pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] New plugin

[Jerome P. <j.p...@pa...>]

Hi,

I've develop a new extension (plug in) for PyMOL : dbSearch.
It enable PyMOL to search a molecular structure (MDL mol format) by her name 
into a database (MySQL) and display it in PyMOL.
You can find the archive there:
http://pansanel.adlp.org/chemistry/resources/pymol_dbsearch.tgz

Cheers,

Jerome Pansanel

[PyMOL] PyMol with MacOS 10.4

[<kh...@ce...>]

Are there other people out there who compile their own PyMol on the  
Mac and who have succeeded with MacOS 10.4 (Tiger)?

After updating my Mac to Tiger, my PyMol installation doesn't work  
anymore:

~> pymol
Traceback (most recent call last):
   File "/usr/local/lib/pymol/modules/pymol/__init__.py", line 90, in ?
     import pymol
   File "/usr/local/lib/pymol/modules/pymol/__init__.py", line 306, in ?
     import _cmd
ImportError: Failure linking new module: /usr/local/lib/pymol/modules/ 
pymol/_cmd.so: Symbol not found: _gluCylinder
   Referenced from: /sw/lib/libglut.3.dylib
   Expected in: /usr/X11R6/lib/libGL.1.dylib


I guess that something has changed in Apple's OpenGL libraries. My  
first reaction was to reinstall PyMol from sources in the same way as  
before (i.e. using the Distutils installation method and Fink's  
installation of Python 2.3). This fails pretty quickly due to some  
problem with the GLUT headers:

In file included from layer0/os_gl.h:95,
                  from layer2/RepNonbondedSphere.c:19:
/sw/include/GL/glut.h:432: error: parse error before "layer"
/sw/include/GL/glut.h:432: warning: function declaration isn't a  
prototype
/sw/include/GL/glut.h:490: error: parse error before "GLfloat"
/sw/include/GL/glut.h:490: warning: function declaration isn't a  
prototype
...

This is perhaps not so surprising, because I didn't update Fink after  
updating to 10.4 - because that didn't work either. In fact, I am  
sufficiently fed up with the fragility of Fink that I would like to  
get rid of it entirely.

So I thought I should try to use MacPython 2.4.1 (my everyday Python  
on the Mac) and Apple's OpenGL and GLUT frameworks. That required a  
few patches to the PyMol sources (the includes need to be changed  
from GL/... to OpenGL/...) and a bit of tweaking setup.py plus some  
manual intervention (Distutils doesn't handle -framework parameters),  
but I got an error-free compile pretty quickly. I can then even start  
PyMol, but it messes up my screen to the point that I need to go to  
sleep mode and then restart to get the Finder redrawn. And I am not  
even sure that my approach is reasonable, given that with MacPython I  
also use Aqua-Tk, and thus no X11 at all. Window handling ought to be  
different then.

Does anyone have more ideas for getting this to work? I don't care  
which Python and which Tk I use, as long as I can add my own Python  
modules and get PyMol with NumPy support.

Konrad.

[PyMOL] PyMol with MacOS 10.4

[<kon...@la...>]

Are there other people out there who compile their own PyMol on the  
Mac and who have succeeded with MacOS 10.4 (Tiger)?

After updating my Mac to Tiger, my PyMol installation doesn't work  
anymore:

~> pymol
Traceback (most recent call last):
   File "/usr/local/lib/pymol/modules/pymol/__init__.py", line 90, in ?
     import pymol
   File "/usr/local/lib/pymol/modules/pymol/__init__.py", line 306, in ?
     import _cmd
ImportError: Failure linking new module: /usr/local/lib/pymol/modules/ 
pymol/_cmd.so: Symbol not found: _gluCylinder
   Referenced from: /sw/lib/libglut.3.dylib
   Expected in: /usr/X11R6/lib/libGL.1.dylib


I guess that something has changed in Apple's OpenGL libraries. My  
first reaction was to reinstall PyMol from sources in the same way as  
before (i.e. using the Distutils installation method and Fink's  
installation of Python 2.3). This fails pretty quickly due to some  
problem with the GLUT headers:

In file included from layer0/os_gl.h:95,
                  from layer2/RepNonbondedSphere.c:19:
/sw/include/GL/glut.h:432: error: parse error before "layer"
/sw/include/GL/glut.h:432: warning: function declaration isn't a  
prototype
/sw/include/GL/glut.h:490: error: parse error before "GLfloat"
/sw/include/GL/glut.h:490: warning: function declaration isn't a  
prototype
...

This is perhaps not so surprising, because I didn't update Fink after  
updating to 10.4 - because that didn't work either. In fact, I am  
sufficiently fed up with the fragility of Fink that I would like to  
get rid of it entirely.

So I thought I should try to use MacPython 2.4.1 (my everyday Python  
on the Mac) and Apple's OpenGL and GLUT frameworks. That required a  
few patches to the PyMol sources (the includes need to be changed  
from GL/... to OpenGL/...) and a bit of tweaking setup.py plus some  
manual intervention (Distutils doesn't handle -framework parameters),  
but I got an error-free compile pretty quickly. I can then even start  
PyMol, but it messes up my screen to the point that I need to go to  
sleep mode and then restart to get the Finder redrawn. And I am not  
even sure that my approach is reasonable, given that with MacPython I  
also use Aqua-Tk, and thus no X11 at all. Window handling ought to be  
different then.

Does anyone have more ideas for getting this to work? I don't care  
which Python and which Tk I use, as long as I can add my own Python  
modules and get PyMol with NumPy support.

Konrad.

Re: [PyMOL] Query variable value

[Ezequiel H P. <za...@pa...>]

Olivier,

> But how do I find out specular's (or ANY variable's) value without 
> changing it?

I wrote a little extension called 'grepset' that does what you want and it 
is great for finding out about other settings.

It is available at the pymol wiki site:

	http://www.pymolwiki.org/index.php/Grepset

Cheers,
Zac

Re: [PyMOL] Query variable value

[Sebastien M. <seb...@ig...>]

> PyExperts:
>=20
> When inside PyMOL, how do I find out the value of a variable without=20
> using 'set'?
>=20
> For example, I can type:
>  set specular, 1
> and then I know, specular =3D 1.
>=20
> But how do I find out specular's (or ANY variable's) value without=20
> changing it?
>=20
> Thanks,
>=20
> Olivier

Hello Olivier,
For PyMOL variables, defined with
	set variable_name,variable_value
, you can get it with
	get variable_name


For other variables (Python variables), defined like it:
	variable_name=3Dvariable_value
you can get it with
	print variable_name
or use it simply with
	variable_name


I hope this will help you.

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

[PyMOL] Re: PyMOL-users digest, Vol 1 #1032 - 3 msgs

[tree <jav...@ut...>]

Oliver,

I know it'll sound crazy but -- "get".  :-)

For example,
 get two_sided_lighting
or
 get bg_rgb

I think this is covered on the Wiki somewhere, too.
(http://www.pymolwiki.org/)

HTH,

-- Jason

On Wed, 2005-10-19 at 20:24 -0700,
pym...@li... wrote:
> Message: 3
> Date: Wed, 19 Oct 2005 16:12:25 -0600
> From: Olivier Julien <oj...@rs...>
> To: PyM...@li...
> Subject: [PyMOL] Query variable value
> 
> PyExperts:
> 
> When inside PyMOL, how do I find out the value of a variable without 
> using 'set'?
> 
> For example, I can type:
>   set specular, 1
> and then I know, specular = 1.
> 
> But how do I find out specular's (or ANY variable's) value without 
> changing it?
> 
> Thanks,
> 
> Olivier
> 
> -- 
> Olivier Julien
> PhD prov student
> Dr Brian D. Sykes Lab
> Department of Biochemistry
> 4-19 Medical Sciences Building
> University of Alberta
> Edmonton (AB) Canada T6G 2H7
> (780) 492-3006
> Email: <oj...@ua...>
> Web: <http://pelican.rsvs.ulaval.ca/oli/olivier.html>
-- 
Jason Vertrees (jav...@ut...)
BSCB Graduate Student @ UTMB, Galveston
http://www.bscb.utmb.edu :: BSCB @ UTMB
http://best.utmb.edu :: B.E.S.T. @ UTMB
http://pymolwiki.org :: PyMol Wiki

RE: [PyMOL] edgelines between molecules

[Mark A S. <sa...@um...>]

Balaji:

I've done this by making a surface of just the domain I want to  
highlight, then bring it into Photoshop.  Select the background, then  
invert the selection.  Then convert selection to path and then stroke  
the path.

