Overlap Analysis

Hi,

To analyze overlaps between two SDF files with ~290000 and ~40000 compounds respectively.

With duplicate search IJC overlap analysis worked smoothly.

And when I tried for Similarity search, an error message *Out of Memory* with other java messages. Let me know how to increase the memory for IJC. I read the following links, but did not help much (as I am not a progammer).

http://www.chemaxon.com/jchem/javaFAQ.html#outofmemory

http://www.chemaxon.com/jchem/doc/admin/Performance.html#cacheSiz

Let me know how to troubleshoot this error and increase memory for overlap analysis.

Thanks,

Giri

giribio wrote:

Hi, To analyze overlaps between two SDF files with ~290000 and ~40000 compounds respectively. With duplicate search IJC overlap analysis worked smoothly. And when I tried for Similarity search, an error message *Out of Memory* with other java messages. Let me know how to increase the memory for IJC. I read the following links, but did not help much (as I am not a progammer). http://www.chemaxon.com/jchem/javaFAQ.html#outofmemory http://www.chemaxon.com/jchem/doc/admin/Performance.html#cacheSiz Let me know how to troubleshoot this error and increase memory for overlap analysis. Thanks, Giri

Just now I found, the SDF file with ~2900000 structures are imported in IJC and table showing 1212499 rows.

Hi Giri,

the maximum heap memory size can be increased in <i>Tools -> Options -> Miscellaneous -> Other settings</i>.
More info can be found at http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/changing_user_settings.html#other .

Does the import of that SDF finished successfully?  If not a *._errors file might be created in the directory with SDF file. The error file contains structures which were not imported. Other reason can be the OutOfMemory error.

Filip

Hi

I'm looking at the Similarity overlap of two sets of compounds each 250000.  Without any tweaks, the maximum number of overlaps I can set is 200 - any more and I get error messages.  With the hints you gave above, setting the max to 2048 MB, I can get this to 280 ish but no higher.  Is there anything else I can do to increase this, maybe to 1000 overlap count ?

Thanks

Steve

Hi Steve,

We've tested it and we see an issue related to large Max hits number. The problem seems to be in too small column for the results so if max hits is too large the whole information doesn't fit into that column.

Could you please confirm that you see this type of error? It would help us if you can send us the errors which you see in the output window in IJC.

I'm afraid I don't see any workaround at the moment as the size of the column can't be modified by user. We will look at this for the next release.

Thanks for reporting it.

Petr

Hi Filip and others,

I managed to perform Overlap analysis by increasing the memory to 256MB as mentioned by Filip.

Now, as Steve mentioned I faced the same issue when there are multiple hits based on similarity search.

Waiting to have a fixed version of IJC.

Thanks,

Giri

Hi All,

the error when there are too many hits has been fixed in the 6.0 version. You can download it at http://www.chemaxon.com/download/instant-jchem/.

Cheers,

Filip