pymol-users Mailing List for PyMOL Molecular Graphics System

Hi,

trying to read a mol2 file I get the following error message;

ReadMOL2File-Error: bad atom count

I compare this file with another one which pymol loads without problems 
and they look very similar (except for the atomic coordiantes)

Do you know what could be the cause ?

Thanks

John,

This is a bug we haven't yet been able to figure out yet.  However, Jack
Howarth has provided the following workaround:

[with] the compile flags...

-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic

Out of those it turns out that "-fstack-protector --param=ssp-buffer-size=4"
triggers the run-time failures. These same flags don't cause a problem on
x86 (-m32) builds. You might want to look into this
to see if the stack protection code is picking up on a real flaw in pymol at
-m64.

I hope this helps!

Cheers,
Warren


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of JJ
> Sent: Saturday, December 22, 2007 4:18 AM
> To: pym...@li...
> Subject: [PyMOL] strange pymol crash
> 
> Hello:
> I have a strange crash problem with pymol.  I've had the 64 
> bit version 1.0r2 installed on two Fedora 8 machines for 
> several weeks and up until yesterday or so everything was 
> working just fine.  Now pymol will not start on either 
> machine.  Here is the error:
> 
> python: Modules/gcmodule.c:276: visit_decref:
> Assertion `gc->gc.gc_refs != 0' failed.
> /usr/local/bin/pymol: line 2:  3127 Aborted           
>      /usr/bin/python
> /usr/lib64/python2.5/site-packages/pymol/__init__.py
> $*
> 
> I tried rebuilding the NVIDIA driver for one machine, but 
> that did not fix the problem.  I also uninstalled and 
> reinstalled pymol, but it didn't help either. 
> Perhaps I did something to both machines to cause pymol to 
> crash, but I don't know what that was.  As far as I know, no 
> Fedora updates were made before the crashes.  I did try 
> installing updates for one machine, but that did not help.  I 
> get the same error if I try to use "import pymol" in an 
> interactive python shell.  Any ideas on how to fix it?
> 
> John
> 
> 
> 
> 
> 
>       
> ______________________________________________________________
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Hello:
I have a strange crash problem with pymol.  I've had
the 64 bit version 1.0r2 installed on two Fedora 8
machines for several weeks and up until yesterday or
so everything was working just fine.  Now pymol will
not start on either machine.  Here is the error:

python: Modules/gcmodule.c:276: visit_decref:
Assertion `gc->gc.gc_refs != 0' failed.
/usr/local/bin/pymol: line 2:  3127 Aborted           
     /usr/bin/python
/usr/lib64/python2.5/site-packages/pymol/__init__.py
$*

I tried rebuilding the NVIDIA driver for one machine,
but that did not fix the problem.  I also uninstalled
and reinstalled pymol, but it didn't help either. 
Perhaps I did something to both machines to cause
pymol to crash, but I don't know what that was.  As
far as I know, no Fedora updates were made before the
crashes.  I did try installing updates for one
machine, but that did not help.  I get the same error
if I try to use "import pymol" in an interactive
python shell.  Any ideas on how to fix it?

John





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Be a better friend, newshound, and 
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dXNlIHdpemFyZC0+bXV0YWdlbmlzaXMuLgoKT24gRGVjIDE5LCAyMDA3IDU6NDMgUE0sIHdhbmcs
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ZQo+IF9fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fCj4gUHlN
T0wtdXNlcnMgbWFpbGluZyBsaXN0Cj4gUHlNT0wtdXNlcnNAbGlzdHMuc291cmNlZm9yZ2UubmV0
Cj4gaHR0cHM6Ly9saXN0cy5zb3VyY2Vmb3JnZS5uZXQvbGlzdHMvbGlzdGluZm8vcHltb2wtdXNl
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ZXJzaXR5IG9mIFdhc2hpbmd0b24KQm94IDM1NTAxMwpTZWF0dGxlLCBXQSA5ODE5NS01MDEzCg==

hi, everyone, I want to make an image to show some structual differences between wild-tye ribosomal protein S12 and mutant type in bacteria. Does anybody know how to substitute wt aa residue with mutant type in an published crystal structed? or it is a mission impossible using PyMol. Thanks a lot!
 
best regards,
 
wangPh.DMicrobial Function LabNational Food Research InstituteTsukuba, 305-8642, JAPANTel: 81-29-838-8124
_________________________________________________________________
MSN圣诞礼物火热登场，免费发放中，快来领取吧！
http://im.live.cn/emoticons/?ID=18

Dear all,

when trying to use the APBS plugin I experience the following problem


The first time I tried to run it it the error message was simply
"ObjectMapLoadDXFile-Error:  Unable to open file!"
Now the second time it pops up an error log:

