pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] RE: EMizing an xray structure (Warren DeLano)

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

Sarina,

I'm not sure where that "3D10" is coming from -- it should simply be the
number 10:

alter all, b=3D10

map_new can take a selection as its fourth argument, so you could
generate an independent map for each subunit, show the surface, and
color it independently.  It's also possible to color a surface by atomic
proximity, but the approach is a bit convoluted:

load some.pdb, prot
util.cbc prot
alter prot,b=3D10
set gaussian_resolution, 9.0
map_new dcalc, gaussian, 3.0
map_double dcalc
isosurface dsurf, dcalc, 1.0, prot
ramp_new dramp, prot, [-10,0,10]
color dramp, dsurf


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
> Sarina Bromberg
> Sent: Thursday, December 01, 2005 9:45 AM
> To: pym...@li...
> Subject: [PyMOL] RE: EMizing an xray structure (Warren DeLano)
>=20
> Warren,
> These commands (see below) go a long way toward solving the=20
> problem of producing low resolution simple structures for my=20
> textbook project. I have some questions:
>=20
> The first command elicits an error:
> PyMOL>alter all,b=3D3D10
> Alter-Error: Aborting on error. Assignment may be incomplete.
>    File "<string>", line 1
>      b=3D3D10
>          ^
> SyntaxError: unexpected EOF while parsing
> Alter-Error: Aborting on error. Assignment may be incomplete.
> Alter: modified 0 atoms.
>=20
> The rest work fine.  For a multimeric protein, how do I get=20
> different surface colors on different chains?  I tried=20
> selecting the chains and coloring them differently before=20
> running the commands below, but the dsurf object was just one=20
> color.  Can I make each chain a different object and add ",=20
> objectname" to each of these commands?
>=20
> Thanks!
> Sarina
>=20
> > Message: 6
> > Subject: RE: [PyMOL] EMizing an xray structure
> > Date: Wed, 30 Nov 2005 16:51:07 -0800
> > From: "Warren DeLano" <wa...@de...>
> > To: =3D?iso-8859-1?Q?Andreas_F=3DF6rster?=3D =
<an...@bi...>,
> > 	<pym...@li...>
> >
> >
> > Try a command sequence like this:
> >
> > alter all,b=3D3D10
> > set gaussian_resolution, 9.0
> > map_new dcalc, gaussian, 3.0
> > map_double dcalc
> > isosurface dsurf, dcalc, 1.0
> >
> > Cheers,
> > Warren
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
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> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
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>=20
>=20
>=20
>=20

[PyMOL] RE: EMizing an xray structure (Warren DeLano)

[Sarina B. <sa...@di...>]

Warren,
These commands (see below) go a long way toward solving the problem  
of producing low resolution simple structures for my textbook  
project. I have some questions:

The first command elicits an error:
PyMOL>alter all,b=3D10
Alter-Error: Aborting on error. Assignment may be incomplete.
   File "<string>", line 1
     b=3D10
         ^
SyntaxError: unexpected EOF while parsing
Alter-Error: Aborting on error. Assignment may be incomplete.
Alter: modified 0 atoms.

The rest work fine.  For a multimeric protein, how do I get different  
surface colors on different chains?  I tried selecting the chains and  
coloring them differently before running the commands below, but the  
dsurf object was just one color.  Can I make each chain a different  
object and add ", objectname" to each of these commands?

Thanks!
Sarina

> Message: 6
> Subject: RE: [PyMOL] EMizing an xray structure
> Date: Wed, 30 Nov 2005 16:51:07 -0800
> From: "Warren DeLano" <wa...@de...>
> To: =?iso-8859-1?Q?Andreas_F=F6rster?= <an...@bi...>,
> 	<pym...@li...>
>
>
> Try a command sequence like this:
>
> alter all,b=3D10
> set gaussian_resolution, 9.0
> map_new dcalc, gaussian, 3.0
> map_double dcalc
> isosurface dsurf, dcalc, 1.0
>
> Cheers,
> Warren

RE: [PyMOL] EMizing an xray structure

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

Try a command sequence like this:

alter all,b=3D10
set gaussian_resolution, 9.0
map_new dcalc, gaussian, 3.0
map_double dcalc
isosurface dsurf, dcalc, 1.0

