Frgment and solvent removal using Standardizer in I-JChem

User 677b9c22ff

13-10-2007 23:24:36


I have a list of molecules and want to remove all solvents and small fragment, this works fine with the Standardizer GUI, but not within

Instant-JChem. Settings in Standardizer are "keep largest".

Example molecules:



Br.CN1CCC[[email protected]@H]1Cc2c[nH]c3ccc(CCS(=O)(=O)c4ccccc4)cc23


Instant JChem Version: 2.1 (build: 071002) JChem Version: 3.2.11 Marvin

Version: 4.1.13 (build date: 2007-9-20) Java: 1.5.0_11; Java HotSpot(TM)

Client VM 1.5.0_11-b03 System: Windows XP version 5.1 running on x86;

Cp1252; en_US (instantjchem)


ChemAxon fa971619eb

14-10-2007 03:56:29

This seems to be working fine.

Are you displaying the structures in their standardized form? The default is the original form. Use the structure display settings to change this.

With a form view you could display in both forms. With the grid view you have to choose which one to use.


User 677b9c22ff

14-10-2007 04:59:12


thanks, I don't know, there are just many things which

seem illogical to me, why would I use a Standardizer

in the first place to remove water, if I still can see it later?

I mean you can see it from the picture, seeing is believing,

now I know I can go to Customize widget settings and

can check "Show standardized form" and the water will

disappear (actually its still there, hidden). The logic path

would be however to turn the widget setting on,

if a Standardizer is selected and/or really remove the water

The second question is, if I use the Standardizer and do a

fragment removal and export some structures from a query,

will it export the standardized structures or the raw structures?

In both cases it will export the water molecule,

but I can toggle the widget display to show water and

not showing water, I don't know what this is good for.

I now use the Standardizer GUI and just perform all

computations including desalting and fragment removal

outside and then import everything into

Instant-JChem. That seems pretty safe right now.

It would be also helpful if some more people

would comment on such issues, because

different people use different approaches.


ChemAxon fa971619eb

14-10-2007 08:04:47

The purpose of a standardizer in a JChem table is to provide consistent SEARCH behaviour. So the standardizer should be thought of as a property of querying, not display. In the majority of cases we find that users are interested in the actual structure, not the one that is used for querying, so that is why the original form is the default, but we provide the option do view it the other way when this is needed.

For instance the fact that salts are present is important to know, even though when searching the salt form is not considered. Also, as aromatisation will will almost always be required as part of a standardizer configuration display in the standardized form will result in structures being displayed in aromatic form, which most chemists find less preferable than the Kekule form.

If you want to load strucutres as if the salt/solvent was never there in the first place then you can use a stand-alone standardizer to convert you file prior to importing it. See here for details: