Dear All,
Here I make my question much clear.
For both PDB 2zan and 2zam, they are for the same protein, they conformation
were similar except that 2zam was apo and 2zam was ATP binding. 2zaz was got by
soaking the 2zam crystal with ATP. Both were P65 space group
However by getting the mate coordinates of 2zam and 2zan by Coot or Chimera,
you will find their 6 mates arrange differently ( viewed by Chimera or by
Pymol). For 2zan, the 6 mates were separated with each other, but for 2zam the
6 mates were connected. Can you explain to me why their 6 mates arrange
differently?
What is more, by pymol I align 2zan onto 2zam, and I get the PDB for 2zan
fitted to 2zam (no any text information from the pdb file left after pymol
saving, except the coordinates). Then I add all the text information from 2zan
(except the coordinates) to the PDB for 2zan fitted to 2zam, and then I get the
mate coordinates by Chimera or Coort and then view the mates got by Chimera or
Coot for the text information added PDB for 2zan fitted to 2zam, I find the 6
mates arrange like 2zam, rather like 2zan (viewed by Chimera).
Thus, will you please explain which remark information decide the mate
arrangement, as in the remark added PDB for 2zan fitted to 2zam? Why after
pymol alignment, the same remark information leads to different mates
arrangement?
I am looking forward to getting a reply from you.
Smith
-------- Forwarding messages --------
From: "Smith Liu" <smith_liu...@163.com>
Date: 2017-02-02 12:06:16
To: pymol-users@lists.sourceforge.net
Subject: symmetry and pdb remark
Dear All,
I have a symmetry problem, which I hope I can get your help.
For both PDB 2zan and 2zam, they are for the same protein, they conformation
were similar except that 2zam was apo and 2zam was ATP binding. 2zaz was got by
soaking the 2zam crystal with ATP. Both were P65 space group
However by getting the mates of 2zam and 2zan, you will find their 6 mates
arrange differently ( viewed by Chimera). Can you explain to me why their 6
mates arrange differently?
What is more, by pymol I align 2zan onto 2zam, and I get the PDB for 2zan
fitted to 2zam (no any remark information left after pymol saving). Then I add
all the remark information from 2zan to the PDB for 2zan fitted to 2zam, and
then I view the mates for the remark added PDB for 2zan fitted to 2zam, I find
the 6 mates arrange like 2zam, rather like 2zan (viewed by Chimera).
Thus, will you please explain which remark information decide the mate
arrangement, as in the remark added PDB for 2zan fitted to 2zam? Why after
pymol alignment, the same remark information leads to different mates
arrangement?
I am looking forward to getting a reply from you.
Smith
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