Standardizer (remove explicit H) doesnt work in IJChem

User 677b9c22ff

27-02-2009 01:15:53


I downloaded some files from PubChem,

created a DB with Standardizer in Instant JCHem

and imported that field. I enabled all fields in the

remove H section.

The explicit Hs are still shown, I tested it with the

external Standardizer and that works fine.

This is version 2.4.1 (general ZIP install with latest update)


User da00f5c453

28-02-2009 04:12:44

try to change to "display as standardized" in molecule widget in your database form or view.

ChemAxon fa971619eb

28-02-2009 05:11:14

Yes, that is correct. Standardization is primarily for query purposes.

It determines how the queries are run, and as such is often not of direct relevance for display purposes.

For this reason the version of the structure that is displayed by default is the unstandardized form, but you can change this by setting the "display as standardized" dispaly setting for molecules.

See here for a related topic:


User 677b9c22ff

02-03-2009 02:37:54

Hello Oleg and Tim,

thanks for your help, yes that resolves the issue.

Tim, now I know I fell into that trap twice....

I have two other problems I can not

1) get rid of the "Absolute" label with the widget property

2) show R/S labels even in case of stereochemistry.


ChemAxon fa971619eb

03-03-2009 16:45:41

We will add the option to show/hide the R/S labels.

I'm not sure whether the "Absolute" label can be hidden, and need to investigate.

Also, I'm not sure its desirable to hide this as it contains important information about the stereo chemistry (the MDL chiral flag).


ChemAxon fa971619eb

12-03-2009 17:53:23

An option for showing/hiding R/S lablels is now present in the IJC 2.4.3 update.