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
> Andreas F=F6rster
> Sent: Wednesday, November 30, 2005 1:32 PM
> To: pym...@li...
> Subject: [PyMOL] EMizing an xray structure
>=20
> Hey all,
>=20
> I'm trying to make a figure from a pdb that's supposed to=20
> look like an EM structure.  According to an older post from=20
> Warren I should increase solvent_radius and alter vdw.
>=20
> For most combinations of the two, artefacts appear all over=20
> the place, like missing surface and surface floating about. =20
> I succeeded in making a figure without artifacts (high vdw=20
> increase, minimal solvent_radius increase), but it looks more=20
> like a lychee than a protein.
>=20
> Has anyone found numbers that work well?  Or a different=20
> approach to creating an EM reconstruction-like figure.
>=20
> Merci bien.
>=20
>=20
> Andreas
>=20
>=20
>=20
> --=20
>     -->       Andreas F=F6rster       <--
> Institut de Biologie Structural, Grenoble
>        www.biochem.utah.edu/~andreas
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
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>=20
>=20
>=20
>=20

Re: [PyMOL] EMizing an xray structure

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

You can create an mrc map from a PDB using the pdb2mrc program in the
EMan package (http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/ and
http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/doc/progs/pdb2mrc.html).

Pdb2mrc allows you to specify parameters that would affect what a
theoretical cryo EM 3D reconstruction would look like. If you are
looking for a theoretical negative stain EM image, EMan can create
flattened projections of the mrc from multiple angles as well.

I don't know if pymol can read MRC though (I know Chimera can).

Andreas F=F6rster wrote:
> Hey all,
>=20
> I'm trying to make a figure from a pdb that's supposed to look like an
> EM structure.  According to an older post from Warren I should increase
> solvent_radius and alter vdw.
>=20
> For most combinations of the two, artefacts appear all over the place,
> like missing surface and surface floating about.  I succeeded in making
> a figure without artifacts (high vdw increase, minimal solvent_radius
> increase), but it looks more like a lychee than a protein.
>=20
> Has anyone found numbers that work well?  Or a different approach to
> creating an EM reconstruction-like figure.
>=20
> Merci bien.
>=20
>=20
> Andreas
>=20
>=20
>=20

[PyMOL] EMizing an xray structure

[<an...@bi...>]

Hey all,

I'm trying to make a figure from a pdb that's supposed to look like an=20
EM structure.  According to an older post from Warren I should increase=20
solvent_radius and alter vdw.

For most combinations of the two, artefacts appear all over the place,=20
like missing surface and surface floating about.  I succeeded in making=20
a figure without artifacts (high vdw increase, minimal solvent_radius=20
increase), but it looks more like a lychee than a protein.

Has anyone found numbers that work well?  Or a different approach to=20
creating an EM reconstruction-like figure.

Merci bien.


Andreas



--=20
    -->       Andreas F=F6rster       <--
Institut de Biologie Structural, Grenoble
       www.biochem.utah.edu/~andreas

RE: [PyMOL] How can I get the color ramp to show up in raytraced images?

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

Michael, =20

There's a scaling bug for raytracing the ramp in perspective mode. =20

set orthoscopic
ray

is the workaround.

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
> Michael George Lerner
> Sent: Wednesday, November 30, 2005 11:34 AM
> To: pym...@li...
> Subject: [PyMOL] How can I get the color ramp to show up in=20
> raytraced images?
>=20
>=20
> Hi,
>=20
> When I use the APBS plugin to look at electrostatic=20
> potentials, I get a color ramp at the bottom of the window=20
> (e.g. red and -1 on the left, blue and +1 on the right) that=20
> shows the color scale that I'm using.  When I raytrace, that=20
> ramp goes away.  How can I make it show up in the raytraced image?
>=20
> Thanks,
>=20
> -michael
>=20
> --
> 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
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] How can I get the color ramp to show up in raytraced images?

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

Hi,

When I use the APBS plugin to look at electrostatic potentials, I get a 
color ramp at the bottom of the window (e.g. red and -1 on the left, blue 
and +1 on the right) that shows the color scale that I'm using.  When I 
raytrace, that ramp goes away.  How can I make it show up in the raytraced 
image?

Thanks,

-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

[PyMOL] how to get the mouse information

[Qingyi Y. <qin...@ya...>]

Hi,

I am wondering how to get the mouse information from
Pymol. For example, when moving the molecule, how to
actually read the "start" and "end" position from the
mouse? Thanks a lot!

