pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Pawel,

the state argument of the select command is only for state sensitive
selection criteria (like around or within operators). The selection will
always be on all states (exception: discrete objects).

The angle_between_helices command itself needs a state argument. Since I
wrote that script, it's my fault that it doesn't have one :) But I
continued to work on that script in the PSICO package and actually added
state support there. So I recommend that you install PSICO and change
your script like this:

import psico.orientation as abh
x=abh.angle_between_helices('hel1','hel2', visualize=0,
                            state1=i+1, state2=i+1, quiet=1)

http://pymolwiki.org/index.php/Psico
https://github.com/speleo3/pymol-psico

Hope that helps.

Cheers,
  Thomas

Pawel wrote, On 07/31/13 20:18:
> Hello,
> 
> I am having trouble running scripts which vary selections on different
> states of a PyMOL object. I've converted an MD trajectory into a pdb
> with 500 models that PyMOL loads as 500 states of 1 object. For example,
> I would then like to run the anglesbetweenhelices.py script (from PyMOL
> wiki) on each state separately. A simple script example:
> 
>     import anglebetweenhelices as abh
>     cmd.load('output.pdb', object="cdp")
>     for i in range(1,501):
>         cmd.set('state',i,'cdp')
>         cmd.select('hel1','/cdp///1-22')
>         cmd.select('hel2','/cdp///25-37')
>         x=abh.angle_between_helices('hel1','hel2', visualize=0, quiet=1)
>         print x
> 
> In theory the select command has a state option but this doesn't seem to
> work (as is confirmed by
> http://www.mail-archive.com/pym...@li.../msg08224.html).
> I then tried using the set state command, but this also does not seem to
> affect the actual coordinates of the selection. The only thing that does
> work is if in the GUI I go to the desired state by pressing the "<" and
> ">" animation buttons. But is there a way to select the state from
> within a script?
> 
> Thanks!
> Pawel

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hello,

I am having trouble running scripts which vary selections on different 
states of a PyMOL object. I've converted an MD trajectory into a pdb 
with 500 models that PyMOL loads as 500 states of 1 object. For example, 
I would then like to run the anglesbetweenhelices.py script (from PyMOL 
wiki) on each state separately. A simple script example:

    import anglebetweenhelices as abh
    cmd.load('output.pdb', object="cdp")
    for i in range(1,501):
         cmd.set('state',i,'cdp')
         cmd.select('hel1','/cdp///1-22')
         cmd.select('hel2','/cdp///25-37')
         x=abh.angle_between_helices('hel1','hel2', visualize=0, quiet=1)
         print x

In theory the select command has a state option but this doesn't seem to 
work (as is confirmed by 
http://www.mail-archive.com/pym...@li.../msg08224.html). 
I then tried using the set state command, but this also does not seem to 
affect the actual coordinates of the selection. The only thing that does 
work is if in the GUI I go to the desired state by pressing the "<" and 
">" animation buttons. But is there a way to select the state from 
within a script?

Thanks!
Pawel

Hi Pawel,

1. PyMOL might have a bug here, or at least the amber file support is
   rather limited at the momemt. Also note that the amber restart file
   is not a trajectory but contains only one frame. PyMOL internally
   treats rst and crd the same (which we should change, actually). So
   this will work for a proper formatted restart file:

   PyMOL> load ../Cdp_UCM.rst7, CDP, 1, crd

2. the load_traj command has an "interval" argument:

   PyMOL> load_traj ../Cdp_UCM.dcd, CDP, 1, interval=10

You'll always get a quick hint about the command arguments like this:
PyMOL>load_traj ?