Error: 1
WindowsError Exception in Tk callback
 Function: <bound method PmwFileDialog.okbutton of
<pmg_tk.startup.apbs_tools.PmwFileDialog instance at 0x05961A30>>
(type: <type 'instancemethod'>)
 Args: ()
Traceback (innermost last):
 File "d:\Program Files\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in
__call__
   return apply(self.func, args)
 File "d:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py", line 1711, in
okbutton
   self.setfilename(fn)
 File "d:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py", line 1745, in
setfilename
   self.configure(directory=dir,filename=value)
 File "d:\Program Files\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 729, in
configureapbs.exe
   func()
 File "d:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py", line 1769, in
newdir
   self.fillit()
 File "d:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py", line 1836, in
fillit
   fl=os.listdir(dir)
WindowsError: [Errno 123] The filename, directory name, or volume
label syntax is incorrect: 'd:APBS-0.5.1\\bin\\d:APBS-0.5.1\\bin/*.*'

Both pymol (1.0edu1) and apbs (0.5.1)are fresh and clean installations.
APBS is installed in D:\APBS-0.5.1

I experienced similiar problems on another Windows machine and a Mac,
but both without the error log above.

I was realizing that when choosing the location of APBS binary pymol
writes: d:APBS-0.5.1 where it should be d:\APBS-0.5.1
I tried to put the correct path manually d:\APBS-0.5.1\bin\apbs.exe,
but did not help.


Any suggestions?


Many thanks,
Thomas

Carsten,

Hmm...this could be a bug.  In the meantime, the way to get this effect is
to duplicate the object, and then configure one object one way, and the
second, another.

Cheers,
Warren


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Schubert,
Carsten [PRDUS]
Sent: Wednesday, December 12, 2007 1:48 PM
To: pym...@li...
Subject: [PyMOL] Cartoon mode not stored in scene description?

Hi

I am trying to define 2 scenes, in one the protein is represented in
"cartoon automatic" mode in the other with "cartoon putty". Pymol (1.0 on
Linux or 1.1b on Windows) both only draw the recalled scenes in putty mode.
Is that expected behaviour? I would have thought that the cartoon mode is
part of a scene description?
The colors do get updated between the scenes. 

Here is a code snipped to make this clearer:

....
cartoon automatic
refresh

scene F1, store

cartoon putty
spectrum b, palette=rainbow, minimum=0, maximum=60,selection=prot and name
CA

scene F2, store


Cheers

	Carsten

Hi

I am trying to define 2 scenes, in one the protein is represented in =
"cartoon automatic" mode in the other with "cartoon putty". Pymol (1.0 =
on Linux or 1.1b on Windows) both only draw the recalled scenes in putty =
mode. Is that expected behaviour? I would have thought that the cartoon =
mode is part of a scene description?
The colors do get updated between the scenes.=20

Here is a code snipped to make this clearer:

....
cartoon automatic
refresh

scene F1, store

cartoon putty
spectrum b, palette=3Drainbow, minimum=3D0, =
maximum=3D60,selection=3Dprot and name CA

scene F2, store


Cheers

	Carsten

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9700 S. Cass Ave.
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Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...

Hi Steve,

You'll need to provide more information if you want to have a chance on a
helpful thought. Maybe you could link the .pdb file and the .xplor map and
show what O does to it.

Cheers,

Tsjerk

On Dec 7, 2007 3:57 PM, W.M. B. <but...@gm...> wrote:

> Hi, All
>
> I'm trying to make a picture of active site with density map. When I
> loaded the pdb and xplor map, I found that map and model are in the diffrent
> position. But in O, they are fine. Would anyone give me a hint how to fix
> it.
>
> Thanks
>
> Steve
>
> -------------------------------------------------------------------------
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>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Thanks to Michael and Warren for a quick and correct but somewhat 
baffling solution.  In OSX, one renames an application and it starts up 
looking quite dissimilar from before.  I'm still new to the Gospel 
according to Steve, and I wouldn't mind enlightenment.

In any case, using MacPyMOL as PyMOLHybrid also solves the problem of 
physically separating the viewer from the external gui, without which 
one couldn't fully harness the power of multiple screens.

