VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Apr 23 2018 - 12:05:44 CDT

I tried that last night, and VMD opened the structure models as 4 frames. I had to save the coordinates of each frame and then merge them back together as one structure. Is there a different way to open it so that VMD recognizes the models as different peptides instead of frames?

Kelly L. McGuire
PhD Scholar
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602

________________________________
From: jrhau lung <jrhaulung_at_gmail.com>
Sent: Monday, April 23, 2018 5:56:53 AM
To: McGuire, Kelly
Cc: VMD Mailing LIst
Subject: Re: vmd-l: PDB Question

Hi Kelly:
    If you download 5C02, it does contain only one chain. But if you download the biological assembly, it will have four chains as a homotetramer structure.

sincerely,

Jrhau

2018-04-23 7:40 GMT+08:00 McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>>:
Sometimes when I download a PDB from pdb.org<http://pdb.org> or request one through QwikMD, only a part of the protein is loaded. For example, 5C02 is a homotetramer crystal structure, but when I download the pdb or request it through QwikMD, I only get one of the peptides, not all 4 i.e. not the whole structure. What is causing that?

Kelly L. McGuire
PhD Scholar
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602