Avogadro 1.1.0 cannot deal with files with certain names?

Dear all,

The attached pdbs are two identical files from Protein Data Bank. The
one with the original name “2K4G.pdb” will cause Avogadro 1.1.0 to crash
(see 2K4G.log) and just changing the name from “2K4G.pdb” to
"2K4G_avo.pdb" will prevent the software from crashing. Avogadro 1.0.3
does not have this problem. Maybe it’s related to the new Open Babel
version (2.3.1) ? Actually this happens to various files containing
large molecules and the error messages are usually different from one to
another.

I can reproduce the bug on both Windows 7 and OpenSUSE 12.2 platforms.
Am I the only one facing the problem or maybe it is really a bug?

Thanks!


Xing Yin
Graduate Student
Department of Chemistry
University of Pittsburgh

On Fri, Feb 1, 2013 at 5:40 PM, Xing xiy25@pitt.edu wrote:

Dear all,

The attached pdbs are two identical files from Protein Data Bank. The one
with the original name “2K4G.pdb” will cause Avogadro 1.1.0 to crash (see
2K4G.log) and just changing the name from “2K4G.pdb” to “2K4G_avo.pdb” will
prevent the software from crashing. Avogadro 1.0.3 does not have this
problem. Maybe it’s related to the new Open Babel version (2.3.1) ?
Actually this happens to various files containing large molecules and the
error messages are usually different from one to another.

I can reproduce the bug on both Windows 7 and OpenSUSE 12.2 platforms. Am
I the only one facing the problem or maybe it is really a bug?

Definitely an odd bug, one that I cannot reproduce here.

But, digging through the sources, I find the error message at the end of
the .log file in the openqube mopac .aux file reader. Are there any files
in the directory with 2K4G.pdb that have a .aux (or similar) extension? Or
have you done any MOPAC calculations on it?

Does it work if you move the pdb file to another directory?

I don’t see this particular error message anywhere else in openbabel or
avogadro, so it definitely seems to be because of a bad .aux file.

If you still see this issue with the pdb file in another directory, we’ll
need to get a backtrace of the crash to really track this down.

Department of Chemistry
University of Pittsburgh

Perhaps Dr. Hutchison could help with the debug build/backtrace if needed
:wink:

Dave

Wow, I do have 2K4G.aux (generated by MOPAC2012) in the same directory
as 2K4G.pdb. Once I copy 2K4G.pdb into a new folder, it can be read by
Avogadro 1.1.0 without a problem just like 2K4G_avo.pdb. Simply symlink
2K4G.pdb to another directory cannot solve the problem.

Thanks very much! Now I know what is the problem and how to avoid it. :wink:
But still, is Avogadro supposed to read an aux file while loading a pdb
file? If so, can Avogadro continue to load the pdb if something is wrong
in the aux file?

Thanks!


Xing Yin
Graduate Student
Department of Chemistry
University of Pittsburgh

On 02/03/2013 09:05 AM, David Lonie wrote:

On Fri, Feb 1, 2013 at 5:40 PM, Xing <xiy25@pitt.edu
mailto:xiy25@pitt.edu> wrote:

Dear all,

The attached pdbs are two identical files from Protein Data Bank.
The one with the original name “2K4G.pdb” will cause Avogadro 1.1.0 to
crash (see 2K4G.log) and just changing the name from “2K4G.pdb” to
"2K4G_avo.pdb" will prevent the software from crashing. Avogadro 1.0.3
does not have this problem. Maybe it’s related to the new Open Babel
version (2.3.1) ? Actually this happens to various files containing
large molecules and the error messages are usually different from one
to another.

I can reproduce the bug on both Windows 7 and OpenSUSE 12.2
platforms. Am I the only one facing the problem or maybe it is really
a bug?

Definitely an odd bug, one that I cannot reproduce here.

But, digging through the sources, I find the error message at the end
of the .log file in the openqube mopac .aux file reader. Are there any
files in the directory with 2K4G.pdb that have a .aux (or similar)
extension? Or have you done any MOPAC calculations on it?

Does it work if you move the pdb file to another directory?

I don’t see this particular error message anywhere else in openbabel
or avogadro, so it definitely seems to be because of a bad .aux file.

If you still see this issue with the pdb file in another directory,
we’ll need to get a backtrace of the crash to really track this down.

Department of Chemistry
University of Pittsburgh

Perhaps Dr. Hutchison could help with the debug build/backtrace if
needed :wink:

Dave


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On Sun, Feb 3, 2013 at 10:26 AM, Xing Yin xiy25@pitt.edu wrote:

Wow, I do have 2K4G.aux (generated by MOPAC2012) in the same directory
as 2K4G.pdb. Once I copy 2K4G.pdb into a new folder, it can be read by
Avogadro 1.1.0 without a problem just like 2K4G_avo.pdb. Simply symlink
2K4G.pdb to another directory cannot solve the problem.

Thanks very much! Now I know what is the problem and how to avoid it. :wink:
But still, is Avogadro supposed to read an aux file while loading a pdb
file? If so, can Avogadro continue to load the pdb if something is wrong in
the aux file?

It should, but there seems to be an issue in the mopac aux file reader. Can
you attach the .aux file? I’d like to see what’s causing the crash.

Dave

It’s attached in my previous reply. Here it is again. :wink:

Sincerely yours
Xing Yin
Department of Chemistry, Univ Pittsburgh
G-3 Chevron Science Center
219 Parkman Ave
Pittsburgh, PA 15260

On 02/03/2013 10:58 AM, David Lonie wrote:

On Sun, Feb 3, 2013 at 10:26 AM, Xing Yin <xiy25@pitt.edu
mailto:xiy25@pitt.edu> wrote:

Wow, I do have 2K4G.aux (generated by MOPAC2012) in the same
directory as 2K4G.pdb. Once I copy 2K4G.pdb into a new folder, it
can be read by Avogadro 1.1.0 without a problem just like
2K4G_avo.pdb. Simply symlink 2K4G.pdb to another directory cannot
solve the problem.

Thanks very much! Now I know what is the problem and how to avoid
it. ;) But still, is Avogadro supposed to read an aux file while
loading a pdb file? If so, can Avogadro continue to load the pdb
if something is wrong in the aux file?

It should, but there seems to be an issue in the mopac aux file
reader. Can you attach the .aux file? I’d like to see what’s causing
the crash.

Dave


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Download AppDynamics Lite for free today:
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This patch should fix it in the next release:

http://review.source.kitware.com/#/t/2057/

Thanks for the report!

Dave

On Sun, Feb 3, 2013 at 11:01 AM, Xing Yin xiy25@pitt.edu wrote:

It’s attached in my previous reply. Here it is again. :wink:

Sincerely yours
Xing Yin
Department of Chemistry, Univ Pittsburgh
G-3 Chevron Science Center
219 Parkman Ave
Pittsburgh, PA 15260

On 02/03/2013 10:58 AM, David Lonie wrote:

On Sun, Feb 3, 2013 at 10:26 AM, Xing Yin xiy25@pitt.edu wrote:

Wow, I do have 2K4G.aux (generated by MOPAC2012) in the same directory
as 2K4G.pdb. Once I copy 2K4G.pdb into a new folder, it can be read by
Avogadro 1.1.0 without a problem just like 2K4G_avo.pdb. Simply symlink
2K4G.pdb to another directory cannot solve the problem.

Thanks very much! Now I know what is the problem and how to avoid it. :wink:
But still, is Avogadro supposed to read an aux file while loading a pdb
file? If so, can Avogadro continue to load the pdb if something is wrong in
the aux file?

It should, but there seems to be an issue in the mopac aux file reader.
Can you attach the .aux file? I’d like to see what’s causing the crash.

Dave


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Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:http://p.sf.net/sfu/appdyn_d2d_jan


Avogadro-Discuss mailing listAvogadro-Discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/avogadro-discuss


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Download AppDynamics Lite for free today:
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This patch should fix it in the next release:

Speaking of which, if you need it on OpenSuse, let me know and I can show you how to get things compiled from source. Windows is a bit trickier.

-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

Yeah, OpenSUSE is much easier for me. I have some experience with OBS so
I checked out the package, applied the patch and built it locally (and
online). It works great now! :slight_smile:

Thanks so much!

Sincerely yours
Xing Yin
Department of Chemistry, Univ Pittsburgh
G-3 Chevron Science Center
219 Parkman Ave
Pittsburgh, PA 15260

On 02/03/2013 02:01 PM, Geoffrey Hutchison wrote:

This patch should fix it in the next release:

Speaking of which, if you need it on OpenSuse, let me know and I can
show you how to get things compiled from source. Windows is a bit
trickier.

-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com mailto:geoffh@pitt.edu
web: http://hutchison.chem.pitt.edu/


Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan


Avogadro-Discuss mailing list
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https://lists.sourceforge.net/lists/listinfo/avogadro-discuss