Re: [PyMOL] Segmentation fault

[João M . Damas]

Thanks for the tips Thomas. I will try and let you know.

João

On Tue, Apr 11, 2017 at 9:12 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi João,
>
> Before diving into the hassle of installing additional compilers (which
> probably won't make a difference) I recommend to get familiar with a
> debugger like gdb and obtain a stack trace of the crash.
>
> To compile PyMOL with debug symbols, do
>
> export DEBUG=1
>
> before running setup.py. Then run PyMOL (actually: python) with gdb. There
> is a bit of a learning curve to get familiar with gdb, but considering that
> you already spend time on this problem and are willing to spend more, I
> think it's worthwhile.
>
> Cheers,
>   Thomas
>
> On 11 Apr 2017, at 19:08, João M. Damas  wrote:
>
> > Thanks for the feedback, Folmer!
> >
> > I am using CentOS. I already used --use-msgpackc=no and it did not
> improve. gcc --version gives me 4.8.5 (I cannot update more). Do you think
> it would be worth it to install gcc 4.9? On the install page there was said
> that a regression to 4.4 could work, but I don’t know.
> >
> > Anyone else using CentOS having problems with pymol installation?
> >
> > Thanks,
> > João
> >
> >
> > On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund 
> wrote:
> > Hi João,
> >
> > On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9
> and "--use-msgpackc=no" I get a working pymol with revision 4170.
> >
> > Have you tried creating a new user and test pymol from that account?
> That should help you identify if it is solely a problem with your own
> account.
> >
> > HTH,
> > Folmer
> >
> >
> > On 2017-03-28 03:15, João M. Damas wrote:
> >> Nobody experiencing the same issues? Any tips on what I may be doing
> wrong on the installation?
> >>
> >> João
> >>
> >> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas 
> wrote:
> >> Dear all,
> >>
> >> I started experiencing segmentation fault on a pymol that I had
> installed through the omnia channel on conda.
> >>
> >> Then, I decided to install from scratch using this recipe:
> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN
> >>
> >> Still getting the segmentation fault, so maybe something changed in my
> system and it's conflicting with?
> >>
> >> The segmentation fault is not on launching PyMOL, but rather when I do
> stuff: loading a PDB file, building a fragment. Like this:
> >>
> >> ```
> >> ./pymol: line 3: 28505 Segmentation fault  "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> >> ```
> >>
> >> Curiously, when I load a 1.740 session (.pse file I had saved), it
> works (no segmentation fault), I can even perform commands like select and
> stuff, and they work. If I load a more recent 1.803 session, it also seg
> faults:
> >>
> >> ```
> >>  Executive: Loading version 1.803 session...
> >> ./pymol: line 3: 29221 Segmentation fault  "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> >> ```
> >>
> >> Any clues? Am I doing something wrong?
> >>
> >> Thanks,
> >> João
> >>
> >> --
> >> João M. Damas
> >> PhD Student
> >> Protein Modelling Group
> >> ITQB-UNL, Oeiras, Portugal
> >> Tel:+351-214469613
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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Re: [PyMOL] Segmentation fault

[Thomas Holder]

Hi João,

Before diving into the hassle of installing additional compilers (which 
probably won't make a difference) I recommend to get familiar with a debugger 
like gdb and obtain a stack trace of the crash.

To compile PyMOL with debug symbols, do

export DEBUG=1

before running setup.py. Then run PyMOL (actually: python) with gdb. There is a 
bit of a learning curve to get familiar with gdb, but considering that you 
already spend time on this problem and are willing to spend more, I think it's 
worthwhile.

Cheers,
  Thomas

On 11 Apr 2017, at 19:08, João M. Damas  wrote:

> Thanks for the feedback, Folmer!
> 
> I am using CentOS. I already used --use-msgpackc=no and it did not improve. 
> gcc --version gives me 4.8.5 (I cannot update more). Do you think it would be 
> worth it to install gcc 4.9? On the install page there was said that a 
> regression to 4.4 could work, but I don’t know.
> 
> Anyone else using CentOS having problems with pymol installation?
> 
> Thanks,
> João
> 
> 
> On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund  wrote:
> Hi João,
> 
> On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 and 
> "--use-msgpackc=no" I get a working pymol with revision 4170.
> 
> Have you tried creating a new user and test pymol from that account? That 
> should help you identify if it is solely a problem with your own account.
> 
> HTH,
> Folmer
> 
> 
> On 2017-03-28 03:15, João M. Damas wrote:
>> Nobody experiencing the same issues? Any tips on what I may be doing wrong 
>> on the installation?
>> 
>> João
>> 
>> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas  wrote:
>> Dear all,
>> 
>> I started experiencing segmentation fault on a pymol that I had installed 
>> through the omnia channel on conda.
>> 
>> Then, I decided to install from scratch using this recipe: 
>> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN
>> 
>> Still getting the segmentation fault, so maybe something changed in my 
>> system and it's conflicting with?
>> 
>> The segmentation fault is not on launching PyMOL, but rather when I do 
>> stuff: loading a PDB file, building a fragment. Like this:
>> 
>> ```
>> ./pymol: line 3: 28505 Segmentation fault  "/usr/bin/python2.7" 
>> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
>> ```
>> 
>> Curiously, when I load a 1.740 session (.pse file I had saved), it works (no 
>> segmentation fault), I can even perform commands like select and stuff, and 
>> they work. If I load a more recent 1.803 session, it also seg faults:
>> 
>> ```
>>  Executive: Loading version 1.803 session...
>> ./pymol: line 3: 29221 Segmentation fault  "/usr/bin/python2.7" 
>> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
>> ```
>> 
>> Any clues? Am I doing something wrong?
>> 
>> Thanks,
>> João
>> 
>> -- 
>> João M. Damas
>> PhD Student
>> Protein Modelling Group
>> ITQB-UNL, Oeiras, Portugal
>> Tel:+351-214469613

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Segmentation fault

[João M . Damas]

Thanks for the feedback, Folmer!

I am using CentOS. I already used --use-msgpackc=no and it did not improve. gcc
--version gives me 4.8.5 (I cannot update more). Do you think it would be
worth it to install gcc 4.9? On the install page there was said that a
regression to 4.4 could work, but I don’t know.

Anyone else using CentOS having problems with pymol installation?

Thanks,
João
​

On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund 
wrote:

> Hi João,
>
> On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9
> and "--use-msgpackc=no" I get a working pymol with revision 4170.
>
> Have you tried creating a new user and test pymol from that account? That
> should help you identify if it is solely a problem with your own account.
>
> HTH,
> Folmer
>
>
> On 2017-03-28 03:15, João M. Damas wrote:
>
> Nobody experiencing the same issues? Any tips on what I may be doing wrong
> on the installation?
>
> João
>
> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas 
> wrote:
>
>> Dear all,
>>
>> I started experiencing segmentation fault on a pymol that I had installed
>> through the omnia channel on conda.
>>
>> Then, I decided to install from scratch using this recipe:
>> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN
>>
>> Still getting the segmentation fault, so maybe something changed in my
>> system and it's conflicting with?
>>
>> The segmentation fault is not on launching PyMOL, but rather when I do
>> stuff: loading a PDB file, building a fragment. Like this:
>>
>> ```
>> ./pymol: line 3: 28505 Segmentation fault  "/usr/bin/python2.7"
>> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
>> ```
>>
>> Curiously, when I load a 1.740 session (.pse file I had saved), it works
>> (no segmentation fault), I can even perform commands like select and stuff,
>> and they work. If I load a more recent 1.803 session, it also seg faults:
>>
>> ```
>>  Executive: Loading version 1.803 session...
>> ./pymol: line 3: 29221 Segmentation fault  "/usr/bin/python2.7"
>> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
>> ```
>>
>> Any clues? Am I doing something wrong?
>>
>> Thanks,
>> João
>>
>> --
>> João M. Damas
>> PhD Student
>> Protein Modelling Group
>> ITQB-UNL, Oeiras, Portugal
>> Tel:+351-214469613 <21%20446%209613>
>>
>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613 <21%20446%209613>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
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>
>
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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Re: [PyMOL] Segmentation fault

[Folmer Fredslund]

Hi João,

On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 
and "--use-msgpackc=no" I get a working pymol with revision 4170.


Have you tried creating a new user and test pymol from that account? 
That should help you identify if it is solely a problem with your own 
account.


HTH,
Folmer

On 2017-03-28 03:15, João M. Damas wrote:
Nobody experiencing the same issues? Any tips on what I may be doing 
wrong on the installation?


João

On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas > wrote:


Dear all,

I started experiencing segmentation fault on a pymol that I had
installed through the omnia channel on conda.

Then, I decided to install from scratch using this recipe:
https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN


Still getting the segmentation fault, so maybe something changed
in my system and it's conflicting with?

The segmentation fault is not on launching PyMOL, but rather when
I do stuff: loading a PDB file, building a fragment. Like this:

```
./pymol: line 3: 28505 Segmentation fault  "/usr/bin/python2.7"
"/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py"
"$@"
```

Curiously, when I load a 1.740 session (.pse file I had saved), it
works (no segmentation fault), I can even perform commands like
select and stuff, and they work. If I load a more recent 1.803
session, it also seg faults:

```
 Executive: Loading version 1.803 session...
./pymol: line 3: 29221 Segmentation fault  "/usr/bin/python2.7"
"/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py"
"$@"
```

Any clues? Am I doing something wrong?

Thanks,
João

-- 
João M. Damas

PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613 




--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613


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Re: [PyMOL] Segmentation fault

[João M . Damas]

Nobody experiencing the same issues? Any tips on what I may be doing wrong
on the installation?

