I am trying to visualize the protein interactions between human lung surfactant protein D (1PW9) and the SARS-CoV-2 spike (6VYB). I used PatchDock and FireDock to generate the structure and put the file into PyMOL. However, I am new to PyMOL and am not sure why my structure does not look correct and has a lot of "extra lines." I have attached a photo as an example. Does anyone have an explanation for this? Thanks!
I have seen similar effects when students failed to ensure that the two docking partners do not carry the same chain label - in this case, programs that strictly follow the order of residues, ignoring the chain and residue labels in the file, display the file OK, while more sophisticated programs that pay attention to the explicit residue labels get thrown off by jumping back and forth between the two binding partners from A1 in one chain to A1 in the second, back to A2 in the first and so on. Even if some programs may lead to a reasonable representation, this can keep causing problems in further processing of the coordinates. Look at the coordinate file in a text editor, e.g. notepad+, to see whether the coordinate file is OK. ( my answer in https://www.researchgate.net/post/Pdb_showed_only_as_sticks_in_PyMOL )
A quick fix in PyMOL is to set the "retain_order" setting. See https://pymolwiki.org/index.php/Retain_order (Thomas Holden)
There is probably something wrong in your pdb. As Annemarie Honegger said this can happen when you have identical chains. I think it can also happen if there is more then one line with the same atom id.
Can you show us your PDB ? Then we can maybe find the problem.
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