Hello.
I'm currently having this problem.
The .pdb I'm showing is a complex from Patchdock, so when I open it on PyMOL, it's showed as lines, even if I select all the residues and then click on 'show->cartoon' nothing happens.
So I tried in console by typing 'cartoon loop/rectangle/oval/automatic/etc' but didn't work either.
Has anyone experienced same problem?
I think PyMOL is showing only some type of contact..
Dear Diana Martínez-Valencia , try to convert your file to .pdbqt with autodock mgltools then reopen it with pymol. Else use another visualization tool like Discovery studio, it may give you better visual...
Best regards
I think the pymol repsesntation style has changed. Fix it to cartoon style. You can try Discovery Studio, ICM browser, or Schrodinger to check whether the downloaded pdb file is correct or not. You can download visualizer of all this three software for free.
Dear Diana Martínez-Valencia, I think you should use Discovery studio or UCSF Chimera for the visualization of your complex. I would also recommend re-checking your file prior to submitting it to Patchdock because sometimes the structures get distorted when we change the file types within the software. When you create the cartoon structures of your molecules through software and then change the file type (eg. from .mol to .pdb) be sure to close the window and re-open the same file to verify that your structures are not distorted.
Can you share the coordinate file (sending it directly to me if you do not want to share with everybody)? It looks like something is wrong with it.
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.
Annemarie Honegger is most likely correct about the chain IDs. A quick fix in PyMOL is to set the "retain_order" setting. See https://pymolwiki.org/index.php/Retain_order
Hello Annemarie Honegger and everyone. Thank you very much for your answers.
I already solved the problem by deleting 'CRYST1 110.348 110.122 110.151 90.00 90.00 90.00 P 1 1' at the beginning of the file.
Also, I needed to add 'TER' at the end of the first chain.
Those simple changes allowed to open the pdb file properly in any visualizer.
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