Cheers,
  Thomas

Pawel wrote, On 07/30/13 22:42:
> Hello Pymol Users. I just started getting into Pymol and encountered two
> issues I'd like to ask about.
> 
> 1. When trying to load amber topology and coordinate files that do not
> have the default extension, I get this error:
> 
>     PyMOL>load ../Cdp_UCM.prmtop, CDP, 1, top
>      ObjectMolecule: Attempting to read Amber7 topology file.
>      CmdLoad: "../Cdp_UCM.prmtop" loaded as "CDP".
>     PyMOL>load ../Cdp_UCM.rst7, CDP, 1, rst
>     CmdLoad-Error: must load object topology before loading restart file!
> 
> 
> If files have the default extension and I don't need to to specify the
> file type, loading works fine:
> 
>     PyMOL>load Cdp_UCM.top, CDP, 1
>      ObjectMolecule: Attempting to read Amber7 topology file.
>      CmdLoad: "Cdp_UCM.top" loaded as "CDP".
>     PyMOL>load Cdp_UCM.rst, CDP, 1
>      ObjectMolecule: read coordinates into state 1...
>      CmdLoad: "Cdp_UCM.rst" appended into object "CDP".
>      CmdLoad: 1 total states in the object.
> 
> Of course I can work around this by modifying the extensions on my files
> before loading, but due to compatibility issues with other scripts I'd
> prefer to leave the extensions I've been using heretofore.
> 
> 2. When using the load_traj command is there a way to select which
> frames are to be loaded? For example to load only every 10th frame?
> 
> Pawel

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

You can also use the builder module. 

Click on the two atoms and then delete bond button

-----Original Message-----
From: Martin Hediger [mailto:ma...@bl...] 
Sent: Wednesday, 31 July 2013 12:40 a.m.
To: pym...@li...
Subject: [PyMOL] Unbond two atoms

Dear PyMOL users

Sometimes PyMOL draws bonds between atoms which are not supposed to be connected. I know it is possible to unbond them using "unbond atom1, atom2", however this requires to always select the atoms and rename the selections to "atom1" and "atom2", respectively. It would be great if I could just click two atoms (using the "Atoms" selection quantifier) and then have them unbonded. How could I do that?

Thanks a lot for any hints.
Martin

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Hello Pymol Users. I just started getting into Pymol and encountered two 
issues I'd like to ask about.

1. When trying to load amber topology and coordinate files that do not 
have the default extension, I get this error:

    PyMOL>load ../Cdp_UCM.prmtop, CDP, 1, top
      ObjectMolecule: Attempting to read Amber7 topology file.
      CmdLoad: "../Cdp_UCM.prmtop" loaded as "CDP".
    PyMOL>load ../Cdp_UCM.rst7, CDP, 1, rst
    CmdLoad-Error: must load object topology before loading restart file!


If files have the default extension and I don't need to to specify the 
file type, loading works fine:

    PyMOL>load Cdp_UCM.top, CDP, 1
      ObjectMolecule: Attempting to read Amber7 topology file.
      CmdLoad: "Cdp_UCM.top" loaded as "CDP".
    PyMOL>load Cdp_UCM.rst, CDP, 1
      ObjectMolecule: read coordinates into state 1...
      CmdLoad: "Cdp_UCM.rst" appended into object "CDP".
      CmdLoad: 1 total states in the object.

Of course I can work around this by modifying the extensions on my files 
before loading, but due to compatibility issues with other scripts I'd 
prefer to leave the extensions I've been using heretofore.

2. When using the load_traj command is there a way to select which 
frames are to be loaded? For example to load only every 10th frame?

Pawel

Hi,

I put some instructions on the PyMOLWiki for those who want to play with
the Leap Motion Controller.

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

Cheers,
  Thomas

David Hall wrote, On 07/29/13 17:18:
> Jason can fill you in if there's an update, but the latest status update
> I'm aware of was:
> http://www.mail-archive.com/pym...@li.../msg11572.html
> 
> -David
> 
> On Monday, July 29, 2013 at 11:04 AM, H. Adam Steinberg wrote:
> 
>> It would be great if we could control PyMOL with a Leap Motion control
>> <https://www.leapmotion.com>.
>>
>> I see it supports molecules.
>>
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi all,

I'm not very experienced with installing things from source, so you'll have to bear with me a bit here….

I'm trying to get pymol 1.6.0.0 working on my macbook (OS X 10.8.4). The install seems to go ok (home directory set to /sw) but when I try to launch pymol, it exits with this message:

Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 1.20.
OpenGL graphics engine:
 GL_VENDOR: NVIDIA Corporation
 GL_RENDERER: NVIDIA GeForce GT 650M OpenGL Engine
 GL_VERSION: 2.1 NVIDIA-8.12.47 310.40.00.05f01
Detected 8 CPU cores.  Enabled multithreaded rendering.
libpng warning: Application built with libpng-1.5.11 but running with 1.6.3
/sw/bin/pymol: line 4: 86592 Segmentation fault: 11  "/sw/bin/python" "/sw/lib/python/pymol/__init__.py" "$@"

The version of python I have is 2.7.5 .
If I just do "python /sw/lib/python/pymol/__init__.py" then I get the segmentation fault 11 error. 
Can anyone help me fix this?

