[PyMOL] Windows PDB file for debugging pymol C extension?

[Gary Oberbrunner]

Hi; I'm running into a crash in Windows pymol, in the C extension part
(_cmd.cp36-win_amd64.pyd) using pymol open source 2.1.0. I'd like to debug
it; is there a symbol file (.pdb) available anywhere? Or failing that, can
I rebuild the C extension from source and create a pdb?

-- 
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Re: [PyMOL] Windows PDB file for debugging pymol C extension?

[Christoph Gohlke]

I put a VS2015 build of svn rev 4189 including debug information files 
for the pymol source at 



Hope this helps.

Christoph

On 5/9/2018 7:34 AM, Gary Oberbrunner wrote:
Hi; I'm running into a crash in Windows pymol, in the C extension part 
(_cmd.cp36-win_amd64.pyd) using pymol open source 2.1.0. I'd like to 
debug it; is there a symbol file (.pdb) available anywhere? Or failing 
that, can I rebuild the C extension from source and create a pdb?


--
Gary Oberbrunner


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[PyMOL] Pymol 2.1 graphics error

[Andreas Tosstorff]

Hi all,

I just installed PyMol 2.1 on my system (Centos 7) and there are some 
issues with displaying any structures.


I get the following error, however I'm not sure whether that's what's 
causing the actual laggy graphics:


 "This Executable Build integrates and extends Open-Source PyMOL.
 Detected OpenGL version 2.0 or greater. Shaders available.
 Geometry shaders not available
 SMAA not available
 Detected GLSL version 1.30.
 OpenGL graphics engine:
  GL_VENDOR:   Intel Open Source Technology Center
  GL_RENDERER: Mesa DRI Intel(R) HD Graphics 530 (Skylake GT2)
  GL_VERSION:  3.0 Mesa 17.0.1
GL_ERROR : 1282"

I'm new to Pymol and Linux so please excuse me if I'm missing something.

Thanks,

Andy


--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059

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[PyMOL] Add ACE and NME terminals

[roja rahmani]

Hi,

I'm beginner in PYMOL. I want to add ACE and NME terminals to helical poly
amino acid which is made by Peptide builder. I load the poly AA pdb file to
pymol. Then:

Edit first (name N)

Then i didn't know how to add residue so i got help from taps and select
ACE.
But when i used this command,
Edit last (name C)
And then select NME from tabs, the NME were not connected to the last
carbon and was completely separated.
Would you please help me how solve this problem?

Best regards
Roja
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Re: [PyMOL] Pymol 2.1 graphics error

[Thomas Holder]

Hi Andy,

Does it help if you launch PyMOL with "-M"?

pymol -M

If not, can you be more specific about the symptoms? Is it just slow or do you 
get flickering, wrong rendering, crashes, etc.?

Thanks,
  Thomas

> On May 9, 2018, at 8:01 PM, Andreas Tosstorff 
>  wrote:
> 
> Hi all,
> 
> I just installed PyMol 2.1 on my system (Centos 7) and there are some issues 
> with displaying any structures.
> 
> I get the following error, however I'm not sure whether that's what's causing 
> the actual laggy graphics:
> 
>  "This Executable Build integrates and extends Open-Source PyMOL.
>  Detected OpenGL version 2.0 or greater. Shaders available.
>  Geometry shaders not available
>  SMAA not available
>  Detected GLSL version 1.30.
>  OpenGL graphics engine:
>   GL_VENDOR:   Intel Open Source Technology Center
>   GL_RENDERER: Mesa DRI Intel(R) HD Graphics 530 (Skylake GT2) 
>   GL_VERSION:  3.0 Mesa 17.0.1
> GL_ERROR : 1282"
> 
> I'm new to Pymol and Linux so please excuse me if I'm missing something.
> 
> Thanks,
> 
> Andy
>  
> 
> -- 
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> Department Pharmazie
> LMU München
> Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
> 
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Add ACE and NME terminals

[Thomas Holder]

Hi Roja,

This could be useful for you:
18 Nov 2017, NME and ACE capping from script
https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg14812.html

I couldn't quite follow your description, which interface were you using? The 
"Builder" panel? The following works for me:
1) Click "Builder" button in the upper right
2) Click "Protein" tab
3) Click "NMe"
4) Click on the last C atom (C-terminus)

If there is an OXT atom, remove that first (e.g. with: "remove name OXT")

Hope that helps.

Cheers,
  Thomas

> On May 9, 2018, at 9:11 PM, roja rahmani  wrote:
> 
> Hi,
> 
> I'm beginner in PYMOL. I want to add ACE and NME terminals to helical poly 
> amino acid which is made by Peptide builder. I load the poly AA pdb file to 
> pymol. Then:
> 
> Edit first (name N) 
> 
> Then i didn't know how to add residue so i got help from taps and select ACE.
> But when i used this command,
> Edit last (name C)
> And then select NME from tabs, the NME were not connected to the last carbon 
> and was completely separated.
> Would you please help me how solve this problem?
> 
> Best regards
> Roja

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Pymol 2.1 graphics error

[David Mathog]

On 09-May-2018 12:52, Thomas Holder wrote:

Hi Andy,

Does it help if you launch PyMOL with "-M"?

pymol -M

If not, can you be more specific about the symptoms? Is it just slow
or do you get flickering, wrong rendering, crashes, etc.?



