Accuracy of re-creating images in marvin view

Hi.





I have a database of structures and smile strings stored in a database. The smile strings are generated using the jchem manager import function.


I am using the smile string to re-create the structure in marvin view however the accuracy of the re-created image is not always 100% e.g for chiral compounds some of the chirality is reversed etc. What is the best method/format to use to re-create the image for viewing so that it is exactly the same as the original mol/sd structure?





E.g. how accurate is to recreate the structure image using molconvert using the following formats:





mol string


smile string


inchi string





thanks

Hello, could you please give some examples where the chirality is not correct so we can have a look?





If you are creating images from SMILES only, the coordinates should be the same. There can be a difference for some of the non-unique SMILES, so when you are generating the SMILES it is worth to try the "smiles:u" format. Could you also send a molecule if possible when the generated image differs?

Hi,





Please see attached file - original_image.gif. This is the original representaion of the compound from a mol file.





JChem manager produces the following chemaxon extended smile string for this compound:

Code:

CN(C)[C@@H]1CCCC[C@H]1N |r,@:1|

If the above smile string is used to recreate the compound in marvin view it comes out as follows - please see attached file using_extended_smile.gif. This is an incorrect representation of the original compound.





If I use a unique smile string as shown below the co-ordinates of the original compound are changed. Whilst it is the same compound the properties would be different with the different representation of the compound. See the resulting image in attachment using_unique_smile.gif

Code:

CN(C)[C@@H]1CCCC[C@H]1N

Hi





The problem is the following here:


1) chemaxon extended smiles exports the local parity information also (this allows to store not only molecules but queries also):


CN(C)[C@@H]1CCCC[C@H]1N |r,@:1|


2) if it is possible the parity/local parity is interpreted at both end of a wedge bond


3) Clean tries to arrange wedges avoiding setting wedge between two stereo center





So in cxsmiles case the N and the C has also local parity and the clean set wedges for both atom.


In case of smiles the local parity information is lost. The N has no parity just local parity information so the problem does not appear.





In a later marvin version it will be possible to set parity interpretation to the narrow end of a wedge only, which will solve this problem.





If you have simple molecules you can use unique smiles format.


For a complete list of supported cxsmiles features see:


http://www.chemaxon.com/marvin/doc/user/cxsmiles-doc.html





Andras

any indication when a new release of marvin will be available which will fix the above problem?

In a few month. Hopefully in one.

Can anyone print a copy of a drawn molecule charge? I tried to print mine out and it wouldn't print.

It works for me. In the charge calculation result window, take a right click to display popup menu and select any option from the print submenu.

volfi wrote:

Hi The problem is the following here: 1) chemaxon extended smiles exports the local parity information also (this allows to store not only molecules but queries also): CN(C)[C@@H]1CCCC[C@H]1N |r,@:1| 2) if it is possible the parity/local parity is interpreted at both end of a wedge bond 3) Clean tries to arrange wedges avoiding setting wedge between two stereo center So in cxsmiles case the N and the C has also local parity and the clean set wedges for both atom. In case of smiles the local parity information is lost. The N has no parity just local parity information so the problem does not appear. In a later marvin version it will be possible to set parity interpretation to the narrow end of a wedge only, which will solve this problem. If you have simple molecules you can use unique smiles format. For a complete list of supported cxsmiles features see: http://www.chemaxon.com/marvin/doc/user/cxsmiles-doc.html Andras

does the new jchem version automatically clean wedge bonds when imporitng an sd file into a database by defualt or does the standerdiser need to be configured to achieve the above? if so what is the syntax using a command line or jchem manager?





also is it possible to apply clean wedge bond as a parameter in marvin view when loading a molecule?

No, currently there is no option to do it by the initalization of MarvinView applet.

does the new jchem version automatically clean wedge bonds when importng an sd file into a database by defualt or does the standerdiser need to be configured to achieve the above? if so what is the syntax using a command line or jchem manager?

Hi,





No, database import does not clean wedge bonds. However, you should use the cd_structure column for displaying the database structure. It contains the original structure source that was imported. (It is also the starting point at table regeneration for a new version.)





The new JChem 5.0 interprets wedge bonds at the narrow end only, so you should just regenerate your JChem tables (I assume that you have molfile/sd file structures imported), and use the cd_structure column for display, and all will be as expected.





Let us know if you still have any questions.





Best Regards,


Szabolcs