Thanks,

Narin

Hi Martin,

that's what edit mode is for. Right-click on the mouse mode panel,
choose "3-Button Editing", pick the two atoms and type "unbond".

Cheers,
  Thomas

Martin Hediger wrote, On 07/30/13 14:40:
> Dear PyMOL users
> 
> Sometimes PyMOL draws bonds between atoms which are not supposed to be 
> connected. I know it is possible to unbond them using "unbond atom1, 
> atom2", however this requires to always select the atoms and rename the 
> selections to "atom1" and "atom2", respectively. It would be great if I 
> could just click two atoms (using the "Atoms" selection quantifier) and 
> then have them unbonded. How could I do that?
> 
> Thanks a lot for any hints.
> Martin

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Dear PyMOL users

Sometimes PyMOL draws bonds between atoms which are not supposed to be 
connected. I know it is possible to unbond them using "unbond atom1, 
atom2", however this requires to always select the atoms and rename the 
selections to "atom1" and "atom2", respectively. It would be great if I 
could just click two atoms (using the "Atoms" selection quantifier) and 
then have them unbonded. How could I do that?

Thanks a lot for any hints.
Martin

Dear PyMOL Users,

I would like to announce you the plugin for PyMOL, which allows to perform
molecular dynamics simulation on PyMOL loaded molecules using GROMACS and
display results back to PyMOL in form of the animation.
You can find more information on PyMOL Wiki:
http://www.pymolwiki.org/index.php/GROMACS_Plugin
and GitHub page of the project:
https://github.com/tomaszmakarewicz/Dynamics
The current work has been publish in scientific paper:
http://pubs.acs.org/doi/abs/10.1021/ci400071x
And you can find ready Ubuntu packages in following repository:
https://launchpad.net/~tomaszm/+archive/dynamics

If you have any question please do not hesitate to ask.

In case of any bug, request or error please fill Issue on the GitHub page.

Best regards,
-- 
Tomasz Makarewicz,
Laboratory of Biomolecular Systems Simulations,
Intercollegiate Faculty of Biotechnology,
University of Gdańsk and Medical University of Gdańsk,
Kładki 24, 80-822 Gdańsk, Poland


-----------------------------------------
Ten list został wysłany z serwera Uniwersytetu Gdańskiego.
http://www.ug.edu.pl/

Jason can fill you in if there's an update, but the latest status update I'm aware of was:
http://www.mail-archive.com/pym...@li.../msg11572.html

-David 

-David


On Monday, July 29, 2013 at 11:04 AM, H. Adam Steinberg wrote:

> It would be great if we could control PyMOL with a Leap Motion control <https://www.leapmotion.com>.
> 
> I see it supports molecules.
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
> 
> 
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 
> 

It would be great if we could control PyMOL with a Leap Motion control <https://www.leapmotion.com>.

I see it supports molecules.

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Greg,

You can also use the alter command to change the vdw to the value you want. This is often done with SAXS bead models so that they can then be surfaced.

alter (n. ca), vdw= 3

If this is set after the show spheres command the rebuild the view

rebuild

Hope this helps.

Best regards,
Mark

Sent from my iPhone

On Jul 26, 2013, at 4:12 PM, "Sampson, Jared" <Jar...@ny...<mailto:Jar...@ny...>> wrote:

[Re-posting to the list because, as usual, I forgot to Reply All...]

Hi Greg -

If I understand correctly (and just on a quick visual inspection in PyMOL it looks like I'm at least close), the sphere_scale setting will scale the size of the sphere relative to the van der Waals radius of the atom.  So at sphere_scale == 1, Carbon will be ~1.70Å, Oxygen will be ~1.52Å, Nitrogen ~1.55Å, and so forth.  To have a CA atom of 3Å radius, you would use sphere_scale of ( 3.0 / 1.7 ) = 1.76.