Here is an example:

[ Attachment only sent to Balaji, available on request ]

Layer 0 is a regular surface of the residues involved in a dimer  
interface.  Layer 1 is the stroked path.  Layer 2 is a surface with  
charge potential of the entire region.  Displaying Layer 1 and Layer  
2 gives the desired figure.

Have fun,
Mark


> Date: Wed, 19 Oct 2005 15:44:35 -0400
> From: Balaji Bhyravbhatla <bal...@um...>
> To:  pym...@li...
> Subject: [PyMOL] edgelines between molecules
>
> Hello All,
> I have a large mega-dalton multi chain structure that I would like to
> make an overview (surface) figure. Instead of using many colors  
> (13subunits)
> I would like to use one color and demarcate the subunits by some other
> means.One way would be to generate some sort of edge lines between the
> molecules. Is that possible, if so how?
>
> If anyone has any other suggestions please send them my way, it  
> would be
> highly appreciated.
>
> Thanks
>
>
> Balaji
>

_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

[PyMOL] Query variable value

[Olivier J. <oj...@rs...>]

PyExperts:

When inside PyMOL, how do I find out the value of a variable without 
using 'set'?

For example, I can type:
  set specular, 1
and then I know, specular = 1.

But how do I find out specular's (or ANY variable's) value without 
changing it?

Thanks,

Olivier

-- 
Olivier Julien
PhD prov student
Dr Brian D. Sykes Lab
Department of Biochemistry
4-19 Medical Sciences Building
University of Alberta
Edmonton (AB) Canada T6G 2H7
(780) 492-3006
Email: <oj...@ua...>
Web: <http://pelican.rsvs.ulaval.ca/oli/olivier.html>

RE: [PyMOL] Stereo

[Warren D. <wa...@de...>]

> Does this mean that until Apple release an OS / OpenGL driver=20
> upgrade, stereo is still not possible on OS X even with new hardware?

Not at all.  Currently shipping hardware http://www.apple.com/powermac
does stereo 3D in a window with currently shipping software
http://www.delsci.com/macpymol  -- I can personally confirm that!

However, the situation for existing G5 owners is less clear.
Ultimately, I expect Apple to make it possible for existing G5 PowerMac
users to upgrade their video card, update to the latest OS X, and then
be able to do stereo in a window too.  Nevertheless, we are still
waiting for confirmation on this ...

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Mark Mayer
> Sent: Wednesday, October 19, 2005 2:22 PM
> To: pym...@li...
> Subject: [PyMOL] Stereo
>=20
> Not sure I understand Warren's post:
>=20
> > Also, quad processors are nice, but for those of us with=20
> recent G5s is=20
> > all we need the new graphics card?
>=20
> I hope -- that along with an OS / OpenGL driver upgrade...
>=20
>=20
> Does this mean that until Apple release an OS / OpenGL driver=20
> upgrade, stereo is still not possible on OS X even with new hardware?
>=20
> Mark
>=20

[PyMOL] Stereo

[Mark M. <ma...@ma...>]

Not sure I understand Warren's post:

>  Also, quad processors are nice, but for those of us with
>  recent G5s is all we need the new graphics card?

I hope -- that along with an OS / OpenGL driver upgrade...

Does this mean that until Apple release an OS / OpenGL driver 
upgrade, stereo is still not possible on OS X even with new hardware?

