pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Yuri,

> I was putting together some movies using pymol and I have some 
> questions.
> First, how can I gradually make a surface go from solid to transparent? 
> Currently what I see is, in scene 1 I have it solid (0% transp.) 
> surface. Then after I show some ligands and aa side chains in scene 2, I 
> try to get the surface to look transparent (60%) in scene 3.
> However when I reinterpolate and play the movie every surface will be 
> 60%, the last setting I entered.

looks like scenes do not save settings. What you need is the "mdo" 
command to register the transparency with a particular movie frame.

http://pymolwiki.org/index.php/Mdo

Example:
mdo 1: set transparency, 0.0
mdo 100: set transparency, 0.6

This might also be interesting for you:
http://pymolwiki.org/index.php/Movie_fade

> Second, how can I make an object (ligand shown as stciks) rotate or 
> flip? I can make it move using "translate" but this happens in a linear 
> fashion.

not sure about this right now, but does "matrix_mode" make a difference?

set matrix_mode, 1

See:
http://www.pymolwiki.org/index.php/MovieSchool_5#Object_Motions

> Lastly, I like to save movies as pngs and later create the movie. How 
> can I change the output frame size, e.g. 1024x1024?

viewport 1024, 1024

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

Hope that helps.

Cheers,
   Thomas

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

Dear Users,
I was putting together some movies using pymol and I have some 
questions.
First, how can I gradually make a surface go from solid to transparent? 
Currently what I see is, in scene 1 I have it solid (0% transp.) 
surface. Then after I show some ligands and aa side chains in scene 2, I 
try to get the surface to look transparent (60%) in scene 3.
However when I reinterpolate and play the movie every surface will be 
60%, the last setting I entered.
Second, how can I make an object (ligand shown as stciks) rotate or 
flip? I can make it move using "translate" but this happens in a linear 
fashion.
Lastly, I like to save movies as pngs and later create the movie. How 
can I change the output frame size, e.g. 1024x1024?

Thank you so much for your time,

-- 
Yuri Pompeu

I'm trying to understand the map_new command, especially the "gaussian" option.

What determines the shape of the gaussian function? What is the relationship between the "b" factor and the variance (or the full-width-half-maxium) of the gaussian? How is the map normalized?

What does the "grid" option of the map_new command do? And the gaussian_resolution setting?

Daniel

Hi Anasuya,

your question is related to this one from September last year:
http://www.mail-archive.com/pym...@li.../msg09588.html

In short (example with heme as ligand):

select ligand, chain A and resn HEM
select shortrange, byres (polymer within 4.5 of ligand)
select midrange, byres ((polymer within 9 of ligand) and not shortrange)

Relevant reading:
http://www.pymolwiki.org/index.php/Selection_Algebra

Cheers,
   Thomas

On 02/28/2012 08:10 PM, Anasuya Dighe wrote:
> Hello ,
>
> I want to extract out complete amino acid residues which fall "within a radius
> of 4 to 9 Angstroms from the ligand".
>
> What do I do in such a case, given the pdb id's, chain ID,  the name of the
> ligand and its residue id?
>
> PS: I want to avoid, extracting out cmplete residues within a 0-4.5A first AND
> THEN getting residues from 4.5-9A.
>
> Is there a direct way to do this?
>
> Please let me know.
>
> - Anasuya
>
>


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

Hi Andreas,

I forgot one step, sorry. The update.py script does not copy the header 
files from the include directory, so you need:

cd $VMD/plugins/include
cp vmdconio.h molfile_plugin.h $PYMOL/contrib/uiuc/plugins/include

Here I put $VMD and $PYMOL as the respective source tree roots.

Hopefully these were all steps now...

Cheers,
   Thomas

On 02/28/2012 07:39 PM, Andreas Förster wrote:
> Thanks for your help, Thomas, but this didn't do the trick for me. I can
> run the python update.py and get a list of available plugins, but python
> setup.py build install (after patching) still crashes at the point of
> compiling the VMD plugins.
>
> gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
> -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE
> -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS
> -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS
> -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_VMD_PLUGINS -Iov/src
> -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5
> -I/usr/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt
> -Igenerated/include -Igenerated/src -Icontrib/uiuc/plugins/include
> -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/include/python2.6 -c
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o
> build/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o
> -ffast-math -funroll-loops -O3 -g
> In file included from
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:43:
> contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function
> ‘init_qmdata’:
> contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error:
> ‘MOLFILE_QMSTATUS_UNKNOWN’ undeclared (first use in this function)
> contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error: (Each
> undeclared identifier is reported only once
> contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error: for each
> function it appears in.)
> contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’:
> contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835: warning:
> ignoring return value of ‘fgets’, declared with attribute
> warn_unused_result
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
> ‘read_basis_rundata’:
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:262: error:
> ‘molfile_qm_basis_t’ has no member named ‘shell_types’
> error: command 'gcc' failed with exit status 1
>
> Looks like I'm tied to VMD.
>
>
> Andreas
>
>
>
> On 28/02/2012 3:02, Thomas Holder wrote:
>> Hi Andreas,
>>
>> this error was introduced in the open-source tree with the updates from
>> PyMOL 1.5. I'm not sure what the easiest fix would be, but here is how I
>> got it to work:
>>
>> Download the latest VMD source code and unpack it:
>> http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
>>
>> In the PyMOL source tree, edit the file
>> contrib/uiuc/plugins/molfile_plugin/update.py
>> and point "molfile_src_path" to the correct path in the VMD source tree.
>> Then run "python update.py".
>>
>> In setup.py, comment out "cpmdlogplugin.c", "cpmdplugin.c" and
>> "gaussianplugin.c" (they are commented out in update.py as well). You
>> may use the attached patch.
>>
>> Cheers,
>> Thomas
>>
>> On 02/28/2012 11:36 AM, Andreas Förster wrote:
>>> Dear all,
>>>
>>> driven beyond the reach of sanity by VMD, I've tried to enable the
>>> loading of DCD trajectories (from NAMD2 molecular dynamics simulations)
>>> in PyMOL. I followed the instructions given on this mailing list a few
>>> weeks back, specifically (setup.py):
>>>
>>> - uncommenting "contrib/uiuc/plugins/include",
>>> "contrib/uiuc/plugins/molfile_plugin/src",
>>> ("_PYMOL_VMD_PLUGINS",None),
>>> - changing the line underneath
>>> # VMD plugin support
>>> # switch the 0 to 1 to activate the additional source code
>>> from ] + 0 * [
>>> to ] + 1 * [
>>>
>>> Compilation (python setup.py build install) crashes because of an error
>>> in the molfile plugin:
>>>
>>> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
>>> ‘read_basis_metadata’:
>>> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208: error:
>>> ‘molfile_qm_metadata_t’ has no member named ‘have_esp’
>>> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209: error:
>>> ‘molfile_qm_metadata_t’ has no member named ‘have_npa’
>>> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211: error:
>>> ‘molfile_qm_metadata_t’ has no member named ‘have_internals’
>>> error: command 'gcc' failed with exit status 1
>>>
>>>
>>> Have others encountered that? Is there a solution or work-around?
>>>
>>> Thanks.
>>>
>>>
>>> Andreas


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

Hello ,

I want to extract out complete amino acid residues which fall "within a radius
of 4 to 9 Angstroms from the ligand".

What do I do in such a case, given the pdb id's, chain ID,  the name of the
ligand and its residue id?

PS: I want to avoid, extracting out cmplete residues within a 0-4.5A first AND
THEN getting residues from 4.5-9A.

Is there a direct way to do this?

Please let me know.

- Anasuya


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Hi Andreas,

this error was introduced in the open-source tree with the updates from 
PyMOL 1.5. I'm not sure what the easiest fix would be, but here is how I 
got it to work:

Download the latest VMD source code and unpack it:
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

In the PyMOL source tree, edit the file
contrib/uiuc/plugins/molfile_plugin/update.py
and point "molfile_src_path" to the correct path in the VMD source tree. 
Then run "python update.py".

In setup.py, comment out "cpmdlogplugin.c", "cpmdplugin.c" and 
"gaussianplugin.c" (they are commented out in update.py as well). You 
may use the attached patch.

