Hey Folks,
It is a relatively new feature to be able to read SDF compound
structure files in Chimera. (I have release 2350 for Windows -
I will be upgrading to the new snapshot that I just saw while looking
around the site)
Anyway - I tried with a compound sdf file that I got from PubChem
(enclosed) - but seemed to have problems.
At first it gave an error shown in the first lines below - and then
seemed to say that it opened the files - but no atoms were displayed
and no new model ID was generated and put into the Model Panel .
Opening C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf
Error reading C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf:
Unexpected end of file (parser state: post header 1) in MOL/SDF file
'C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf'
Done opening C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf
Opening C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf
Error reading C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf:
Unexpected end of file (parser state: post header 1) in MOL/SDF file
'C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf'
Done opening C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf
I tried various atom selections and displaying all - but it seems
obvious that it has not read in atoms and bonds.
I have browsed around the documentation and only found a link to the
sdf file formats.
(I checked this out and tried editing out two of the header lines - )
It seems the error is unexpected end of file past the header.
When checking the sdf file format information it seems that the $$$$
should be the only end of file mark -
and there is only one at the end of my file.
I also tried the whole procedure with a different sdf file from PubChem.
Can anyone recognize what is causing the error in the enclosed file?
Beyond that - are there other instructions on sdf file use in chimera
that I did not see in searching the documentation?
Thanks in advance,
Mark
--
contactinfo
Mark Andrake, Ph.D.
Research Associate
Fox Chase Cancer Center
ICR428
7701 Burholme Ave.
Philadelphia, PA 19111
215-728-3654
mark.andrake@fccc.edu