Hello Smith, I had a look at the two structures. In some crystallographic space groups there are alternate choices for the origin that are all equivalent. It appears that this is what you are seeing here.
If you look carefully at the mates generated separately for 2zam and 2zan, they are equivalent in their position and orientation relative to the original coordinates for each structure. There is simply a translational shift along two axes that relates the coordinates of 2zam and its mates to 2zan and its mates. There is a slight difference in the unit cell dimensions as well, which could make very small differences in the packing contacts. Cheers, Rob On Thu, 2017-02-02 12:37 +0800, Smith Liu <smith_liu...@163.com> wrote: > 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 -- Robert L. Campbell, Ph.D. Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