Cheers,
   Thomas

On 02/28/2012 11:36 AM, Andreas Förster wrote:
> Dear all,
>
> driven beyond the reach of sanity by VMD, I've tried to enable the
> loading of DCD trajectories (from NAMD2 molecular dynamics simulations)
> in PyMOL.  I followed the instructions given on this mailing list a few
> weeks back, specifically (setup.py):
>
> - uncommenting "contrib/uiuc/plugins/include",
>                  "contrib/uiuc/plugins/molfile_plugin/src",
>                 ("_PYMOL_VMD_PLUGINS",None),
> - changing the line underneath
>          # VMD plugin support
>          # switch the 0 to 1 to activate the additional source code
>     from    ] + 0 * [
>     to      ] + 1 * [
>
> Compilation (python setup.py build install) crashes because of an error
> in the molfile plugin:
>
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
> ‘read_basis_metadata’:
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208: error:
> ‘molfile_qm_metadata_t’ has no member named ‘have_esp’
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209: error:
> ‘molfile_qm_metadata_t’ has no member named ‘have_npa’
> contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211: error:
> ‘molfile_qm_metadata_t’ has no member named ‘have_internals’
> error: command 'gcc' failed with exit status 1
>
>
> Have others encountered that?  Is there a solution or work-around?
>
> Thanks.
>
>
> Andreas

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

Dear all,

driven beyond the reach of sanity by VMD, I've tried to enable the 
loading of DCD trajectories (from NAMD2 molecular dynamics simulations) 
in PyMOL.  I followed the instructions given on this mailing list a few 
weeks back, specifically (setup.py):

- uncommenting "contrib/uiuc/plugins/include",
                "contrib/uiuc/plugins/molfile_plugin/src",
               ("_PYMOL_VMD_PLUGINS",None),
- changing the line underneath
        # VMD plugin support
        # switch the 0 to 1 to activate the additional source code
   from    ] + 0 * [
   to      ] + 1 * [

Compilation (python setup.py build install) crashes because of an error 
in the molfile plugin:

contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function 
‘read_basis_metadata’:
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208: error: 
‘molfile_qm_metadata_t’ has no member named ‘have_esp’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209: error: 
‘molfile_qm_metadata_t’ has no member named ‘have_npa’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211: error: 
‘molfile_qm_metadata_t’ has no member named ‘have_internals’
error: command 'gcc' failed with exit status 1


Have others encountered that?  Is there a solution or work-around?

Thanks.


Andreas



-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk

Hi Gudrun,

Gudrun Lotze wrote:
> Dear all,
>
> I wish to ray trace my object so it looks nice. I have chosen a mesh as surface representation.
>
> I did 
> viewport 1024, 768
> ray 1024, 768
>
> But the mesh is black afterwards and not anymore blue.
> Is there a chance to keep the color and have less dominant lines for the mesh?
>
>   
May be this could help:
bg_color white
set mesh_radius, 0.015
ray 1024, 768

> Is there a chance to view the object in question for example in the XY, YZ plane? Are there somewhere easy rotation matrix available?
> I tried to bring my object manually into the YZ plane view, for example, but it works only halfhearted. 
> It would be nice to be able to tell pymol in a very easy way which view I would like to see the object.
>
>   
http://www.pymolwiki.org/index.php/Rotate

Best,
Zhijian Xu

> Thank you for your patience.
> Kind regards
> Gudrun
>
>  
> ------------------------------------------------------------------------------
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>
>
>   

Hi Gudrun,

> But the mesh is black afterwards and not anymore blue.

You may want to check your light position, or try a slighter blue.

> Is there a chance to keep the color and have less dominant lines for the mesh?

I'm not artistically skilled enough to know about less dominant lines, 
but the mesh_width setting can be used to make thinner (or thicker) lines.

> Is there a chance to view the object in question for example in the XY, YZ plane? Are there somewhere easy rotation matrix available?
> I tried to bring my object manually into the YZ plane view, for example, but it works only halfhearted. 
> It would be nice to be able to tell pymol in a very easy way which view I would like to see the object.

The turn/rotate commands can be used fairly easily for 90 degree turns; 
but I'm not sure if that's what you're asking about.

Pete

Dear all,

I wish to ray trace my object so it looks nice. I have chosen a mesh as surface representation.

I did 
viewport 1024, 768
ray 1024, 768

But the mesh is black afterwards and not anymore blue.
Is there a chance to keep the color and have less dominant lines for the mesh?

Is there a chance to view the object in question for example in the XY, YZ plane? Are there somewhere easy rotation matrix available?
I tried to bring my object manually into the YZ plane view, for example, but it works only halfhearted. 
It would be nice to be able to tell pymol in a very easy way which view I would like to see the object.

Thank you for your patience.
Kind regards
Gudrun

 

Dear Gudrun,

I have no experience with PyMOL on Mac. Maybe this helps:
http://pymolwiki.org/index.php/Mouse_Controls

Deselecting objects does not help, because by default you transform in 
camera space, which affects all objects. What you need is transformation 
in model space, which is achieved by "A > drag" or "A > drag matrix" for 
a particular object.

