Draw a structure with data like ISIS draw

  Hello,

We'd like to draw some special structures in Marvin, and the exported SDF from Marvin databse can be identified by ISIS database

Could you tell us how to draw a better structure in Marvin as the attached file drew by ISIS?

Thanks

Dear User !

To draw the structures in Marvin you have to do the following :

1. structure :

Draw the structure in Marvin. Then select the whole structure with the Selection tool and
use Structure > Add > Data to add different data to the structure as a group :

- choose Context > Group (Selection), Name > ROLE  and Value > Parent and Adduct (Salt) respectively.
- unable query with 'none'.
- choose Placement > Absolute

2. structure :

Draw the structure in Marvin. To add the absolute stereo flags select the corresponding atom and
use Right Click > Stereo > R/S > S and R respectively. That will set the correct stereo bonds.
Then to add labels to the stereo atoms

- choose Context > Atom , Name > c , Value > a and Value > ab, respectively  
- choose Placement > Next to objects to have them appear next to the atom

To add the text under the structure use a text box. (Insert > Text Box)

3. structure :

Draw the structure in Marvin. Then select the whole structure with the Selection tool and
use Structure > Add > Data to add different data to the structure as a group :

- choose Context > Group (Selection), Name > QUALIFIER and Value > ISOMER 1  
- unable query with 'none'.
- choose Placement > Absolute

Then choose the central C of the ring branch and

- choose Context > Group (Selection), Name > STEREO and Value > unknown absolute
- unable query with 'none'.
- choose Placement > Absolute

These should give the same result as in ISIS.

I hope this helps.

Hi, thank you for help

We have a further question, If our database was set as duplicate filtering on, how can both two compounds with the same structure but with different data pass through? for example about the third compound in "Sgroup Field.docx", there is another compound with the same structure but with data of "ISOMER 2"

Hi,

Could you send the sdf-file created by ISIS draw which works in this case?

Best Regards,

Efi

ehoffmann wrote:

Hi, Could you send the sdf-file created by ISIS draw which works in this case? Best Regards, Efi

Hello

this problem is still troubling us, please see the attached file, A1,A2,B1,B2 are exported from ISIS. Our question is if there is possibility to change some setting about duplicate filter to allow these structures as different data in the structure database(Jchem 5.4.1), or add some symbol to differentiate those structure, but without influence on SMILES, as pseudo atom will become "*" in SMILES. Alternatively, it is ok if there is a way to remove a sepcific pseudo remark(eg."remark") in the strucure by batch processing in SDF file

Thanks for help

Sorry for the late answer. I am moving to this issue to the JChem forum. My colleagues can help you in this question.

Hi,

The difference between A1 and A2, and B1 and B2 structures in your sdf file is found in their attached data  (qualifier: isomer1 (in A1) and isomer3 (in A3), (count: 1 (in B1) and 1.5 (in B2)). In JChem, there is a search option implemented, called  AttachedDataMatch, with 3 possible values (ignore, general, exact); its default value is 'ignore'. This search option makes possible to differentiate structures upon their attached data during search processes. During database import into a table with 'Filter out duplicate structures' setting, however, the default value of AttachedDataMatch  (ignore) is valid. Therefore, during the import, JChem can't filter out structures which differ only in their attached data.

So we suggest not to apply 'Filter out duplicate structure' table settings if you would like to import all of these structures; and use the AttachedDataMatch search option when you run duplicate, full, full-fragment, sub - or superstructure searches in these tables.

Best regards,

Krisztina

Thank you very much.

 Your measure give us a great help

One more comment from our above linked documentation:

"To help represent new molecular features during duplication control,
from JChem 5.3 duplicate search uses special attached data with name starting with "[DUP]".
These attached data names are automatically checked during duplicate searches"

According to this rule both attached structures (isomer1.sdf and isomer2.sdf) will be successfully imported into tables with "Filter out duplicate structures"  settings.

Best regards,

Krisztina