I am trying to carry out some docking experiments: I have the structure of my protein in .PDB and then the cofactor NADP in .sdf.
I think that I have some problem with the output: I can only open the structure of the protein and then the .sdf of the cofactor which is not docked.
The main thing you need to know is that I am not an expert at all in this field, and I would be grateful if someone could help me to carry out the docking and visualizing it. Currently, I am using Pymol to visualize structures.
I thank you in advance for your consideration.
Which Rosie job are you seeing the issue with? If you have a successful run, like http://rosie.rosettacommons.org/ligand_docking/viewjob/14330 you can click on the individual structures in the table, which should have both the ligand and the protein in them. If you have an unsuccessful run, like http://rosie.rosettacommons.org/ligand_docking/viewjob/14281, you won't get the table of output structures. Instead, you'll get an error message.
Which run are you having problems on, and which links are you clicking to get the structures you do?
If you have an output file containing models info, depending on its type, dragging the file directly to pymol instead of open it from pull down menu might work.
Another program "chimera" also has a function under pull down menu "tools/surface binding analysis/viewdock" to open many types of docking results file for visualization. Hope this helps.