Mark

[PyMOL] Stereo 3D Monitors & Equipment

[Warren D. <wa...@de...>]

Here is some current information for those of you ordering yourself a
new "Quad" Quadro-based Mac for doing Stereo 3D visualization.  You will
also need a good CRT, a stereo signal emitter, and shutter glasses. =20

Stereo 3D glasses & emitters:

- More expensive: StereoGraphics
<http://www.stereographics.com/products/crystaleyesworkstation/index.htm
l>

- Less expensive: NuVision3D
<http://www.nuvision3d.com/the60gx.html>

Thanks to LCD dominance, it is getting mucher harder to find a good CRT.
You may need to hunt around a bit and perhaps buy "pre-owned".

The critical monitor specifications for Stereo 3D are:

- Must be a CRT (not an LCD).
- Should be as big as you can afford (20-22").
- HD15 VGA input (DVI very rare).
- Vertical refresh must be at least 120 Hz.
- Horizontal sync frequency must be at least 130 kHz (ideally 140 kHz).

Note that the last point is CRITICAL.  Do not buy a CRT monitor for
stereo 3D until you have confired that it can do a horizontal sync of at
least 130 kHz.  Beware of consumer monitors have horizontal sync limits
of 80-120 kHz and thus cannot do stereo well.

Good stereo-capable CRT displays still available NEW:

- Philips 202P73=20
<http://www.cdw.com/shop/products/specs.aspx?EDC=3D812337>=20
<http://www.insight.com/site/product/detail/index.cfm?item_number=3D201B4=
5
74>

- Iiyama Vision Master Pro 514 / HM204DT
<http://www.cdw.com/shop/products/default.aspx?EDC=3D453522>

Good stereo-capable displays that are discontinued (buy USED on eBay,
etc.):

- IBM ThinkVision C220p (discontinued)
- HP p1230 CRT Monitor (P9613W) (discontinued)
- DELL p1230 (discontinued)
- Sony GDM-C520K (discontinued)
- NEC FP2141SB-BK (discontinued)
- NEC-Mitsubishi Diamond Pro 2070SB-BK (discontinued)
- Sun X7149A (discontinued)

Borderline displays:
=20
- ViewSonic, P225FB (H-sync: 127 kHz - good for 1280x960 @ ~110 Hz)
- Samsung SyncMaster 1100 DF (H-sync: 121 kHz)
- Sun X7149A (H-sync: 121 kHz)

Unsuitable displays:

- ViewSonic G220f/fb, G810, G90f/fb
- Philips 201B40, 201B45
- NEC Accusync 120
- Mitsubishi Diamond Pro 930SB
- Samsung SyncMaster 1000 P, 997DF/997MB=20

See: http://monitors.alege.net for info on tons of monitors, old & new.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20

[PyMOL] edgelines between molecules

[Balaji B. <bal...@um...>]

Hello All,
I have a large mega-dalton multi chain structure that I would like to
make an overview (surface) figure. Instead of using many colors (13subunits)
I would like to use one color and demarcate the subunits by some other
means.One way would be to generate some sort of edge lines between the
molecules. Is that possible, if so how?

If anyone has any other suggestions please send them my way, it would be
highly appreciated.

Thanks


Balaji

[PyMOL] CRT vs flat panel stereo on Mac question

[Mark M. <ma...@ma...>]

Warren

Exciting news.

Any thoughts on whether it will be possible to run stereo on a flat 
panel? At minimum seems like we can retire SGIs and use the CRT 
monitors?

Also, quad processors are nice, but for those of us with recent G5s 
is all we need the new graphics card?
-- 
Mark Mayer Ph.D.
LCMN NICHD NIH DHHS
Bldg 35, Room 3B 1002 MSC 3712
35 Lincoln Drive
Bethesda MD 20892 3712
Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
Lab web site: http://mayerlab.nichd.nih.gov

Send packages, Fedex and anything requiring a signature to:

Bldg 35, Room 3B 1004
35 Lincoln Drive
Bethesda MD 20892

Re: [PyMOL] PyMOL featured on Apple Store site?

[Michael G. L. <ml...@um...>]

On Wed, 19 Oct 2005, Sabuj Pattanayek wrote:

> nm, I found the url:
>
> http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/72303/wo/iG1ZdpmENibK2kKdLwyNuAAR9NW/0.SLID?nclm=PowerMac&mco=586014F6

That URL complains that the session has expired.

