license for more information.
  import pymol
  pymol.finish_launching()
  2011-12-19 12:32:21.895 Python[243:5d03] -[GLUTApplication _setup:]:
 unrecognized selector sent to instance 0x1805490
 2011-12-19 12:32:21.898 Python[243:5d03] An uncaught exception was raised
 2011-12-19 12:32:21.899 Python[243:5d03] -[GLUTApplication _setup:]:
 unrecognized selector sent to instance 0x1805490
  selector sent to instance 0x1805490'
 *** Call stack at first throw:
 (
 0   CoreFoundation  0x906e36ca __raiseError + 410
 1   libobjc.A.dylib 0x990c15a9
 objc_exception_throw + 56
 2   CoreFoundation  0x9073090b
 -[NSObject(NSObject) doesNotRecognizeSelector:] + 187
 3   CoreFoundation  0x90689c06 ___forwarding___ +
 950
 4   CoreFoundation  0x906897d2
 _CF_forwarding_prep_0 + 50
 5   Tk  0x17e11ea8 TkpInit + 601
 6   Tk  0x17d7d60a
 Tk_PkgInitStubsCheck + 2489
 7   _tkinter.so 0x01d9afe8 Tcl_AppInit + 130
 8   _tkinter.so 0x01d9af09 var_perform + 2295
 9   Python  0x0007ad4d PyEval_EvalFrameEx
 + 16241
 10  Python  0x0007cac6 PyEval_EvalCodeEx
 + 1734
 11  Python  0x000274ce PyClassMethod_New
 + 2213
 12  Python  0xc2a8 PyObject_Call + 50
 13  Python  0x00015db7 PyClass_New + 1710
 14  Python  0xc2a8 PyObject_Call + 50
 15  Python  0x00076130
 PyEval_CallObjectWithKeywords + 211
 16  Python  0x0001566f PyInstance_New +
 330
 17  Python  0xc2a8 PyObject_Call + 50
 18  Python  0x0007c332 PyEval_EvalFrameEx
 + 21846
 19  Python  0x0007cac6 PyEval_EvalCodeEx
 + 1734
 20  Python  0x000274ce PyClassMethod_New
 + 2213
 21  Python  0xc2a8 PyObject_Call + 50
 22  Python  0x00015db7 PyClass_New + 1710
 23  Python  0xc2a8 PyObject_Call + 50
 24  Python  0x00076130
 PyEval_CallObjectWithKeywords + 211
 25  Python  0x0001566f PyInstance_New +
 330
 26  Python  0xc2a8 PyObject_Call + 50
 27  Python  0x0007c332 PyEval_EvalFrameEx
 + 21846
 28  Python  0x0007cac6 PyEval_EvalCodeEx
 + 1734
 29  Python  0x00027461 PyClassMethod_New
 + 2104
 30  Python  0xc2a8 PyObject_Call + 50
 31  Python  0x0007c363 PyEval_EvalFrameEx
 + 21895
 32  Python  0x0007aedc PyEval_EvalFrameEx
 + 16640
 33  Python

Re: [PyMOL] Color states as rainbow

2011-12-19 Thread Jacob Keller

Yes, now it works perfectly--thanks very much! Also, did you see some
advantage of doing the b-factor idea over your script, or just a good
parallel strategy?

Jacob

On Mon, Dec 19, 2011 at 2:41 AM, Thomas Holder
spel...@users.sourceforge.net wrote:
 Hi Jacob,

 I fixed the color_obj script in the wiki, it had a bug.

 Btw. I like Tsjerk's suggestion best, using b-factors.

 Cheers,
  Thomas

 Jacob Keller wrote, On 12/19/11 03:38:

 Dear Pymol list,

 I have been trying to color the states in a morph by spectrum to try
 to show the motion in still form, using the following method:

 split_states foo,     # after which I get the states as new objects as
 expected
 color_obj(rainbow=1)     # after which I get the following error message:

 Error: unknown type: 'models'

 Can someone help me out here--what's the error about? Or, still
 better, can you tell me the most efficient way to color the states by
 some color pattern (presumably I will just use the spectrum). This
 kind of thing should have been used in NMR or MD figures all the time,
 no?

 Thanks very much,

 Jacob Keller


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



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

--
Write once. Port to many.
Get the SDK and tools to simplify cross-platform app development. Create 
new or port existing apps to sell to consumers worldwide. Explore the 
Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
http://p.sf.net/sfu/intel-appdev
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[PyMOL] Pymol Crashes Despite Plenty of Extra Memory

2011-12-19 Thread Jacob Keller

Dear Pymol Users,

I have 6 GB of RAM, but I am still getting crashes when I try to
render my 30-state figure, even when I don't raise the hash_max
(lowering it makes it take really long). When I look at the task
manager to see how much RAM is being used, it still is very far from
being maxed out, say at ~2 GB max, with 4 GB to go. Is there some
limitation to Pymol's access to my RAM (hopefully that can be changed?

Jacob

-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

--
Write once. Port to many.
Get the SDK and tools to simplify cross-platform app development. Create 
new or port existing apps to sell to consumers worldwide. Explore the 
Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
http://p.sf.net/sfu/intel-appdev
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Re: [PyMOL] Color states as rainbow

[PyMOL] Annual CCP4 summer school in USA, at APS, June 19-26

[PyMOL] Problem with open source pymol

Re: [PyMOL] Problem with open source pymol

[PyMOL] Center of screen?

Re: [PyMOL] Center of screen?

Re: [PyMOL] Color states as rainbow

Re: [PyMOL] Problem with open source pymol

Re: [PyMOL] Color states as rainbow

[PyMOL] Pymol Crashes Despite Plenty of Extra Memory

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