So the problem really is that in the file that doesn't work there is a blank line following the '$$$$' -- and that line is gone in the cut- and-paste version of the file which is why that one works. SDF files can have multiple compounds in them, each ended with a '$$$$', and the first lines of the compound description can be blank, so when Chimera sees the blank line following the '$$$$' it assumes that is the start of another compound description -- and then the file ends. I have now amended the code so that if it never sees anything but blank lines following a '$$$$' it doesn't throw an error. --Eric On May 4, 2007, at 3:59 PM, Mark Andrake wrote:
Hey Folks,
It is a relatively new feature to be able to read SDF compound structure files in Chimera. (I have release 2350 for Windows - I will be upgrading to the new snapshot that I just saw while looking around the site)
Anyway - I tried with a compound sdf file that I got from PubChem (enclosed) - but seemed to have problems. At first it gave an error shown in the first lines below - and then seemed to say that it opened the files - but no atoms were displayed and no new model ID was generated and put into the Model Panel .
Opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs \Cy3_CID_16048627.sdf Error reading C:\Documents and Settings\andrake\My Documents\WORK f \PDBs\Cy3_CID_16048627.sdf: Unexpected end of file (parser state: post header 1) in MOL/SDF file 'C:\Documents and Settings\andrake\My Documents\WORK f\PDBs \Cy3_CID_16048627.sdf' Done opening C:\Documents and Settings\andrake\My Documents\WORK f \PDBs\Cy3_CID_16048627.sdf Opening C:\Documents and Settings\andrake\My Documents\WORK f\PDBs \Cy3_CID_16048627.sdf Error reading C:\Documents and Settings\andrake\My Documents\WORK f \PDBs\Cy3_CID_16048627.sdf: Unexpected end of file (parser state: post header 1) in MOL/SDF file 'C:\Documents and Settings\andrake\My Documents\WORK f\PDBs \Cy3_CID_16048627.sdf' Done opening C:\Documents and Settings\andrake\My Documents\WORK f \PDBs\Cy3_CID_16048627.sdf
I tried various atom selections and displaying all - but it seems obvious that it has not read in atoms and bonds.
I have browsed around the documentation and only found a link to the sdf file formats. (I checked this out and tried editing out two of the header lines - )
It seems the error is unexpected end of file past the header. When checking the sdf file format information it seems that the $$$ $ 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
-- Mark Andrake, Ph.D. Research Associate
Fox Chase Cancer Center ICR428 7701 Burholme Ave. Philadelphia, PA 19111 215-728-3654 mark.andrake@fccc.edu 16048627