João

On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas  wrote:

> Dear all,
>
> I started experiencing segmentation fault on a pymol that I had installed
> through the omnia channel on conda.
>
> Then, I decided to install from scratch using this recipe:
> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN
>
> Still getting the segmentation fault, so maybe something changed in my
> system and it's conflicting with?
>
> The segmentation fault is not on launching PyMOL, but rather when I do
> stuff: loading a PDB file, building a fragment. Like this:
>
> ```
> ./pymol: line 3: 28505 Segmentation fault  "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> ```
>
> Curiously, when I load a 1.740 session (.pse file I had saved), it works
> (no segmentation fault), I can even perform commands like select and stuff,
> and they work. If I load a more recent 1.803 session, it also seg faults:
>
> ```
>  Executive: Loading version 1.803 session...
> ./pymol: line 3: 29221 Segmentation fault  "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> ```
>
> Any clues? Am I doing something wrong?
>
> Thanks,
> João
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613 <21%20446%209613>
>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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[PyMOL] Segmentation fault

[João M . Damas]

Dear all,

I started experiencing segmentation fault on a pymol that I had installed
through the omnia channel on conda.

Then, I decided to install from scratch using this recipe:
https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN

Still getting the segmentation fault, so maybe something changed in my
system and it's conflicting with?

The segmentation fault is not on launching PyMOL, but rather when I do
stuff: loading a PDB file, building a fragment. Like this:

```
./pymol: line 3: 28505 Segmentation fault  "/usr/bin/python2.7"
"/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
```

Curiously, when I load a 1.740 session (.pse file I had saved), it works
(no segmentation fault), I can even perform commands like select and stuff,
and they work. If I load a more recent 1.803 session, it also seg faults:

```
 Executive: Loading version 1.803 session...
./pymol: line 3: 29221 Segmentation fault  "/usr/bin/python2.7"
"/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
```

Any clues? Am I doing something wrong?

Thanks,
João

-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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[PyMOL] segmentation fault

[henry tang]

Dear developer,

I had this segmentation fault problem whenever using plugin like apbs or
autodock etc. it crashes when I click button "APBS binary location" etc,
Tried both pymol 1.7.4 and 1.8.0 and gave the same error. Any help would be
greatly appreciated.

Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 4.50.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: GeForce GTX 850M/PCIe/SSE2
  GL_VERSION:  4.5.0 NVIDIA 352.68
 Detected 4 CPU cores.  Enabled multithreaded rendering.

/pymol: line 3: 20414 Segmentation fault  (core dumped)
"/usr/bin/python" "/home/protein/pymol/lib/python/pymol/__init__.py" "$@"

Henry
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Re: [PyMOL] Segmentation fault when I tried to load a pdb file

[Thomas Holder]

Hi Beibei,

Googling for "gallium llvmpipe" suggests that your system is running on the 
wrong graphics driver:

https://www.google.com/search?q=gallium+llvmpipe

People solved this by reinstalling the correct driver and/or fixing permission 
problems.

Cheers,
  Thomas

On 14 Oct 2015, at 17:05, bbw...@msu.edu wrote:

> Hello I just installed pymol on my machine (ubuntu 14; Graphics: Gallium 0.4 
> on llvmpipe): sudo apt-get install pymol. And I could open pymol, but when I 
> tried to load a pdb file. It crashed and closed, and I got the following 
> errorsF pymol: line 3: 17889 Segmentation fault. Could you help me to fix 
> this please? Thanks. Beibei

-- 
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PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Segmentation fault when I tried to load a pdb file

[bbwang]

HelloI just installed pymol on my machine (ubuntu 14; Graphics: Gallium 0.4 on 
llvmpipe): sudo apt-get install pymol. And I could open pymol, but when I tried 
to load a pdb file. It crashed and closed, and I got the following errorsF 
pymol: line 3: 17889 Segmentation fault.Could you help me to fix this 
please?Thanks.Beibei--
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[PyMOL] Segmentation fault with pymol2

[Alessia Visconti]

Dear all,
I have implemented a software in python/pyQT to draw chemical structure.
For the visualisation it uses a pymol widget (using the pymol2 package). I
haven't used it for a while (it was part of an old project), but today I
noticed that it is no longer working.
When I run the following code:

def paintGL(self):
print(Paint)
glViewport(0, 0, self.width(), self.height())
self._pymol.idle()
self._pymol.draw()

the last line returns me a segmentation fault 11.
I am using Python 2.7, PyMOL 1.6 and Mac OS X Yosemite, but the problem is
present also with Mavericks.  Both python and PyMOL have been installed
using homebrew.
Does anyone have any suggestion?

Thank you for your help,
Alessia
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[PyMOL] Segmentation fault when using APBS Tool 2

[Ooker]

The newest version of PyMOL (1.7.1.3) 
solves this problem, just to announce you 
to know that.

Thank you.
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[PyMOL] Segmentation fault when using APBS Tool 2

[Ooker]

Hi all,

When I want to using the APBS Tool 2 to show the solvent 
accessible surface, pyMOL crashes and auto close, no matter the 
Solvent accessible surface and Color by potential on sol. acc. surf. 
are checked. The trace back is:

Could not find pymol-generated.dx so searching for pymol-
generated-PE0.dx
 ObjectMapLoadDXFile: Loading from 'pymol-generated-PE0.dx'.
 DXStrToMap: Dimensions: 129 161 161
 DXStrToMap: Origin   -9.311  -48.159  -47.641
 DXStrToMap: Grid0.4960.4040.455
 DXStrToMap: 3343809 data points.
 APBS Tools: range is [-5.0, 0.0, 5.0]
Segmentation fault (core dumped)

I meet this error in Linux, not Windows. My tcl version is 8.5

echo 'puts $tcl_version;exit 0' | tclsh
8.5

What should I do? Thank you so much.

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[PyMOL] segmentation fault with pymol 1.6 (r4050)

[ccp4 pymol]

Hi to everyone

Recently moved to latest pymol (from subversion r4050) on linux (ubuntu
12.10). Installation was fine and could launch pymol successfully. Using
builder crashes with a segmentation fault.
Has anyone encountered this? Please give suggestions to overcome this issue.

Thanks

Best Regards
Priyadarshan
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Re: [PyMOL] Segmentation Fault

[Sampson, Jared]

Hi Narin -

Hope you don't mind me reviving an old thread, but I just ran into this same 
problem trying to build Pymol from source (and using fink for the dependencies) 
on my laptop.  What solved it for me was the following:

fink remove libpng16 libpng16-shlibs

I guess pymol was trying to use libpng-1.6 because it was available at runtime, 
but the fink package still specifies version 1.5 as a dependency.  Fortunately, 
I had nothing else that depended on version 1.6, so uninstalling it was no 
problem.

Hope that helps,
Jared

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On Jul 30, 2013, at 9:33 AM, Narin Hengrung 
narin.hengr...@chch.ox.ac.ukmailto:narin.hengr...@chch.ox.ac.uk wrote:

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
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[PyMOL] segmentation fault in Ubuntu12.10

[管泓翔]

Dear Sir,
 When I load the map,big-sized map of virus, in pymol v1.5
 on my computer with 64bit ubuntu 12.10, the pymol run very slow and then
 showed segmentation fault. On my old computer with Ubuntu 9.10, the same
 map can run very smooth.


 Thank you Hong-Hsiang

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Re: [PyMOL] Segmentation fault while cmd.read_pdbstr on MacOS

[Jason Vertrees]

Hi Dominik,

This looks like a bug. We're looking into it.

Cheers,

-- Jason

On Thu, Mar 1, 2012 at 11:35 AM, Dominik G tno...@gmail.com wrote:
 Hi pymolers,

 I attempt to send a structure from a program to PyMol, which doesn't work.
 After some time I've managed to extract the smallest data making the crash.

 So the segfault always happens when I do this:

 ~/bin/MacPyMOL.app/Contents/MacOS/MacPyMOL -p  incmd

 where the incmd file contains solely the test below:

 cmd.read_pdbstr(ATOM      1  N   MET A   1     -14.152   0.961   4.712
  1.00  1.26           N\nATOM      2  CA  MET A   1     -13.296   0.028
 3.924  1.00  0.43           C\nATOM      3  C   MET A   1     -11.822
 0.338   4.193  1.00  0.41           C\nATOM      4  O   MET A   1
 -11.358   1.432   3.941  1.00  0.68           O\nATOM      5  CB  MET A   1
     -13.571   0.173   2.426  1.00  1.24           C\nATOM      6  CG  MET A
   1     -15.046  -0.135   2.144  1.00  1.63           C\nATOM      7  SD
  MET A   1     -16.174   1.270   1.982  1.00  2.41           S\nATOM      8
  CE  MET A   1     -17.702   0.313   1.823  1.00  2.91           C\nATOM
  9  N   THR A   2     -11.121  -0.642   4.703  1.00  0.23           N\nATOM
     10  CA  THR A   2      -9.669  -0.447   4.998  1.00  0.19
 C\nATOM     11  C   THR A   2      -8.861  -1.586   4.373  1.00  0.15
     C\nATOM     12  O   THR A   2      -9.036  -2.736   4.724  1.00  0.20
         O\nATOM     13  CB  THR A   2      -9.462  -0.447   6.516  1.00
  0.20           C\nATOM     14  OG1 THR A   2     -10.399   0.505   7.010
  1.00  0.31           O\nATOM     15  CG2 THR A   2      -8.090   0.103
 6.896  1.00  0.23           C\n,a)

 (its just a single line)

 I use PyMOL 1.5.0.1 on MacOS. Interestingly, it doesn't crash when the input
 line comprises about 5 to 7 atoms. Moreover, Pymol version 1.2r1 also
 crashes, but work until appx 20 atoms in a line.

