docking in rosetta 3.3

If you’re having a specific problem with Rosetta, we can try to help you sort it out. It seems to me that you need to figure out what you want to do before we can help you do it. Have you read any of the docking related papers? Look for papers by Jeff Gray’s lab for protein docking, and Ora Schueler-Furman’s lab for peptide-protein docking.

What do you not understanding about the manuals? They’re full of gaps but I don’t usually hear that they’re incomprehensible.

It may be worthwhile to also look through the demos and the RosettaCON2011 Tutorials Collection. (I believe each are available as a separate download from the same location you got the code from.)

Working through the examples (e.g. by actually running the code on the example structures provided) will help to give a better sense of what Rosetta can do, and how to use which programs for what type of problems.

Your laptop will have about the same power available as the RosettaDock server. You will have much finer-grained control over what Rosetta is doing locally, so you can try different experiments. Running Rosetta on a laptop for long periods may overheat it (Rosetta will max the processor out consistently). It’s your choice.

For PyMOL:
http://lmgtfy.com/?q=pymol
http://www.pymol.org/
http://www.pymolwiki.org/index.php/Main_Page

If it’s two proteins with no docked structure, then just open their PDBs in a text editor, combine the two files, and delete any line that doesn’t start with ATOM. You’ll need to make sure the two proteins have different chains (read the PDB format specs at RSCB to learn which is the chain column; I think it’s the 5th column after the residue type and before the residue number. There are other things you may or may not need to do depending on what errors you may or may not encounter – this works for properly formatted crystal-sourced PDBs with no nonprotein residues. You haven’t told us enough about your system to anticipate other problems.

I don’t know anything about cleanpdb.pl – where did you see it mentioned so I can ask that person where it is? All it’s likely to do is remove unnecessary atoms, etc.