Are you working directly on the machine's console or over a network to a 
remote X11 server?  Graphics intensive programs which are smooth when 
running locally are often quite jerky when displayed remotely, even on a 
wired local network.





On May 9, 2018, at 8:01 PM, Andreas Tosstorff 
 wrote:


Hi all,

I just installed PyMol 2.1 on my system (Centos 7) and there are some 
issues with displaying any structures.


I get the following error, however I'm not sure whether that's what's 
causing the actual laggy graphics:


 "This Executable Build integrates and extends Open-Source PyMOL.
 Detected OpenGL version 2.0 or greater. Shaders available.
 Geometry shaders not available
 SMAA not available
 Detected GLSL version 1.30.
 OpenGL graphics engine:
  GL_VENDOR:   Intel Open Source Technology Center
  GL_RENDERER: Mesa DRI Intel(R) HD Graphics 530 (Skylake GT2)
  GL_VERSION:  3.0 Mesa 17.0.1
GL_ERROR : 1282"

I'm new to Pymol and Linux so please excuse me if I'm missing 
something.


Thanks,

Andy


--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059




--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: [PyMOL] Windows PDB file for debugging pymol C extension?

[Gary Oberbrunner]

Thanks -- unfortunately it seems to be heap corruption. I can see where
it's detected:

  ntdll.dll!RtlpLogHeapFailure () Unknown
  ntdll.dll!RtlFreeHeap() Unknown
  ucrtbase.dll!_free_base() Unknown
  _cmd.cp36-win_amd64.pyd!VLAFree(void * ptr) Line 222 C++
  _cmd.cp36-win_amd64.pyd!CGOFreeImpl(CGO * I, short withVBOs) Line 447 C++
  _cmd.cp36-win_amd64.pyd!CGOFree(CGO * & I) Line 435 C++
  _cmd.cp36-win_amd64.pyd!OrthoInvalidateDoDraw(_PyMOLGlobals * G) Line 2808
C++
  _cmd.cp36-win_amd64.pyd!OrthoAddOutput(_PyMOLGlobals * G, const char *
str) Line 1175 C++
  _cmd.cp36-win_amd64.pyd!PCatchWrite(_object * self, _object * args) Line
2738 C++

But that doesn't really tell me anything about where the actual heap
corruption happened.

On Wed, May 9, 2018 at 1:54 PM, Christoph Gohlke  wrote:

> I put a VS2015 build of svn rev 4189 including debug information files for
> the pymol source at  ke/download/pymol-svn-4189.zip>
>
> Hope this helps.
>
> Christoph
>
>
> On 5/9/2018 7:34 AM, Gary Oberbrunner wrote:
>
>> Hi; I'm running into a crash in Windows pymol, in the C extension part
>> (_cmd.cp36-win_amd64.pyd) using pymol open source 2.1.0. I'd like to debug
>> it; is there a symbol file (.pdb) available anywhere? Or failing that, can
>> I rebuild the C extension from source and create a pdb?
>>
>> --
>> Gary Oberbrunner
>>
>
> 
> --
> 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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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



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Re: [PyMOL] Windows PDB file for debugging pymol C extension?

[Christoph Gohlke]

Try to turn on heap verification for python.exe using the following 
registration key and then start pymol with `python.exe -m pymol`


[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image 
File Execution Options\python.exe]

"GlobalFlag"="0x0200"
"VerifierFlags"=dword:0001
"PageHeapFlags"="0x3"


Christoph


On 5/9/2018 5:32 PM, Gary Oberbrunner wrote:
Thanks -- unfortunately it seems to be heap corruption. I can see where 
it's detected:


         ntdll.dll!RtlpLogHeapFailure ()Unknown
ntdll.dll!RtlFreeHeap()Unknown
ucrtbase.dll!_free_base()Unknown
_cmd.cp36-win_amd64.pyd!VLAFree(void * ptr) Line 222C++
_cmd.cp36-win_amd64.pyd!CGOFreeImpl(CGO * I, short withVBOs) Line 447C++
_cmd.cp36-win_amd64.pyd!CGOFree(CGO * & I) Line 435C++
_cmd.cp36-win_amd64.pyd!OrthoInvalidateDoDraw(_PyMOLGlobals * G) Line 
2808C++
_cmd.cp36-win_amd64.pyd!OrthoAddOutput(_PyMOLGlobals * G, const char * 
str) Line 1175C++
_cmd.cp36-win_amd64.pyd!PCatchWrite(_object * self, _object * args) Line 
2738C++


But that doesn't really tell me anything about where the actual heap 
corruption happened.


On Wed, May 9, 2018 at 1:54 PM, Christoph Gohlke > wrote:


I put a VS2015 build of svn rev 4189 including debug information
files for the pymol source at
>

Hope this helps.

Christoph


On 5/9/2018 7:34 AM, Gary Oberbrunner wrote:

Hi; I'm running into a crash in Windows pymol, in the C
extension part (_cmd.cp36-win_amd64.pyd) using pymol open source
2.1.0. I'd like to debug it; is there a symbol file (.pdb)
available anywhere? Or failing that, can I rebuild the C
extension from source and create a pdb?

-- 
Gary Oberbrunner




--
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)
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