pymol-users Mailing List for PyMOL Molecular Graphics System

Hello All.

Having a electrostatic potentials map loaded in PyMOL
(an apbs map), does somebody know if there is a way to
get the potential associated with a given point in
space (i.e. to give a set of 3 spatial coordinates and
get the value for the potential at that point)?

Thanks in advance,

Raul

__________________________________________________
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Alan,

Okay, I found the glitch with the OSX defines -- my bad.

However, I also rediscovered what the hidden difficultly is with compiling
PyMOL under X11, and that is: Mac OS X's built-in python has an Aqua-based
Tcl/Tk/Tkinter implementation NOT bound to X11 and which does not work with
PyMOL due to conflicts in the threading and event model.  

So to compile PyMOL for X11 on Mac OS X, one needs a separate
Python/Tcl/Tk/Tkinter instance that has been built for X11.  Where you do
get that?  Fink.  

So the bottom line message is: Open-source PyMOL for X11 under Mac OS X must
be compiled under the Fink environment, not straight Mac OS X.  We need to
fix the default setup.py to reflect this fact.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of DeLano Scientific
> Sent: Wednesday, June 27, 2007 7:59 AM
> To: 'Alan'; 'Pymol'
> Subject: Re: [PyMOL] compiling pymol on Mac intel
> 
> Alan,
> 
> Hmm...the Darwin "setup.py" build is definitely broken...I'll 
> need to look into why -- it shouldn't be trying to link to 
> any MacPyMOL symbols (MacPyMOL is beyond the scope of the 
> open-source project).  
> 
> In the meantime, you can probably try an in-place 
> autotools-based compile instead.
> 
> ./configure
> make
> make install
> 
> Note that "make install" just installs into the current 
> source directory.
> 
> As for the Fink build, that looks like an X11 / OpenGL / GLX 
> problem on your system.  Does the precompiled X11 build work? 
> 
> Cheers,
> Warren
> 
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de...
>  
> "Not yet a PyMOL Subscriber, but want to support the project? 
>  Email sa...@de... to quote your lab, school, or 
> employer.  Thank you for sponsoring this open-source endeavor!" -WLD
>  
> 
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of Alan
> > Sent: Wednesday, June 27, 2007 4:46 AM
> > To: Pymol
> > Subject: [PyMOL] compiling pymol on Mac intel
> > 
> > Hi List!
> > 
> > I am trying to compile pymol via 2 ways on my Macbook pro Intel:
> > 
> > 1) Via fink:
> > fink install pymol-py24
> > (installs version 0.99-1005)
> > 
> > All seems to be ok, but when running
> > /sw/lib/pymol-py24/bin/pymol, I got this:
> > X Error of failed request:  BadAlloc (insufficient resources for 
> > operation)
> >   Major opcode of failed request:  150 (GLX)
> >   Minor opcode of failed request:  3 (X_GLXCreateContext)
> >   Serial number of failed request:  19
> >   Current serial number in output stream:  20
> >  PyMOL: abrupt program termination.
> > 
> > 2) Via SVN Pymol 1.0
> > python setup.py build
> > 
> > Failed with:
> > 
> > [...]
> > gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp 
> > -mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes 
> > -D_PYMOL_MODULE -D_PYMOL_OSX -Iov/src -Ilayer0 -Ilayer1 -Ilayer2
> > -Ilayer3 -Ilayer4 -Ilayer5
> > -I/System/Library/Frameworks/OpenGL.framework/Headers
