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schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
https://pymol.org/
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Error saving PDB file #294

Closed 404-xianjin closed 5 months ago

404-xianjin commented 1 year ago

I have two pdb files, 4hkz and GSTP1, I use 4hkz's variable region "SRWGGDGFYAMDY" to combine with GSTP1's "DQGQSWKEEVVTVETWQE". as the picture shows, image I try to save this two pdb files as a new pdb file, but the pdb file I saved is like this. image I'm not sure what is causing this and I need your help. Thank you so much @JarrettSJohnson @TstewDev @pslacerda

JarrettSJohnson commented 1 year ago

Can you try this setting before saving it as PDB: https://pymolwiki.org/index.php/Retain_order

YaoYinYing commented 1 year ago

These chain ids from pdbs are identical, try something like this before saving the merged pdb: 

alter prot_A and chain A, chain='A'
alter prot_B and chain A, chain='B'
save merged.pdb, (prot_A and chain A) or (prot_B and chain B)