pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] PyMol segmentation fault while starting from external python program

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

Dmitriy,

I spent a few minutes yesterday trying to track down the seg. fault -- =
there are at least three issues here...

One appears to be a race condition inside of Tcl/Tk-to-Python call =
interface, which is most apparent on multi-cpu systems, and for which I =
have no solution yet other than disabling the external GUI altogether.

The second is a blunder on my part in the CmdReady function in =
layer4/Cmd.c:

static PyObject *CmdReady(PyObject *dummy, PyObject *args)=20
{
return(APIResultCode(TempPyMOLGlobals->Ready));
}

should be

static PyObject *CmdReady(PyObject *dummy, PyObject *args)=20
{
   if(TempPyMOLGlobals) {
      return(APIResultCode(TempPyMOLGlobals->Ready));
   } else {
      return(APIResultCode(0));
   }
}

since TempPyMOLGlobals can't be derefrenced until it exists. =20

The third issue appears to be a Python initialization issue that also =
only rears its ugly head on SMP machines:

finish_launching() in modules/pymol/__init__.py needs to be updated as =
follows:

    def finish_launching():
        e=3Dthreading.Event()
        while not hasattr(__main__,'pymol'):
            e.wait(0.01)
        while not _cmd.ready():
            e.wait(0.01)
        while not hasattr(__main__.pymol,'xray'):
            e.wait(0.01)

in order to allow time for the xray module to initialize before loading =
structures.

These changes have been committed to CVS.

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: Dmitriy Igor Bryndin [mailto:bry...@ms...]=20
> Sent: Tuesday, October 11, 2005 5:06 AM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: Re: [PyMOL] PyMol segmentation fault while starting=20
> from external python program
>=20
> Warren=20
>=20
> It seems like PyMol should have time to load after  import=20
> pymol and before anything else can be done with it.
> If I=B4ll do
>  ------------------------------
> pymol_argv =3D ['pymol', '-qx']
> import pymol
> # let`s give pymol some time to load
> for a in range(1000000):
> 	b=3D0=20
>=20
> pymol.finish_launching()=20
>=20
> from pymol import cmd=20
>=20
> cmd.load("$HOME/pept.pdb")
> cmd.show("sticks")
>  ------------------------------
> everything is fine. It loads and shows the picture.
> =B4for a in range(100)=B4  for example will produce segmentation =
fault.=20
>=20
> As far as I understand =B4pymol.finish_launching()=B4 is meant to=20
> produce such delay. Correct me if I=B4m wrong. But this call=20
> produce segm fault by itself without a waiting cycle.=20
>=20
> Can you recommend some workaround for this problem? This=20
> stupid cycle may work on my machine, but may not work on a=20
> faster one. Is there any way to find out that PyMol window=20
> had loaded?=20
>=20
> Thanks
>  Dmitriy Bryndin=20
>=20
> =20
>=20
> =20
>=20
> =20
>=20
>=20
> Warren DeLano writes:=20
>=20
> > Dmitriy,
> >=20
> > Due to problem with multithreading (especially with the Tcl/Tk=20
> > external GUI), we haven't been able to get the "import=20
> pymol" approach to work in
> > a stable robust manner across different OSes and environments.  =20
> >=20
> > So sight now, as per comments in=20
> "modules/pymol/__init__.py", the only=20
> > supported way to launch PyMOL is to run the __init__.py script on=20
> > startup.
> >=20
> > %python modules/pymol/__init__.py
> >=20
> > Hoever, if you disable the external GUI, then you might be=20
> able to get=20
> > "import pymol" to work...
> >=20
> > pymol_argv =3D ['pymol', '-qx']
> > import pymol
> > pymol.finish_launching()
> >=20
> > from pymol import cmd
> >=20
> > cmd.load(...etc.=20
> >=20
> >=20
> > Cheers,
> > Warren
> >=20
> >=20
> > --
> > Warren L. DeLano, Ph.D.                    =20
> > Principal Scientist
> >=20
> > . 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
> >=20
> >> -----Original Message-----
> >> From: pym...@li...
> >> [mailto:pym...@li...] On Behalf=20
> Of Dmitriy=20
> >> Igor Bryndin
> >> Sent: Monday, October 10, 2005 2:33 PM
> >> To: pym...@li...
> >> Subject: [PyMOL] PyMol segmentation fault while starting from=20
> >> external python program
> >>=20
> >> Launching PyMol form external python script will produce=20
> >> segmaentation fault.
> >> For example starting "launch.py" from "/pymol/examples/launching"
> >>  ----------------------------------------------
> >> $ python launch.py
> >> zsh: segmentation fault  python launch.py
> >>  ----------------------------------------------
> >> Crashes without even showing PyMol windows. =20
> >>=20
> >> Tried it on Fedora Core 1, Fedora Core 4, Mandriva 2005. The same=20
> >> story.
> >> Different pythons and compiling different versions of=20
> PyMol does not=20
> >> change anything.
> >>=20
> >> It will launch PyMol windows if there is only
> >>    import pymol
> >> line. =20
> >>=20
> >> Adding
> >>    pymol.finish_launching()
> >> or
> >>    from pymol import cmd
> >>    cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
> >> will produce segmentation fault. With no windows shown. =20
> >>=20
> >> The same time if I'll try to debug step by step, let's say,=20
> >> "launch_demo.py"
> >> (from "/pymol/examples/launching")
> >>  -------------------------------
> >> pymol.finish_launching()
> >> from pymol import cmd
> >> cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
> >> cmd.show("sticks")
> >>  -------------------------------
> >> using IDLE. Everything will work. It starts windows, loads a file,=20
> >> changes to sticks...
> >> Running it "python launch_demo.py" will wait for a second=20
> and return=20
> >> segmentation fault.
> >>=20
> >> If someone knows what's going on, please help me. =20
> >>=20
> >>  Thanks
> >>    Dmitriy Bryndin
> >>=20
> >> =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
> >=20
> =20
>=20
>=20
>=20
>=20
>=20
>=20

