Centroid pharmacophore features

Hi,





Is it possible in MarvinSpace to define the centroid of multiple atoms as a pharmacophore feature, for example the centre of an aromatic ring as an aromatic feature? Would be very useful to have.

Hi,





yes, it's possible. Though pharmacophore regions (currently represented by spheres) can initially be placed on atoms but then they can be translated (and resized). Also, the pharmacophore type of the sphere can be changed.





1. load a small molecule


2. click the "Place pharmacophore point on a selected atom" button (this is the 7th in the toolbar) (this action is only available on this toolbar... - mspacae has an experimental gui)


3. then click an atom (eg a ring atom): a sphere is placed around the atom and a new item is shown in the right hand side selection panel


4. click the sphere to make it selected (then it's highlighted in purple), or right click in the selection panel and click the first item in the menu: selected


5. to move the pharmacophore sphere away form the initial atom click "Translate ligand in the space" button (actually, the 4th in the toolbar, and don't be confused by the inaccurate tooltip), then a double arrow is put in the middle of the sphere


5. use mouse drag + ctrl to translate the sphere along in the x-y plane, also hold down shift to move it in z direction


6. similarly, the sphere can be resized, just press the 6th button in the icon toolbar ("Resize resizable object...")..


7. to change the pharmacophore type rightclick the pharmacophore point (eg. Hydrophobic point) label in the selection panel then Properties->Type





It is important to note that the MSpace application is not capable of saving, loading the pharmacophore points. (Actually, we are working on a 3D pharmacophore search project and MSpace will be applied as visualization from-end for the search, so these missing features will be implemented.)





Does this help? What would be the ideal solution for you, what features you could use?





Regards


Miklos

Thanks, the repositioning and resizing works satisfactory. It is a pity though that the pharmacophore features cannot be saved yet, I hope you will implement this also.





Cheers

Yes, we will save it in MRV primarily. In the longer term we plan to support major formats (Catalyst, MOE, Phase etc.), import first.








Thanks


Miklos