-----原始邮件-----
发件人:"Elaine Meng" <meng@cgl.ucsf.edu>
发送时间:2016-04-14 03:21:16 (星期四)
收件人: "赵思雨" <154612254@csu.edu.cn>
抄送: chimera-users@cgl.ucsf.edu
主题: Re: [Chimera-users] PDB file created by a protein—protien docking tool ZDOCK can not opened by Chimera
Dear Siyu Zhao,
The file from ZDOCK does not follow the PDB format description because it has extra numbers in the wrong places after the X,Y,Z coordinates. Probably Jmol and DSV are not bothered by those extra numbers, but Chimera does not tolerate them. If you just remove the columns after the coordinates, the file will display in Chimera. Below I attached an edited copy of your file which includes only columns 1-54.
ZDOCK output before editing:
ATOM 1 N LYS A 2 -1.022 -5.354 37.251 4 1 1.63 -0.15
ATOM 2 CA LYS A 2 -1.230 -4.312 38.301 4 1 2.03 0.10
ATOM 3 C LYS A 2 0.011 -3.410 38.417 4 0 1.67 0.60
…after editing (OK for Chimera):
ATOM 1 N LYS A 2 -1.022 -5.354 37.251
ATOM 2 CA LYS A 2 -1.230 -4.312 38.301
ATOM 3 C LYS A 2 0.011 -3.410 38.417
Example from RCSB PDB:
ATOM 1 N ALA A 1 46.457 12.189 21.556 1.00 56.69 N
ATOM 2 CA ALA A 1 47.614 11.997 22.448 1.00 55.96 C
ATOM 3 C ALA A 1 47.538 12.947 23.645 1.00 55.17 C
About PDB format:
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco