bugGnome Chemistry Utils - Bugs: bug #36582, gchem3d crashes when trying to...

 
 

You are not allowed to post comments on this tracker with your current authentication level.

bug #36582: gchem3d crashes when trying to open lysozyme molecule

Submitted by:  Julian Sikorski <belegdol>
Submitted on:  Sun 03 Jun 2012 10:21:02 AM UTC  
 
Category: NoneSeverity: 3 - Normal
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: Jean Bréfort <jean_brefort>
Open/Closed: Closed

(Jump to the original submission Jump to the original submission)

Sun 10 Jun 2012 02:51:26 PM UTC, comment #13:

Confirmed.

Julian Sikorski <belegdol>
Project Member
Sun 10 Jun 2012 11:02:55 AM UTC, comment #12:

This file is correctly displayed again.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 02:06:14 PM UTC, comment #11:

I see. I guess this is fixed then.

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 02:02:53 PM UTC, comment #10:

The pdb file is not displayed because it actually describe a crystal. I need to fix that. In the future, it will propose to open the file in gcrystal instead, but I didn't implement it for 0.14. The mol file should be displayed.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 01:47:31 PM UTC, comment #9:

You were right, I guess mixing rpm and self-built code is a bad idea.
Anyhow, it does not crash anymore, but nothing is shown either. Is that expected?

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 01:43:52 PM UTC, comment #8:

I removed the g_free code, you need to reinstall the cml plugin.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 01:35:48 PM UTC, comment #7:

I am not sure where did the backtrace go. Here it is.

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 01:34:13 PM UTC, comment #6:

PDB still crashes here, mol contintues to work from the homedir:

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 01:15:43 PM UTC, comment #5:

This one does not crash for me, but the original one doesn't either now that I removed the g_free. I just commited this fix, can you try again after updating?

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 01:11:37 PM UTC, comment #4:

Actually the error in comment #3 seems to be caused by either spaces or the unusually long filename - moving the file to the home folder allows gchem3d to open it properly.

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 12:57:32 PM UTC, comment #3:

Attempting to open a .mol file also results in a crash:

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 12:42:04 PM UTC, comment #2:

Hmm, looks like when babel converts the pdb to cml, it uses XFract and others since the file actually describes a crystal. This looks like a severe regression.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 12:27:00 PM UTC, comment #1:

Thanks for reporting. This g_free call is just stupid and, worse, seems to be somewhat ancient. Now I'm facing another issue: I don't see any thin in the view.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 10:21:02 AM UTC, original submission:

Since I upgraded to Fedora 17 I could finally test gchemutils-0.13. Unfortunately, gchem3d seems to crash when opening lysozyme:
I have also tested SVN trunk built without any RPM magic to eliminate the possibility of the latter interfering.

Julian Sikorski <belegdol>
Project Member

 

Attached Files
file #25971:  merged0.mol added by belegdol (18KiB - chemical/x-mdl-molfile - file in question)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by belegdol (Submitted the item)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.

     

    Please enter the title of George Orwell's famous dystopian book (it's a date):

     

     

    Follow 4 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Sun 12 Aug 2012 10:09:26 AM UTCjean_brefortOpen/ClosedOpen=>Closed
    Sun 10 Jun 2012 11:02:55 AM UTCjean_brefortStatusNone=>Fixed
      Assigned toNone=>jean_brefort
    Sun 03 Jun 2012 12:58:28 PM UTCbelegdolAttached File-=>Added merged0.mol, #25971

    Back to the top


    Powered by Savane 3.1-cleanup1