> > -I/System/Library/Frameworks/GLUT.framework/Headers
> > -I/System/Library/Frameworks/CoreFoundation.framework/Headers
> > -I/System/Library/Frameworks/AppKit.framework/Headers
> > -I/System/Library/Frameworks/ApplicationServices.framework/Headers
> > -I/System/Library/Frameworks/Cocoa.framework/Headers
> > -I/System/Library/Frameworks/IOKit.framework/Headers
> > -I/sw/include/python2.4 -c layer5/main.c -o 
> > build/temp.darwin-8.10.1-i386-2.4/layer5/main.o
> > In file included from layer0/os_gl.h:44,
> >                  from layer5/main.c:27:
> > /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:269:
> > warning: function declaration isn't a prototype
> > /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:281:
> > warning: function declaration isn't a prototype
> > /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:290:
> > warning: function declaration isn't a prototype
> > layer5/main.c: In function 'launch':
> > layer5/main.c:1484: error: 'MacPyMOLOption' undeclared 
> (first use in 
> > this function)
> > layer5/main.c:1484: error: (Each undeclared identifier is reported 
> > only once
> > layer5/main.c:1484: error: for each function it appears in.)
> > layer5/main.c:1485: error: 'MacPyMOLReady' undeclared (first use in 
> > this function)
> > error: command 'gcc' failed with exit status 1
> > 
> > I am using:
> > ri  python24       2.4.3-1001     Interpreted, 
> > object-oriented language
> > ii  python24-shlib 2.4.3-1001     Interpreted, 
> > object-oriented language
> > 
> > ii  freeglut       2.4.0-1        Opengl utility toolkit
> > ii  freeglut-shlib 2.4.0-1        Opengl utility toolkit
> > ii  glut-shlibs    3.7-1025       Opengl utility toolkit
> > 
> > ii  libpng3        1.2.18-1       PNG image format handling library
> > ii  libpng3-shlibs 1.2.18-1       Shared libraries for 
> libpng3 package
> > 
> > ii  tcltk          8.4.13-3       Tool Command Language and 
> > the Tk toolkit
> > ii  tcltk-dev      8.4.13-3       Tool Command Language and 
> > the Tk toolkit
> > ii  tcltk-shlibs   8.4.13-3       Tool Command Language and 
> > the Tk toolkit
> > 
> > ii  freetype2      2.1.4-12       TrueType font rendering 
> > library, (dummy)
> > ii  freetype219    2.2.1-4        TrueType font rendering 
> > library, headers
> > ii  freetype219-sh 2.2.1-4        TrueType font rendering 
> > library, shared libs
> > 
> > And MacOSX OpenGL.
> > 
> > I also tried with python 2.4.3 OSX Framework version, same error.
> > 
> > My guess is it's trying to install MacPymol, but I don't 
> know if I am 
> > even allowed (although I use pymol only visualisation and 
> have several 
> > scripts written for it). Otherwise, how to tell setup to 
> install pymol 
> > for X11? If I can use MacPymol (and compile it), that's would be 
> > great.
> > 
> > So, any hint here would be very appreciated.
> > 
> > Many thanks in advance.
> > Cheers,
> > Alan
> > --
> > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate 
> Department of 
> > Biochemistry, University of Cambridge.
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >>http://www.bio.cam.ac.uk/~awd28<<
> > 
> > --------------------------------------------------------------
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> 
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Alan,

Hmm...the Darwin "setup.py" build is definitely broken...I'll need to look
into why -- it shouldn't be trying to link to any MacPyMOL symbols (MacPyMOL
is beyond the scope of the open-source project).  

In the meantime, you can probably try an in-place autotools-based compile
instead.

./configure
make
make install

Note that "make install" just installs into the current source directory.

As for the Fink build, that looks like an X11 / OpenGL / GLX problem on your
system.  Does the precompiled X11 build work? 

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of Alan
> Sent: Wednesday, June 27, 2007 4:46 AM
> To: Pymol
> Subject: [PyMOL] compiling pymol on Mac intel
> 
> Hi List!
> 
> I am trying to compile pymol via 2 ways on my Macbook pro Intel:
> 
> 1) Via fink:
> fink install pymol-py24
> (installs version 0.99-1005)
> 
> All seems to be ok, but when running 
> /sw/lib/pymol-py24/bin/pymol, I got this:
> X Error of failed request:  BadAlloc (insufficient resources 
> for operation)
>   Major opcode of failed request:  150 (GLX)
>   Minor opcode of failed request:  3 (X_GLXCreateContext)
>   Serial number of failed request:  19
>   Current serial number in output stream:  20
>  PyMOL: abrupt program termination.
> 
> 2) Via SVN Pymol 1.0
> python setup.py build
> 
> Failed with:
> 
> [...]
> gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp 
> -mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes 
> -D_PYMOL_MODULE -D_PYMOL_OSX -Iov/src -Ilayer0 -Ilayer1 -Ilayer2
> -Ilayer3 -Ilayer4 -Ilayer5
> -I/System/Library/Frameworks/OpenGL.framework/Headers
> -I/System/Library/Frameworks/GLUT.framework/Headers
> -I/System/Library/Frameworks/CoreFoundation.framework/Headers
> -I/System/Library/Frameworks/AppKit.framework/Headers
> -I/System/Library/Frameworks/ApplicationServices.framework/Headers
> -I/System/Library/Frameworks/Cocoa.framework/Headers
> -I/System/Library/Frameworks/IOKit.framework/Headers
> -I/sw/include/python2.4 -c layer5/main.c -o 
> build/temp.darwin-8.10.1-i386-2.4/layer5/main.o
> In file included from layer0/os_gl.h:44,
>                  from layer5/main.c:27:
> /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:269:
> warning: function declaration isn't a prototype
> /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:281:
> warning: function declaration isn't a prototype
> /System/Library/Frameworks/OpenGL.framework/Headers/glu.h:290:
> warning: function declaration isn't a prototype
> layer5/main.c: In function 'launch':
> layer5/main.c:1484: error: 'MacPyMOLOption' undeclared (first 
> use in this function)
> layer5/main.c:1484: error: (Each undeclared identifier is 
> reported only once
> layer5/main.c:1484: error: for each function it appears in.)
> layer5/main.c:1485: error: 'MacPyMOLReady' undeclared (first 
> use in this function)
> error: command 'gcc' failed with exit status 1
> 
> I am using:
> ri  python24       2.4.3-1001     Interpreted, 
> object-oriented language
> ii  python24-shlib 2.4.3-1001     Interpreted, 
> object-oriented language
> 
> ii  freeglut       2.4.0-1        Opengl utility toolkit
> ii  freeglut-shlib 2.4.0-1        Opengl utility toolkit
> ii  glut-shlibs    3.7-1025       Opengl utility toolkit
> 
> ii  libpng3        1.2.18-1       PNG image format handling library
> ii  libpng3-shlibs 1.2.18-1       Shared libraries for libpng3 package
> 
> ii  tcltk          8.4.13-3       Tool Command Language and 
> the Tk toolkit
> ii  tcltk-dev      8.4.13-3       Tool Command Language and 
> the Tk toolkit
> ii  tcltk-shlibs   8.4.13-3       Tool Command Language and 
> the Tk toolkit
> 
> ii  freetype2      2.1.4-12       TrueType font rendering 
> library, (dummy)
> ii  freetype219    2.2.1-4        TrueType font rendering 
> library, headers
> ii  freetype219-sh 2.2.1-4        TrueType font rendering 
> library, shared libs
> 
> And MacOSX OpenGL.
> 
> I also tried with python 2.4.3 OSX Framework version, same error.
> 
> My guess is it's trying to install MacPymol, but I don't know 
> if I am even allowed (although I use pymol only visualisation 
> and have several scripts written for it). Otherwise, how to 
> tell setup to install pymol for X11? If I can use MacPymol 
> (and compile it), that's would be great.
> 
> So, any hint here would be very appreciated.
> 
> Many thanks in advance.
> Cheers,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate 
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Tsjerk,

Sometimes the archives can be misleading...

Actually, settings do now work on selections and bonds as well (with
set_bond).  However, only a small set of per-atom and per-bond settings are
currently implemented, since each can require a significant amount of new
code.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Tsjerk Wassenaar
> Sent: Tuesday, June 26, 2007 9:26 PM
> To: Dr. Mark Mayer
> Cc: pym...@li...
> Subject: Re: [PyMOL] Sticks and distances with individual 
> transparencies
> 
> Hi Mark,
> 
> You could've found this one in the archives of this list. 
> Settings work on objects, not on selections. The solution is 
> to make an object for the solid sticks and one for the 
> transparent sticks, using create.
> 
> Cheers,
> 
> Tsjerk
> 
> On 6/26/07, Dr. Mark Mayer <ma...@ma...> wrote:
> >
> >
> > Dear All,
> >
> >
> > I'm trying to write a Pymol script with which produces a mixture of 
> > both solid and transparent sticks I'm using the current 1.0 
> incentive 
> > release of MacPymol. After drawing all my sticks I issue following 
> > commands, but nothing changes although the log output suggests the 
> > change is being set.
> >
> >
> > PyMOL>set stick_transparency=0.2, /sca//A/228  and !mc
> >  Setting: stick_transparency set for 5 atoms in object "mol1".
> >
> >  I'd also like to draw selected H-bonds with control of 
> transparency 
> > with the rest solid, but have no idea how to do this.
> >
> >
> > --
> > 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
> >
> > 
> ----------------------------------------------------------------------
> > --- This SF.net email is sponsored by DB2 Express Download 
> DB2 Express 
> > C - the FREE version of DB2 express and take control of 
> your XML. No 
> > limits. Just data. Click to get it now.
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> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> 
> 
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express Download DB2 
> Express C - the FREE version of DB2 express and take control 
> of your XML. No limits. Just data. Click to get it now.
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

* Andreas Henschel <ah...@bi...> [2007-06-27 15:49] wrote:
> Hi Julio,
> 
> If I understood you right, you can simply use translate, eg.:
> translate [20,0,0], mol_to_dislocate
> 
> The important thing is that "turn" and "move" modify the camera, while 
> translate and rotate modify the coordinates.
> 
> Cheers,
> Andreas
> 
> 
> Júlio César wrote:
> > Hi,
> >
> > I have loaded two structure and tried to dislocate one independent on the
> > other, but I couldn't. Is it possible to do thit?
> > I would like to know how to dislocate independently each structure when you
> > have loaded two structures?
> >

Or you can put the mouse in editing mode (click in the bottom corner of
the main graphics window where the mouse functions are described) and
you'll now see that "Shift middle-button" is labelled "MovO" and "Shift
left-button" is labelled "RotO". So you can use "Shift middle-button"
to translate one object and "Shift left-button" to rotate one object
relative to the other. You just have to be careful that you pick your
atom carefully if the two objects are superimposed.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Am Mittwoch, 27. Juni 2007 schrieb Robert Campbell:

Hey Robert,

> You are welcome to modify it to add new features, of course. You can
> find it at:
>
>    http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/color_b.py

I found it this morning via google and the pictures are now really great. If i 
need it more often, i consider adding a simple gui with sliders. I'll tell 
you if I did so.

Thanks for the script

Cheers
	Martin

Hi Julio,

If I understood you right, you can simply use translate, eg.:
translate [20,0,0], mol_to_dislocate

The important thing is that "turn" and "move" modify the camera, while 
translate and rotate modify the coordinates.

Cheers,
Andreas


Júlio César wrote:
> Hi,
>
> I have loaded two structure and tried to dislocate one independent on the
> other, but I couldn't. Is it possible to do thit?
> I would like to know how to dislocate independently each structure when you
> have loaded two structures?
>
> Thanks,
>
> Julio Cesar da Silva
> ----------------------
> SAXS / Studies of protein Structure using SAXS
> Brazilian Synchrotron Light Laboratory
> Brazil
> Phone: +55 19 3512-1115
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>   

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...

Hi,

I have loaded two structure and tried to dislocate one independent on the
other, but I couldn't. Is it possible to do thit?
I would like to know how to dislocate independently each structure when you
have loaded two structures?

Thanks,

Julio Cesar da Silva
----------------------
SAXS / Studies of protein Structure using SAXS
Brazilian Synchrotron Light Laboratory
Brazil
Phone: +55 19 3512-1115

* Martin Höfling <mar...@gm...> [2007-06-27 01:33] wrote:
> Am Dienstag, 26. Juni 2007 schrieb Eva Vanamee:
> > Hi,
> >
> > I'd like to color a molecule based on its sequence similarity to another
> > molecule.
> > Can this be done in Pymol?
> 
> If you can quantify "similarity" in a number you can write it into the 
> b-factors of the atoms and then color it by them.

I have a script:

  http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/variability.py

that takes a FASTA or Clustal format sequence alignment and calculates
the variability of the sequence at each position by:

   variability = (# different a.a.) / (frequency of the most common a.a)

The output can be either the complete set of information (a set of
columns of data showing each sequence, the number of different a.a, the
number of the most common a.a., the frequency of the most common a.a and
finally the variability) or a simple file that can be imported into
PyMOL via my data2bfactor.py script to change the B-factor into the
variability. Then one can color on that property.

The variability.py script depends on having biopython installed and it
calls my seq_convert.py script as well. See:

  http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/seq_convert.py

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hi Martin,

* Martin Höfling <mar...@ph...> [2007-06-26 15:15] wrote:
> Hi there,
> 
> i am trying to map b factors on a surface representation. 
> 
> I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there a 
> way to fine tune the color spectrum, such as with the "Midpoint" and "Offset" 
> sliders in vmd?