  - go to www.apple.com
  - click on the Store tab at the top
  - click on the big Power Mac G5 Quad image (top center)
  - scroll down a bit

Just the image:

http://store.apple.com/Catalog/US/Images/pm_infoblock_graphics.jpg

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

>
> D. Joe Anderson wrote:
>> So, that sure looks like PyMOL to me (actually, four instances
>> of it) running on the display of a PowerMac G5 on the
>> newly-updated Apple Store website today.
>>
>> My question is, which structure is that?
>>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>

RE: [PyMOL] PyMOL featured on Apple Store site?

[Warren D. <wa...@de...>]

They've got MacPyMOL two places on this site:

http://www.apple.com/powermac/graphics.html

Be sure to note the explicit mention of stereo 3D "in a window" down
near the bottom. =20

Amazing!  The "Stereo 3D Matters to Me" campaign actually worked. =20

Apple really *is* serious about meeting our needs. =20

Cheers,
Warren

PS. IL2 on top, hexameric insulin in the bottom right.

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Sabuj Pattanayek
> Sent: Wednesday, October 19, 2005 10:38 AM
> To: pym...@li...
> Subject: Re: [PyMOL] PyMOL featured on Apple Store site?
>=20
> Do you have the URL?
>=20
> D. Joe Anderson wrote:
> > So, that sure looks like PyMOL to me (actually, four=20
> instances of it)=20
> > running on the display of a PowerMac G5 on the newly-updated Apple=20
> > Store website today.
> >=20
> > My question is, which structure is that?
> >=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] PyMOL featured on Apple Store site?

[Sabuj P. <sab...@va...>]

nm, I found the url:

http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/72303/wo/iG1ZdpmENibK2kKdLwyNuAAR9NW/0.SLID?nclm=PowerMac&mco=586014F6

D. Joe Anderson wrote:
> So, that sure looks like PyMOL to me (actually, four instances
> of it) running on the display of a PowerMac G5 on the
> newly-updated Apple Store website today.
> 
> My question is, which structure is that?
> 

Re: [PyMOL] PyMOL featured on Apple Store site?

[Sabuj P. <sab...@va...>]

Do you have the URL?

D. Joe Anderson wrote:
> So, that sure looks like PyMOL to me (actually, four instances
> of it) running on the display of a PowerMac G5 on the
> newly-updated Apple Store website today.
> 
> My question is, which structure is that?
> 

[PyMOL] PyMOL featured on Apple Store site?

[D. J. A. <de...@ia...>]

So, that sure looks like PyMOL to me (actually, four instances
of it) running on the display of a PowerMac G5 on the
newly-updated Apple Store website today.

My question is, which structure is that?

-- 
D. Joe Anderson, Asst. Sci.    2252 Molecular Biology Bldg   
  Biochem, Biophys, & Mol Bio  Iowa State Univ, Ames, IA 50010
How to Report Bugs Effectively
        http://www.chiark.greenend.org.uk/~sgtatham/bugs.html

[PyMOL] Mac Stereo 3D: Breaking News

[Warren D. <wa...@de...>]

See "New Power Macs" on

http://www.macworld.com/news/2005/10/19/liveupdate/index.php

The first Quad-core Mac and the the first with a Quadro FX 4500 graphics
card!=20

Do you know what this implies?

Cheers,
Warren
--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20

Re: [PyMOL] Need testers for new MacPyMOL on Tiger

[<kh...@ce...>]

On Oct 14, 2005, at 17:50, Warren DeLano wrote:


> For cutting-edge Mac users, there is a new MacPyMOL for Tiger that
> integrates into a single window and links to the system Python instead
> of bringing its own copy (in part this is necessary preparation for
> Intel...).
>
> http://delsci.com/beta
>
> Please let me know how it works for you!
>

It works fine on the few quick tests that I did. It looks fine as =20
well, I much prefer the single window approach. Using the system =20
Python is also a step in the right direction... now... if it also =20
came with NumPy support compiled in... I might actually use it!