Hope that helps,

Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/




On Jul 26, 2013, at 3:23 PM, Gregory Ryslik <rs...@co...<mailto:rs...@co...>> wrote:

Hi,

I'm a fairly new user to PyMol and am having some trouble with the sphere_scale command. I understand that if I want to draw a sphere around the x'th ca atom, I can use:

show spheres, ////X/ca

However, what if I want that sphere to have a radius of 3 angstroms, or 6 angstroms, etc.

 I understand I can use set sphere_scale, 1, ///X/ca but what is the default scale of 1? Is it 1A, is it something else?

Thank you for your help!

Kind regards,
Greg
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[Re-posting to the list because, as usual, I forgot to Reply All...]

Hi Greg -

If I understand correctly (and just on a quick visual inspection in PyMOL it looks like I'm at least close), the sphere_scale setting will scale the size of the sphere relative to the van der Waals radius of the atom.  So at sphere_scale == 1, Carbon will be ~1.70Å, Oxygen will be ~1.52Å, Nitrogen ~1.55Å, and so forth.  To have a CA atom of 3Å radius, you would use sphere_scale of ( 3.0 / 1.7 ) = 1.76.

Hope that helps,

Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/




On Jul 26, 2013, at 3:23 PM, Gregory Ryslik <rs...@co...<mailto:rs...@co...>> wrote:

Hi,

I'm a fairly new user to PyMol and am having some trouble with the sphere_scale command. I understand that if I want to draw a sphere around the x'th ca atom, I can use:

show spheres, ////X/ca

However, what if I want that sphere to have a radius of 3 angstroms, or 6 angstroms, etc.

 I understand I can use set sphere_scale, 1, ///X/ca but what is the default scale of 1? Is it 1A, is it something else?

Thank you for your help!

Kind regards,
Greg
------------------------------------------------------------------------------
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Hi,

I'm a fairly new user to PyMol and am having some trouble with the 
sphere_scale command. I understand that if I want to draw a sphere 
around the x'th ca atom, I can use:

/show spheres, ////X/ca/

However, what if I want that sphere to have a radius of 3 angstroms, or 
6 angstroms, etc.

  I understand I can use set sphere_scale, 1, ///X/ca but what is the 
default scale of 1? Is it 1A, is it something else?

Thank you for your help!

Kind regards,
Greg

Hi Suhas,

have you looked at pymol/examples/devel/gl03.py ?

http://sourceforge.net/p/pymol/code/4037/tree/trunk/pymol/examples/devel/gl03.py

Cheers,
  Thomas

On Jul 26, 2013, at 11:21 AM, Narendra Suhas Jagannathan <su...@nu...> wrote:
> Hello,
>   I am relatively new to PyMol. I understand that using a CGO helps import an OpenGL object into the Pymol GUI. But does anyone know if it is possible to integrate an OpenGL stream like say, glxgears into the Pymol viewer?
> 
> Thanks
> Suhas

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hello,
   I am relatively new to PyMol. I understand that using a CGO helps import an OpenGL object into the Pymol GUI. But does anyone know if it is possible to integrate an OpenGL stream like say, glxgears into the Pymol viewer?

Thanks
Suhas

Hi Jordan,

If ray_trace_frames is on, and ray_opaque_background is off then
during the moviemaking process PyMOL uses the background color in the
movie.

At present, I think your only workaround is to export the PNGs with
transparencies and use a professional-quality movie exporter, like
Adobe Premier Pro (or similar).

Cheers,

-- Jason



On Tue, Jul 23, 2013 at 7:23 PM, Jordan Willis <jwi...@gm...> wrote:
> Hello,
>
> I'm using MacPymol 1.5.0.4
>
> When I save a ray traced .PNG file with set ray_opaque_background, 0 It does gives me a transparent background when I put the picture into other apps, e.g. Powerpoint. However, when I save it as a .mov file, I can see that pymol is trying for a transparent background (I can see each frame as a checkerboard), but the finished product is a solid black background that looks terrible. Has anyone encountered this problem and have a possible solution or workaround?
>
> Jordan
>
>
>
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
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-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

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

Hello,

I'm using MacPymol 1.5.0.4

When I save a ray traced .PNG file with set ray_opaque_background, 0 It does gives me a transparent background when I put the picture into other apps, e.g. Powerpoint. However, when I save it as a .mov file, I can see that pymol is trying for a transparent background (I can see each frame as a checkerboard), but the finished product is a solid black background that looks terrible. Has anyone encountered this problem and have a possible solution or workaround?