Here an example to use the command line:
translate [10,0,0], object=axes

Hope that helps.

Cheers,
   Thomas

On 02/27/2012 03:21 PM, Gudrun Lotze wrote:
> Dear Thomas Thank you for your reply. The mouse dragging does not
> work because the Mac starts to move windows in a very beautiful way
> which I never came across. :-) So I used a 2-button mouse. But there
> is still a problem. The dummy atom model and the three axes object
> are always moving together when dragging around. Even when I deselect
> the model, drag the cross, and re-select the model, the model has
> moved as well. May I have to shift the cross within the script?
>
> Kind regards Gudrun
>
> Am 27.02.2012 um 12:50 schrieb Thomas Holder:
>
>> Hi Gudrun,
>>
>> On 02/27/2012 01:36 PM, Gudrun Lotze wrote:
>>> The axes appear, but the screen in pymol is now split into two
>>> sections with the cross covering one part. Is there a chance to
>>> move the cross closer to the model in one screen section? A bit
>>> like shown in picture on page http://pymolwiki.org/index.php/Axes
>>> .
>>
>> You can drag the axes object with the mouse. In the right panel,
>> click on "A>  drag" and then use Shift+MiddleMouseButton to drag
>> it.
>>
>> If you prefer the command line over mouse, you could use translate
>> and rotate commands: http://pymolwiki.org/index.php/Translate
>> http://pymolwiki.org/index.php/Rotate
>>
>> Cheers, Thomas

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

Try install tkinter

Tkinter uses tcl 8.4 (something...)



Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234



2012/2/27 <Gre...@mh...>

> Hi Jason,
>
> I just installed pymol 1.5.0.3 on our linux machines and the segfault in
> libtcl8.5.so upon help->about is still present. Do you have any hint when
> this will be fixed?
>
> Best regards,
> Joachim
> --
> Dr. rer. nat. Joachim Greipel
> Med. Hochschule Hannover
> Biophys. Chem. OE 4350
> Carl-Neuberg-Str. 1
> 30625 Hannover
> Germany
>
> Fon: +49-511-532-3718
> Fax: +49-511-532-16-3718
>
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: Jason Vertrees [mailto:jas...@sc...]
> > Gesendet: Donnerstag, 19. Mai 2011 17:53
> > An: Greipel, Joachim Dr.
> > Cc: pym...@li...; he...@sc...
> > Betreff: Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon
> > "help->about"
> >
> > Hi Joachim,
> >
> > > I always get a segmentation fault, when I click
> > "help"->"about" to see the
> > > version details of pymol. The respective entry in
> > /var/log/messages is:
> > >
> > > pymol.exe[4991]: segfault at 3e0019b ip 00000000f74857a0 sp
> > 00000000f3bab9a8
> > > error 4 in libtcl8.5.so[f7410000+ed0
> > > 00]
> >
> > Indeed on a few Linux distros, there is a crash when selecting Help >
> > About.  We're trying to track down the cause.  The error happens in
> > our pure Python code and the segfault happens in the libtcl8.5 shared
> > library.
> >
> > If you're checking for the PyMOL version number, please use
> > "get_version" in the meantime.
> >
> > Cheers,
> >
> > -- Jason
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrodinger, LLC
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
> >
>
>
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Gudrun,

On 02/27/2012 01:36 PM, Gudrun Lotze wrote:
> The axes appear, but the screen in pymol is now split into two sections
> with the cross covering one part. Is there a chance to move the cross
> closer to the model in one screen section?
> A bit like shown in picture on page http://pymolwiki.org/index.php/Axes .

You can drag the axes object with the mouse. In the right panel, click 
on "A > drag" and then use Shift+MiddleMouseButton to drag it.

If you prefer the command line over mouse, you could use translate and 
rotate commands:
http://pymolwiki.org/index.php/Translate
http://pymolwiki.org/index.php/Rotate

Cheers,
   Thomas

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

Hi Jason,

I just installed pymol 1.5.0.3 on our linux machines and the segfault in
libtcl8.5.so upon help->about is still present. Do you have any hint when
this will be fixed?

