obtain visualization changes in screen3d aligned structures

Hi,
I was a bit unsure where to post my question as I use command line screen3d, but my question refers to the visualization.

I run command line screen3d comparisons on many molecule pairs. I would also like to automatically obtain nice figures of the aligned molecule pairs.
Attached are two example sd files, on which I show what I do:

1) run screen3d to generate 3D pharmacophore structures
screen3d g AKE.sdf -F -pharm
screen3d g MIX.sdf -F -pharm

2) run screen3d to compare the structures, save overlayed structures as well
screen3d s -q AKEF.ser -t MIXF.ser -writeQuery

Now I have a file with aligned structures. If I view it with mview, both structures are coloured using the same
schema (C atoms are black, O red, N blue), so it is hard to differentiate between the 2 molecules.
Also, the lone electron pairs are explicitly shown as 'LP'.

My questions are as follows:
    1) Would it be possible to remove the LP notation? It is very confusing like this.
    2) Would it be possible to colour the two molecules differently? One with one single colour and the other with another single colour?

Thanks,
Anna

Hi Anna, 

There are no direct solutions for your question in MarvinView/Space. Currently only they can be solved with using the API. 

We are going to investigate other possibilities to solve them differently with ChemAxon tools. 

Dani

Hi Dani,

Could you give me an example how to do it using the API?

Thanks,

Anna

Dear Anna,

Please see the attached code example.
You can compile and run it with the following commands:

javac -cp jchem.jar FragmentColoring.java
cat AKEF_MIXF_shape_aligned.mrv | java -cp jchem.jar:. FragmentColoring | mview -

Best regards,
Laszlo 

Dear Laszlo,

Thanks for the code example. It worked, and was perfect in terms of the colouring. Is it also possible to remove the LP notation (or replace with the more conventional dot notation)?

Thanks,
Anna

Dear Anna,

Sorry for the late answer.

I have updated the example with a new method which remove the LP atoms from the molecule.
If you want to see the lone pairs (dot notation) of the molecule you have to set View > Advanced > Lone Pairs menu in MarvinSketch.

Best regards,
Laszlo 

Dear Laszlo, thanks, I really like the result. Best, Anna