Chemical terms

Hi,

I just downloaded Instant JChem and opened a new project and view.  I added a structure by copying from MarvinSketch but can not add cLogP or other property calculators to my table view.  Did the required plug-in's come with the download?

thanks, Ron

Hi Ron,

this is most likely to be a licensing issue. Most calcuator plugins, including logP, require licenses. WIthout the appropriate license the calcuations are disabled. You can check this by using one of the calculations that does not need a license, such as composition.

The second, less likely, possibiltiy is that you have created a standard table, not a structure table. Chemical terms calcuations are only possible for structure tables.

For more info on how to use chemical terms fields in IJC see here:
https://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/editing_database/fields_chem_terms.html

For an animation of this in action see here:
https://www.chemaxon.com/instant-jchem-animations/working-with-data/structure-based-predictions/

Tim

Hi,

 

I have a table of screening results and would like to calculate ligand efficiency by dividing the EC50 by molecular weight. I can't see how to do this in IJChem (most recent version).

 

If I resort to calculating the values in another program, I don't see how to merge a new column with an existing table.

 

Yvonne

This can't be done in the current version without working directly at the database level, which is not suitable for normal users (but see here for examples: http://www.chemaxon.com/instantjchem/ijc_latest/docs/admin/tips/triggers/index.html).

We are currently adding the ability to perform generic calculations, and hope it will be ready for the next version.

Until then probably the easiest approach is to create two columns in IJC containing the EC50 and MW, then Copy & Paste those values into Excel, generate the calculated column in Excel, then paste the results back into a new (empty) column in IJC.

Tim

 

Tim,

I can't seem to do this. I highlighted the column in IJChem table view and selected Copy. However, Excel has nothing to paste.

I guess that I have to save a list--will try that.

I saved a list from IJChem and it appears that this is not a file--at least it is nowhere to be found.
I then exported a file as .tab, read it into Excel, performed the calculations, and saved the file. I also checked that the file actually has numbers.
In IJChem I then "Import list from file" and it is empty.
I then "New File", highlight columns of interest, "Copy", return to grid view of original data. Again "paste" is greyed out.

I finally figured out that I had to right-click on the database name and then I could import/merge. Just reading in the file didn't let me merge.

All of this is overly complicated. It seems to me that cut-and-paste should work or that importing a file should let one merge.

Yvonne

Hi Yvonne,

I think this just needs to get Excel to play ball. I tried repeating this, but I'm on Mac, so was using using OpenOffice as the spreadsheet, not Excel, but it worked exactly as expected. I'll try this soon with Windows and see how it works.

I suspect the problem is to get Excel to allow the Copy/Paste commands. MS Office products do unhelpfully clear the clipboard when they start, so try having Excel open already before you do the Copy command and seeing if that helps.

Tim

Hi Yvonne,

Windows/Excel seems OK too.

See the attached movie that shows this.

 

Tim

Hi Tim,

I'm working on a mac with an ancient version of Excel (2001)--to cheap to update. I did try restarting Excel, but I suspect that the problem is this old version.

That said, it should be more obvious how to merge a file into an existing database. Once I figured it out, it worked smoothly. I also couldn't copy-and-paste from one grid view to another--I had imported the calculations, but they went to a new something-or-other?? a view but not a database. Again, I could copy, but in my main database paste was greyed out. I hunted around if there were some protections on that database, but didn't see anywhere that they could be set.

Yvonne

Hi Yvonne,

Merging data is a relatively advanced topic. It is described here:
http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/moving_data/merging_data.html

But in your case I think using copy and paste will be much simpler.

Tim

Tim,

I actually think that Merge can be safer than copy and paste. Whenever I paste into a spreadsheet I include some identifier so that I can double check that the new columns refer to the same object as do the original columns. Merge does this automatically.

At any rate, I have now added several more columns to my database, so all is well.

Yvonne