Joy


		
__________________________________ 
Yahoo! Music Unlimited 
Access over 1 million songs. Try it free. 
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[PyMOL] Residue numbering using fuse

[<ma...@xr...>]

Hi,

I'm trying to use PyMol to create a polysaccharide (or poly-anything) 
out of a disaccharide building block. The disaccharide consists of two 
residues with different residue names and residue numbers "1" and "2". 
When I use the "fuse" command in PyMol to fuse one disaccharide to 
another, two things happen which I'm hoping can be prevented with some 
kind of setting:
1.   The residue numbers of the polysaccharide are all "1" or "2", i.e. 
the residue numbers are 1-2-1-2-1-2-1-2....
2.   The atom names in the polysaccharide are not the same as in the 
disaccharide building block.

Is there a way to prevent this behaviour?
One possible solution to "1." is to renumber the residues afterwards. 
However I can't figure out how to do it since trying to select one of 
the residues in the polysaccharide results in PyMol selecting all 
residues with that residue name (since all residues have the same 
residue number)

Martin

Re: [PyMOL] Listing secondary structure assignments

[Robert C. <rl...@po...>]

* J. Evan Sadler <es...@im...> [2005-11-23 13:08] wrote:
> I need a list of the secondary structure assigned to each residue by dss in
> pymol. Is there a simple way to write this information to a file, or dump it
> to the screen?

To dump it to the screen, try:

  iterate <object name> & n. ca, print resn,resi,ss

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] Listing secondary structure assignments

[J. E. S. <es...@im...>]

I need a list of the secondary structure assigned to each residue by dss in
pymol. Is there a simple way to write this information to a file, or dump it
to the screen?

Thanks,

Evan Sadler

-- 
J. Evan Sadler, M.D., Ph.D.
Howard Hughes Medical Institute
Washington University
660 S. Euclid Ave., Box 8022
St. Louis, MO   63110
Tel: 314-362-9067
FAX: 314-454-3012
email: es...@im...

RE: [PyMOL] Raytracing interior surfaces. Problems in both PyMoland PovRay

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

Yep, Daniel's has it!

To lessen the darkness of shadows, increase "direct" and if necessary,
lower "reflect"

get reflect
get direct

set reflect, 0.7
set direct, 0.4

ray

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
> Daniel Rigden
> Sent: Wednesday, November 23, 2005 5:03 AM
> To: Jacob Poehlsgaard
> Cc: pym...@li...
> Subject: Re: [PyMOL] Raytracing interior surfaces. Problems=20
> in both PyMoland PovRay
>=20
> Hi Jacob
>=20
> In Pymol, have you tried adding in a direct light source? e.g.
>=20
> set direct, 0.5
>=20
> It worked nicely in a similar situation for me
>=20
> Daniel
>=20
> On Wed, 2005-11-23 at 11:42 +0100, Jacob Poehlsgaard wrote:
> > Hi folks
> >=20
> > =20
> >=20
> >  I'm trying to visualize a section of the inner workings of the=20
> > ribosome. To this end I've generated a surface and clipped it to=20
> > reveal the internal structure I want to look at. This looks really=20
> > good in the normal openGL view. When I raytrace it however,=20
> the part=20
> > that's clipped away still throws a shadow, so everything is=20
> completely=20
> > dark. I know I could turn shadows off, but I'd really like to keep=20
> > them for things that's visible.
> >=20
> > =20
> >=20
> >  I also tried exporting to PovRay, but unfortunately the clipping=20
> > plane isn't really implemented in the export methods I tried (using=20
> > the renderer=3D1 command and the script from=20
> > http://adelie.biochem.queensu.ca/~rlc/work/pymol/ ).
> >=20
> > =20
> >=20
> >  I can extract the coordinates for the plane and put it=20
> into pov-ray,=20
> > but because the surface is exported as thousands of little mesh2=20
> > objects, I can't seem to explain to povray that they should all be=20
> > "clipped_by" the plane. If I make a union or merge of the mesh2=20
> > objects, it works, but this is not a realistic solution, as the=20
> > processor time needed is massive, even for simple test objects.
> >=20
> > =20
> >=20
> >  Does anyone have suggestions to fix this, using either the=20
> internal=20
> > renderer og pov-ray?
> >=20
> > =20
> >=20
> > Sincerely
> > Jacob Poehlsgaard
> >=20
> > SDU, Denmark
> >=20
> >=20
> --=20
> Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
> School of Biological Sciences             FAX:(+44) 151 795 4406
> Room 101, Biosciences Building
> University of Liverpool
> Crown St.,
> Liverpool L69 7ZB, U.K.
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today Register for a JBoss Training Course.  Free=20
> Certification Exam for All Training Attendees Through End of=20
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> _______________________________________________
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>=20
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>=20
>=20

