Failed to import text file with CAS number into Chemaxon

User b993cfcb8f

21-01-2015 16:44:28

Dear all,

I read that IJC is capable of converting CAS numbers into structures from this post

Following one of the suggestions:

1.I created a text file containing lines of CAS numbers

2. File > import file > clicked next twice (keeping everything default) > error

Warning: Failed to import row 1,818: Empty structures not allowed
Warning: Failed to import row 1,819: Empty structures not allowed
Warning: Failed to import row 1,820: Empty structures not allowed

Import completed in 2s.
0 entries successfully imported.

I am not sure what went wrong.

My ultimate goal is to convert the chemicals I have now (all in the form of CAS number) to SDF format.

Would really appreciate your help.


Thanks all.

User 247c00dc1d

22-01-2015 13:26:20

Had you mapped the CAS field to the structure before run importing?

User b993cfcb8f

23-01-2015 15:21:11

Thanks Igorlab! I have tried your method but what appeared on my computer screen was not the same as the picture.

I have attached two files with this reply -

1) showing the screen shots and error I got

2) my casnumber.txt

Would really appreciate your help. thank you!

User 247c00dc1d

23-01-2015 15:53:58

In your file before each cas# is extra space, if you will del it, import will be ok


User b993cfcb8f

23-01-2015 16:13:09

Hi Igor

Thanks so much for the speedy response, I have removed the spaces but this time there is no "structure" to map to so I just continued to click on "next" until "finished".

This table was what I got - is this what it is supposed to be like?

User 247c00dc1d

23-01-2015 16:49:35, actually not, it absolutely necessary to map your "Field 1" to the structure field as shown in my picture. moreover if you want get a structures, instead of cas# you should import file not into the standard table but into a structure table

The way to add a structure table is on the picture

User b993cfcb8f

23-01-2015 17:16:47

Hi Igor

Really really appreciate your helping hand- however I am still at a lost ...

I have done according to what you said and still getting error - bad molecule format

Please see attached files for new screenshots and the cas number text file (without space in front).

Thanks a lot!

Hui Wen

User 247c00dc1d

23-01-2015 17:40:42

Did you update the ijc?

I did in same way and all 9 structures have been imported...

User b993cfcb8f

23-01-2015 17:55:44

Hi Igor

I am using IJC 6.2.1 - may i know which version are you using?

I just found out the latest versions are IJC 15.x

Will ask our system administrator to upgrade the version...

Thank you so much for guiding me through! Really grateful.

Best wishes,

Hui Wen

User 247c00dc1d

23-01-2015 21:05:55

Hi Hui Wen

I am using IJC 15.1 



Hope that you will deal with this problem :)

sorry for my English

Best regards,

Igor T.