Dear All,
I got the each of 6 mates coordination for each pdb by Coot or by Chimera. Then
viewed the arrangement of the 6 mates for 2zan or 2zao by Pymol or by Chimera.
You will find, for the 6 mates of 2zan, they were separated, but for 2zao they
were connected.
Then 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 (in fact all text information except the coordination information)
from 2zan to the PDB for 2zan fitted to 2zam, and then I view the mates for the
remark （all text except coordination） added PDB for 2zan fitted to 2zam by
Chimera or Pymol, I find the 6 mates of the remark （all text except
coordination）added PDB for 2zan fitted to 2zam were connected, rather than
separated.
Based on what advised by Jared, by increasing the radius to 20 A by pymol, I am
not sure they have the same molecule arrangement in the crystal.
I hope I can get more advice on my question.
Best regards.
Smith
On Thursday, February 2, 2017 12:03 PM, "Sampson, Jared"
<[email protected]> wrote:
Hi Smith -
It seems that you may need to increase the radius of symmetry mate generation.
Looking at these two PDBs after superimposition in PyMOL with symmetry mates
generated within 20Å shows what appear to me as essentially identical lattice
structures.
Also, the symmetry information is not stored in REMARK records, but rather in
the CRYST1, ORIGXn, and SCALEn records
(seehttp://deposit.rcsb.org/adit/docs/pdb_atom_format.html, for example).
Hope that helps.
Cheers,Jared
On Feb 1, 2017, at 10:00 PM, Smith Lee
<[email protected]> wrote:
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. 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.
Thus, will you please explain whi ch 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