 Best,
 Tim

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[PyMOL] Segmentation fault while cmd.read_pdbstr on MacOS

[Dominik G]

Hi pymolers,

I attempt to send a structure from a program to PyMol, which doesn't work.
After some time I've managed to extract the smallest data making the crash.

So the segfault always happens when I do this:

~/bin/MacPyMOL.app/Contents/MacOS/MacPyMOL -p  incmd

where the incmd file contains solely the test below:

cmd.read_pdbstr(ATOM  1  N   MET A   1 -14.152   0.961   4.712
 1.00  1.26   N\nATOM  2  CA  MET A   1 -13.296   0.028
3.924  1.00  0.43   C\nATOM  3  C   MET A   1 -11.822
0.338   4.193  1.00  0.41   C\nATOM  4  O   MET A   1
-11.358   1.432   3.941  1.00  0.68   O\nATOM  5  CB  MET A   1
-13.571   0.173   2.426  1.00  1.24   C\nATOM  6  CG  MET A
  1 -15.046  -0.135   2.144  1.00  1.63   C\nATOM  7  SD
 MET A   1 -16.174   1.270   1.982  1.00  2.41   S\nATOM  8
 CE  MET A   1 -17.702   0.313   1.823  1.00  2.91   C\nATOM
   9  N   THR A   2 -11.121  -0.642   4.703  1.00  0.23
N\nATOM 10  CA  THR A   2  -9.669  -0.447   4.998  1.00  0.19
C\nATOM 11  C   THR A   2  -8.861  -1.586   4.373  1.00  0.15
C\nATOM 12  O   THR A   2  -9.036  -2.736   4.724  1.00
 0.20   O\nATOM 13  CB  THR A   2  -9.462  -0.447   6.516
 1.00  0.20   C\nATOM 14  OG1 THR A   2 -10.399   0.505
7.010  1.00  0.31   O\nATOM 15  CG2 THR A   2  -8.090
0.103   6.896  1.00  0.23   C\n,a)

(its just a single line)

I use PyMOL 1.5.0.1 on MacOS. Interestingly, it doesn't crash when the
input line comprises about 5 to 7 atoms. Moreover, Pymol version 1.2r1 also
crashes, but work until appx 20 atoms in a line.

Best,
Tim
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Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

[Tao-wei Huang]

Hi Jason,

My version of Ubuntu was 11.04 and the graphics card is the Intel
integrated card. I don't know what's the problem, but I upgrade to
11.10 today. It works now. Thank you very much for your reply.

Cheers,
Tao

On Tue, Oct 18, 2011 at 10:10 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
 Hi Tao,

 What version of Ubuntu are you running? I'm running 11.04 (and
 recently upgraded to 11.10). It works fine for me. What video card do
 you have? How did you install?

 Cheers,

 -- Jason

 On Mon, Oct 17, 2011 at 6:08 PM, Tao-wei Huang yelve...@gmail.com wrote:
 Hi all,

 I have problems with starting pymol in ubuntu. When I started it from
 terminal, I just received the error message: Segmentation fault. I
 tried googling pymol segmentation fault, but I don't find effective
 information to fix this problem. If you have any idea or experience
 about this, please tell me. Thank you very much.


 Cheers,
 Tao

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Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

[Jason Vertrees]

Hi Tao,

What version of Ubuntu are you running? I'm running 11.04 (and
recently upgraded to 11.10). It works fine for me. What video card do
you have? How did you install?

Cheers,

-- Jason

On Mon, Oct 17, 2011 at 6:08 PM, Tao-wei Huang yelve...@gmail.com wrote:
 Hi all,

 I have problems with starting pymol in ubuntu. When I started it from
 terminal, I just received the error message: Segmentation fault. I
 tried googling pymol segmentation fault, but I don't find effective
 information to fix this problem. If you have any idea or experience
 about this, please tell me. Thank you very much.


 Cheers,
 Tao

 --
 All the data continuously generated in your IT infrastructure contains a
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(o) +1 (603) 374-7120

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[PyMOL] Segmentation fault while starting Pymol in ubuntu 11

[Tao-wei Huang]

Hi all,

I have problems with starting pymol in ubuntu. When I started it from
terminal, I just received the error message: Segmentation fault. I
tried googling pymol segmentation fault, but I don't find effective
information to fix this problem. If you have any idea or experience
about this, please tell me. Thank you very much.


Cheers,
Tao

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Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

[Troels Emtekær Linnet]

What version do you have installed?

Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/10/17 Tao-wei Huang yelve...@gmail.com

 Hi all,

 I have problems with starting pymol in ubuntu. When I started it from
 terminal, I just received the error message: Segmentation fault. I
 tried googling pymol segmentation fault, but I don't find effective
 information to fix this problem. If you have any idea or experience
 about this, please tell me. Thank you very much.


 Cheers,
 Tao


 --
 All the data continuously generated in your IT infrastructure contains a
 definitive record of customers, application performance, security
 threats, fraudulent activity and more. Splunk takes this data and makes
 sense of it. Business sense. IT sense. Common sense.
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Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

[lina]

On Tue, Oct 18, 2011 at 12:08 AM, Tao-wei Huang yelve...@gmail.com wrote:
 Hi all,

 I have problems with starting pymol in ubuntu. When I started it from
 terminal, I just received the error message: Segmentation fault. I
 tried googling pymol segmentation fault, but I don't find effective
 information to fix this problem. If you have any idea or experience
 about this, please tell me. Thank you very much.

Last time I met segment fault when I updated some graphic-driver packages.



 Cheers,
 Tao

 --
 All the data continuously generated in your IT infrastructure contains a
 definitive record of customers, application performance, security
 threats, fraudulent activity and more. Splunk takes this data and makes
 sense of it. Business sense. IT sense. Common sense.
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Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

[Tsjerk Wassenaar]

Hey :)

After removing the svn source copy, as well as the pymol version
installed globally through apt-get, followed by downloading the source
anew and compiling, I ended up with a working copy. Apparently there
were some version conflicts...

The take home message: clean up before cooking :)

Cheers, and thumbs up for Jason!

Tsjerk

On Mon, Apr 11, 2011 at 2:03 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
 Hi,

 The problem did not occur on another machine (Intel Core i7, 64bit),
 running Ubuntu 10.10.
 On my EeePC loading a python CGO file worked fine, while loading an
 empty PDB file segfaulted. So it seems to be related to loading the
 coordinates, not to the displaying.

 Cheers,

 Tsjerk


 On Mon, Apr 11, 2011 at 12:06 PM, Abhinav Verma abhinav1...@gmail.com wrote:
 Hi Jason  Tsjerk ...
  Just for the info that  I just downloaded, compiled and tried it on
 OpenSuse 11.4 and it ran without any problems:

 PyMOLload ../../3lzt.pdb
 HEADER    HYDROLASE   23-MAR-97   3LZT
 TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
   unsuccessful in guessing valences.
  CmdLoad: ../../3lzt.pdb loaded as 3lzt.

 hth,
 abhi


 On Mon, Apr 11, 2011 at 9:43 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Jason,

 I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running
 Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens
 regardless of the contents of the PDB file, but loading something with
 hetatms gives some insight in how far it goes:

 PyMOLload ../../../3lzt.pdb
 HEADER    HYDROLASE                               23-MAR-97   3LZT
 TITLE     REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in
 heteroatom,
  unsuccessful in guessing valences.
 Segmentation fault

 If you need any information on libraries or such, let me know.

 Best,

 Tsjerk

 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands


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 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands




-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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[PyMOL] segmentation fault pymol 1.4 rev 3938

[Tsjerk Wassenaar]

Hi Jason,

I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running
Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens
regardless of the contents of the PDB file, but loading something with
hetatms gives some insight in how far it goes:

PyMOLload ../../../3lzt.pdb
HEADERHYDROLASE   23-MAR-97   3LZT
TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
COMPNDMOL_ID: 1;
COMPND   2 MOLECULE: LYSOZYME;
COMPND   3 CHAIN: A;
COMPND   4 EC: 3.2.1.17;
COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 1 symmetry operators.
 ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
  unsuccessful in guessing valences.
Segmentation fault

If you need any information on libraries or such, let me know.

Best,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

[Abhinav Verma]

Hi Jason  Tsjerk ...
 Just for the info that  I just downloaded, compiled and tried it on
OpenSuse 11.4 and it ran without any problems:

PyMOLload ../../3lzt.pdb
HEADERHYDROLASE   23-MAR-97   3LZT
TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
COMPNDMOL_ID: 1;
COMPND   2 MOLECULE: LYSOZYME;
COMPND   3 CHAIN: A;
COMPND   4 EC: 3.2.1.17;
COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 1 symmetry operators.
 ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
  unsuccessful in guessing valences.
 CmdLoad: ../../3lzt.pdb loaded as 3lzt.

hth,
abhi


On Mon, Apr 11, 2011 at 9:43 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Jason,

 I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running
 Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens
 regardless of the contents of the PDB file, but loading something with
 hetatms gives some insight in how far it goes:

 PyMOLload ../../../3lzt.pdb
 HEADERHYDROLASE   23-MAR-97   3LZT
 TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPNDMOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
  unsuccessful in guessing valences.
 Segmentation fault

 If you need any information on libraries or such, let me know.

