I have 2 different files with prediction results of a protein protein interaction from 2 servers, and I want to align them to see how similar the structures are. I would normally fetch the PDB molecule to align but in this case I can't because the structures obviously don't have PDB codes.
type command on prompt.....
align obj01, obj02 (press enter)
You can do it by clicking in Action > Align > to molecule.
Do you have problems loading your structures? you can use "open" in the file menuor the command "load filepath/yourfilename.pdb, objectname" to load your structures. Under MacOSX, you can also drag-and drop yourstructure files onto the program icon or into the open PyMOL display window.
Besides "align", which does a sequence based alignment, there are other options: cealign, super, pairfit - which one is best depends on the level of sequence similarity and whether you need to get an informative rmsd (no throwing out badly matching atom pairs) or a good alignment of the core structure. Consult the pymol wiki ( http://pymolwiki.org/index.php/Main_Page) for the exact syntax.
The PyMOL modules tmalign http://www.pymolwiki.org/index.php/TMalign and colorbyrmsd http://www.pymolwiki.org/index.php/ColorByRMSD may also come in handy when comparing multiple structures.
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