Best regards,
Joachim 
--
Dr. rer. nat. Joachim Greipel
Med. Hochschule Hannover
Biophys. Chem. OE 4350
Carl-Neuberg-Str. 1
30625 Hannover
Germany
 
Fon: +49-511-532-3718
Fax: +49-511-532-16-3718
 
 

> -----Ursprüngliche Nachricht-----
> Von: Jason Vertrees [mailto:jas...@sc...] 
> Gesendet: Donnerstag, 19. Mai 2011 17:53
> An: Greipel, Joachim Dr.
> Cc: pym...@li...; he...@sc...
> Betreff: Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon 
> "help->about"
> 
> Hi Joachim,
> 
> > I always get a segmentation fault, when I click 
> "help"->"about" to see the
> > version details of pymol. The respective entry in 
> /var/log/messages is:
> >
> > pymol.exe[4991]: segfault at 3e0019b ip 00000000f74857a0 sp 
> 00000000f3bab9a8
> > error 4 in libtcl8.5.so[f7410000+ed0
> > 00]
> 
> Indeed on a few Linux distros, there is a crash when selecting Help >
> About.  We're trying to track down the cause.  The error happens in
> our pure Python code and the segfault happens in the libtcl8.5 shared
> library.
> 
> If you're checking for the PyMOL version number, please use
> "get_version" in the meantime.
> 
> Cheers,
> 
> -- Jason
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
> 

Dear all,

I used the following script David pointed out:

from pymol.cgo import *
from pymol import cmd
 
w = 0.06 # cylinder width 
l = 0.75 # cylinder length
h = 0.25 # cone hight
d = w * 1.618 # cone base diameter
 
obj = [CYLINDER, 0.0, 0.0, 0.0,   l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0,
       CYLINDER, 0.0, 0.0, 0.0, 0.0,   l, 0.0, w, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0,
       CYLINDER, 0.0, 0.0, 0.0, 0.0, 0.0,   l, w, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0,
       CONE,   l, 0.0, 0.0, h+l, 0.0, 0.0, d, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 
       CONE, 0.0,   l, 0.0, 0.0, h+l, 0.0, d, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0, 
       CONE, 0.0, 0.0,   l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0]
 
cmd.load_cgo(obj, 'axes')


The axes appear, but the screen in pymol is now split into two sections with the cross covering one part. Is there a chance to move the cross closer to the model in one screen section?
A bit like shown in picture on page http://pymolwiki.org/index.php/Axes .

Kind regards
Gudrun 





Am 27.02.2012 um 12:01 schrieb David Hall:

> http://pymolwiki.org/index.php/Axes
> 
> -David
> 
> On Feb 27, 2012, at 5:38 AM, Gudrun Lotze <gud...@gm...> wrote:
> 
>> Dear all,
>> 
>> is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please?
>> I have a protein made from dummy atoms and there is no unit cell.
>> I just want to show clearly which plane is shown when presenting the model in my document.
>> 
>> Thank you for your help.
>> Kind regards
>> Gudrun Lotze
>> 
>> 
>> ------------------------------------------------------------------------------
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http://pymolwiki.org/index.php/Axes

-David

On Feb 27, 2012, at 5:38 AM, Gudrun Lotze <gud...@gm...> wrote:

> Dear all,
> 
> is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please?
> I have a protein made from dummy atoms and there is no unit cell.
> I just want to show clearly which plane is shown when presenting the model in my document.
> 
> Thank you for your help.
> Kind regards
> Gudrun Lotze
> 
> 
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Dear all,

is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please?
I have a protein made from dummy atoms and there is no unit cell.
I just want to show clearly which plane is shown when presenting the model in my document.

Thank you for your help.
Kind regards
Gudrun Lotze

Hi Shane,

I have a script which saves a colored sequence in HTML format. See 
attachment.

Example usage:

     run save_colored_fasta.py
     save_colored_fasta seq.html

It should be possible to copy&paste the colored sequence from your 
browser to excel.

Cheers,
   Thomas

Shane Neeley wrote, On 02/27/12 01:45:
>     Hi Pymol Network,
> 
>     I would appreciate someones help in extracting the sequence in the
>     viewer above the protein. I have gone through the sequence and
>     changed AAs to different colors based on their position. I would
>     ideally like to be able to copy that sequence with the colors that
>     they are coded so that I could export it to an excel file. Is this
>     possible? 
> 
>     Thanks very much.
> 
>     Shane

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

Hi Pymol Network,
>
> I would appreciate someones help in extracting the sequence in the viewer
> above the protein. I have gone through the sequence and changed AAs to
> different colors based on their position. I would ideally like to be able
> to copy that sequence with the colors that they are coded so that I could
> export it to an excel file. Is this possible?
>
> Thanks very much.
>
> Shane
>

Hi pymolers.

