Way to highlight chiral centers in Marvinsketch/view?

Hi,

Is there a way to highlight chiral/asymm atoms in marvinview or marvinsketch?  If a user has drawn a structure with all flat bonds at chiral centers is can be hard to quickly find all chiral atoms.

Thanks for any information.

Best,

Andrew

Hi Andrew,

Marvin does not have this  feature currently, however we are aware that it would be useful. (You have to draw single up and/or single down wedge bonds and set  menu: "View">"Stereo">"R/S labels">"all" to see the chirality center. See documentation also: http://www.chemaxon.com/marvin/help/sci/stereo-doc.html).

Best regards,

Efi

Thank you very much for the reply.

You can use JChem to find out which atoms in a molecule are stereogenic with unspecified configuration.    

Molecule mol = MolImporter.importMol(substrate);

int numAtoms = mol.getAtomCount();

for (int atomNum = 0; atomNum < numAtoms; atomNum++) { 

	int parity = mol.getParity(atomNum);

	int localParity = mol.getLocalParity(atomNum);

	if (parity == StereoConstants.PARITY_EITHER && localParity == 0) {

		System.out.println("Atom " + (atomNum + 1) + " is stereogenic with unspecified configuration.");

	}

}

 See this page.

Hi,

Bob, I would like to thank you for your kind cooperation, and useful comment on this.

Andrew, if you have any further questions please do not hesitate to ask, I hope one of the suggested solutions will work fine for you.

Regards,
Istvan

Hi Bob and Andrew,

from Marvin 14.11.10 we will highlight atoms with possible but undefined chirality with a (?) label.

BRs,

Peter

Can I suggest making this optional, not mandatory? I assume it will be in View R/S labels; you can add a checkbox to include unspecified stereocenters.

It will be turned on/off together with the R/S labels in 14.11.10, but we might add this as an option in one of our later release.