Hi Alexa,
Thanks for your reply.
I used Marvin 5.8 test version which says that "Automatic text OCR (optical character recognition) has been added to support document to structure conversion of scanned (non searchable) PDF documents. " as mentioned here. I could extract a lot of srtuctures from the full pdf file but these particular pages were not converted.
Lets take the following four names as a case study :
(4S)-4-{[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]amino}-1-{3-[(phenylcarbonyl)sulfanyl]propanoyl}-L-proline ditrifluoroacetate salt
N-[(1S)-1-carboxy-3-phenylpropyl]-L-alanyl-(4S)-4-{[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]amino}-L-proline ditrifluoroacetate salt
Methyl N-[(2S)-1-ethoxy-1-oxo-4-phenylbutan-2-yl]-L-alanyl-(4S)-4-{[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]amino}-L-prolinate ditrifluoroacetate salt
N-[(1S)-1-carboxy-3-phenylpropyl]-L-valyl-(4S)-4-{[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]amino}-L-proline dilithium salt.
if I type the first name in MarvinSketch->edit->Import name without the "ditrifluoroacetate salt" the structure is retrieved.
but all the rest give error with/without the salt component. I have attached the error log.