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Hey Folks,<br>
<br>
It is a relatively new feature to be able to read SDF compound
structure files in Chimera. (I have release 2350 for Windows - <br>
I will be upgrading to the new snapshot that I just saw while looking
around the site)<br>
<br>
Anyway - I tried with a compound sdf file that I got from PubChem
(enclosed) - but seemed to have problems.<br>
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 .<br>
<br>
Opening C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf<br>
Error reading C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf:<br>
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'<br>
Done opening C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf<br>
Opening C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf<br>
Error reading C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf:<br>
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'<br>
Done opening C:\Documents and Settings\andrake\My Documents\WORK
f\PDBs\Cy3_CID_16048627.sdf<br>
<br>
I tried various atom selections and displaying all - but it seems
obvious that it has not read in atoms and bonds.<br>
<br>
I have browsed around the documentation and only found a link to the
sdf file formats.<br>
(I checked this out and tried editing out two of the header lines - )<br>
<br>
It seems the error is unexpected end of file past the header.<br>
When checking the sdf file format information it seems that the $$$$
should be the only end of file mark - <br>
and there is only one at the end of my file.<br>
I also tried the whole procedure with a different sdf file from PubChem.<br>
Can anyone recognize what is causing the error in the enclosed file?<br>
<br>
Beyond that - are there other instructions on sdf file use in chimera
that I did not see in searching the documentation?<br>
<br>
Thanks in advance, <br>
Mark<br>
<br>
<div class="moz-signature">-- <br>
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<title>contactinfo</title>
<i><b>Mark Andrake, Ph.D.</b></i><br>
Research Associate<br>
<b><br>
Fox Chase Cancer Center<br>
</b>ICR428<br>
7701 Burholme Ave.<br>
Philadelphia, PA 19111<br>
215-728-3654<br>
<a class="moz-txt-link-abbreviated" href="mailto:mark.andrake@fccc.edu">mark.andrake@fccc.edu</a>
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