 Best,

 Tsjerk

 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands


 --
 Xperia(TM) PLAY
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 smartphone on the nation's most reliable network.
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Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

[Tsjerk Wassenaar]

Hi,

The problem did not occur on another machine (Intel Core i7, 64bit),
running Ubuntu 10.10.
On my EeePC loading a python CGO file worked fine, while loading an
empty PDB file segfaulted. So it seems to be related to loading the
coordinates, not to the displaying.

Cheers,

Tsjerk


On Mon, Apr 11, 2011 at 12:06 PM, Abhinav Verma abhinav1...@gmail.com wrote:
 Hi Jason  Tsjerk ...
  Just for the info that  I just downloaded, compiled and tried it on
 OpenSuse 11.4 and it ran without any problems:

 PyMOLload ../../3lzt.pdb
 HEADER    HYDROLASE   23-MAR-97   3LZT
 TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
   unsuccessful in guessing valences.
  CmdLoad: ../../3lzt.pdb loaded as 3lzt.

 hth,
 abhi


 On Mon, Apr 11, 2011 at 9:43 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Jason,

 I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running
 Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens
 regardless of the contents of the PDB file, but loading something with
 hetatms gives some insight in how far it goes:

 PyMOLload ../../../3lzt.pdb
 HEADER    HYDROLASE                               23-MAR-97   3LZT
 TITLE     REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in
 heteroatom,
  unsuccessful in guessing valences.
 Segmentation fault

 If you need any information on libraries or such, let me know.

 Best,

 Tsjerk

 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands


 --
 Xperia(TM) PLAY
 It's a major breakthrough. An authentic gaming
 smartphone on the nation's most reliable network.
 And it wants your games.
 http://p.sf.net/sfu/verizon-sfdev
 ___
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

--
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
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Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

[Jason Vertrees]

Hi,

 The problem did not occur on another machine (Intel Core i7, 64bit),
 running Ubuntu 10.10.
 On my EeePC loading a python CGO file worked fine, while loading an
 empty PDB file segfaulted. So it seems to be related to loading the
 coordinates, not to the displaying.

Is anyone else having this problem?  We found and fixed a similar
HETATM-related issue a few weeks ago.  PyMOL's HETATM bonding
determination needs improvement.

Tsjerk, can you please send me a stack trace.  Have you done a clean
build?  Also, are your drivers up to date?  (Is this an Intel GMA 9x5
video card?)

Cheers,

-- Jason

 Cheers,

 Tsjerk


 On Mon, Apr 11, 2011 at 12:06 PM, Abhinav Verma abhinav1...@gmail.com wrote:
 Hi Jason  Tsjerk ...
  Just for the info that  I just downloaded, compiled and tried it on
 OpenSuse 11.4 and it ran without any problems:

 PyMOLload ../../3lzt.pdb
 HEADER    HYDROLASE   23-MAR-97   3LZT
 TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
   unsuccessful in guessing valences.
  CmdLoad: ../../3lzt.pdb loaded as 3lzt.

 hth,
 abhi


 On Mon, Apr 11, 2011 at 9:43 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Jason,

 I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running
 Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens
 regardless of the contents of the PDB file, but loading something with
 hetatms gives some insight in how far it goes:

 PyMOLload ../../../3lzt.pdb
 HEADER    HYDROLASE                               23-MAR-97   3LZT
 TITLE     REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in
 heteroatom,
  unsuccessful in guessing valences.
 Segmentation fault

 If you need any information on libraries or such, let me know.

 Best,

 Tsjerk

 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands


 --
 Xperia(TM) PLAY
 It's a major breakthrough. An authentic gaming
 smartphone on the nation's most reliable network.
 And it wants your games.
 http://p.sf.net/sfu/verizon-sfdev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands

 --
 Xperia(TM) PLAY
 It's a major breakthrough. An authentic gaming
 smartphone on the nation's most reliable network.
 And it wants your games.
 http://p.sf.net/sfu/verizon-sfdev
 ___
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-- 
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PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

[Tsjerk Wassenaar]

Hey Jason,

Intel GMA 950 card, 945GSE chipset, check :(

So this is a known problem, and is there a workaround? Do you need
additional information from my side?

Cheers,

Tsjerk

On Mon, Apr 11, 2011 at 6:06 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
 Hi,

 The problem did not occur on another machine (Intel Core i7, 64bit),
 running Ubuntu 10.10.
 On my EeePC loading a python CGO file worked fine, while loading an
 empty PDB file segfaulted. So it seems to be related to loading the
 coordinates, not to the displaying.

 Is anyone else having this problem?  We found and fixed a similar
 HETATM-related issue a few weeks ago.  PyMOL's HETATM bonding
 determination needs improvement.

 Tsjerk, can you please send me a stack trace.  Have you done a clean
 build?  Also, are your drivers up to date?  (Is this an Intel GMA 9x5
 video card?)

 Cheers,

 -- Jason

 Cheers,

 Tsjerk


 On Mon, Apr 11, 2011 at 12:06 PM, Abhinav Verma abhinav1...@gmail.com 
 wrote:
 Hi Jason  Tsjerk ...
  Just for the info that  I just downloaded, compiled and tried it on
 OpenSuse 11.4 and it ran without any problems:

 PyMOLload ../../3lzt.pdb
 HEADER    HYDROLASE   23-MAR-97   3LZT
 TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
   unsuccessful in guessing valences.
  CmdLoad: ../../3lzt.pdb loaded as 3lzt.

 hth,
 abhi


 On Mon, Apr 11, 2011 at 9:43 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Jason,

 I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running
 Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens
 regardless of the contents of the PDB file, but loading something with
 hetatms gives some insight in how far it goes:

 PyMOLload ../../../3lzt.pdb
 HEADER    HYDROLASE                               23-MAR-97   3LZT
 TITLE     REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
 COMPND    MOL_ID: 1;
 COMPND   2 MOLECULE: LYSOZYME;
 COMPND   3 CHAIN: A;
 COMPND   4 EC: 3.2.1.17;
 COMPND   5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in
 heteroatom,
  unsuccessful in guessing valences.
 Segmentation fault

 If you need any information on libraries or such, let me know.

 Best,

 Tsjerk

 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands


 --
 Xperia(TM) PLAY
 It's a major breakthrough. An authentic gaming
 smartphone on the nation's most reliable network.
 And it wants your games.
 http://p.sf.net/sfu/verizon-sfdev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands

 --
 Xperia(TM) PLAY
 It's a major breakthrough. An authentic gaming
 smartphone on the nation's most reliable network.
 And it wants your games.
 http://p.sf.net/sfu/verizon-sfdev
 ___
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 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120




-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

--
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
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Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

[Jason Vertrees]

Hi Tsjerk,

 Intel GMA 950 card, 945GSE chipset, check :(

The mobile Intel video drivers have been problematic for us and quite
a few other graphics software groups.  Some of our users have been
reporting success after they upgrade their drivers.  For others
though, it doesn't help.  On Windows this sometimes shows up as bad
stick rendering and as a problem where the user cannot restore the
PyMOL window, once minimized.  On Linux, it's usually just bad stick
coloring.

Any chance you can send me a stack trace and exact commands used to
crash PyMOL?  Multiple examples would help.  Please send them directly
to me so we do not clog up the list with debugging messages.  We've
tried to debug these drivers for months now.  On all machines I've
tried, we cannot ever get them to fail locally, making debugging
extremely challenging.

Cheers,

-- Jason

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

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
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[PyMOL] Segmentation fault rendering CGO object with all_states one

[Tsjerk Wassenaar]

Hi Jason,

It appears that Pymol segfaults rendering when a cgo object spans
multiple states, and all_states is set on:

from pymol import cmd

set all_states,1
cmd.load_cgo([COLOR,1,1,0,SPHERE,3,0,0,1],name=bla,state=2)
cmd.load_cgo([COLOR,1,0,0,SPHERE,0,0,0,2],name=bla,state=3)
ray

This happened with 1.0r2 under Ubuntu on an EEE PC, and with 1.2r2 on
an i7 also running Ubuntu.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

--
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and, 
should the need arise, upgrade to a full multi-node Oracle RAC database 
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Re: [PyMOL] Segmentation fault rendering CGO object with all_states one

[Jason Vertrees]

Hi Tsjerk,

That is indeed a bug.  I'll look into it and post the changes back to
SVN when it's fixed.

Cheers,

-- Jason

On Mon, Jan 3, 2011 at 11:34 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
 Hi Jason,

 It appears that Pymol segfaults rendering when a cgo object spans
 multiple states, and all_states is set on:

 from pymol import cmd

 set all_states,1
 cmd.load_cgo([COLOR,1,1,0,SPHERE,3,0,0,1],name=bla,state=2)
 cmd.load_cgo([COLOR,1,0,0,SPHERE,0,0,0,2],name=bla,state=3)
 ray

 This happened with 1.0r2 under Ubuntu on an EEE PC, and with 1.2r2 on
 an i7 also running Ubuntu.