My color_b.py script has some controls, although I'm not sure it will
do quite what you want. It has a number of different gradients built
in, plus you can adjust the overall saturation or value (brightness).
Like the spectrum command you can set the minimum and maximum values
to use, which can help to adjust the midpoint. It also has two modes,
histogram, in which the spacing of B-values (or other values) is equal
or "ramp", in which the number of atoms in each bin is kept constant,
but the widths of the bins vary.

You are welcome to modify it to add new features, of course. You can
find it at:

   http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/color_b.py


Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hi List!

I am trying to compile pymol via 2 ways on my Macbook pro Intel:

1) Via fink:
fink install pymol-py24
(installs version 0.99-1005)

All seems to be ok, but when running /sw/lib/pymol-py24/bin/pymol, I got this:
X Error of failed request:  BadAlloc (insufficient resources for operation)
  Major opcode of failed request:  150 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Serial number of failed request:  19
  Current serial number in output stream:  20
 PyMOL: abrupt program termination.

2) Via SVN Pymol 1.0
python setup.py build

Failed with:

[...]
gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp
-mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes
-D_PYMOL_MODULE -D_PYMOL_OSX -Iov/src -Ilayer0 -Ilayer1 -Ilayer2
-Ilayer3 -Ilayer4 -Ilayer5
-I/System/Library/Frameworks/OpenGL.framework/Headers
-I/System/Library/Frameworks/GLUT.framework/Headers
-I/System/Library/Frameworks/CoreFoundation.framework/Headers
-I/System/Library/Frameworks/AppKit.framework/Headers
-I/System/Library/Frameworks/ApplicationServices.framework/Headers
-I/System/Library/Frameworks/Cocoa.framework/Headers
-I/System/Library/Frameworks/IOKit.framework/Headers
-I/sw/include/python2.4 -c layer5/main.c -o
build/temp.darwin-8.10.1-i386-2.4/layer5/main.o
In file included from layer0/os_gl.h:44,
                 from layer5/main.c:27:
/System/Library/Frameworks/OpenGL.framework/Headers/glu.h:269:
warning: function declaration isn't a prototype
/System/Library/Frameworks/OpenGL.framework/Headers/glu.h:281:
warning: function declaration isn't a prototype
/System/Library/Frameworks/OpenGL.framework/Headers/glu.h:290:
warning: function declaration isn't a prototype
layer5/main.c: In function 'launch':
layer5/main.c:1484: error: 'MacPyMOLOption' undeclared (first use in
this function)
layer5/main.c:1484: error: (Each undeclared identifier is reported only once
layer5/main.c:1484: error: for each function it appears in.)
layer5/main.c:1485: error: 'MacPyMOLReady' undeclared (first use in
this function)
error: command 'gcc' failed with exit status 1

I am using:
ri  python24       2.4.3-1001     Interpreted, object-oriented language
ii  python24-shlib 2.4.3-1001     Interpreted, object-oriented language

ii  freeglut       2.4.0-1        Opengl utility toolkit
ii  freeglut-shlib 2.4.0-1        Opengl utility toolkit
ii  glut-shlibs    3.7-1025       Opengl utility toolkit

ii  libpng3        1.2.18-1       PNG image format handling library
ii  libpng3-shlibs 1.2.18-1       Shared libraries for libpng3 package

ii  tcltk          8.4.13-3       Tool Command Language and the Tk toolkit
ii  tcltk-dev      8.4.13-3       Tool Command Language and the Tk toolkit
ii  tcltk-shlibs   8.4.13-3       Tool Command Language and the Tk toolkit

ii  freetype2      2.1.4-12       TrueType font rendering library, (dummy)
ii  freetype219    2.2.1-4        TrueType font rendering library, headers
ii  freetype219-sh 2.2.1-4        TrueType font rendering library, shared libs

And MacOSX OpenGL.

I also tried with python 2.4.3 OSX Framework version, same error.

My guess is it's trying to install MacPymol, but I don't know if I am
even allowed (although I use pymol only visualisation and have several
scripts written for it). Otherwise, how to tell setup to install pymol
for X11? If I can use MacPymol (and compile it), that's would be
great.

