On 07/03/2024 07:18, 신진우(생명과학과) wrote:
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Dear Coot,
Hello. My name is Jinwoo Shin. I'm a structural biologist in South Korea.
I am deeply grateful to your service for developing coot program.
I have a question.
I recently deposited a cryo-EM structure to RCSB (PDB: 8IEP,
https://www.rcsb.org/structure/8IEP). I found that downloaded cif file
from RCSB has some issues in coot program.
By using color by atom mode, there is no issue.
However, by using color by chain mode, it is shown that the backbone
of structure is broken. (please see the attached pictures)
Also, by using Ca/Backbone mode, only atoms are shown. (please see the
attached pictures)
The original PDB file, which has not been deposited, does not exhibit
any issues in the cootprogram regardless of the mode I use. Thus, I
speculate that there may be some problematic elements during the
deposition process.
I am unsure of the exact reason. Even the staff of RCSB does not know;
he said, 'I don't know, and if I find out any causes, I will let you know.
He also said that asking the coot staffs would be faster.
Dear Jinwoo Shin,
Rest easy.
The problem is entirely ours. Briefly, there is a bug in parsing mmCIF
files in Coot. To fix this is taking some time, but it's on the way!
You will see, I think, that your molecule looks fine in ChimeraX.
Paul.
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