Entering edit mode
4.7 years ago
anndybud
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0
Hi all, Does anybody know how to export distances measured in pymol in fasta format or text format? Thank you very much!
FASTA contains sequences with headers. How does the information you're trying to export map to that? Plain text should be doable, as almost every format in bioinformatics is plain text :-)
Hi RamRS, So how to export to plain text in pymol? I have tried, but failed. Thank you very much!
I don't know pymol, but if you were to say what you've tried, others might be able to point you to the changes you need to make.
Hi RamRS, I will try to express the details later. Thank you very much!
See if this helps you.
I will sound like a broken record, but probably there are other programs or scripts that can do this more efficiently than PyMol if you truly need it done on a large scale. The distance formula is not very complicated and here is one way to do it using BioPython.
Hi Mensur, First I have to measure the distances in pymol, which is a visualization tool for 3D structures. Then I would like to export the values for these distances. I will try biopython later, though I have no idea where to start. Thank you very much anyway!