question on protein structure change after matchmaker (position-change) operation
Dear users, After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001). Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation? Thanks! Lei
Hi Lei, Matchmaker itself does not change the structure. However, if you save a PDB file after moving any atomic structure (by any method), because of rounding you may get tiny differences comparing the structures before and after. PDB file format only has 3 digits after the decimal in X,Y,Z coordinates. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 25, 2021, at 10:17 AM, Lei Qian via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear users, After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001). Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation? Thanks! Lei
Hi Elaine, Thank you very much for your explanation! Best, Lei ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Monday, September 27, 2021 12:11 AM To: Lei Qian leiqian@temple.edu Cc: chimera-users@cgl.ucsf.edu chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] question on protein structure change after matchmaker (position-change) operation
Hi Lei, Matchmaker itself does not change the structure. However, if you save a PDB file after moving any atomic structure (by any method), because of rounding you may get tiny differences comparing the structures before and after. PDB file format only has 3 digits after the decimal in X,Y,Z coordinates. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 25, 2021, at 10:17 AM, Lei Qian via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear users, After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001). Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation? Thanks! Lei
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Elaine Meng -
Lei Qian