[Chimera-users] importing sdf files from PubChem

[Mark Andrake]

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 at fccc.edu
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