Importing Custom Ligands in Pymol - (Sep/18/2013 )

I'm currently working on a fourth year molecular biology project and I'm having some trouble importing files into pymol. What I want to do is create a custom ligand and import it into pymol with a pdb protein file. So far, I have tried using marvin sketch to create the molecule and trying to import the file via different file types (pdb,cube,mol ect...). Pymol either crashes or it makes the original protein disappear. Does anyone have any suggestions? Should I maybe use a new program altogether?

When you import your new ligand and your orignal protein dissappers, does it still list the original protein in the right side bar? It could be that you are entering a very small ligand (compared to your protein) and it blowing out your protein from view.  I would try centering on your protein (easily done in protein drop down menu) and then moving your ligand to your protein.

Depending on the complexity of your ligand, you can easily draw it within Pymol.  I have found that for some projects, this is much easier.

I think the issue is that when you upload your ligand, your protein gets pushed out of frame.

Let me know if that works.

Thanks for the suggestion, I finally found the protein. The pymol zoom function and viewing model can be a real irritation.

David