Re: [PyMOL] Small problem or inconsistency in showing cgo objects?

[Terry J. <tc...@ca...>]

| Seems that "hide" means roughly the same as setting the  
| representation to "none".
| 
| "Enable/disable" are the equivalents to clicking on the "name-button".
| 
| So, if you change the test script to have "cmd.disable('two')" at the  
| end instead of 'hide', then it seems to do what you wanted it to do...

Thanks (again)  Gilleain, that's exactly what I needed.

Regards,
Terry.

[PyMOL] Transparency w/o rendering

[Anders P. <and...@ch...>]

Hi all! Just wondering whether it is possible to write movie pngs  
with transparent background (as with the set ray_opaque_background)  
without ray-tracing, i.e. to save time but still get rather nice  
movies...

/Anders

Re: [PyMOL] Small problem or inconsistency in showing cgo objects?

[Gilleain T. <gil...@gm...>]

Hi,

I was curious, and tried this out.

Seems that "hide" means roughly the same as setting the  
representation to "none".

"Enable/disable" are the equivalents to clicking on the "name-button".

So, if you change the test script to have "cmd.disable('two')" at the  
end instead of 'hide', then it seems to do what you wanted it to do...

gilleain torrance

On 10 Oct 2005, at 22:12, Terry Jones wrote:

> Hi. I've run into a slight pymol UI problem with cgo objects and I'm
> wondering if I should be doing something differently or if it's a  
> pymol
> idiosyncrasy.
>
> Here's a script:
>
>     from pymol.cgo import *
>     from pymol import cmd
>
>     one = [ SPHERE, 0.0, 0.0, 0.0, 1.0 ]
>     two = [ SPHERE, 2.0, 0.0, 0.0, 1.0 ]
>
>     cmd.load_cgo(one, 'one')
>     cmd.load_cgo(two, 'two')
>     cmd.hide('cgo', 'two')
>
> When I load it into pymol (using the run command on the command  
> line), the
> 'one' sphere appears. I expected to be able to click on the gray  
> 'two' item
> on the right side of the pymol GUI and have the two sphere appear.  
> But this
> doesn't work. Instead, I have to click on 'S' next to the two  
> indicator,
> drag down to 'cgo' and then the sphere appears. After this initial  
> step I
> can turn the display of sphere two on and off with the 'two' toggle  
> just
> like I can do from the outset with the 'one' toggle/button.
>
> Should the 'two' button toggle right away? If not, is there some pymol
> command I can issue to enable that?
>
> I hope this is clear enough. Please let me know if there's not enough
> detail. I'm doing this with pymol 0.98 on Mac OSX 10.3.9. I get the  
> same
> behavior in both the Aqua pymol and the X11 hybrid.
>
> Regards,
> Terry
>
>
> -------------------------------------------------------
> 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] RGB values for preset colors in PyMol

