[PyMOL] symmetry and pdb remark

[honegger]

You have to generate the symmetry mates before you align the two structures. 
Then you can generate an object containing all symmetry mates for one 
structure, e.g by putting them as different frames on one object, and do the 
alignment with this object.

Annemarie


 Forwarding messages 
From: "Smith Liu" 
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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[PyMOL] symmetry and pdb remark

[Smith Liu]

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--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net