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: kh...@ce...
---------------------------------------------------------------------

Re: [PyMOL] Missing parts in cartoon mode

[<ran...@ic...>]

Well ill be d......! The .pse file you send me shows the loops just
fine. I=B4m still puzzled as to why PyMol 0.98 on win2000 fails to show
those loops but now I can just use your .pse file as a template and work
my way around it. Ill also try upgrading as Warren suggest. Anyways,
thanks a lot for the help, it is greatly appreciated!
=20
Cheers=20
kasper

<-----Original Message----->

 	  	 From: Joel Tyndall
Sent: 10/18/2005 10:17:30 PM
To: ran...@ic...
Subject: Re: [PyMOL] Missing parts in cartoon mode=20

Hi again,=20

Hmmm had a look and it looks fine to me. I'm assuming you're looking at=20
chain H. See if you can open this pse file which is displaying the=20
cartoon. The only strange thing is that there is no residue 218. sorry I
can't be of any more help. might be worth sending Warren/me a pse of the
problem?=20

See ya=20

J=20

PS thats a windows pse file and should work=20

ran...@ic... wrote:=20

> Hi Joel=20
> The two missing loops of the 1DAN structure when in cartoon mode are=20
> located to res. 183-189 and 220-220. I=B4m using a standard PC with=20
> Windows 2000.=20
> Any suggestions? A fellow collegue in my lab is having identical=20
> troubles but he=B4s also using a PC with win2000. Its quite =
frustrating=20
> because the rest of the structure looks great in PyMol!=20
>=20
> Cheers Kasper=20
> The two missing loops of the 1DAN structure when in cartoon mode are=20
> located to res. 183-189 and 220-220. I=B4m using a standard PC with=20
> Windows 2000.=20
> Any suggestions? A fellow collegue in my lab is having identical=20
> troubles but he=B4s also using a PC with win2000. Its quite =
frustrating=20
> because the rest of the structure looks great in PyMol!=20
>=20
> Cheers Kasper=20
>=20
>=20
> <-----Original Message----->=20
> *From: Joel Tyndall*=20
> Sent: 10/17/2005 12:07:00 AM=20
> To: ran...@ic...=20
> Subject: Re: [PyMOL] Missing parts in cartoon mode=20
>=20
> Hey Kasper,=20
>=20
> which loops can't you see (amino acid nos./chain/)? what OS are you on
> (OSX, PC, Linux?) I have had a look and it looks ok on windows=20
>=20
> Cheers=20
>=20
> J=20
>=20
> ran...@ic... wrote:=20
>=20
> > Hi everybody=20
> > I am getting quite desperate! For some strange reason PyMol do not=20
> > display certain areas (several loops) of my .pdb file (1DAN) when in
> > cartoon display mode. When I display the structure in "lines" or=20
> > "sticks" everything is ok. Other pdb-viewers dont have this problem=20
> > with the same .pdb file. I have tried several things:=20
> > 1. Upgraded to the newest version og PyMol.=20
> > 2. Redefined secondary structure using the "alter" command.=20
> > 3. Imported the .pdb file into SwissViewer, saved as the imported=20
> > structure as a .pdb file, and then imported into PyMOl.=20
> >=20
> > None of these things have solved the problem. Help please! (I would=20
> > hate to have to start using another pdb-viewer!!) Cheers Kasper=20
> >=20
> > _______________________________________________________________=20
> > ICQ - You get the message, anywhere!=20
> > Get it @ http://www.icq.com=20
> >=20
> >=20
> >=20
>=20
> --=20
> Joel Tyndall, PhD=20
>=20
> Lecturer=20
> National School of Pharmacy=20
> University of Otago=20
> PO Box 913 Dunedin=20
> NNew Zealand=20
>=20
> Pukenga=20
> Te Kura Taiwhanga Putaiao=20
> Te Whare Wananga o Otago=20
> Pouaka Poutapeta 913 Otepoti=20
> Aotearoa=20
>=20
> Ph / Waea +64 3 4797293=20
> Fax / Waeawhakaahua +64 3 4797034=20
>=20
>=20
> .=20
>=20
> _______________________________________________________________=20
> ICQ - You get the message, anywhere!=20
> Get it @ http://www.icq.com=20
>=20
>=20
>=20