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

Mark,

print cmd.get_color_indices() will retrieve the color indices

print cmd.get_color_tuple(index-number) will retrieve individual RGB
components.

set_color color-name, [r,b,g]=20

will create a new color that will appear in the GUI list.  From the
open-source GUI you can use the "add" button in the color list viewer.
In MacPyMOL, enter the new name into the MacPyMOL color editor window,
set the RGBs, and then click Apply.

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: Monday, October 10, 2005 2:04 PM
> To: pym...@li...
> Subject: [PyMOL] RGB values for preset colors in PyMol
>=20
> Hi,
>=20
> Is it possible to get a listing of the RGB values for the=20
> present color palette used in PyMol? Related to this anyone=20
> know how to add user defined colors to the GUI interface.
>=20
> Thanks
> --
> 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=20
> 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov
>=20
> Send packages, Fedex and anything requiring a signature to:
>=20
> Bldg 35, Room 3B 1004
> 35 Lincoln Drive
> Bethesda MD 20892
>=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 segmentation fault while starting from external python program

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

Dmitriy,

Due to problem with multithreading (especially with the Tcl/Tk external
GUI), we haven't been able to get the "import pymol" approach to work in
a stable robust manner across different OSes and environments. =20

So sight now, as per comments in "modules/pymol/__init__.py", the only
supported way to launch PyMOL is to run the __init__.py script on
startup.

%python modules/pymol/__init__.py

Hoever, if you disable the external GUI, then you might be able to get
"import pymol" to work...

pymol_argv =3D ['pymol', '-qx']
import pymol
pymol.finish_launching()

from pymol import cmd

cmd.load(...etc.


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
> Dmitriy Igor Bryndin
> Sent: Monday, October 10, 2005 2:33 PM
> To: pym...@li...
> Subject: [PyMOL] PyMol segmentation fault while starting from=20
> external python program
>=20
> Launching PyMol form external python script will produce=20
> segmaentation fault.
> For example starting "launch.py" from "/pymol/examples/launching"
>  ----------------------------------------------
> $ python launch.py
> zsh: segmentation fault  python launch.py
>  ----------------------------------------------
> Crashes without even showing PyMol windows.=20
>=20
> Tried it on Fedora Core 1, Fedora Core 4, Mandriva 2005. The=20
> same story.
> Different pythons and compiling different versions of PyMol=20
> does not change anything.=20
>=20
> It will launch PyMol windows if there is only
>    import pymol
> line.=20
>=20
> Adding
>    pymol.finish_launching()
> or
>    from pymol import cmd
>    cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
> will produce segmentation fault. With no windows shown.=20
>=20
> The same time if I'll try to debug step by step, let's say,=20
> "launch_demo.py"=20
> (from "/pymol/examples/launching")
>  -------------------------------
> pymol.finish_launching()
> from pymol import cmd
> cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
> cmd.show("sticks")
>  -------------------------------
> using IDLE. Everything will work. It starts windows, loads a=20
> file, changes to sticks...
> Running it "python launch_demo.py" will wait for a second and=20
> return segmentation fault.=20
>=20
> If someone knows what's going on, please help me.=20
>=20
>  Thanks
>    Dmitriy Bryndin=20
>=20
>=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

[PyMOL] Correction: New PX beamline at APS

[Sanishvili, R. <rsa...@an...>]

Oops, please use the site
http://www.gmca.aps.anl.gov/user_program/EnvelopeIDin.html
For current beamline capabilities.
Sorry for any confusion.
Nukri




Ruslan Sanishvili (Nukri), Ph.D.

GM/CA-CAT, Bld. 436, D007
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...