Re: [PyMOL] Raytracing interior surfaces. Problems in both PyMol and PovRay

[Daniel R. <dr...@li...>]

Hi Jacob

In Pymol, have you tried adding in a direct light source? e.g.

set direct, 0.5

It worked nicely in a similar situation for me

Daniel

On Wed, 2005-11-23 at 11:42 +0100, Jacob Poehlsgaard wrote:
> Hi folks
>=20
> =20
>=20
>  I=FFm trying to visualize a section of the inner workings of the
> ribosome. To this end I=FFve generated a surface and clipped it to
> reveal the internal structure I want to look at. This looks really
> good in the normal openGL view. When I raytrace it however, the part
> that=FFs clipped away still throws a shadow, so everything is completely
> dark. I know I could turn shadows off, but I=FFd really like to keep
> them for things that=FFs visible.
>=20
> =20
>=20
>  I also tried exporting to PovRay, but unfortunately the clipping
> plane isn=FFt really implemented in the export methods I tried (using
> the renderer=3D1 command and the script from
> http://adelie.biochem.queensu.ca/~rlc/work/pymol/ ).
>=20
> =20
>=20
>  I can extract the coordinates for the plane and put it into pov-ray,
> but because the surface is exported as thousands of little mesh2
> objects, I can=FFt seem to explain to povray that they should all be
> =B4clipped_by=A1 the plane. If I make a union or merge of the mesh2
> objects, it works, but this is not a realistic solution, as the
> processor time needed is massive, even for simple test objects.
>=20
> =20
>=20
>  Does anyone have suggestions to fix this, using either the internal
> renderer og pov-ray?
>=20
> =20
>=20
> Sincerely
> Jacob Poehlsgaard
>=20
> SDU, Denmark
>=20
>=20
--=20
Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.

[PyMOL] Raytracing interior surfaces. Problems in both PyMol and PovRay

[Jacob P. <ja...@bm...>]

Hi folks

 

 I'm trying to visualize a section of the inner workings of the ribosome. To
this end I've generated a surface and clipped it to reveal the internal
structure I want to look at. This looks really good in the normal openGL
view. When I raytrace it however, the part that's clipped away still throws
a shadow, so everything is completely dark. I know I could turn shadows off,
but I'd really like to keep them for things that's visible.

 

 I also tried exporting to PovRay, but unfortunately the clipping plane
isn't really implemented in the export methods I tried (using the renderer=1
command and the script from
http://adelie.biochem.queensu.ca/~rlc/work/pymol/ ).

 

 I can extract the coordinates for the plane and put it into pov-ray, but
because the surface is exported as thousands of little mesh2 objects, I
can't seem to explain to povray that they should all be "clipped_by" the
plane. If I make a union or merge of the mesh2 objects, it works, but this
is not a realistic solution, as the processor time needed is massive, even
for simple test objects.

 

 Does anyone have suggestions to fix this, using either the internal
renderer og pov-ray?

 

Sincerely
Jacob Poehlsgaard

SDU, Denmark

[PyMOL] Nvidia question (7676 driver)! - NOT SOLVED

[Joel T. <joe...@ot...>]

Hi folks,

I was a little pre-emptive. The flicker is back! so no solution yet.

J

-- 
Joel Tyndall, PhD

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

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

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

[PyMOL] Another Nvidia question (7676 driver)! - SOLVED -use 7664

[Joel T. <joe...@ot...>]

Hi folks,

Thanks to those who responded. I uninstalled the 7676 driver and 
installed an earlier driver (7664) which seems to be a trusted nvidia 
driver (see mailing list) and has solved the problem (and pymol doesn't 
crash. I did try the 6629 but the x sever refused to start ( at least on 
my system).

Anyway thanks again

J

-- 
Joel Tyndall, PhD

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

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

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

[PyMOL] problem using raster3d *.r3d files

[J. E. S. <es...@im...>]

Hello,

I'm trying to load *.r3d files made by raster3d, as described in the pymol
user guide. The test file supplied with pymol fails with the following
output:

PyMOL>load test/dat/pept.r3d
Traceback (most recent call last):
  File 
"/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/parser.py",
line 188, in parse
    result=apply(kw[nest][0],args[nest],kw_args[nest])
  File 
"/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/importing.py"
, line 549, in load
    discrete,quiet,multiplex,zoom)
  File 
"/users/warren/pymol/products/MacPyMOL.app/pymol/modules/pymol/cmd.py", line
755, in _load
    obj = cgo.from_r3d(finfo)
  File "/Applications/MacPyMOL.app/pymol/modules/pymol/cgo.py", line 167, in
from_r3d
    if (mode[0:1]=='r') and (string.find(fname,':')>1):
NameError: global name 'mode' is not defined


Does anyone know how to make *.r3d files work with pymol?