--=20
Joel Tyndall, PhD=20

Lecturer=20
National School of Pharmacy=20
University of Otago=20
PO Box 913 Dunedin=20
New Zealand=20

Pukenga=20
Te Kura Taiwhanga Putaiao=20
Te Whare Wananga o Otago=20
Pouaka Poutapeta 913 Otepoti=20
Aotearoa=20

Ph / Waea +64 3 4797293=20
Fax / Waeawhakaahua +64 3 4797034=20


=09


<P><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">_______________________________________________________________<BR><font face="Arial, Helvetica, sans-serif" size="2" style="font-size:13.5px">ICQ - You get the message, anywhere!<br>Get it @ <a href="http://www.icq.com" target=new>http://www.icq.com</a></font><br><br>&nbsp;</font></font>

Re: [PyMOL] How to raw_input() from windows Pymol?

[evangelos p. <eva...@db...>]

Warren,
Thank you for the prompt answer. Defining the function/script as you 
said in a way that I pass arguments through the calling command should 
work. Although there could be other nicer ways.
I intend to use it in order to input a filename with constrain data that 
the user wants to open. I work with NMR structures and I have writen a 
Pymol script that can take the NMR constrains and display them atop the 
NMR structure or ensemble.  You can see an example in this snapshot:
http://www.biophys.su.se/~evangelo/mDpl/cnstr3.gif
It can work for CNS format or Cyana/Dyana upl. I inted to share it 
either from this email list or deposit it in pymol wiki. I have a 
slightly working version already but the user has to correct the 
filename from within the script file which is rather clumpsy.

I would like to point out also to this script from Pymol wiki:

http://www.pymolwiki.org/index.php/Key_Wait

It is suposed to call a raw_input() from pymol and even get an input. 
But I never made it work and had some errors like:

PyMOL>spawn spawn_demo.py, local
Exception in thread Thread-5:
Traceback (most recent call last):
  File "E:\Program Files\DeLano Scientific\PyMOL\py23\lib\threading.py", 
line 436, in __bootstrap
    self.run()
  File "E:\Program Files\DeLano Scientific\PyMOL\py23\lib\threading.py", 
line 416, in run
    self.__target(*self.__args, **self.__kwargs)
  File "spawn_demo.py", line 2
     within pymol
                ^
 SyntaxError: invalid syntax

How should this key_wait script be used?

Thanks again for the help. Are there any  further beter suggestions? I 
am comming soon hopefully back on it with the script
./Evangelos

Re: [PyMOL] Re:

[Jules J. <jo...@he...>]

Kostas,

This command:
dist name, sel1, sel2, mode=3D2

doesn't work because the move value should be a whole number ie. 1,2,3 etc.

Also unless you have some objects actually called sel1 and sel2 you 
won't get anything meaningful back.

something like this:

dist name, resn lys, resn glu, mode=2

will give you a new object called name, which shows the distances 
between all lysine and glutamate N-O atoms within approxmately 3.5 
Angstroms.

Is this clearer?

Jules


Kostas Tripsianes wrote:
> On Tuesday 18 October 2005 16:36, pym...@li... 
> wrote:
> Hi Warren
> It's been a long time since my last post. Anyway I tried the polar contacts 
> identifier as written below
> 
>>dist name, sel1, sel2, mode=3D2
> 
> and I get the following error
> Traceback (most recent call last):
>   File "/home/kostas/pymol/modules/pymol/parser.py", line 191, in parse
>     result=apply(kw[nest][0],args[nest],kw_args[nest])
>   File "/home/kostas/pymol/modules/pymol/querying.py", line 400, in distance
>     str(selection2),int(mode),float(cutoff),
> ValueError: invalid literal for int(): 3D2
> using the last version  pymol-0_99beta20
> Any clue
> Another important notion regarded the 0.99 versions and on is that incorrectly 
> draw bonds between methyl protons. As you understand I work with NMR 
> structures but I don't have this misinterpretation with previous versions. 
> The same appeared with 13 and 20 releases. Please keep it in mind.
> 
> cheers kostas
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

