Originally mis-sent because I used reply and did not check the address.
>Hello,
>
>Are you using the Format Convert to do the import (it sounds like it but I
>thought I would check)?
This was with Structure -> Structures -> import
Also, for my 56 residue peptide, the python idle window gives:
[0, <ccp.molecule.MolSystem.Residue ['MS1', 'A', 1]>]
[1, <ccp.molecule.MolSystem.Residue ['MS1', 'A', 2]>]
[2, <ccp.molecule.MolSystem.Residue ['MS1', 'A', 3]>]
[3, <ccp.molecule.MolSystem.Residue ['MS1', 'A', 4]>]
...
[55, <ccp.molecule.MolSystem.Residue ['MS1', 'A', 56]>]
If instead I use Format Converter to try to import this pdb, I get an error
window that claims no model found, and in the python idle window I get:
##############################################
# FormatConverter: executing readCoordinates #
##############################################
Error: /Bruce/PDB_files/ovomucoid/dom3_md_min/dom3_H_num.pdb is not a file originating from PDB. Cannot be read.
Interestingly, if I try Format Converter in a new project and try to import
the coordinates without a sequence previously entered, I get an error output
of:
##############################################
# FormatConverter: executing readCoordinates #
##############################################
Error: /Bruce/PDB_files/ovomucoid/dom3_md_min/dom3_H_num.pdb is not a file originating from PDB. Cannot be read.
Exception in Tkinter callback
Traceback (most recent call last):
File "/sw/lib/python2.6/lib-tk/Tkinter.py", line 1410, in __call__
return self.func(*args)
File "/programs/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 979, in ok
if (not self.apply()):
File "/programs/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 992, in apply
returnValue = self.importExportFile(self.component) # If none, will do all components
File "/programs/ccpnmr/ccpnmr2.1/python/ccpnmr/format/gui/ImportExportFormatPopup.py", line 799, in importExportFile
returnValue = rwFunc(*addArgs,**addKeywds)
File "/programs/ccpnmr/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py", line 1278, in readCoordinates
self.getCoordinates()
File "/programs/ccpnmr/ccpnmr2.1/python/ccpnmr/format/converters/DataFormat.py", line 4372, in getCoordinatesGeneric
self.getCoordinatesSetSequenceFile()
File "/programs/ccpnmr/ccpnmr2.1/python/ccpnmr/format/converters/PdbFormat.py", line 121, in getCoordinatesSetSequenceFile
self.sequenceFile.read(pdbFile = self.coordinateFile, **readKeywds)
File "/programs/ccpnmr/ccpnmr2.1/python/ccp/format/pdb/sequenceIO.py", line 215, in read
modelCoordRefKey = modelCoordKeys[0]
IndexError: list index out of range
Why the origin of a pdb file should trigger an error somewhat escapes me.
>Also, you should be able to run Analysis (and the Format Converter) in an
>ordinary terminal window. So all you need X for is to exist, you don't
>need an X terminal to run the program.
Thank-you for this.
>Wayne
>
>On Mon, 30 May 2011, Bruce D. Ray wrote:
>
>> I'm using analysis 2.1.5 with the latest updates installed on MAC OS X 10.6.8
>> with XQuartz 2.3.6.
>>
>> On set up of my project, I read in a text file of the protein sequence along
>> with a number of spectra converted to azara format. I then began assigning
>> the spectra. I also derived by a structure by homology to this protein as
>> found in other species followed with molecular dynamics energy minimization
>> (OPLS AA force field). I have a pdb of this structure. However, if I try to
>> include these coordinates in the project, I get an error message stating that
>> the structure is truncated by more than 10 residues. A lot of material about
>> the sequence is als spewed onto the x-terminal so fast that I am not able to
>> see the initial messages and cannot recover them because the x-terminal does
>> not have any scroll bars. Furthermore, the text of the pdb file shows complete
>> residues for the entire sequence. In addition, if I start a new project and
>> import the coordinates without a sequence previously entered, the coordinates
>> are read and appear to be correct in the viewer, and a sequence is generated
>> that has all of the residues. Therefore, I believe there may be a bug in
>> reading and linking coordinates to a pre-existing sequence.
>>
>>
>> Sincerely,
>>
>>
>> --
>> Bruce D. Ray, Ph.D.
>> Associate Scientist
>> IUPUI
>> Physics Dept.
>> 402 N. Blackford St., Rm. LD-061
>> Indianapolis, IN 46202-3273
>>
--
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN 46202-3273
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