Best regards,

Evan Sadler

Re: [PyMOL] mixing ray_shadows states

[Tim F. <fe...@st...>]

On Mon, Nov 21, 2005 at 11:24:23PM -0800, Nat Echols wrote:
> 
> I'm trying to make a high-quality figure showing ligand binding in a 
> cleft, incorporating sticks, electron density, and some combination of 
> cartoon/surface/lines for the protein.  Ray-traced shadows make the 
> perspective much clearer but also add visual "noise" - for instance, the 
> electron density casts mesh-shaped shadows everywhere.  Is there a way to 
> prevent specific objects from casting shadows?  I tried
> 
> set ray_shadows = 0, mesh1
> 
> but this doesn't seem to have any effect.  (This is with a very recent 
> beta.)  Is it even possible in theory for the raytracer to support such an 
> option?
> 

POVRay can, if you're itching to do it.  Check out the no_shadow
object modifier.

-Tim

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

        Tim Fenn
        fe...@st...
        Stanford University, School of Medicine
        James H. Clark Center
        318 Campus Drive, Room E300
        Stanford, CA  94305-5432
        Phone:  (650) 736-1714
        FAX:  (650) 736-1961

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

RE: [PyMOL] mixing ray_shadows states

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

Nat,

ray_shadows is a global setting (only) -- changing it for individual =
objects has no effect.

set ray_shadows, 0
ray

will work.

Cheers,
Warren



-----Original Message-----
From: pym...@li... on behalf of Nat Echols
Sent: Mon 11/21/2005 11:28 PM
To: pym...@li...
Subject: [PyMOL] mixing ray_shadows states
=20

I'm trying to make a high-quality figure showing ligand binding in a=20
cleft, incorporating sticks, electron density, and some combination of=20
cartoon/surface/lines for the protein.  Ray-traced shadows make the=20
perspective much clearer but also add visual "noise" - for instance, the =

electron density casts mesh-shaped shadows everywhere.  Is there a way =
to=20
prevent specific objects from casting shadows?  I tried

set ray_shadows =3D 0, mesh1

but this doesn't seem to have any effect.  (This is with a very recent=20
beta.)  Is it even possible in theory for the raytracer to support such =
an=20
option?


-------------------------------------------------------
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[PyMOL] errors compiling fink pymol 0.98

[Jean-Christophe A. <am...@es...>]

Hello,

I tried to compile pymol 0.98 from fink distribution but I got the =20
following error (see bellow) during gmp-4.1.4-2 which seems to be =20
required for pymol compilation. I got the same result on both =20
MacOSX10.3.9 and 10.4.3. How can I overcome this problem? Did anybody =20=

got the same error?
Thank a lot for any responses.
Jean-Christophe



Making check in misc
make  t-printf t-scanf t-locale
gcc-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests  -I/sw/=20
include  -g -O2 -mpowerpc -no-cpp-precomp -c `test -f t-printf.c || =20
echo './'`t-printf.c
/bin/sh ../../libtool --mode=3Dlink gcc-3.3  -g -O2 -mpowerpc -no-cpp-=20=

precomp  -L/sw/lib -o t-printf  t-printf.o ../../tests/=20
libtests.la ../../libgmp.la
mkdir .libs
gcc-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-printf t-=20
printf.o  -L/sw/lib ../../tests/.libs/libtests.a -L/sw/src/fink.build/=20=

gmp-4.1.4-2/gmp-4.1.4/.libs -L../../.libs -lgmp
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmp.3.dylib is not prebound
creating t-printf
gcc-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests  -I/sw/=20
include  -g -O2 -mpowerpc -no-cpp-precomp -c `test -f t-scanf.c || =20
echo './'`t-scanf.c
/bin/sh ../../libtool --mode=3Dlink gcc-3.3  -g -O2 -mpowerpc -no-cpp-=20=

precomp  -L/sw/lib -o t-scanf  t-scanf.o ../../tests/=20
libtests.la ../../libgmp.la
gcc-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-scanf t-scanf.o  -=20=