RE: [PyMOL] Missing parts in cartoon mode

[Warren D. <wa...@de...>]

Kasper,

Those regions show up fine with the latest beta versions (e.g. beta19 =
tested), so please upgrade.

http://delsci.com/beta=20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> ran...@ic...
> Sent: Tuesday, October 18, 2005 8:39 AM
> To: pym...@li...
> Subject: Re: [PyMOL] Missing parts in cartoon mode
>=20
> The two missing loops of the 1DAN structure when in cartoon=20
> mode are located to res. 183-189 and 220-220. I=B4m using a=20
> standard PC with Windows 2000.
>=20
> Any suggestions? A fellow collegue in my lab is having=20
> identical troubles but he=B4s also using a PC with win2000. Its=20
> quite frustrating because the rest of the structure looks=20
> great in PyMol!
>=20
> =20
>=20
> Cheers Kasper
>=20
> =20
>=20
>=20
>=20
> <-----Original Message----->
>=20
>  	  	 From: Joel Tyndall
> Sent: 10/17/2005 12:07:00 AM
> To: ran...@ic...
> Subject: Re: [PyMOL] Missing parts in cartoon mode=20
>=20
> Hey Kasper,=20
>=20
> which loops can't you see (amino acid nos./chain/)? what OS=20
> are you on (OSX, PC, Linux?) I have had a look and it looks=20
> ok on windows=20
>=20
> Cheers=20
>=20
> J=20
>=20
> ran...@ic... wrote:=20
>=20
> > Hi everybody
> > I am getting quite desperate! For some strange reason PyMol do not=20
> > display certain areas (several loops) of my .pdb file=20
> (1DAN) when in=20
> > cartoon display mode. When I display the structure in "lines" or=20
> > "sticks" everything is ok. Other pdb-viewers dont have this problem=20
> > with the same .pdb file. I have tried several things:
> > 1. Upgraded to the newest version og PyMol.=20
> > 2. Redefined secondary structure using the "alter" command.=20
> > 3. Imported the .pdb file into SwissViewer, saved as the imported=20
> > structure as a .pdb file, and then imported into PyMOl.
> >=20
> > None of these things have solved the problem. Help please! (I would=20
> > hate to have to start using another pdb-viewer!!) Cheers Kasper
> >=20
> > _______________________________________________________________
> > ICQ - You get the message, anywhere!=20
> > Get it @ http://www.icq.com
> >=20
> >=20
> >=20
>=20
> --
> Joel Tyndall, PhD=20
>=20
> Lecturer
> National School of Pharmacy
> University of Otago
> PO Box 913 Dunedin
> New Zealand=20
>=20
> Pukenga
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 913 Otepoti
> Aotearoa=20
>=20
> Ph / Waea +64 3 4797293
> Fax / Waeawhakaahua +64 3 4797034=20
>=20
>=20
> .=20
> =09
>=20
> _______________________________________________________________
> ICQ - You get the message, anywhere!
> Get it @ http://www.icq.com
>=20
> =20
>=20

[PyMOL] macpymol beta

[Dan W. <da...@ch...>]

Hi,

just downloaded the new single window macpymol beta,
runs fine on imacG4

looks very nice, with the handle to minimise the tool bar and command =20=

line etc.

just noticed the
find polar contacts
feature, very handy!

cheers

Dan



Dr. Daniel James White BSc. (Hons.) PhD
Bioimaging Coordinator
Nanoscience Centre and Department of Biological and Environmental =20
Sciences
Division of Molecular Recognition
Ambiotica C242
PO Box 35
University of Jyv=E4skyl=E4
Jyv=E4skyl=E4
FIN 40014
Finland

+358 14 260 4183 (work)
+358 468102840 (mobile)
http://www.bioimagexd.org
http://www.chalkie.org.uk
da...@ch...
wh...@cc...