PyMol - molecule export problem
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12 months ago
macbas ▴ 20

Dear all,

I have a molecule in PyMol which I want to open in ChimeraX. But after exporting the molecule as .pdb, some structural information seems to be lost - regions that in the PyMol session file are embedded into helices are now loops (this regards to several residues only). If I open the .pdb in PyMol, it looks the same as in chimeraX. I have no idea what I keep doing wrong, any hints? The first 14 residues of the original protein (from PDB, corresponding to Histag) were removed with a custom PyMol script which changed residues enumeration so that it properly starts with 1 - that is why the molecule from PyMol is needed. I would be grateful for the help.

best,

maciek

PyMol molecule format PDB export • 1.2k views
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12 months ago
Mensur Dlakic ★ 20k

PDB files have information about secondary structure elements that looks like this:

HELIX   11  11 GLY A  219  ASP A  222  1                                   4
HELIX   12  12 GLN A  235  CYS A  240  1                                   6
HELIX   13  13 TYR A  248  SER A  252  1                                   5
SHEET    1   A 6 ASN A  53  HIS A  57  0
SHEET    2   A 6 VAL A  65  THR A  69 -1  N  THR A  69   O  ASN A  53
SHEET    3   A 6 VAL A  29  GLN A  33 -1  N  LEU A  32   O  ALA A  66


Most visualization programs will use this information when rendering molecules. However, I don't know if this information is preserved when you save the file in PyMol. If not, PyMol will use its internal algorithm to calculate helices and strands, which can give different results from the original file. I think something similar could be true for Chimera.

Long story short: I suggest you open the original file in a text editor and delete the HIS-tag by hand - you will have to scroll down a while to find ATOM residues and delete the histidines. As long as you don't change anything else, you should be able to get the original secondary structure elements when you open the file afterwards. If you don't know how to do this, open the original PDB file and find all the lines that begin with either HELIX or SHEET. Copy and paste them into the file created by PyMol, and make sure they are right before the line that starts with CRYST1.

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Thank you! It helped a lot.

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12 months ago
macbas ▴ 20

For anyone who might be interested: 1 - open original .pdb in text editor 2 - remove all atoms (lines starting with ATOMS) corresponding to unwanted residues, save file 3 - go to https://wenmr.science.uu.nl/pdbtools/ and renumber your sequence (saved file) as desired 4 - go back to your original structure file and find all lines starting with HELIX or SHEET and copy them to the beginning of your corrected file (just before the first residue) and apply corrections to the secondary elements ranges (for example, I deleted 14 residues from the beginning, so need to shift back secondary elements ranges by 14) 5 - save the file and check if the structure adheres to what you expect

For me, it worked perfectly.