L/sw/lib ../../tests/.libs/libtests.a -L/sw/src/fink.build/=20
gmp-4.1.4-2/gmp-4.1.4/.libs -L../../.libs -lgmp
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmp.3.dylib is not prebound
creating t-scanf
gcc-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests  -I/sw/=20
include  -g -O2 -mpowerpc -no-cpp-precomp -c `test -f t-locale.c || =20
echo './'`t-locale.c
/bin/sh ../../libtool --mode=3Dlink gcc-3.3  -g -O2 -mpowerpc -no-cpp-=20=

precomp  -L/sw/lib -o t-locale  t-locale.o ../../tests/=20
libtests.la ../../libgmp.la
gcc-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-locale t-=20
locale.o  -L/sw/lib ../../tests/.libs/libtests.a -L/sw/src/fink.build/=20=

gmp-4.1.4-2/gmp-4.1.4/.libs -L../../.libs -lgmp
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmp.3.dylib is not prebound
ld: warning multiple definitions of symbol _localeconv
t-locale.o definition of _localeconv in section (__TEXT,__text)
/usr/lib/libSystem.dylib(localeconv.So) definition of _localeconv
creating t-locale
make  check-TESTS
PASS: t-printf
Warning, sscanf("","%d",&x) doesn't return EOF.
This affects gmp_sscanf, tests involving it will be suppressed.
You should try to get a fix for your libc.
PASS: t-scanf
PASS: t-locale
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
All 3 tests passed
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Making check in cxx
make  t-cast t-headers t-ostream t-constr t-expr
g++-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests  -I/sw/=20
include  -g -O2 -mpowerpc -no-cpp-precomp -c -o t-cast.o `test -f t-=20
cast.cc || echo './'`t-cast.cc
In file included from t-cast.cc:23:
../../gmpxx.h:2379: warning: use of `long double' type; its size may =20
change in
    a future release
../../gmpxx.h:2379: warning: (Long double usage is reported only once =20=

for each
    file.
../../gmpxx.h:2379: warning: To disable this warning, use -Wno-long-=20
double.)
/bin/sh ../../libtool --mode=3Dlink g++-3.3  -g -O2 -mpowerpc -no-cpp-=20=

precomp  -L/sw/lib -o t-cast  t-cast.o ../../tests/libtests.la ../../=20
libgmpxx.la ../../libgmp.la
mkdir .libs
g++-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-cast t-cast.o  -L/=20=

sw/lib ../../tests/.libs/libtests.a ../../.libs/libgmpxx.dylib /sw/=20
src/fink.build/gmp-4.1.4-2/gmp-4.1.4/.libs/libgmp.dylib -L/usr/lib/=20
gcc/darwin/3.3 -L/usr/lib/gcc/darwin -L/usr/libexec/gcc/darwin/ppc/=20
3.3/../../.. /usr/local/lib/libstdc++.a -L/Users/logan/Development/=20
CVS/1008/powerpc-apple-darwin6.1/libstdc++-v3/src -L/Users/logan/=20
Development/CVS/1008/powerpc-apple-darwin6.1/libstdc++-v3/src/.libs -=20
lm -lm -lm -L/Users/logan/Development/CVS/1008/gcc -L/usr/local/lib/=20
gcc-lib/powerpc-apple-darwin6.1/3.3 -L/usr/local/lib/gcc-lib/powerpc-=20
apple-darwin6.1/3.3/../../.. -lgcc -lSystem -L: -lm -lgcc -lSystem -=20
lgcc -lSystem ../../.libs/libgmp.dylib
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src/.libs) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
gcc) does not exist
ld: warning -L: directory name (:) does not exist
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmpxx.3.dylib is not prebound
creating t-cast
g++-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests  -I/sw/=20
include  -g -O2 -mpowerpc -no-cpp-precomp -c -o t-headers.o `test -f =20
t-headers.cc || echo './'`t-headers.cc
In file included from t-headers.cc:22:
../../gmpxx.h:2379: warning: use of `long double' type; its size may =20
change in
    a future release
../../gmpxx.h:2379: warning: (Long double usage is reported only once =20=

for each
    file.
../../gmpxx.h:2379: warning: To disable this warning, use -Wno-long-=20
double.)
/bin/sh ../../libtool --mode=3Dlink g++-3.3  -g -O2 -mpowerpc -no-cpp-=20=

precomp  -L/sw/lib -o t-headers  t-headers.o ../../tests/=20
libtests.la ../../libgmpxx.la ../../libgmp.la
g++-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-headers t-=20
headers.o  -L/sw/lib ../../tests/.libs/libtests.a ../../.libs/=20
libgmpxx.dylib /sw/src/fink.build/gmp-4.1.4-2/gmp-4.1.4/.libs/=20
libgmp.dylib -L/usr/lib/gcc/darwin/3.3 -L/usr/lib/gcc/darwin -L/usr/=20
libexec/gcc/darwin/ppc/3.3/../../.. /usr/local/lib/libstdc++.a -L/=20
Users/logan/Development/CVS/1008/powerpc-apple-darwin6.1/libstdc++-v3/=20=

src -L/Users/logan/Development/CVS/1008/powerpc-apple-darwin6.1/=20
libstdc++-v3/src/.libs -lm -lm -lm -L/Users/logan/Development/CVS/=20
1008/gcc -L/usr/local/lib/gcc-lib/powerpc-apple-darwin6.1/3.3 -L/usr/=20
local/lib/gcc-lib/powerpc-apple-darwin6.1/3.3/../../.. -lgcc -lSystem =20=

-L: -lm -lgcc -lSystem -lgcc -lSystem ../../.libs/libgmp.dylib
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src/.libs) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
gcc) does not exist
ld: warning -L: directory name (:) does not exist
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmpxx.3.dylib is not prebound
creating t-headers
g++-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests  -I/sw/=20
include  -g -O2 -mpowerpc -no-cpp-precomp -c -o t-ostream.o `test -f =20
t-ostream.cc || echo './'`t-ostream.cc
/bin/sh ../../libtool --mode=3Dlink g++-3.3  -g -O2 -mpowerpc -no-cpp-=20=

precomp  -L/sw/lib -o t-ostream  t-ostream.o ../../tests/=20
libtests.la ../../libgmpxx.la ../../libgmp.la
g++-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-ostream t-=20
ostream.o  -L/sw/lib ../../tests/.libs/libtests.a ../../.libs/=20
libgmpxx.dylib /sw/src/fink.build/gmp-4.1.4-2/gmp-4.1.4/.libs/=20
libgmp.dylib -L/usr/lib/gcc/darwin/3.3 -L/usr/lib/gcc/darwin -L/usr/=20
libexec/gcc/darwin/ppc/3.3/../../.. /usr/local/lib/libstdc++.a -L/=20
Users/logan/Development/CVS/1008/powerpc-apple-darwin6.1/libstdc++-v3/=20=

src -L/Users/logan/Development/CVS/1008/powerpc-apple-darwin6.1/=20
libstdc++-v3/src/.libs -lm -lm -lm -L/Users/logan/Development/CVS/=20
1008/gcc -L/usr/local/lib/gcc-lib/powerpc-apple-darwin6.1/3.3 -L/usr/=20
local/lib/gcc-lib/powerpc-apple-darwin6.1/3.3/../../.. -lgcc -lSystem =20=

-L: -lm -lgcc -lSystem -lgcc -lSystem ../../.libs/libgmp.dylib
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src/.libs) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
gcc) does not exist
ld: warning -L: directory name (:) does not exist
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmpxx.3.dylib is not prebound
ld: Undefined symbols:
virtual thunk to std::basic_istream<char, std::char_traits<char> =20
 >::~basic_istream()
virtual thunk to std::basic_istream<char, std::char_traits<char> =20
 >::~basic_istream()
virtual thunk to std::basic_ostream<char, std::char_traits<char> =20
 >::~basic_ostream()
virtual thunk to std::basic_ostream<char, std::char_traits<char> =20
 >::~basic_ostream()
make[3]: *** [t-ostream] Error 1
make[2]: *** [check-am] Error 2
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1
### execution of /var/tmp/tmp.5.gja4ng failed, exit code 2
Removing build lock...
/sw/bin/dpkg-lockwait -r fink-buildlock-gmp-4.1.4-2
(Reading database ... 22053 files and directories currently installed.)
Removing fink-buildlock-gmp-4.1.4-2 ...
Failed: phase compiling: gmp-4.1.4-2 failed

Before reporting any errors, please run "fink selfupdate" and
try again.  If you continue to have issues, please check to see if the
FAQ on fink's website solves the problem.  If not, ask on the fink-users
or fink-beginners mailing lists.  As a last resort, you can try e-=20
mailing
the maintainer directly:

         Dave Morrison <dm...@us...>

________________________
Jean-Christophe Am=E9, PhD
D=E9partement Int=E9grit=E9 du G=E9nome, UMR 7175-LC1 du CNRS
=C9cole Sup=E9rieure de Biotechnologie de Strasbourg
P=F4le API
Parc d'innovation, Boulevard S=E9bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: +33 (0)3 90 24 47 05
Fax.: +33 (0)3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html

=AB Science sans conscience n'est que ruine de l'=E2me ...=BB (Fran=E7ois =
=20
Rabelais, 1483-1553)

[PyMOL] mixing ray_shadows states

[Nat E. <ec...@uc...>]

I'm trying to make a high-quality figure showing ligand binding in a 
cleft, incorporating sticks, electron density, and some combination of 
cartoon/surface/lines for the protein.  Ray-traced shadows make the 
perspective much clearer but also add visual "noise" - for instance, the 
electron density casts mesh-shaped shadows everywhere.  Is there a way to 
prevent specific objects from casting shadows?  I tried

set ray_shadows = 0, mesh1

but this doesn't seem to have any effect.  (This is with a very recent 
beta.)  Is it even possible in theory for the raytracer to support such an 
option?

Re: [PyMOL] Another Nvidia question (7676 driver)!

[Nat E. <ec...@uc...>]

> Any body know how to fix this. Have people tested this driver? Should I load 
> an earlier driver?

When dealing with NVidia cards, I've found this is always the first thing 
to try whenever a problem arises.  Their Linux drivers are updated to 
support new hardware and fix old bugs, but they often introduce new bugs 
on old(er) hardware.  I have encountered several situations where the 
latest driver simply would not work on hardware that was fairly standard 
(e.g. Dell laptop!).  This was not due to the graphics card, but the rest 
of the system conflicting somehow with the driver.  I'm using 7676 with no 
problems here, but I doubt we have the same laptop.

[PyMOL] Another Nvidia question (7676 driver)!

[Joel T. <joe...@ot...>]

Hi folks,

Sorry for the slightly of topic question but I figure you guys know 
whats going on.

I have a linux box with RHE WS 4 and I have just installed the nvidia 
driver (7676 x86) which at least works so far! The problem is that the 
screen will occasionally (and randomly) start flickering badly rendering 
pymol and any other program essentially useless (flicker is the whole 
screen and the desktop shape changes to a trapezoid shape).

Any body know how to fix this. Have people tested this driver? Should I 
load an earlier driver?

Many thanks

Joel

-- 
Joel Tyndall, PhD

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

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

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

[PyMOL] apbs and pymol in fink (OS X)

[William S. <wg...@ch...>]

> I have the same problem on a mac G5 dual processor with newly  
> compiled pymol
> 0.98 and apbs 3.2, installed by fink. Also occurs with the standalone
> mac/xll hybrid executable, calling apbs 3.2 using the plug in menu.
>
> Interestingly, the programs work fine together on my mac G4 laptop,  
> with
> single processor apbs 3.2 but an older version of the mac/x11  
> hybrid pymol,
> using the same pdb files.

Hi Evan:

Could you go into a little more detail about what is going wrong?   
These compile ok for me on both the G4 and G5. I can also take one  
compiled on my G4 and run it on my G5.  Are you running from a  
directory in which you have write permissions?

FWIW there are now fink packages for both X-11 based pymol and for  
apbs (both vanilla and mpi) in fink.  If anyone experiences problems  
with the apbs packages, please let me know, and I will try to fix  
it.  Jack Howarth put together the pymol package, and it permits apbs  
to be used in the plug-in mode.  By default it runs with an x-windows  
based tkinter and display, but you can make an inverse-hybrid that  
uses an X-windows based display and the aqua tkinter in 10.4.x by  
substituting the line /usr/bin/python for /sw/bin/python in the /sw/ 
bin/pymol shell script.

Thanks,

Bill





William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

[PyMOL] Re: Slowwwww ray

[Michele F. <mfu...@me...>]

Stuart,

>  Stuart Endo-Streeter <stu...@du...>
> Default view, white with black background (sticks):
> Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.)
>
> Surface ray (white w/ black background):
> Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.)
>

thanks a lot for the test. I guess I'm in the right spot.


Warren,

> Did you just migrate from an older version?

yes sir,

> set orthoscopic
> =3D>2.58 seconds on 2 X 2 Ghz opteron
>
> load 1alk.pdb
> show surface
> set hash_max=3D160
> =3D>10.7 seconds on 2 x 2 Ghz opteron


that explains it. I did the same test and it "went back" to the speed  
I remember.
How do you determine the hash_max, 160? just by testing it?

Thanks


Michele