So, any hint here would be very appreciated.

Many thanks in advance.
Cheers,
Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

Hi Mark,

You could've found this one in the archives of this list. Settings
work on objects, not on selections. The solution is to make an object
for the solid sticks and one for the transparent sticks, using create.

Cheers,

Tsjerk

On 6/26/07, Dr. Mark Mayer <ma...@ma...> wrote:
>
>
> Dear All,
>
>
> I'm trying to write a Pymol script with which produces a mixture of both
> solid and transparent sticks
> I'm using the current 1.0 incentive release of MacPymol. After drawing all
> my sticks I issue following commands, but nothing changes although the log
> output suggests the change is being set.
>
>
> PyMOL>set stick_transparency=0.2, /sca//A/228  and !mc
>  Setting: stick_transparency set for 5 atoms in object "mol1".
>
>  I'd also like to draw selected H-bonds with control of transparency
> with the rest solid, but have no idea how to do this.
>
>
> --
> 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
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Greetings!

As some of you have noticed, PyMOL 1.0 is out (at last!).  Though it lacks
many of the features and enhancements I had hoped to deliver in the big
"1.0", we were long overdue for a major release and so the line was drawn.
 
For those of you new to PyMOL within the past year or so, our software
releases are a relatively low-key event:  The last thing we want is for
everyone to race out and download the latest version, suddenly to discover
some horrendous bug right in the middle of orals or a critical corporate
presentation.  No, no, not that! 

Instead, we ask people to gradually ease into new versions at a safe time &
place, while reporting any problems that come up so that we can quickly fix
the source and builds before too many other folks encounter them.  In terms
of features, PyMOL 1.0 is not a huge leap beyond the latest 1.0 beta builds,
but there were some last minute tweaks, so please do use caution.

So far, so good: the 1.0r0 builds appear stable, and current sponsors can
download builds from <." rel="nofollow">http://delsci.com/ip>.  Non-sponsors are welcome to
pull & compile the open-source code from the Subversion repository hosted at
SourceForge <http://pymol.sf.net>.  Free educational-use-only builds of
PyMOL 1.0 will be released in early August, before the start of the fall
semester.

The other big announcement is the opening of our official documentation
site, which has also been in the works for over a year.  As opposed to the
PyMOL Community Wiki, this read-only resource at <" rel="nofollow">http://delsci.info/dsc> is
something you need a paid subscription to access, and it also involves a
somewhat tedious email-based registration & login process.  I apologize in
advance for that inconvenience.  

However, if your company or institution maintains an entity-wide PyMOL
subscription, then we can simply reverse-DNS through your whole domain so
that you and all your colleagues can access documentation without logging
in, much the same way transparent entity-wide access is granted for
scientific journals. 

By the way, if you are thinking of sponsoring the effort or of renewing an
existing subscription, please do look into whether we might all save time &
effort by going entity-wide.  Processing of individual and/or laboratory
subscriptions takes precious time & resources away from development and
documentation relative to broader subscriptions.  Plus, in addition to
saving paperwork, entity-wide subscriptions can potentially benefit a much
larger base of users at a much lower per-user cost.

So a hearty "thank you" to everyone who has made PyMOL possible over the
past 7 years, whether at the individual, laboratory, departmental,
corporate, or institutional level.  Although I do not have permission to
name most PyMOL sponsors, they include many top universities, research
institutes, pharmaceutical companies, and biotech giants, as well as a wide
assortment of startup companies, laboratories, and individuals.  Thanks also
to the contributors of various open-source components and capabilities!
Together we are all working together to ensure that PyMOL continues to
thrive under terms that remain compatible with the open-source code.

Enjoy!

Cheers,
Warren L. DeLano, Ph.D.
DeLano Scientific LLC

Sponsorship info at http://pymol.org/funding.html

Martin,

Unfortunately not -- you would need to use a PyMOL command script or =
Python
program to achieve finer control over coloring.  However, you can set =
the
minimum and maximum values by passing those as arguments to "spectrum".