A side note regarding Michael's instructions:  APBS doesn't require 
fink.  (I haven't even figured out what fink is yet.  Some sort of yum 
for OSX?)  One can just download the Mac OSX binary from WUSTL and 
install it as per default.  Works like a charm, as does APBS itself. 
Much better than on my Fedora 7 system, I'm embarrassed to admit ;-)


Andreas


Michael Lerner wrote:
>> I would like to use apbs from within PyMOL.  I have downloaded and
>> installed the latest version of apbs, and apbs_tools.py exists in
>> $PYMOL_PATH/modules/pmg_tk/startup/.  However, I find no "plugins" entry
>> in any of the PyMOL menus.
> 
> I think that you need to rename the application bundle to
> "PyMOLX11Hybrid" in order to use plugins.
> 
>> Am I blind or daft?  But the question I'd
>> really like to have answered is how do I get abps to work.
> 
> I would suggest
> 
> 1) register APBS here http://agave.wustl.edu/apbs/download/
> 2) Install fink ( http://finkproject.org/ ) and then use it to install
> apbs (e.g. by typing "fink install apbs" on the command line).
> 
> hope that helps,
> 
> -michael
> 
>> I'm using educational MacPyMOL, which "integrates and extends
>> Open-Source PyMOL 1.0r1".
>>
>> Thanks.
>>
>>
>> Andreas
>>

Hi, All

I'm trying to make a picture of active site with density map. When I loaded
the pdb and xplor map, I found that map and model are in the diffrent
position. But in O, they are fine. Would anyone give me a hint how to fix
it.

Thanks

Steve

Hello everybody.
Does anybody know how to perform sequence to structure fit with pymol?
For example this feature in swiss-pdb-viewer is called "Fit" or "Magic
fit". So,
1/ Is there a command to fit sequence to pdb&
2/ If yes, could I specify the region to fit on?

Thanks!

> I would like to use apbs from within PyMOL.  I have downloaded and
> installed the latest version of apbs, and apbs_tools.py exists in
> $PYMOL_PATH/modules/pmg_tk/startup/.  However, I find no "plugins" entry
> in any of the PyMOL menus.

I think that you need to rename the application bundle to
"PyMOLX11Hybrid" in order to use plugins.

> Am I blind or daft?  But the question I'd
> really like to have answered is how do I get abps to work.

I would suggest

1) register APBS here http://agave.wustl.edu/apbs/download/
2) Install fink ( http://finkproject.org/ ) and then use it to install
apbs (e.g. by typing "fink install apbs" on the command line).

hope that helps,

-michael

>
> I'm using educational MacPyMOL, which "integrates and extends
> Open-Source PyMOL 1.0r1".
>
> Thanks.
>
>
> Andreas
>
> -------------------------------------------------------------------------
> SF.Net email is sponsored by:
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner

Hey all,

I would like to use apbs from within PyMOL.  I have downloaded and 
installed the latest version of apbs, and apbs_tools.py exists in 
$PYMOL_PATH/modules/pmg_tk/startup/.  However, I find no "plugins" entry 
in any of the PyMOL menus.  Am I blind or daft?  But the question I'd 
really like to have answered is how do I get abps to work.

I'm using educational MacPyMOL, which "integrates and extends 
Open-Source PyMOL 1.0r1".

Thanks.


Andreas

The command 'png' has image width and height as possible arguments,
while the command 'mpng' doesn't. Is there a way to get mpng write files
with some chosen dimensions?

Thank you.
Paride

Hi Alain,

I think this problem is raised because you try to open the file,
whose path includes non-us-ascii charactors.

Pymol (and many other programs) doesn't recognize "multilingual" path,
so when you specify the file under such folder, pymol will return some errors.

To resolve this error, copy the file to the root directory of C:\ etc.,
and try to open it again.

If you'd like to open the file without copying, go to 'Start' menu and
select 'Run' command, enter the command:
x:\path\to\pymol\pymol.exe "x:\path\to\the\file.pdb"

It's important to enclose the file path/name in double-quotes.


> dear users,
> 
> Since recently, I've got an error message when I try to 'open' a pdb (or
> mol2) from the pymol tcl/tk GUI File/Open menu.
> No problem when I open directly from the file (doble-clic)
> 
> Thanks
> 
> 
> Alain
> 
> ==========
> Error: 1
> CmdException Exception in Tk callback
>   Function: <bound method Normal.file_open of <pmg_tk.skins.normal.Normal
> instance at 0x04A9A8A0>> (type: <type 'instancemethod'>)
>   Args: ()
> Traceback (innermost last):
>   File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in
> __call__
>     return apply(self.func, args)
>   File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pmg_tk\skins\normal\__init__.py", line 438, in
> file_open
>     self.cmd.load(ofile,quiet=0)
>   File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\importing.py", line 585, in load
>     if _raising(r): raise pymol.CmdException
> CmdException: <pymol.CmdException instance at 0x031E51C0>



-- 
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

YOSHIMURA, Takuya
Dept. of Applied Life Sceinces,
Facl. of Agriculture, Kyoto University.

Mail: ta...@ka...