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

 
 
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sr #2998: PDB reading bug in relax

Submitted by:  None
Submitted on:  Mon 14 Jan 2013 02:50:26 PM UTC  
 
Category: NonePriority: 5 - Normal
Severity: 3 - NormalStatus: Done
Assigned to: Edward d Auvergne <bugman>Originator Email: -unavailable-
Open/Closed: ClosedOperating System: None

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

Mon 04 Feb 2013 12:06:52 PM UTC, 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 01 Feb 2013 01:29:07 PM UTC, 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 01 Feb 2013 12:41:29 PM UTC, 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 31 Jan 2013 02:12:28 PM UTC, 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 31 Jan 2013 10:30:18 AM UTC, 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 31 Jan 2013 10:11:39 AM UTC, 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 31 Jan 2013 10:03:11 AM UTC, comment #2:

This appears to be a relax bug reported here.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 14 Jan 2013 09:24:54 PM UTC, 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 14 Jan 2013 02:50:26 PM UTC, 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

 

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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

 

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  • -unavailable- added by bugman (Posted a comment)
  • -unavailable- added by None (Submitted the item)
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    Follow 22 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon 04 Feb 2013 12:06:52 PM UTCNoneAttached File-=>Added log0204, #17119
      Attached File-=>Added 1RTE_H_trunc.pdb, #17120
      Attached File-=>Added dauvergne_protocol.py, #17121
    Fri 01 Feb 2013 12:41:29 PM UTCNoneAttached File-=>Added log0201, #17084
      Attached File-=>Added dauvergne_protocol.py, #17085
    Fri 01 Feb 2013 10:49:16 AM UTCbugmanStatusIn Progress=>Done
      Open/ClosedOpen=>Closed
    Thu 31 Jan 2013 02:12:28 PM UTCNoneAttached File-=>Added dauvergne_protocol.py, #17075
      Attached File-=>Added log0131, #17076
    Thu 31 Jan 2013 02:12:27 PM UTCNoneAttached File-=>Added 1RTE_H.pdb, #17073
      Attached File-=>Added 1RTE_H_trunc.pdb, #17074
    Thu 31 Jan 2013 11:04:04 AM UTCbugmanStatusNone=>In Progress
      Operating SystemMicrosoft Windows=>None
      SummaryImport BMRB data to Relax=>PDB reading bug in relax
    Thu 31 Jan 2013 11:03:18 AM UTCbugmanAttached File-=>Added 1RTE_trunc.pdb, #17070
    Thu 31 Jan 2013 10:59:10 AM UTCbugmanAttached File-=>Added patch_sr_2998, #17068
    Thu 31 Jan 2013 10:03:11 AM UTCbugmanAssigned toNone=>bugman
    Mon 14 Jan 2013 09:24:54 PM UTCNoneAttached File-=>Added 1RTE.pdb, #16943
      Attached File-=>Added 17226.txt, #16944
      Attached File-=>Added dauvergne_protocol.py, #16945
      Attached File-=>Added log0114, #16946
    Mon 14 Jan 2013 02:50:26 PM UTCNoneAttached File-=>Added 0114.rar, #16936
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