Dear Bruce,

The problem about the origin of the PDB files is well known.

FormatConverter distinguishes between PDB files (properly formatted, with 
all headers, coming from the PDB), and psudoPdb files (just Atom records).

The user needs to be aare of the distinction and choose 'pdb' or 
'pseudoPdb' import as appropriate.

I have always hated this behaviour - when we get to rewriting the 
FormatConverter interface we will change it but right now we are busy with 
other things.

It sounds like there is more to it than this, though.

Yours,

Rasmus

---------------------------------------------------------------------------
Dr. Rasmus H. Fogh                  Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK.     FAX (01223)766002

On Mon, 30 May 2011, Bruce D. Ray wrote:

> 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
>