Jordan

numpy issue fixed in svn r4036.

Cheers,
  Thomas

Thomas Holder wrote, On 07/23/13 11:18:
> Hi Andreas,
> 
> I recently made a small change regarding numpy support. Can you please
> send me the output of the following command:
> 
> ls /usr/lib64/python2.6/site-packages/numpy/core/include/numpy
> 
> Meanwhile, just disable numpy support by removing the try/except block
> in setup.py line 221.
> 
> Thanks,
>   Thomas

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Dear all,

following up on my previous post, pymol-v1.6.0.0.tar.bz2 from 
http://sourceforge.net/projects/pymol/ compiles just fine on my machine. 
  It's the most recent source from svn that doesn't.



Andreas




-- 
                   Andreas Förster
      Crystallization and Xray Facility Manager
            Centre for Structural Biology
               Imperial College London

Hi Andreas,

I recently made a small change regarding numpy support. Can you please
send me the output of the following command:

ls /usr/lib64/python2.6/site-packages/numpy/core/include/numpy

Meanwhile, just disable numpy support by removing the try/except block
in setup.py line 221.

Thanks,
  Thomas

Andreas Förster wrote, On 07/23/13 11:05:
> Dear all,
> 
> I'm installing PyMOL from svn on a RHEL 6.2 machine.  This has always 
> worked.  Today, I get an "command 'gcc' failed with exit status 1" error 
> (see below).
> 
> Any suggestions?  Is there something amiss with the source?
> 
> Thanks.
> 
> Andreas
> 
> 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_VMD_PLUGINS -D_PYMOL_LIBPNG 
> -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS 
> -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS 
> -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 
> -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src 
> -Imodules/cealign/src/tnt -Ibuild/generated 
> -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src 
> -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include 
> -I/usr/include/freetype2 -I/usr/include/python2.6 -c layer3/Executive.c 
> -o build/temp.linux-x86_64-2.6/layer3/Executive.o -ffast-math 
> -funroll-loops -O3 -fcommon
> layer2/ObjectMap.c:42:32: error: numpy/ndarraytypes.h: No such file or 
> directory
> layer2/ObjectMap.c:43: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or 
> ‘__attribute__’ before ‘MyArrayObject’
> layer2/ObjectMap.c: In function ‘ObjectMapNumPyArrayToMapState’:
> layer2/ObjectMap.c:5555: error: ‘MyArrayObject’ undeclared (first use in 
> this function)
> layer2/ObjectMap.c:5555: error: (Each undeclared identifier is reported 
> only once
> layer2/ObjectMap.c:5555: error: for each function it appears in.)
> layer2/ObjectMap.c:5555: error: ‘pao’ undeclared (first use in this 
> function)
> layer2/ObjectMap.c:5559: error: expected expression before ‘)’ token
> error: command 'gcc' failed with exit status 1
> 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_VMD_PLUGINS -D_PYMOL_LIBPNG 
> -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS 
> -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS 
> -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 
> -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src 
> -Imodules/cealign/src/tnt -Ibuild/generated 
> -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src 
> -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include 
> -I/usr/include/freetype2 -I/usr/include/python2.6 -c layer4/Export.c -o 
> build/temp.linux-x86_64-2.6/layer4/Export.o -ffast-math -funroll-loops 
> -O3 -fcommon
> csbadmin@csb6 in pymol-src: layer2/RepSurface.c: In function 
> ‘SurfaceJobRun’:
> layer2/RepSurface.c:4506: warning: ‘solv_map’ may be used uninitialized 
> in this function
> layer1/CGO.c: In function ‘CGOOptimizeGLSLCylindersToVBOIndexedImpl’:
> layer1/CGO.c:4344: warning: ‘org_colorVals’ may be used uninitialized in 
> this function
> layer1/CGO.c:4337: warning: ‘col2[1]’ may be used uninitialized in this 
> function
> layer1/CGO.c:4337: warning: ‘col2[2]’ may be used uninitialized in this 
> function
> layer1/CGO.c: In function ‘CGOProcessCGOtoArrays’:
> layer1/CGO.c:2815: warning: ‘normalValsDA’ may be used uninitialized in 
> this function
> layer1/CGO.c:2815: warning: ‘accessibilityValsDA’ may be used 
> uninitialized in this function
> layer1/CGO.c:2816: warning: ‘pickColorValsDA’ may be used uninitialized 
> in this function
> layer1/CGO.c: In function ‘CGORenderGL’:
> layer1/CGO.c:7954: warning: ‘normalVals_tmp’ may be used uninitialized 
> in this function
> layer1/CGO.c: In function ‘CGOOptimizeToVBONotIndexedWithReturnedData’:
> layer1/CGO.c:3371: warning: ‘normalValsDA’ may be used uninitialized in 
> this function
> layer1/CGO.c:3372: warning: ‘pickColorValsDA’ may be used uninitialized 
> in this function
> layer1/CGO.c: In function ‘CGORenderRay’:
> layer1/CGO.c:6185: warning: ‘vertexVals’ may be used uninitialized in 
> this function
> layer1/CGO.c: In function ‘CGOSimplify’:
> layer1/CGO.c:5136: warning: ‘normalVals’ may be used uninitialized in 
> this function