-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of
Sanishvili, Ruslan
Sent: Monday, October 10, 2005 4:42 PM
To: pym...@li...
Subject: [PyMOL] New PX beamline at APS

Dear Colleague,

We are pleased to announce our first call for proposals for beam time at
sector 23 of the APS.  Beamline 23ID-D, currently operational, is the
first of two undulator beamlines being constructed at GM/CA CAT, funded
by NIGMS and NCI of the U.S. NIH.

Proposals for beamtime should be submitted to the APS on-line proposal
system (see
http://www.aps.anl.gov/Users/Scientific_Access/General_User/index.html).
For time at GM/CA CAT, indicate 23ID-D as your first choice.

For administrative questions about GM/CA CAT, please contact Sheila
Rossi at sr...@an... or (630)252-0662.  For current beamline
capabilities and updates, please visit
http://www.gmca.aps.anl.gov/user_program/Envelope/Idin.html

With best regards,
GM/CA staff.=20




-------------------------------------------------------
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

[PyMOL] New PX beamline at APS

[Sanishvili, R. <rsa...@an...>]

Dear Colleague,

We are pleased to announce our first call for proposals for beam time at
sector 23 of the APS.  Beamline 23ID-D, currently operational, is the
first of two undulator beamlines being constructed at GM/CA CAT, funded
by NIGMS and NCI of the U.S. NIH.

Proposals for beamtime should be submitted to the APS on-line proposal
system (see
http://www.aps.anl.gov/Users/Scientific_Access/General_User/index.html).
For time at GM/CA CAT, indicate 23ID-D as your first choice.

For administrative questions about GM/CA CAT, please contact Sheila
Rossi at sr...@an... or (630)252-0662.  For current beamline
capabilities and updates, please visit
http://www.gmca.aps.anl.gov/user_program/Envelope/Idin.html

With best regards,
GM/CA staff.=20

[PyMOL] PyMol segmentation fault while starting from external python program

[Dmitriy I. B. <bry...@ms...>]

Launching PyMol form external python script will produce segmaentation 
fault.
For example starting "launch.py" from "/pymol/examples/launching"
 ----------------------------------------------
$ python launch.py
zsh: segmentation fault  python launch.py
 ----------------------------------------------
Crashes without even showing PyMol windows. 

Tried it on Fedora Core 1, Fedora Core 4, Mandriva 2005. The same story.
Different pythons and compiling different versions of PyMol does not change 
anything. 

It will launch PyMol windows if there is only
   import pymol
line. 

Adding
   pymol.finish_launching()
or
   from pymol import cmd
   cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
will produce segmentation fault. With no windows shown. 

The same time if I'll try to debug step by step, let's say, "launch_demo.py" 
(from "/pymol/examples/launching")
 -------------------------------
pymol.finish_launching()
from pymol import cmd
cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
cmd.show("sticks")
 -------------------------------
using IDLE. Everything will work. It starts windows, loads a file, changes 
to sticks...
Running it "python launch_demo.py" will wait for a second and return 
segmentation fault. 

If someone knows what's going on, please help me. 

 Thanks
   Dmitriy Bryndin 

Re: [PyMOL] alpha helices as cylinders in Pymol

[Tsjerk W. <ts...@gm...>]

Hi Mark,

Try:

set cartoon_cylindrical_helices,1

I think it should do the trick. For more cartoon related settings, type

set cartoon_ and press <TAB>; pymol will then give you the list of all
settings which match.

Cheers,

Tsjerk

On 10/10/05, Mark Mayer <ma...@ma...> wrote:
>
> Hi,
>
> Is it possible to draw alpha helices as cylinders in PyMol? The
> effect I'm looking for is like the Molscript/render version of
> cylinders.
>
> Related to this, when I read into pymol an r3d script generated by
> molscript with helices drawn as flat ended cylinders, PyMol draws the
> cylinders as sausages with found tops and bottoms. If anyone knows of
> a fix I'd be grateful to know; PyMol is fantastic for making movies
> from r3d scripts if you already have figs made in this format.
>
> Thanks
>
>
> --
> 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:
> 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
>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

[PyMOL] Small problem or inconsistency in showing cgo objects?

