I have a ligand-protein complex in Pymol, but Maestro is not recognizing it. How do I save this session so that Maestro can recognize it
That's bit strange, because Maestro can recognize wide variety of formats. Did u try .pdb format?
Well tell me the file format in pymol, Is C:Users\Name\Document\Ligand-protein.pdb correct?
Cosmas O. Okoro Yes, that should be correct. Did you try opening other .pdb files using maestro? If you don't mind can you post the file here ?
To import the structure into a different program, you do not use the PyMOL session file (.pse), but need to save the coordinates as .pdb or other standard coordinate file. If you use the graphical interface for saving, you do not use "save as", but "export molecule". More easily, you type "save name.pdb, selection"
where name is the name you want to use for the file and selection can be an object, a selection representing a part of an object or a selection representing multiple objects. If you save multiple objects into a single pdb file, make sure that you do not use the same chain labels in the different objects.
Sorry y'all my problem could be due to the version of Maestro that I'm using. I am using an open source version for Academic Institution. It has limited functionality.
Cosmas O. Okoro Even i use the same but never faced any problem during analysis.
I think I am misunderstood. I did docking with PyRx and generated 9 best binding affinity. How do I save the result in order to view 2D Ligand-Receptor Interaction in Maestro. I am doing fine with viewing the interaction in Pymol and Discovery studio.
Look - we are trying to help you, but is extremely difficult to diagnose your problem without seeing the problematic file itself. I assume you have tested that you can open an ordinary pdb file downloaded from the database in maestro - therefore the program is working OK. Therefore the problem has to be with the file rather than the program. You don't need to make the file public, you can send it to me directly.
Dear Cosmas O. Okoro
I will suggest first you need to convert the pdbqt file generated via Pyrx into PBD format, the odb will work in any program
HTH
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