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Dear all,

I'm installing PyMOL from svn on a RHEL 6.2 machine.  This has always 
worked.  Today, I get an "command 'gcc' failed with exit status 1" error 
(see below).

Any suggestions?  Is there something amiss with the source?

Thanks.


Andreas


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_VMD_PLUGINS -D_PYMOL_LIBPNG 
-D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS 
-D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS 
-D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 
-Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src 
-Imodules/cealign/src/tnt -Ibuild/generated 
-Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src 
-I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include 
-I/usr/include/freetype2 -I/usr/include/python2.6 -c layer3/Executive.c 
-o build/temp.linux-x86_64-2.6/layer3/Executive.o -ffast-math 
-funroll-loops -O3 -fcommon
layer2/ObjectMap.c:42:32: error: numpy/ndarraytypes.h: No such file or 
directory
layer2/ObjectMap.c:43: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or 
‘__attribute__’ before ‘MyArrayObject’
layer2/ObjectMap.c: In function ‘ObjectMapNumPyArrayToMapState’:
layer2/ObjectMap.c:5555: error: ‘MyArrayObject’ undeclared (first use in 
this function)
layer2/ObjectMap.c:5555: error: (Each undeclared identifier is reported 
only once
layer2/ObjectMap.c:5555: error: for each function it appears in.)
layer2/ObjectMap.c:5555: error: ‘pao’ undeclared (first use in this 
function)
layer2/ObjectMap.c:5559: error: expected expression before ‘)’ token
error: command 'gcc' failed with exit status 1
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_VMD_PLUGINS -D_PYMOL_LIBPNG 
-D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS 
-D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS 
-D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 
-Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src 
-Imodules/cealign/src/tnt -Ibuild/generated 
-Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src 
-I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include 
-I/usr/include/freetype2 -I/usr/include/python2.6 -c layer4/Export.c -o 
build/temp.linux-x86_64-2.6/layer4/Export.o -ffast-math -funroll-loops 
-O3 -fcommon
csbadmin@csb6 in pymol-src: layer2/RepSurface.c: In function 
‘SurfaceJobRun’:
layer2/RepSurface.c:4506: warning: ‘solv_map’ may be used uninitialized 
in this function
layer1/CGO.c: In function ‘CGOOptimizeGLSLCylindersToVBOIndexedImpl’:
layer1/CGO.c:4344: warning: ‘org_colorVals’ may be used uninitialized in 
this function
layer1/CGO.c:4337: warning: ‘col2[1]’ may be used uninitialized in this 
function
layer1/CGO.c:4337: warning: ‘col2[2]’ may be used uninitialized in this 
function
layer1/CGO.c: In function ‘CGOProcessCGOtoArrays’:
layer1/CGO.c:2815: warning: ‘normalValsDA’ may be used uninitialized in 
this function
layer1/CGO.c:2815: warning: ‘accessibilityValsDA’ may be used 
uninitialized in this function
layer1/CGO.c:2816: warning: ‘pickColorValsDA’ may be used uninitialized 
in this function
layer1/CGO.c: In function ‘CGORenderGL’:
layer1/CGO.c:7954: warning: ‘normalVals_tmp’ may be used uninitialized 
in this function
layer1/CGO.c: In function ‘CGOOptimizeToVBONotIndexedWithReturnedData’:
layer1/CGO.c:3371: warning: ‘normalValsDA’ may be used uninitialized in 
this function
layer1/CGO.c:3372: warning: ‘pickColorValsDA’ may be used uninitialized 
in this function
layer1/CGO.c: In function ‘CGORenderRay’:
layer1/CGO.c:6185: warning: ‘vertexVals’ may be used uninitialized in 
this function
layer1/CGO.c: In function ‘CGOSimplify’:
layer1/CGO.c:5136: warning: ‘normalVals’ may be used uninitialized in 
this function