Cheers,
Warren

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Martin H=F6fling
> Sent: Tuesday, June 26, 2007 6:15 AM
> To: pym...@li...
> Subject: [PyMOL] spectral coloring
>=20
> Hi there,
>=20
> i am trying to map b factors on a surface representation.=20
>=20
> I am using spectrum b,blue_white_red,mymol and the colors are=20
> fine. Is there a way to fine tune the color spectrum, such as=20
> with the "Midpoint" and "Offset"=20
> sliders in vmd?
>=20
> Best
> 	Martin
>=20
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express Download DB2=20
> Express C - the FREE version of DB2 express and take control=20
> of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Mark,
 
Your confusion arises from the new "set_bond" command, which must be used
when setting bond-specific properties.  Please see the official docs on
"set_bond".
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Dr. Mark
Mayer
Sent: Tuesday, June 26, 2007 10:18 AM
To: pym...@li...
Subject: [PyMOL] Sticks and distances with individual transparencies -
repost


Apologies for prior post message font was nearly unreadable


Dear All,


I'm trying to write a Pymol script with which produces a mixture of both
solid and transparent sticks
I'm using the current 1.0 incentive release of MacPymol. After drawing all
my sticks I issue following commands, but nothing changes although the log
output suggests the change is being set.


PyMOL>set stick_transparency=0.2, /sca//A/228  and !mc
Setting: stick_transparency set for 5 atoms in object "mol1".

I'd also like to draw selected H-bonds with control of transparency
with the rest solid, but have no idea how to do this.

--
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

Minh,
 
This type of use is now covered under the "rotate" command in the official
documentation for PyMOL 1.0 ( http://delsci.info/dsc ) as well as in the
current open-source code.
 
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Minh Nhat
Sent: Friday, June 22, 2007 11:56 AM
To: pym...@li...
Subject: [PyMOL] rotate about an abitrary axis


Hi everyone,
Is it possible to make a selection rotate about an arbitrary axis (which we
can actively define ourself (not x,y, z) ?)
Thanks,



Send instant messages to your online friends http://uk.messenger.yahoo.com 

Am Dienstag, 26. Juni 2007 schrieb Eva Vanamee:
> Hi,
>
> I'd like to color a molecule based on its sequence similarity to another
> molecule.
> Can this be done in Pymol?

If you can quantify "similarity" in a number you can write it into the=20
b-factors of the atoms and then color it by them.

Best
	Martin

=2D-=20
Wenn Theorie und Realit=E4t nicht =FCbereinstimmen, mu=DF entweder die
Theorie oder die Realit=E4t ge=E4ndert werden. Das erste nennt man
Wissenschaft, das zweite Religion. [Achim Stoesser, 12.8.1999]

Hi,

I'd like to color a molecule based on its sequence similarity to another 
molecule.
Can this be done in Pymol?
Thanks in advance.

- Eva

Apologies for prior post message font was nearly unreadable

Dear All,

I'm trying to write a Pymol script with which produces a mixture of 
both solid and transparent sticks
I'm using the current 1.0 incentive release of MacPymol. After 
drawing all my sticks I issue following commands, but nothing changes 
although the log output suggests the change is being set.

PyMOL>set stick_transparency=0.2, /sca//A/228  and !mc
Setting: stick_transparency set for 5 atoms in object "mol1".

I'd also like to draw selected H-bonds with control of transparency
with the rest solid, but have no idea how to do this.

--
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

Dear All,

I'm trying to write a Pymol script with which produces a mixture of 
both solid and transparent sticks
I'm using the current 1.0 incentive release of MacPymol. After 
drawing all my sticks I issue following commands, but nothing changes 
although the log output suggests the change is being set.

PyMOL>set stick_transparency=0.2, /sca//A/228  and !mc
Setting: stick_transparency set for 5 atoms in object "mol1".

I'd also like to draw selected H-bonds with control of transparency
with the rest solid, but have no idea how to do this.

-- 
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

Hi there,

i am trying to map b factors on a surface representation. 

I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there a 
way to fine tune the color spectrum, such as with the "Midpoint" and "Offset" 
sliders in vmd?

Best
	Martin

Hi, 

I understood the question a little differently than Andreas, and I have a
different answer to you. 

If what you want to do is to be able to define your own x, y and z axis and
rotate about them, I can help you. I've made a script that will make a
transformation matrix that can be input to transform_selection().  This will
enable you to choose the x, y and z axis yourself, and after you've performed
transform_selection(), you can rotete about your newly defined x, y and z axis
using the rotate command as you would normally do. 

I'm including the script along with an example of a run here, so you can see how
it works. 

Basically, you have to choose three atoms, given with a selection string each,
and these three atoms will form a 2D plane. From the unit vectors the z axis can
also be computed, and thus a transformation matrix can be generated. 

Note that transform_selection() is currently unsupported, so I don't know if
this script will work through newer versions of Pymol. Also, I made this script
purely for myself, so it doesn't contain alot of error checking :) 

Hope this helps! 

Example of usage: 

PyMOL>import coordinateOperations
PyMOL>a =  "r. CLA and i. 612 and n. C1B"
PyMOL>b =  "r. CLA and i. 612 and n. CHA"
PyMOL>c =  "r. CLA and i. 612 and n. C4C"
PyMOL>matrix = coordinateOperations.getTransformationMatrix(a, b, c)
PyMOL>m_list = coordinateOperations.listOfTransformationMatrix(matrix)
PyMOL>cmd.transform_selection("all", m_list)

Cheers, 
Siv

On 2007-06-24 16:07:00, Andreas Henschel wrote:

> you define a rotation axis by the rotation axis x, y or z (first 
> argument in cmd.rotate) and a point in 3d (origin argument in cmd.rotate).
> Instead of rotations around axes that are not parallel to the x, y or z 
> axis you can do composite rotations.
> 
> Btw, for the case of GroEL (PDB 2c7e), the structure is oriented along 
> the Z axis, so you can flap the flexible regions with a single rotation 
> around the axis that goes through the regions center of mass and is 
> parallel to the z-axis.
> See the attached file.
> 
> repeat the last rotate command from the gray window
> cmd.rotate("z", 30, "flexregion", camera=0, origin=rotationCenter)
> 
> Minh Nhat wrote:
> >Hi everyone,
> >Is it possible to make a selection rotate about an arbitrary axis 
> >(which we can actively define ourself (not x,y, z) ?)
> >Thanks,
> >
> >Send instant messages to your online friends 
> >http://uk.messenger.yahoo.com
> >
> >------------------------------------------------------------------------
> >
> >-------------------------------------------------------------------------
> >This SF.net email is sponsored by DB2 Express
> >Download DB2 Express C - the FREE version of DB2 express and take
> >control of your XML. No limits. Just data. Click to get it now.
> >http://sourceforge.net/powerbar/db2/
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >PyMOL-users mailing list
> >PyM...@li...
> >https://lists.sourceforge.net/lists/listinfo/pymol-users
> >  
> 
> -- 
> Andreas Henschel
> Bioinformatics Group
> TU Dresden
> Tatzberg 47-51
> 01307 Dresden, Germany
> 
> Phone: +49 351 463 40063
> EMail: ah...@bi...
> 
> 


> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users


-- 
Siv Midtun Hollup 
PhD Student
Dept. of Informatics
University of Bergen, Norway
si...@ii... (NOTE: new email adress)
- Blessed are the flexible, for they can be tied into knots. -

Hi Minh,

you define a rotation axis by the rotation axis x, y or z (first 
argument in cmd.rotate) and a point in 3d (origin argument in cmd.rotate).
Instead of rotations around axes that are not parallel to the x, y or z 
axis you can do composite rotations.

Btw, for the case of GroEL (PDB 2c7e), the structure is oriented along 
the Z axis, so you can flap the flexible regions with a single rotation 
around the axis that goes through the regions center of mass and is 
parallel to the z-axis.
See the attached file.

repeat the last rotate command from the gray window
cmd.rotate("z", 30, "flexregion", camera=0, origin=rotationCenter)

hope that makes sense.

Minh Nhat wrote:
> Hi everyone,
> Is it possible to make a selection rotate about an arbitrary axis 
> (which we can actively define ourself (not x,y, z) ?)
> Thanks,
>
> Send instant messages to your online friends 
> http://uk.messenger.yahoo.com
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> ------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>   

-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...

Hi everyone,
Is it possible to make a selection rotate about an arbitrary axis (which we can actively define ourself (not x,y, z) ?)
Thanks,


 Send instant messages to your online friends http://uk.messenger.yahoo.com 

Hi,

What's the minimum recommend version of python against which pymol 1.0r0 
should be run? I've seen that it doesn't work at all with 2.3 but does 
with 2.4. Latest is 2.5.1.

Thanks,
Sabuj