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands

 --
 Learn how Oracle Real Application Clusters (RAC) One Node allows customers
 to consolidate database storage, standardize their database environment, and,
 should the need arise, upgrade to a full multi-node Oracle RAC database
 without downtime or disruption
 http://p.sf.net/sfu/oracle-sfdevnl
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and, 
should the need arise, upgrade to a full multi-node Oracle RAC database 
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
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Re: [PyMOL] Segmentation fault rendering CGO object with all_states one

[Jason Vertrees]

Hi Tsjerk,

Thanks for bringing this to my attention.  The fix (revision 3929) has
been pushed to the open-source SVN on SourceForge.  You can try out
the following code segments to verify:

###
# TEST 1
from pymol import cmd
from pymol.cgo import *
from pymol.vfont import plain
cgo = []
axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]]
pos = [0.0,0.0,0.0]
wire_text(cgo,plain,pos,'Hello World',axes)
pos = [0.0,-3.0,0.0]
cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes)
cmd.load_cgo(cgo,'txt',state=2)
cmd.zoom(all,2.0)

set all_states
ray


###
# TEST 2
from pymol import cmd
from pymol.cgo import *

cmd.load_cgo([COLOR,1,1,0,SPHERE,3,0,0,1],name=bla,state=2)
cmd.load_cgo([COLOR,1,0,0,SPHERE,0,0,0,2],name=bla,state=3)

set all_states,1
ray

Cheers,

-- Jason

On Mon, Jan 3, 2011 at 11:34 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
 Hi Jason,

 It appears that Pymol segfaults rendering when a cgo object spans
 multiple states, and all_states is set on:

 from pymol import cmd

 set all_states,1
 cmd.load_cgo([COLOR,1,1,0,SPHERE,3,0,0,1],name=bla,state=2)
 cmd.load_cgo([COLOR,1,0,0,SPHERE,0,0,0,2],name=bla,state=3)
 ray

 This happened with 1.0r2 under Ubuntu on an EEE PC, and with 1.2r2 on
 an i7 also running Ubuntu.

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands

 --
 Learn how Oracle Real Application Clusters (RAC) One Node allows customers
 to consolidate database storage, standardize their database environment, and,
 should the need arise, upgrade to a full multi-node Oracle RAC database
 without downtime or disruption
 http://p.sf.net/sfu/oracle-sfdevnl
 ___
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 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and, 
should the need arise, upgrade to a full multi-node Oracle RAC database 
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
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[PyMOL] Segmentation fault r3910 on linux with Python 2.5/2.6 and tcl/tk 8.5.5 and 8.6b1.

[Edward d'Auvergne]

Hi,

I have a similar problem to Ben in this post:

http://sourceforge.net/mailarchive/message.php?msg_id=20100512182803.GA21563%40crystal.harvard.edu

I am using the svn r3910 with various versions of python and tcl/tk.
I see the following message:

IRQ's not enabled, falling back to busy waits: 2 0
 PyMOL(TM) Molecular Graphics System, Version 1.3.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

Created by Warren L. DeLano, Ph.D.

PyMOL is user-supported open-source software.  Although some versions
are freely available, PyMOL is not in the public domain.

If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.

More information can be found at http://www.pymol.org;.

Enter help for a list of commands.
Enter help command-name for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 OpenGL graphics engine:
  GL_VENDOR: Advanced Micro Devices, Inc.
  GL_RENDERER: Mesa DRI R600 (RV635 9598) 20090101  TCL
  GL_VERSION: 2.0 Mesa 7.8.1
 Detected 2 CPU cores.  Enabled multithreaded rendering.
./pymol: line 2:  7161 Segmentation fault
/media/disk/bin/python2.5
/media/disk/lib/python2.5/site-packages/pymol/__init__.py $@

This specific message is with:

pymol:  r3910
python:  2.5.5
tck/tk:  8.5.8
pmw:  1.3.2
GPU:  dual head ATI Radeon HD 2000 and later (radeon/fglrx) GPU
driver:  radeon (x11-driver-video-ati)
OS:  Mandriva 2010 spring (rc2)

Is this a known issue?  Is there a way of disabling multithreaded
rendering for testing this?  Some conspicuous dmseg messages are:

python2.5[8829]: segfault at 0 ip (null) sp 7fff00eabee8 error 14
in python2.5[40+11c000]
python2.5[8846]: segfault at 0 ip (null) sp 7fffd0c51f68 error 14
in python2.5[40+11c000]
python2.5[8871]: segfault at 0 ip (null) sp 7fff515419c8 error 14
in python2.5[40+11c000]
python2.5[9051]: segfault at 0 ip (null) sp 7fffba96bda8 error 14
in python2.5[40+11c000]
python2.5[9198]: segfault at 0 ip (null) sp 7fff56bf19d8 error 14
in python2.5[40+11c000]
[drm] Resetting GPU
[drm] Resetting GPU
python2.5[2825]: segfault at 8 ip 7f090d03e626 sp 7f08f5701e30
error 4 in libX11.so.6.3.0[7f090cfec000+134000]
python2.5[5640]: segfault at 8 ip 7f6403be9626 sp 7f63ec43de30
error 4 in libX11.so.6.3.0[7f6403b97000+134000]
python2.5[7168]: segfault at 8 ip 7f07fb138626 sp 7f07e37fbe30
error 4 in libX11.so.6.3.0[7f07fb0e6000+134000]
python2.5[8252]: segfault at 8 ip 7fb3d38ae626 sp 7fb3bbf71e30
error 4 in libX11.so.6.3.0[7fb3d385c000+134000]
python2.5[8302]: segfault at 8 ip 7f00abd88626 sp 7f009444be30
error 4 in libX11.so.6.3.0[7f00abd36000+134000]

Cheers,

Edward

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Re: [PyMOL] Segmentation fault r3910 on linux with Python 2.5/2.6 and tcl/tk 8.5.5 and 8.6b1.

[Jason Vertrees]

Hi Edward,

Choosing the correct Tcl/Tk version is necessary, and sometimes easy
to overlook.  Glad to hear it works.

Cheers,

-- Jason

On Thu, Jun 10, 2010 at 2:01 PM, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Hi,

 Sorry, this was not compiled properly!  catchsegv showed that tcl/tk
 8.6 was being used.  Setting LD_LIBRARY_PATH for the alternative
 tcl/tk libraries for the Python and PyMOL compilation fixed the
 problem.  The segfault is gone when using Python 2.5.5 with tcl/tk
 8.5.  It also works with Python 2.6.5 with tcl/tk 8.5.  So the problem
 looks like it is triggered by the new tck/tk 8.6 libraries.

 Regards,

 Edward



 On 10 June 2010 17:46, Edward d'Auvergne edward.dauver...@gmail.com wrote:
 Hi,

 I have a similar problem to Ben in this post:

 http://sourceforge.net/mailarchive/message.php?msg_id=20100512182803.GA21563%40crystal.harvard.edu

 I am using the svn r3910 with various versions of python and tcl/tk.
 I see the following message:

 IRQ's not enabled, falling back to busy waits: 2 0
  PyMOL(TM) Molecular Graphics System, Version 1.3.
  Copyright (c) Schrodinger, LLC.
  All Rights Reserved.

    Created by Warren L. DeLano, Ph.D.

    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at http://www.pymol.org;.

    Enter help for a list of commands.
    Enter help command-name for information on a specific command.

  Hit ESC anytime to toggle between text and graphics.

  OpenGL graphics engine:
  GL_VENDOR: Advanced Micro Devices, Inc.
  GL_RENDERER: Mesa DRI R600 (RV635 9598) 20090101  TCL
  GL_VERSION: 2.0 Mesa 7.8.1
  Detected 2 CPU cores.  Enabled multithreaded rendering.
 ./pymol: line 2:  7161 Segmentation fault
 /media/disk/bin/python2.5
 /media/disk/lib/python2.5/site-packages/pymol/__init__.py $@

 This specific message is with:

 pymol:  r3910
 python:  2.5.5
 tck/tk:  8.5.8
 pmw:  1.3.2
 GPU:  dual head ATI Radeon HD 2000 and later (radeon/fglrx) GPU
 driver:  radeon (x11-driver-video-ati)
 OS:  Mandriva 2010 spring (rc2)

 Is this a known issue?  Is there a way of disabling multithreaded
 rendering for testing this?  Some conspicuous dmseg messages are:

 python2.5[8829]: segfault at 0 ip (null) sp 7fff00eabee8 error 14
 in python2.5[40+11c000]
 python2.5[8846]: segfault at 0 ip (null) sp 7fffd0c51f68 error 14
 in python2.5[40+11c000]
 python2.5[8871]: segfault at 0 ip (null) sp 7fff515419c8 error 14
 in python2.5[40+11c000]
 python2.5[9051]: segfault at 0 ip (null) sp 7fffba96bda8 error 14
 in python2.5[40+11c000]
 python2.5[9198]: segfault at 0 ip (null) sp 7fff56bf19d8 error 14
 in python2.5[40+11c000]
 [drm] Resetting GPU
 [drm] Resetting GPU
 python2.5[2825]: segfault at 8 ip 7f090d03e626 sp 7f08f5701e30
 error 4 in libX11.so.6.3.0[7f090cfec000+134000]
 python2.5[5640]: segfault at 8 ip 7f6403be9626 sp 7f63ec43de30
 error 4 in libX11.so.6.3.0[7f6403b97000+134000]
 python2.5[7168]: segfault at 8 ip 7f07fb138626 sp 7f07e37fbe30
 error 4 in libX11.so.6.3.0[7f07fb0e6000+134000]
 python2.5[8252]: segfault at 8 ip 7fb3d38ae626 sp 7fb3bbf71e30
 error 4 in libX11.so.6.3.0[7fb3d385c000+134000]
 python2.5[8302]: segfault at 8 ip 7f00abd88626 sp 7f009444be30
 error 4 in libX11.so.6.3.0[7f00abd36000+134000]

 Cheers,

 Edward


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Re: [PyMOL] segmentation fault -- fedora 13

[Kevin Abbey]

The version that seg faults in fedora 13 is the edu build: *PyMOL 
1.2edu1* (August 2009)

Linux: pymol-1_2edu1-bin-linux-x86-centos45.tgz

The fedora 13 rpm build does not segfault.


I am really confused on the differences between the RPM and the official 
builds by PyMol via supscription.

http://www.pymol.org/reasons.html

Where can I find the document to clarify the differences for the current 
builds, not the pre1.0 since the rpm is 1.2.x?


Thank you,
Kevin




On 06/17/2010 07:11 PM, pymol-users-requ...@lists.sourceforge.net wrote:

Date: Thu, 17 Jun 2010 13:41:23 -0400
From: Kevin Abbeykab...@biomaps.rutgers.edu
Subject: [PyMOL] segmentation fault  -- fedora 13
To:pymol-users@lists.sourceforge.net
Message-ID:4c1a5e43.7010...@biomaps.rutgers.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Help,
I'm getting a seg fault on fedora 13.
What could be wrong?
Kevin
=


pymol
Segmentation fault (core dumped)

more /etc/fedora-release
Fedora release 13 (Goddard)


ldd pymol.exe
  linux-gate.so.1 =   (0x5000)
  libpthread.so.0 =  /lib/libpthread.so.0 (0x00d25000)
  libutil.so.1 =  /lib/libutil.so.1 (0x5558d000)
  libGL.so.1 =  /usr/lib/libGL.so.1 (0x55592000)
  libGLU.so.1 =  /usr/lib/libGLU.so.1 (0x5565d000)
  libfontconfig.so.1 =  /usr/lib/libfontconfig.so.1 (0x004c8000)
  libXss.so.1 =  /usr/lib/libXss.so.1 (0x556c6000)
  libXrender.so.1 =  /usr/lib/libXrender.so.1 (0x00df3000)
  libdl.so.2 =  /lib/libdl.so.2 (0x00d89000)
  libstdc++.so.6 =  /usr/lib/libstdc++.so.6 (0x556ca000)
  libm.so.6 =  /lib/libm.so.6 (0x00d9)
  libgcc_s.so.1 =  /lib/libgcc_s.so.1 (0x557b5000)
  libc.so.6 =  /lib/libc.so.6 (0x00b8a000)
  libXext.so.6 =  /usr/lib/libXext.so.6 (0x02f95000)
  libX11.so.6 =  /usr/lib/libX11.so.6 (0x0029d000)
  /lib/ld-linux.so.2 (0x00b68000)
  libnvidia-tls.so.256.25 =  /usr/lib/libnvidia-tls.so.256.25
(0x557d4000)
  libnvidia-glcore.so.256.25 =  /usr/lib/libnvidia-glcore.so.256.25
(0x557d6000)
  libfreetype.so.6 =  /usr/lib/libfreetype.so.6 (0x00203000)
  libexpat.so.1 =  /lib/libexpat.so.1 (0x003d7000)
  libxcb.so.1 =  /usr/lib/libxcb.so.1 (0x00487000)
  libXau.so.6 =  /usr/lib/libXau.so.6 (0x005fa000)
   


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Re: [PyMOL] segmentation fault in 1.2r3pre 64-bit on linux

[Jason Vertrees]

Hi Ben,

A couple things come to mind:

(1) Always use the latest proven NVidia drivers; 180.xx is not current.
(2) Some RH versions use Tcl/Tk 8.4 over 8.5.  Which is yours using?
(3) Could you please send me the md5 sum for your copy?  We should
make sure it's not corrupted.

Cheers,

-- Jason

On Wed, May 12, 2010 at 2:28 PM, Ben Eisenbraun
b...@hkl.hms.harvard.edu wrote:

 Hi,

 One of my users is getting this:

  PyMOL(TM) Incentive Product - PyMOL Executable Build
  Copyright (C) 2009-2010 Schrodinger, LLC

  This PyMOL Executable Build is available only to PyMOL Power, Casual, and
  Developer Users who have a valid license to use this software product.  Any
  other usage is specifically prohibited and may constitute a violation of
  United States and international copyright laws.

  This Executable Build integrates and extends Open-Source PyMOL 1.2r3pre.
  OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro FX 4600/PCI/SSE2
  GL_VERSION: 3.0.0 NVIDIA 180.51
  Adapting to Quadro hardware.
  Detected 8 CPU cores.  Enabled multithreaded rendering.
  OpenGL quad-buffer stereo 3D detected and enabled.
 Segmentation fault

 This is Red Hat EL 5.3 on x86_64, and the PyMOL version is the incentive build
 of 1.2r3.  Any ideas on how to troubleshoot this?  Could it be related to the
 3d?  I can probably get a core dump, but I don't think the available builds
 have debugging symbols, so that may not be of much use.


 Any ideas on how to proceed would be appreciated.

 Thanks.

 -ben

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Re: [PyMOL] segmentation fault!

[Michael Lerner]

Hi,

I can try to look into this, although I'm not sure what's causing it. Can
you tell me

 - what version of PyMOL you have and how it was installed
 - what version of APBS you have and how it was installed
 - when exactly the segmentation fault happens (are you working with a
particular PDB file, etc.)

Thanks,

-Michael

On Sun, Nov 22, 2009 at 4:00 PM, Mehdi Talebzadeh Farooji 
mahdi...@yahoo.com wrote:

 Dear All,

 I run pymol on laptop ubuntu 9.10 with ATI raedon gaphic card. when I try
 to call plugin of pymol for APBS, pymol crashes with segmentation fault
 message.  Every suggestion would be welcomed!

 Thanks,

 Mehdi

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[PyMOL] segmentation fault!

[Mehdi Talebzadeh Farooji]

Dear All,

I run pymol on laptop ubuntu 9.10 with ATI raedon gaphic card. when I try to 
call plugin
of pymol for APBS, pymol crashes with segmentation fault message.  Every 
suggestion
would be welcomed!

Thanks,

Mehdi


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[PyMOL] Pymol segmentation fault

[Ian Berke]

Hi,

I'm having an issue trying to run various plugins in pymol (apbs and
autodock).  Whenever I select a button that should bring up a file browser
to choose a file (e.g. Choose Externally generated pqr in apbs) Pymol
exits with: Segmentation fault (core dumped).  Same thing happens when I go
to HelpAbout.  I can open and save files normally, and just about
everything else works.

I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin
window to open, as well as the 1.2 trunk from svn (downloaded and compiled
last week) which just crashes when I try to open the apbs window (I can
install autodock.py and the window opens, but it crashes when I try to
choose the location of files).  I'm guessing this is something to do with
the gui and tcl/tk, but don't have any idea how to troubleshoot (see the
catchsegv output below).  I'm running Ubuntu 9.10 on x86_64 and have  a
GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36.

Does anyone have any thoughts?

Here is the backtrace portion from catchsegv:
Backtrace:
/usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
/usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
/usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
/usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
/usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
/usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
/usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
/usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
/usr/lib/libtcl8.5.so.0[0x7f639777dee6]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
/usr/lib/libtcl8.5.so.0[0x7f63977926d1]
/usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
/usr/lib/libtcl8.5.so.0[0x7f6397793192]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/bin/python[0x49c06f]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
/usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0[0x7f63977527b9]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
/usr/lib/libtk8.5.so.0[0x7f6397a556f6]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
/usr/lib/libtcl8.5.so.0[0x7f639779668f]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
/usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
/usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
/usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
/usr/lib/libtk8.5.so.0[0x7f6397a37b48]
/usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
/usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52beed]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]

Re: [PyMOL] Pymol segmentation fault

[Warren DeLano]

Ian,
 
Based on that traceback, it looks like you have two conflicting versions
of Tcl (8.4 as well as 8.5) linked against and running in the same
process...that could be the source of the crash.
 
Cheers,
Warren



From: Ian Berke [mailto:ian.be...@yale.edu] 
Sent: Thursday, September 24, 2009 11:26 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Pymol segmentation fault


Hi,

I'm having an issue trying to run various plugins in pymol (apbs
and autodock).  Whenever I select a button that should bring up a file
browser to choose a file (e.g. Choose Externally generated pqr in
apbs) Pymol exits with: Segmentation fault (core dumped).  Same thing
happens when I go to HelpAbout.  I can open and save files normally,
and just about everything else works.

I've tried this in pymol 1.1r2pre, where I can at least get the
apbs plugin window to open, as well as the 1.2 trunk from svn
(downloaded and compiled last week) which just crashes when I try to
open the apbs window (I can install autodock.py and the window opens,
but it crashes when I try to choose the location of files).  I'm
guessing this is something to do with the gui and tcl/tk, but don't have
any idea how to troubleshoot (see the catchsegv output below).  I'm
running Ubuntu 9.10 on x86_64 and have  a GeForce 8400M GS/PCI/SSE2 with
the proprietory nvidia driver 185.18.36.

Does anyone have any thoughts?

Here is the backtrace portion from catchsegv:
Backtrace:
/usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]

/usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]

/usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
/usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
/usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
/usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
/usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
/usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
/usr/lib/libtcl8.5.so.0[0x7f639777dee6]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]

/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
/usr/lib/libtcl8.5.so.0[0x7f63977926d1]
/usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
/usr/lib/libtcl8.5.so.0[0x7f6397793192]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/bin/python[0x49c06f]
/usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
/usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
/usr/bin/python[0x52bdf0]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python[0x4254ff]
/usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
/usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]

/usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]
/usr/lib/libtcl8.5.so.0[0x7f63977527b9]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
/usr/lib/libtk8.5.so.0[0x7f6397a556f6]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
/usr/lib/libtcl8.5.so.0[0x7f639779668f]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f63977543b8]

/usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
/usr/lib/libtcl8.5.so.0[0x7f63977102f1]
/usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
/usr/lib/libtk8.5.so.0

Re: [PyMOL] Pymol segmentation fault

[Pete Meyer]

 Does anyone have any thoughts?

