helprelax - Support: sr #2998, PDB reading bug in relax

 
 
Show feedback again

sr #2998: PDB reading bug in relax

Submitted by:  None
Submitted on:  Mon Jan 14 14:50:26 2013  
 
Category: NonePriority: 5 - Normal
Severity: 3 - NormalStatus: Done
Assigned to: Edward d Auvergne <bugman>Originator Email: -unavailable-
Open/Closed: ClosedOperating System: None

Add a New Comment (Rich MarkupRich Markup):
   

You are not logged in

Please log in, so followups can be emailed to you.

 

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

Mon Feb 4 12:06:52 2013, comment #8:

Hi Edward,

I have tried the new relax version 2.2.1 to load the BMRB data again, this time the relax error come up:

RelaxError: Multiple alternate location indicators are present in the PDB file, but the desired coordinate set has not been specified.

How to avoid this error?

Thank you.

Regards,

Mengjun

(file #17119, file #17120, file #17121)

Anonymous
Fri Feb 1 13:29:07 2013, comment #7:

Comment #6 has been converted into the bug report https://gna.org/bugs/?20471.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Fri Feb 1 12:41:29 2013, comment #6:

Hi Edward,

As you suggested, I have replaced the argument 'sampleconditions' with 'sample_conditions'. And run the script again, this time bug come up.

Attached please find the script and bug report. Thank you.

Regards,

Mengjun

Hi,

Try replacing the argument 'sampleconditions' with 'sample_conditions' in your call to bmrb.read in your relax script ;). There is nothing wrong with the Bmrb file.

Regards,

Edward

(file #17084, file #17085)

Anonymous
Thu Jan 31 14:12:28 2013, comment #5:

Hi Edward,

Thank you very much for your answers. I have add H atoms to 1RTE.pdb by program reduce, and get 1RTE_H.pdb, after that, I delete all the "CONECT records" in 1RTE_H.pdb, and get 1RTE_H_trunc.pdb. And run dauvergne_protocol.py again, this time, the RelaxError: The keyword argument 'sampleconditions' is unknown.

Attached please find the file 1RTE_H.pdb, 1RTE_H_trunc.pdb,dauvergne_protocol.py, log0131. Thank you.

Regards,

Mengjun

(file #17073, file #17074, file #17075, file #17076)

Anonymous
Thu Jan 31 10:30:18 2013, comment #4:

The problem is that the PDB file 1RTE is corrupt (specifically in the CONECT records which point to non-existent atoms), and relax's PDB reader cannot currently handle such corruptions. One fix is to delete all CONECT records in the PDB file. The other is to use the ScientificPython parser instead of the internal relax parser.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu Jan 31 10:11:39 2013, comment #3:

The script tries to load the PDB file '2L55.pdb', but the attached file is called '1RTE.pdb'. However the following two user function calls trigger the bug:

pipe.create('test', 'mf')
structure.read_pdb('1RTE.pdb')

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu Jan 31 10:03:11 2013, comment #2:

This appears to be a relax bug reported here.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon Jan 14 21:24:54 2013, comment #1:

Hi Edward,

I am sorry about that, attached please find the BMRB and pdb files.

http://thread.gmane.org/gmane.science.nmr.relax.user/1381

Regards,

Mengjun

(file #16943, file #16944, file #16945, file #16946)

Anonymous
Mon Jan 14 14:50:26 2013, original submission:

Hi Edward,

I am trying to import some published demo relax data (17226.txt from BMRB and 1RTE.pdb from protein data bank)to Relax, so that I can learn how to use dauvergne_protocol.py to analyze multi-field nmr relax data. However, the analysis stop somewhere in Relax.

Attached please find the output log file. Thank you

Regards,

Mengjun

Anonymous

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

Attached Files
file #17119:  log0204 added by None (13kB - text/plain)
file #17120:  1RTE_H_trunc.pdb added by None (175kB - chemical/x-pdb)
file #17121:  dauvergne_protocol.py added by None (12kB - text/plain)
file #17084:  log0201 added by None (33kB - text/plain)
file #17085:  dauvergne_protocol.py added by None (12kB - text/plain)
file #17076:  log0131 added by None (31kB - text/plain)
file #17073:  1RTE_H.pdb added by None (204kB - chemical/x-pdb)
file #17074:  1RTE_H_trunc.pdb added by None (175kB - chemical/x-pdb)
file #17075:  dauvergne_protocol.py added by None (12kB - text/plain)
file #17070:  1RTE_trunc.pdb added by bugman (1kB - chemical/x-pdb - This is a minimal PDB file with broken CONECT records to demonstrate the problem.)
file #17068:  patch_sr_2998 added by bugman (669B - application/octet-stream - This patch file fixes the relax internal parsing of broken CONECT records in broken PDB files.)
file #16943:  1RTE.pdb added by None (145kB - chemical/x-pdb)
file #16944:  17226.txt added by None (283kB - text/plain)
file #16945:  dauvergne_protocol.py added by None (12kB - text/plain)
file #16946:  log0114 added by None (15kB - text/plain)
file #16936:  0114.rar added by None (9kB - application/octet-stream)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by bugman (Posted a comment)
  • -unavailable- added by None (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.

     

    Error: not logged in

     

     

    Follow 22 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon Feb 4 12:06:52 2013NoneAttached File-=>Added log0204, #17119
      Attached File-=>Added 1RTE_H_trunc.pdb, #17120
      Attached File-=>Added dauvergne_protocol.py, #17121
    Fri Feb 1 12:41:29 2013NoneAttached File-=>Added log0201, #17084
      Attached File-=>Added dauvergne_protocol.py, #17085
    Fri Feb 1 10:49:16 2013bugmanStatusIn Progress=>Done
      Open/ClosedOpen=>Closed
    Thu Jan 31 14:12:28 2013NoneAttached File-=>Added dauvergne_protocol.py, #17075
      Attached File-=>Added log0131, #17076
    Thu Jan 31 14:12:27 2013NoneAttached File-=>Added 1RTE_H.pdb, #17073
      Attached File-=>Added 1RTE_H_trunc.pdb, #17074
    Thu Jan 31 11:04:04 2013bugmanStatusNone=>In Progress
      Operating SystemMicrosoft Windows=>None
      SummaryImport BMRB data to Relax=>PDB reading bug in relax
    Thu Jan 31 11:03:18 2013bugmanAttached File-=>Added 1RTE_trunc.pdb, #17070
    Thu Jan 31 10:59:10 2013bugmanAttached File-=>Added patch_sr_2998, #17068
    Thu Jan 31 10:03:11 2013bugmanAssigned toNone=>bugman
    Mon Jan 14 21:24:54 2013NoneAttached File-=>Added 1RTE.pdb, #16943
      Attached File-=>Added 17226.txt, #16944
      Attached File-=>Added dauvergne_protocol.py, #16945
      Attached File-=>Added log0114, #16946
    Mon Jan 14 14:50:26 2013NoneAttached File-=>Added 0114.rar, #16936
    Show feedback again

    Back to the top


    Powered by Savane 3.1-cleanup