I was trying to test our lab pymol installation from home.
But i ran into an error in freeglut, when executing over SSH.
I have found a solution, but is unsure what it does, and if means something
for
speed and 3D rendering.

*When I ran:*
*[software@elvis ~]$ pymol*
*freeglut (pymol):  ERROR:  Internal error <FBConfig with necessary
capabilities not found> in function fgOpenWindow*
*X Error of failed request:  BadWindow (invalid Window parameter)*
*  Major opcode of failed request:  4 (X_DestroyWindow)*
*  Resource id in failed request:  0x0*
*  Serial number of failed request:  33*
*  Current serial number in output stream:  36*
* PyMOL: abrupt program termination.*

I found a solution here:
http://superuser.com/questions/203587/remotely-connecting-to-ubuntu-server-from-a-macbook-cant-run-pymol
http://unix.stackexchange.com/questions/1437/what-does-libgl-always-indirect-1-actually-do
http://ubuntuforums.org/showthread.php?t=1682020

*I then changed the pymol exexution script.*
*
*
*[software@elvis ~/pymolsvn]$ ls*
*modules  pymol  pymolMPEG.sh  pymolplugins  Pymol-script-repo
 pymolsvn.desktop  svnfreemol  svnpymol  updatepymol.sh*
*[software@elvis ~/pymolsvn]$ cat pymolMPEG.sh *
*#!/bin/bash*
*if [ ! -f $HOME/.local/share/applications/pymolsvn.desktop ];*
*then*
*ln -s /sbinlab2/software/pymolsvn/pymolsvn.desktop
$HOME/.local/share/applications/pymolsvn.desktop*
*fi*
*
*
*export FREEMOL=/sbinlab2/software/pymolsvn/svnfreemol/freemol*
*export PYMOL_GIT_MOD=/sbinlab2/software/pymolsvn/Pymol-script-repo/modules*
*export
PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/PIL
*
*export
PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-tk
*
*export
PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-dynload
*
*export PYTHONPATH=/sbinlab2/software/pymolsvn:$PYTHONPATH*
*export
PYTHONPATH=/sbinlab2/software/pymolsvn/Pymol-script-repo/modules:$PYTHONPATH
*
*export PYTHONPATH=/sbinlab2/software/pymolsvn/Pymol-script-repo:$PYTHONPATH
*
*export PYMOL_PATH=/sbinlab2/software/pymolsvn/modules/pymol/pymol_path*
*export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sbinlab2/software/x64/lib/pymollib
*
*export LIBGL_ALWAYS_INDIRECT=no*
*
*
*/usr/bin/python /sbinlab2/software/pymolsvn/modules/pymol/__init__.py "$@"*


It now works fine when running pymol.
And it also works when i set: *export LIBGL_ALWAYS_INDIRECT=yes*
*
*
But what is the fastest solution, so pymol can use Direct rendering?
Locally, when sitting at the computer and over SSH.

Best
Troels

Francis,

Great suggestion. We've taken note.

Cheers,

-- Jason

On Fri, Feb 24, 2012 at 11:47 AM, Francis E Reyes
<Fra...@co...> wrote:
> Would love the ability to have thicker outlines on labels. I need the labels in stereo so I'm doing this in pymol.
>
> Any suggestions?
>
> Thanks!
>
> F
>
>
>
>
>
> ---------------------------------------------
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Would love the ability to have thicker outlines on labels. I need the labels in stereo so I'm doing this in pymol.

Any suggestions?

Thanks!

F
 




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

You can see the requirements here:

http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit

Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234



2012/2/24 Andreas Förster <doc...@gm...>

> Hi Yuri,
>
> I'd say yes.  It runs under RHEL 6.2.  In contrast to what was
> officially said, there is no requirement for python 2.7.  Version 2.6.6
> works fine.
>
>
> Andreas
>
>
>
> On 24/02/2012 4:12, Yuri wrote:
> > Hello everyone,
> > Does the latest free Pymolv1.5.0.1 from sourceforge run on CentOS 6?
> > Thanks
>
> --
>          Andreas Förster, Research Associate
>         Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>             http://www.msf.bio.ic.ac.uk
>
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Yuri,

I'd say yes.  It runs under RHEL 6.2.  In contrast to what was 
officially said, there is no requirement for python 2.7.  Version 2.6.6 
works fine.


Andreas



On 24/02/2012 4:12, Yuri wrote:
> Hello everyone,
> Does the latest free Pymolv1.5.0.1 from sourceforge run on CentOS 6?
> Thanks

-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk