3D alignment

Hi!

I'm trying to use the 3D alignment option in MarvinView (Marvin5.2.3_1) and i'm wondering that i'm totally incapable to use it.

I have a set of similar molecules (from a Markush enumeration) and I wanted to align them. I used the standardizer for addH and clean3D, molecules are saved in sdf format.

First, if i don't select any specific molecules, I have an error message:

no molecule selected, select a molecule first.

If I select one, it says

2 or more molecules are requested to align.

How can I select ALL molecules, and what I'm doing wrong???

Thanks,

Panni

 

Hi Panni,

The 3D alignment overlays molecules within the same cell. Hence all the molecules, you want to align, must be copy/pasted into a single msketch window and saved as a single molecule containing multiple fragments.

The alignment can be launched from mskech also.

Please note that the alignment process can take long for simultaneous alignment of 10s of molecules.

Below I attach the alignment help.

Than you for your comment.

Adrian

 

http://www.chemaxon.com/product/align.html

The "User guide" link is currently broken please use:

http://www.chemaxon.com/marvin/help/calculations/conformation.html

Thanks, Adrian.

But how can I select ALL molecules together? It is still not clear for me? Or it doesn't exist as option in Marvin View - I mean select all molecules together and copy-paste it?

And it is a little bit disturbing, that the 3D alignment exists as option in marvinView and as you said it works only in MarvinSpace under special conditions :(.

Panni

 

 

panni wrote:

Thanks, Adrian. But how can I select ALL molecules together? It is still not clear for me? Or it doesn't exist as option in Marvin View - I mean select all molecules together and copy-paste it? If you read the documentation at: http://www.chemaxon.com/marvin/help/calculations/conformation.html There stands a command line: molconvert mrv m1.mol -R m2.mol -o m_all.mrv Based on this you can convert your sdf into the desired one molecule-multi fragment file. This can be used for alignment. And it is a little bit disturbing, that the 3D alignment exists as option in marvinView and as you said it works only in MarvinSpace under special conditions :(. I dont understand your complain. Alignment has nothing to do with MarvinSpace. Though if you had Mspace installed you get nicer output. Under I attach a step-by-step manual for alignment. Panni

 

panni wrote:

Thanks, Adrian. But how can I select ALL molecules together? It is still not clear for me? Or it doesn't exist as option in Marvin View - I mean select all molecules together and copy-paste it? If you read the documentation at: http://www.chemaxon.com/marvin/help/calculations/conformation.html There stands a command line: molconvert mrv m1.mol -R m2.mol -o m_all.mrv Based on this you can convert your sdf into the desired one molecule-multi fragment file. This can be used for alignment. And it is a little bit disturbing, that the 3D alignment exists as option in marvinView and as you said it works only in MarvinSpace under special conditions :(. I dont understand your complain. Alignment has nothing to do with MarvinSpace. Though if you had Mspace installed you get nicer output. Under I attach a step-by-step manual for alignment. Panni

 

Suppose you have a sdf file contaning some molecules (called wish.sdf) that you wish to align.
 This must be converted for the alignment to a single molecule multi fragment file where each fragment is a molecule from "wish.sdf" .

This can be done as:

-go to msketch and create an empty file called eg.: empty.mol

-then type at command prompt:

molconvert mol empty.mol -R wish.sdf -o wish_fused.mol

-load wish_fused into MSketch

-If you know which atoms to overlap use "reaction mapping arrow"  to connect them. This can improve the alignment.

-If you have only 3D molecules as input and you select one of them, its
original conformation will be preserved during the alignment, while
others remains flexible.

-select Tools>Conformation>3D Alignment

-untick "Display in MarvinSpace" (only in 5.2.3_2)

-press "Ok"

-Alignment process can take a while, around a minute for 4 durgsize molecules

-Click on the result window with the second mouse button and select "Save As" from the pop menu.

 

Hi!

Is there a way of using the 3D alignment tool from the command line? I found out that cxcalc can give me conformers and do MD but I can't seem to find how to do the alignment. I'd like to extract the aligned coordinates of the two molecules and the 3D similarity value.

Thanks for any help!

Marci

Hi Marci,

please use screen3d in the jchem suite. Type simply screen3d for the command line help. Feel free to ask further help if needed.

Good luck,

Adrian