Two things to try that may or may not help:

1. Check if the problem persists when running pymol in single-threaded 
mode (cmd.set('max_threads',1)).  libpthread in the trace might 
indicate that one of the libraries is having issues with multiple threads.

2. On Kubuntu 8.04.3 LTS x64, I can't reproduce the problem with 1.2 
from svn trunk.  This is using Tcl/Tk 8.4 (with pymol using it's own 
source build of python 2.4.2, which may or may not be relevant); so 
installing Tcl/Tk 8.4 instead of 8.5 (source or binary) might help 
resolve the problem, or at least eliminate one possible source.

Pete

 Here is the backtrace portion from catchsegv:
 Backtrace:
 /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
 /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
 /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
 /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
 /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
 /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
 /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
 /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
 /usr/lib/libtcl8.5.so.0[0x7f639777dee6]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
 /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
 /usr/lib/libtcl8.5.so.0[0x7f63977926d1]
 /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
 /usr/lib/libtcl8.5.so.0[0x7f6397793192]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
 /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
 /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python[0x52bdf0]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python[0x4254ff]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
 /usr/bin/python[0x49c06f]
 /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python[0x52bdf0]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python[0x4254ff]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
 /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
 /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
 /usr/lib/libtcl8.5.so.0[0x7f63977527b9]
 /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
 /usr/lib/libtk8.5.so.0[0x7f6397a556f6]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
 /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
 /usr/lib/libtcl8.5.so.0[0x7f639779668f]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
 /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
 /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
 /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
 /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
 /usr/lib/libtk8.5.so.0[0x7f6397a37b48]
 /usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
 /usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
 /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
 /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python[0x52beed]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python[0x52bdf0]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python[0x4254ff]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
 /usr/bin/python[0x4d0c4d]
 /lib/libpthread.so.0[0x7f639cf69a04]
 /lib/libc.so.6(clone+0x6d)[0x7f639c4317bd]
 
 Thanks,
 Ian
 

Re: [PyMOL] Pymol segmentation fault

[Ian Berke]

Thank you!  This was indeed the case.  I have no idea why tcl/tk 8.4 was
installed with 8.5 at the same time.  Removing 8.4 and using 8.5 seems to
have fixed the problem.

Ian

On Thu, Sep 24, 2009 at 2:38 PM, Warren DeLano war...@delsci.com wrote:

  Ian,

 Based on that traceback, it looks like you have two conflicting versions of
 Tcl (8.4 as well as 8.5) linked against and running in the same
 process...that could be the source of the crash.

 Cheers,
 Warren

  --
 *From:* Ian Berke [mailto:ian.be...@yale.edu]
 *Sent:* Thursday, September 24, 2009 11:26 AM
 *To:* pymol-users@lists.sourceforge.net
 *Subject:* [PyMOL] Pymol segmentation fault

 Hi,

 I'm having an issue trying to run various plugins in pymol (apbs and
 autodock).  Whenever I select a button that should bring up a file browser
 to choose a file (e.g. Choose Externally generated pqr in apbs) Pymol
 exits with: Segmentation fault (core dumped).  Same thing happens when I go
 to HelpAbout.  I can open and save files normally, and just about
 everything else works.

 I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin
 window to open, as well as the 1.2 trunk from svn (downloaded and compiled
 last week) which just crashes when I try to open the apbs window (I can
 install autodock.py and the window opens, but it crashes when I try to
 choose the location of files).  I'm guessing this is something to do with
 the gui and tcl/tk, but don't have any idea how to troubleshoot (see the
 catchsegv output below).  I'm running Ubuntu 9.10 on x86_64 and have  a
 GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36.

 Does anyone have any thoughts?

 Here is the backtrace portion from catchsegv:
 Backtrace:
 /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
 /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
 /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
 /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
 /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
 /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
 /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
 /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
 /usr/lib/libtcl8.5.so.0[0x7f639777dee6]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
 /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
 /usr/lib/libtcl8.5.so.0[0x7f63977926d1]
 /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
 /usr/lib/libtcl8.5.so.0[0x7f6397793192]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
 /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
 /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python[0x52bdf0]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python[0x4254ff]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
 /usr/bin/python[0x49c06f]
 /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
 /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
 /usr/bin/python[0x52bdf0]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python[0x4254ff]
 /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
 /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
 /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
 /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
 /usr/lib/libtcl8.5.so.0[0x7f63977527b9]
 /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
 /usr/lib/libtk8.5.so.0[0x7f6397a556f6]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
 /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
 /usr/lib/libtcl8.5.so.0[0x7f639779668f]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
 /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
 /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
 /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
 /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
 /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
 /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
 /usr/lib/libtk8.5.so.0[0x7f6397a37b48]
 /usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
 /usr

[PyMOL] Segmentation Fault / Bus Error

[Martin Höfling]

Hey Folks - I am trying to assign colors via APBS plugin to a surface  
which fails with a Bus error on Mac and Segfault on Linux.


Versions are 1.1r2pre on Linux and Mac, as well as the latest from svn- 
trunk on Mac as well...


The command that actually fails is ramp_new, as I found out by doing  
it by hand.


Any Ideas where I could look for?

Best
Martin

Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

[Christian Seifert]

$PYTHONPATH is not set on my machine.



You wrote:

  Re: segmentation fault after switching mainwindow between visualisation 
and commandline
  From: Martin martin.hoefl...@gm... - 2006-11-13 05:15

   ... i had a similar Problem this morning. What is your PYTHONPATH? For 
me, 
   unsetting it solved the problems.
   
   Cheers   
Martin
   


segmentation fault after switching mainwindow between visualisation and 
commandline
From: Christian Seifert cseif...@bp... - 2006-11-13 02:07

 Hi,
 
 I found a critical and reproducible bug using the 0.99rc6-binarys on my
 machine.
 
 Stepps:
 - starting pymol from a kde terminal with user-rights
 - loading a pdb-file (e.g. 1K5D from pdb-database)
 - rotate the molecule with the mouse in any direction
 - hitting Esc to get to the commandline-mode
 - hitting Esc again to get back to the visualisation-mode
 - trying to rotate the molecule again with the mouse
 
 The programm crashes, the two windows of pymol disappear and my
 terminal-window show the following error:
 
 ./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe $@
 
 Speicherzugriffsfehler is the german word for segmentation fault.
 
 There is nothing in dmseg.
 
 The full output:
 cseif...@lexx ~/pymol $ ./pymol
 
  PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.
 
  A current PyMOL Maintenance and/or Support Subscription may be required
  for legal use of this Build beyond a finite honor-system evaluation period.
  Please visit http://www.pymol.org/funding.html for more information.
 
  This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
  OpenGL graphics engine:
   GL_VENDOR: ATI Technologies Inc.
   GL_RENDERER: ATI MOBILITY FireGL V5200 Pentium 4 (SSE2) (FireGL) (GNU_ICD)
   GL_VERSION: 2.0.5946 (8.27.10)
  Detected 2 CPUs.  Enabled multithreaded rendering.
 HEADERSIGNALING PROTEIN/SIGNALING ACTIVATOR   10-OCT-01   1K5D
 TITLE CRYSTAL STRUCTURE OF RAN-GPPNHP-RANBP1-RANGAP COMPLEX
 COMPNDMOL_ID: 1;
 COMPND   2 MOLECULE: GTP-BINDING NUCLEAR PROTEIN RAN;
 COMPND   3 CHAIN: A, D, G, J;
 COMPND   4 SYNONYM: RAN, TC4, RAN GTPASE, ANDROGEN RECEPTOR-
 COMPND   5 ASSOCIATED PROTEIN 24;
 COMPND   6 ENGINEERED: YES;
 COMPND   7 MOL_ID: 2;
 COMPND   8 MOLECULE: RAN-SPECIFIC GTPASE-ACTIVATING PROTEIN;
 COMPND   9 CHAIN: B, E, H, K;
 COMPND  10 SYNONYM: RANBP1, RAN BINDING PROTEIN 1;
 COMPND  11 ENGINEERED: YES;
 COMPND  12 MUTATION: YES;
 COMPND  13 MOL_ID: 3;
 COMPND  14 MOLECULE: RAN GTPASE ACTIVATING PROTEIN 1;
 COMPND  15 CHAIN: C, F, I, L;
 COMPND  16 SYNONYM: RANGAP, PROTEIN RNA1;
 COMPND  17 ENGINEERED: YES
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  CmdLoad: /home/cseifert/Desktop/1K5D.pdb loaded as 1K5D.
 ./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe $@
 
 Thanks,
 
 Christian Seifert.

[PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

[Christian Seifert]

Hi,

I found a critical and reproducible bug using the 0.99rc6-binarys on my
machine.

Stepps:
- starting pymol from a kde terminal with user-rights
- loading a pdb-file (e.g. 1K5D from pdb-database)
- rotate the molecule with the mouse in any direction
- hitting Esc to get to the commandline-mode
- hitting Esc again to get back to the visualisation-mode
- trying to rotate the molecule again with the mouse

The programm crashes, the two windows of pymol disappear and my
terminal-window show the following error:

./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe $@

Speicherzugriffsfehler is the german word for segmentation fault.

There is nothing in dmseg.

The full output:
cseif...@lexx ~/pymol $ ./pymol

 PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.