[Terry J. <tc...@ca...>]

Hi. I've run into a slight pymol UI problem with cgo objects and I'm
wondering if I should be doing something differently or if it's a pymol
idiosyncrasy.

Here's a script:

    from pymol.cgo import *
    from pymol import cmd

    one = [ SPHERE, 0.0, 0.0, 0.0, 1.0 ]
    two = [ SPHERE, 2.0, 0.0, 0.0, 1.0 ]

    cmd.load_cgo(one, 'one')
    cmd.load_cgo(two, 'two')
    cmd.hide('cgo', 'two')

When I load it into pymol (using the run command on the command line), the
'one' sphere appears. I expected to be able to click on the gray 'two' item
on the right side of the pymol GUI and have the two sphere appear. But this
doesn't work. Instead, I have to click on 'S' next to the two indicator,
drag down to 'cgo' and then the sphere appears. After this initial step I
can turn the display of sphere two on and off with the 'two' toggle just
like I can do from the outset with the 'one' toggle/button.

Should the 'two' button toggle right away? If not, is there some pymol
command I can issue to enable that?

I hope this is clear enough. Please let me know if there's not enough
detail. I'm doing this with pymol 0.98 on Mac OSX 10.3.9. I get the same
behavior in both the Aqua pymol and the X11 hybrid.

Regards,
Terry

[PyMOL] PyMol does not compile with python 2.4.1

[Dmitriy I. B. <bry...@ms...>]

I've tried to compile PyMol 0.99beta15 (one from CVS)
using:
python setup.py install 

it fails while comiling layer0/Crystal.c 

the problem in gcc  "-Wp,-D_FORTIFY_SOURCE=2" parameter, which fails
compilation of PRINTF macro inside of Crystal.c 

If I compile Crystal.c without this parameter everything is fine. 

The python is 2.4.1 which comes with Fedora Core 4.
gcc version 4.0.1 20050727 (Red Hat 4.0.1-5) 

I can't find a nice way of getting rid of this "-Wp,-D_FORTIFY_SOURCE=2"
parameter without getting inside python and killing it manually.
If someone knows the way, it will be helpful.
But the main question is WHY it does not compile. Is it somthing wrong
with PyMol code?
As much as I know, this parameter do additional code checks for things like
buffer owerflow. Which itent to be useful. 

 Thanks
   Dmitriy Bryndin 


it fails with this error:
 ----------------------------------------------------------------------
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe 
 -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 
 -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE 
 -D_PYMOL_INLINE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 
 -Ilayer4 -Ilayer5 -I/usr/include/python2.4 -c layer0/Crystal.c -o 
build/temp.linux-i686-2.4/layer0/Crystal.o -ffast-math -funroll-loops -O3
In file included from /usr/include/python2.4/Python.h:8,
                from layer0/os_python.h:26,
                from layer1/Setting.h:19,
                from layer1/CGO.h:21,
                from layer0/Crystal.c:21:
/usr/include/python2.4/pyconfig.h:835:1: warning: "_POSIX_C_SOURCE" 
redefined
In file included from /usr/include/stdio.h:28,
                from layer0/os_std.h:23,
                from layer0/Crystal.c:18:
/usr/include/features.h:150:1: warning: this is the location of the previous 
definition
layer0/Crystal.c:314:1: error: unterminated argument list invoking macro 
"sprintf"
layer0/Crystal.c: In function ‘CrystalDump’:
layer0/Crystal.c:201: error: syntax error at end of input
error: command 'gcc' failed with exit status 1
 ---------------------------------------------------------------------- 

[PyMOL] RGB values for preset colors in PyMol

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

Hi,

Is it possible to get a listing of the RGB values for the present 
color palette used in PyMol? Related to this anyone know how to add 
user defined colors to the GUI interface.

Thanks
-- 
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

[PyMOL] alpha helices as cylinders in Pymol

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

Hi,

Is it possible to draw alpha helices as cylinders in PyMol? The 
effect I'm looking for is like the Molscript/render version of 
cylinders.

Related to this, when I read into pymol an r3d script generated by 
molscript with helices drawn as flat ended cylinders, PyMol draws the 
cylinders as sausages with found tops and bottoms. If anyone knows of 
a fix I'd be grateful to know; PyMol is fantastic for making movies 
from r3d scripts if you already have figs made in this format.

Thanks


-- 
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] grid/cube representation

[Terry J. <tc...@ca...>]

| | As a follow up to my last email asking whether there is a way to make 3D
| grid representations of molecules....  I have found a picture of the kind
| of thing I am after. Is there a way to make anything similar to this
| http://www.techfak.uni-bielefeld.de/ags/ai/projects/docking/images/align.2ptci-6pti_small.png
| with PyMol?

If you don't mind using spheres or cylinders instead of cubes (or whatever
they are in that image), this is quite easy using CGO in pymol. See

  http://pymol.sourceforge.net/newman/user/S0500cgo.html#14

Terry

Re: [PyMOL] PyMol training

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

Hi,

I've planned to write a french training document for PyMOL. I would enjoy t=
hat=20
some people help me by reading my draft, before I release it. This document=
=20
will be released under a Creative Common License (cc).

Thanks,

Jerome Pansanel

Le Lundi 10 Octobre 2005 09:29, Kristian Rother a =E9crit=A0:
> Dear PyMOL users,
>
> there will be a PyMOL training in the area of Berlin,
> Germany, soon. It is scheduled for October 19th, 15.00
> at the beamlines of the BESSY II synchrotron.
>
> Please contact me for details.
>
>     Kristian Rother
>
>     Charite - Universitaetsmedizin Berlin
>     kri...@ch...
>
>
>
>
>
>
>
> __________________________________
> Yahoo! Mail - PC Magazine Editors' Choice 2005
> http://mail.yahoo.com
>
>
> -------------------------------------------------------
> 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 training

[Kristian R. <k_r...@ya...>]

Dear PyMOL users,

there will be a PyMOL training in the area of Berlin,
Germany, soon. It is scheduled for October 19th, 15.00
at the beamlines of the BESSY II synchrotron.

Please contact me for details.

    Kristian Rother

    Charite - Universitaetsmedizin Berlin
    kri...@ch...





	
		
__________________________________ 
Yahoo! Mail - PC Magazine Editors' Choice 2005 
http://mail.yahoo.com

[PyMOL] grid/cube representation

[Sebastien G. <sge...@ma...>]

As a follow up to my last email asking whether there is a way to make 3D 
grid representations of molecules....
I have found a picture of the kind of thing I am after. Is there a way 
to make anything similar to this 
http://www.techfak.uni-bielefeld.de/ags/ai/projects/docking/images/align.2ptci-6pti_small.png 

with PyMol?
thanks,
Sebastien

Re: [PyMOL] How could I modify the secondary structures after superimpose of 2 or more structure?

[Tsjerk W. <ts...@gm...>]

Hi Chung-Ming Yu,

You can change the secondary structure identifiers as follows:

alter helix_selection,ss=3D'H'
alter sheet_selection,ss=3D'S'
alter loop_selection, ss=3D'L'

The RMS deviation gives you information about the quality of the fit. The
lower the number, the better the fit.

Cheers,

Tsjerk

On 10/8/05, yucmbuu <yu...@ga...> wrote:
>
> Dear All:
>
> I made two protein models from one known pdb by using SWISS-MODEL server.
> I
> superimpose these three pdb with pymol. However, I need to modified the
> secondary structure of these structures after "procheck". How could I
> using
> "alter" command to modified one structure at once? Is it meaningful that
> RMS scores were obtained by using "align" command in pymol? Thanks for
> your
> help.
>
> Chung-Ming Yu
> Inst. Biol. Chem.
> Academia Sinica
>
>
>
>
> -------------------------------------------------------
> 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
>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

[PyMOL] How could I modify the secondary structures after superimpose of 2 or more structure?

[yucmbuu <yu...@ga...>]

Dear All:

I made two protein models from one known pdb by using SWISS-MODEL server. I
superimpose these three pdb with pymol. However, I need to modified the
secondary structure of these structures after "procheck". How could I using
"alter" command to modified one structure at once? Is it meaningful that
RMS scores were obtained by using "align" command in pymol? Thanks for your
help.

Chung-Ming Yu
Inst. Biol. Chem.
Academia Sinica

[PyMOL] cube/grid representation

[Sebastien G. <sge...@ma...>]

This may sound like a strange question and I am guessing the answer is 
just a simple "no" but is there any way to represent the structure of a 
protein in cubes with pymol? So say for example take the surface 
representation and change that into a whole lot of cube stuck together 
to fill in the surface? Basically a 3D grid representation...
thanks,
Sebastien

RE: [PyMOL] PyMol training

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

Emmanuel,

There is a SF-Bay PyMOL mailing list for local annnouncements:

http://groups.yahoo.com/group/pymol-sfbay/

We don't have any training events currently planned, but our next PUG
(PyMOL Users Group) meeting will likely be on the 28th of Oct, focused
on the version 0.99 release expected around Nov 1st.  There's always
time for questions and answers at these meetings.

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
> Emmanuel Mayssat
> Sent: Friday, October 07, 2005 9:10 AM
> To: pym...@li...
> Subject: [PyMOL] PyMol training
>=20
> Hello,
>=20
> I am new to PyMol and was wondering if there is any training=20
> session planned in the next few months.=20
> I live in Bay Area.
> Thanks,
>=20
> --
> Emmanuel Mayssat
> Lyncean Technologies, Inc.
> Palo Alto, CA94306
> Cell: 650/793-0626
> "See the invisible"
>=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

[PyMOL] PyMol training

[Emmanuel M. <emm...@ly...>]

Hello,

I am new to PyMol and was wondering if there is any training session
planned in the next few months. 
I live in Bay Area.
Thanks,

-- 
Emmanuel Mayssat
Lyncean Technologies, Inc.
Palo Alto, CA94306
Cell: 650/793-0626
"See the invisible"

RE: [PyMOL] Using a seperate python installation

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

There is always this trade off between (A) shipping PyMOL with its own
Python, to guarantee reliable installation, or (B) using a system PyMOL
install, for enabling integration and extensibility.  One of PyMOL's
advantages is that you aren't locked in to either approach, embedding or
extension -- the program supports both.
=20
The challenge with (B) is that installed Python versions vary from
system to system, so recompilation of PyMOL is the only sure way to
guarantee binary compatibility between PyMOL's compiled code and the
system Python install. =20

Setting PYTHONPATH (note no underscore) only works if the modules you
import are native Python (with no binary C-language dependencies).

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
> Jules Jacobsen
> Sent: Friday, October 07, 2005 5:07 AM
> To: 'pymol'
> Subject: [PyMOL] Using a seperate python installation
>=20
> Hello All,
>=20
> Can someone tell me wether it is possible to use a=20
> stand-alone python installation alongside the latest PyMol=20
> releases? I have a few things set up in my main python=20
> installation which an older (python free) version of Pymol=20
> was happy to use, having installed the newer version it uses=20
> it's own version of python. Is this possible to specify in=20
> the .pymolrc? If so what do I write? I've tried the obvious=20
> PYTHON_PATH =3D 'C:\\Python24\\'
>=20
> Many thanks,
>=20
> Jules
>=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] Using a seperate python installation

[Peter A. M. <pa...@co...>]

> Can someone tell me wether it is possible to use a stand-alone python
> installation alongside the latest PyMol releases? I have a few things
> set up in my main python installation which an older (python free)
> version of Pymol was happy to use, having installed the newer version it
> uses it's own version of python. Is this possible to specify in the
> .pymolrc? If so what do I write? I've tried the obvious PYTHON_PATH =
> 'C:\\Python24\\'

If I'm understanding you correctly, you'd like to use a currently
installed python with a newer version of pymol.  It sounds like you may
need to re-install the new pymol (possibly rebuild, with the new python
paths (include/lib) set to your system version of python).
There's always the standard sys.path workaround (start new version of
pymol, add system python lib directory to sys.path, import your other
modules and check them to make sure they still give the same
results)...but that may cause version conflicts between pymol/system
python module imports (it might not too, I've never tried it).

Hopefully somebody more farmiliar (sp?) with python/pymol on windows (I'm
assuming you're using that from the c:\python24 reference) has a better
solution than this.

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University