User f7c6611bf1
02-12-2010 20:22:02
Hi;
I'm experiencing some problems when using MarvinView to edit some structures from a file with multiple compounds. I have a SMILES file with 200+ compounds that need some editing. After I finish editing, lets say, the 25th molecule, if I ask to "Save All..." as a SMILES file, the application only saves the file up to the file I visualized last (if I scrolled down to the 25th, it would save only the 25 first molecules) instead of saving all 200+ molecules. Then, if I scroll down in the table, all other molecules are blank.
My system specs:
bfd@nequim-153:~$ uname -a
Linux nequim-153 2.6.32-25-generic #45-Ubuntu SMP Sat Oct 16 19:52:42 UTC 2010 x86_64 GNU/Linux
Other Specs (attached file)
ChemAxon 7c2d26e5cf
06-12-2010 12:18:58
I have tried to reproduce the issue but I did not manage it. Can you give a detailed scenario?
I tested the reported problem with the following scenarios (on the same platform):
Case #1:
- Open a file with 250 compounds from NCI in MarvinView.
mview NCI_aug00_250.smi
- Do not scroll (first 16 compounds are visible), just save structures by "Save All" then close the application.
Result: all compounds are saved:
wc -l vis1-16.smi
250 vis1-16.smi
Case #2:
- Open NCI_aug00_250.smi again in MarvinView.
- Scroll down to the 25th structure.
- Edit the structure #25.
- Close detached sketcher (from the viewer).
- Save everything by "Save All" in MarvinView then close the application.
Result: all compounds are saved:
wc -l edit25.smi
250 edit25.smi
Case #3:
- Open NCI_aug00_250.smi again in MarvinView.
- Scroll down to the 25th structure.
- Edit the structure #25.
- Close detached sketcher.
- Scroll up (till the first structure).
- Save compounds by "Save All" then close the application
Result: all compounds are saved:
wc -l vis1-16_after_edit25.smi
250 vis1-16_after_edit25.smi
Please give a step by step scenario.
In your scenario, please also give the exact number of records in the input file.
Do the SMILES records contain extra fields?
Does the updated compound contain any extra information (like query information) that is not exportable into SMILES format?