 A current PyMOL Maintenance and/or Support Subscription may be required
 for legal use of this Build beyond a finite honor-system evaluation period.
 Please visit http://www.pymol.org/funding.html for more information.

 This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
 OpenGL graphics engine:
  GL_VENDOR: ATI Technologies Inc.
  GL_RENDERER: ATI MOBILITY FireGL V5200 Pentium 4 (SSE2) (FireGL) (GNU_ICD)
  GL_VERSION: 2.0.5946 (8.27.10)
 Detected 2 CPUs.  Enabled multithreaded rendering.
HEADERSIGNALING PROTEIN/SIGNALING ACTIVATOR   10-OCT-01   1K5D
TITLE CRYSTAL STRUCTURE OF RAN-GPPNHP-RANBP1-RANGAP COMPLEX
COMPNDMOL_ID: 1;
COMPND   2 MOLECULE: GTP-BINDING NUCLEAR PROTEIN RAN;
COMPND   3 CHAIN: A, D, G, J;
COMPND   4 SYNONYM: RAN, TC4, RAN GTPASE, ANDROGEN RECEPTOR-
COMPND   5 ASSOCIATED PROTEIN 24;
COMPND   6 ENGINEERED: YES;
COMPND   7 MOL_ID: 2;
COMPND   8 MOLECULE: RAN-SPECIFIC GTPASE-ACTIVATING PROTEIN;
COMPND   9 CHAIN: B, E, H, K;
COMPND  10 SYNONYM: RANBP1, RAN BINDING PROTEIN 1;
COMPND  11 ENGINEERED: YES;
COMPND  12 MUTATION: YES;
COMPND  13 MOL_ID: 3;
COMPND  14 MOLECULE: RAN GTPASE ACTIVATING PROTEIN 1;
COMPND  15 CHAIN: C, F, I, L;
COMPND  16 SYNONYM: RANGAP, PROTEIN RNA1;
COMPND  17 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 1 symmetry operators.
 CmdLoad: /home/cseifert/Desktop/1K5D.pdb loaded as 1K5D.
./pymol: line 14:  7110 Speicherzugriffsfehler  $PYMOL_PATH/pymol.exe $@

Thanks,

Christian Seifert.

Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

[Martin Höfling]

... i had a similar Problem this morning. What is your PYTHONPATH? For me, 
unsetting it solved the problems.

Cheers  
Martin

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

[Warren DeLano]

Dmitriy,

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

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

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

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

should be

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

since TempPyMOLGlobals can't be derefrenced until it exists.  

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

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

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

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

These changes have been committed to CVS.

Cheers,
Warren


--
Warren L. DeLano, Ph.D. 
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

 -Original Message-
 From: Dmitriy Igor Bryndin [mailto:brynd...@msu.edu] 
 Sent: Tuesday, October 11, 2005 5:06 AM
 To: Warren DeLano
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] PyMol segmentation fault while starting 
 from external python program
 
 Warren 
 
 It seems like PyMol should have time to load after  import 
 pymol and before anything else can be done with it.
 If I´ll do
  --
 pymol_argv = ['pymol', '-qx']
 import pymol
 # let`s give pymol some time to load
 for a in range(100):
   b=0 
 
 pymol.finish_launching() 
 
 from pymol import cmd 
 
 cmd.load($HOME/pept.pdb)
 cmd.show(sticks)
  --
 everything is fine. It loads and shows the picture.
 ´for a in range(100)´  for example will produce segmentation fault. 
 
 As far as I understand ´pymol.finish_launching()´ is meant to 
 produce such delay. Correct me if I´m wrong. But this call 
 produce segm fault by itself without a waiting cycle. 
 
 Can you recommend some workaround for this problem? This 
 stupid cycle may work on my machine, but may not work on a 
 faster one. Is there any way to find out that PyMol window 
 had loaded? 
 
 Thanks
  Dmitriy Bryndin 
 
  
 
  
 
  
 
 
 Warren DeLano writes: 
 
  Dmitriy,
  
  Due to problem with multithreading (especially with the Tcl/Tk 
  external GUI), we haven't been able to get the import 
 pymol approach to work in
  a stable robust manner across different OSes and environments.   
  
  So sight now, as per comments in 
 modules/pymol/__init__.py, the only 
  supported way to launch PyMOL is to run the __init__.py script on 
  startup.
  
  %python modules/pymol/__init__.py
  
  Hoever, if you disable the external GUI, then you might be 
 able to get 
  import pymol to work...
  
  pymol_argv = ['pymol', '-qx']
  import pymol
  pymol.finish_launching()
  
  from pymol import cmd
  
  cmd.load(...etc. 
  
  
  Cheers,
  Warren
  
  
  --
  Warren L. DeLano, Ph.D. 
  Principal Scientist
  
  . DeLano Scientific LLC  
  . 400 Oyster Point Blvd., Suite 213   
  . South San Francisco, CA 94080 USA   
  . Biz:(650)-872-0942  Tech:(650)-872-0834 
  . Fax:(650)-872-0273  Cell:(650)-346-1154
  . mailto:war...@delsci.com  

  
  -Original Message-
  From: pymol-users-ad...@lists.sourceforge.net
  [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf 
 Of Dmitriy 
  Igor Bryndin
  Sent: Monday, October 10, 2005 2:33 PM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] PyMol segmentation fault while starting from 
  external python program
  
  Launching PyMol form external python script will produce 
  segmaentation fault.
  For example starting launch.py from /pymol/examples/launching
   --
  $ python launch.py
  zsh: segmentation fault  python launch.py
   --
  Crashes without even showing PyMol windows.  
  
  Tried it on Fedora Core 1, Fedora Core 4, Mandriva 2005. The same 
  story.
  Different pythons and compiling different versions of 
 PyMol does not 
  change anything.
  
  It will launch PyMol windows if there is only
 import pymol
  line.  
  
  Adding
 pymol.finish_launching

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

[Warren DeLano]

Update:

With respect to import pymol, I think all of the reported segmentation
fault and race conditions have now been eliminated from the very latest
source code.  Since everyone doesn't have CVS access, I have posted a
source tar-gz file on http://delsci.com/beta with updated instructions
on building and usage.

So if you are a unix-based Python developer with an interest in calling
PyMOL from you own stadalone applications, then this would be a good
time to try building from source into your own Python environment in
order to see whether or not it can work for you.  Windows is a
possibility too, but getting all the dependencies satisfied under Win32
is a bit of a chore.

Cheers,
Warren

--
Warren L. DeLano, Ph.D. 
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

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

[Warren DeLano]

Dmitriy,

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

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

%python modules/pymol/__init__.py

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

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

from pymol import cmd

cmd.load(...etc.


Cheers,
Warren


--
Warren L. DeLano, Ph.D. 
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

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

[Sebastien Moretti]

Hello,
I use a script to build pml script file for PyMOL.
Sometimes, the selection of individual residues are huge for PyMOL (0.98 
or 0.97) and produces a segmentation fault.


Is there a way to avoid this behavior ?
Like a configuration file with a manageable memory quantity ?

Thanks

--
Sébastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

[PyMOL] Pymol segmentation fault - fedora core 1

[Roger Dodd]

Hi everyone,

I've recently updated to the 0.97 release of pymol and although it ran 
fine to start with, it's now generating a segmentation fault. I 
installed from the * pymol-0_97-bin-linux-libc6-i386.tgz* 
http://prdownloads.sourceforge.net/pymol/pymol-0_97-bin-linux-libc6-i386.tgz?download 
file into /usr/local/pymol and ran setup.sh. Then when running the 
pymol.com script I get the following:


./pymol.com: line 14: 31156 Segmentation fault  $PYMOL_PATH/pymol.exe $*

I'm not sure exactly what's causing this and any help would be 
appreciated. I've tried completely removing the pymol directory and 
reinstalling but I still get the same error.


Cheers

Roger

Re: [PyMOL] Pymol segmentation fault - fedora core 1

[Filipe Maia]

On Mon, 26 Jul 2004 10:40:47 +0100, Roger Dodd rb...@hermes.cam.ac.uk  
wrote:



Hi everyone,

I've recently updated to the 0.97 release of pymol and although it ran  
fine to start with, it's now generating a segmentation fault. I  
installed from the * pymol-0_97-bin-linux-libc6-i386.tgz*  
http://prdownloads.sourceforge.net/pymol/pymol-0_97-bin-linux-libc6-i386.tgz?download  
file into /usr/local/pymol and ran setup.sh. Then when running the  
pymol.com script I get the following:


./pymol.com: line 14: 31156 Segmentation fault   
$PYMOL_PATH/pymol.exe $*


I'm not sure exactly what's causing this and any help would be  
appreciated. I've tried completely removing the pymol directory and  
reinstalling but I still get the same error.


$PYMOL_PATH/pymol.exe $* - this looks suspicious.

Did you tried to compile pymol as a monolythic thing? I don't beleive that  
still works.

I use $PYMOL_PATH/ext/bin/python $PYMOL_PATH/modules/pymol/__init__.py $*

I'll send you my Rules.make and pymol.com.
I was able to build it simply with a symlink from ext to /usr




Cheers

Roger


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[PyMOL] Segmentation Fault

[Michael Tallhamer]

Dear PyMOL Users,

This may have been answered before but I haven't found the answer yet. I 
have a script that has to iterate over a very large selection of atoms and 
when it runs it comes to a point where pymol shuts down and I recieve the 
message Segmentation Fault in my terminal window. I'm looking at trying to 
find out what this problem is and how do I go abot trying to correct it?


Thanks for all your help,
Michael Tallhamer
Undergraduate Researcher
Cleveland State University

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