-- 
                   Andreas Förster
      Crystallization and Xray Facility Manager
            Centre for Structural Biology
               Imperial College London

Hi Gianluigi,

PyMOL might find more pymolrc files than you are aware of. Just to be
sure, try this to get a hint:

PyMOL> print invocation.options.deferred

Also, check which plugins are installed and eventually disable them.

Cheers,
  Thomas

Gianluigi Caltabiano wrote, On 07/23/13 10:44:
> Hi Thomas,
> 
> thank you for answering so fast.
> 
> I do not have set retain_order, 1 in my pymolrc, but you are right, if I
> set retain_order, 0 the problem disappears. It  is strange because I  do
> not generally use retain_order, but still I might have used it and for
> some reason it have been kept by pymol.
> 
> cheers,
> 
> Gianluigi 
> 
> ------------------------------------------------------------------------
> Da: Thomas Holder <tho...@sc...>
> A: Gianluigi Caltabiano <chi...@ya...>
> Cc: pymol-users <pym...@li...>
> Inviato: Martedì 23 Luglio 2013 9:27
> Oggetto: Re: Residue numeration problem
> 
> Hi Gianluigi,
> 
> I can only reproduce your problem with retain_order=1, not with
> retain_order=0 (which is the default). Could it be that in your pymolrc,
> you do "set retain_order, 1"?
> 
> I don't think there is a difference between 1.6 and previous versions.
> 
> Cheers,
>   Thomas
> 
> Gianluigi Caltabiano wrote, On 07/23/13 09:48:
>> Hi all,
>>
>> Since 1.6.0.0  on my Mac (OSX 10.8.4) I am experiencing an annoying
>> behaviour both when creating a new object from two existing and when
>> mutating a residue via mutagenesis wizard (both with Macpymol and X11)
>>
>> Creating a new object from two existing, mess up the two (different)
> chains.
>> set retain_order, 1 does not change this behaviour.
>>
>> As for the new object creating try to reproduce this:
>>
>> fetch 4DAJ
>> create MA, 4DAJ and chain A
>> create MB, MA
>> alter MB, chain='B'
>> create dim, MA MB
>>
>>
>> The new object is not ordered on a chain basis, but on residue number.
>>
>> Something very similar happens using mutagenesis wizard, in that case it
>> mess the new residue with the first residue. In this cases closing PyMol
>> and reopening (or chainging to Hybrid) often, but not always, works.
>> Still is a pain in the back.
>>
>> Any clues?
>>
>> cheers,
>>
>> Gianluigi

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Gianluigi,

I can only reproduce your problem with retain_order=1, not with
retain_order=0 (which is the default). Could it be that in your pymolrc,
you do "set retain_order, 1"?

I don't think there is a difference between 1.6 and previous versions.

Cheers,
  Thomas

Gianluigi Caltabiano wrote, On 07/23/13 09:48:
> Hi all,
> 
> Since 1.6.0.0  on my Mac (OSX 10.8.4) I am experiencing an annoying
> behaviour both when creating a new object from two existing and when
> mutating a residue via mutagenesis wizard (both with Macpymol and X11)
> 
> Creating a new object from two existing, mess up the two (different) chains.
> set retain_order, 1 does not change this behaviour. 
> 
> As for the new object creating try to reproduce this:
> 
> fetch 4DAJ
> create MA, 4DAJ and chain A
> create MB, MA
> alter MB, chain='B'
> create dim, MA MB
> 
> 
> The new object is not ordered on a chain basis, but on residue number. 
> 
> Something very similar happens using mutagenesis wizard, in that case it
> mess the new residue with the first residue. In this cases closing PyMol
> and reopening (or chainging to Hybrid) often, but not always, works.
> Still is a pain in the back.
> 
> Any clues?
> 
> cheers,
> 
> Gianluigi

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor