(P6(1) or P6(5), not P6!)
On 06/11/2018 10:16 AM, Edward A. Berry wrote:
Hi Yao-Wang,
If I understand the problem correctly, then if you have built two adjacent
molecules, you can superimpose molecule 1 on molecule 2 to get the operator.
Then apply this operator to molecule 2 to make 3, to moolecule 3 to make 4, and
so on around the helix for as far as you want to go. The operator from two
adjacent molecules won't be very accurate, and errors will add up as you go
unless you rigid-body refine each new monomer in the density before using it to
make the next.
The superposition can be done in coot (LSQ-fit) or from command line with LSQMAN or
(LSQKAB?). For applying the operator to one molecule to generate the next, a quick
survey of coot functions shows "new molecule from symop" but that won't help
you in P1. I didn't see an option to use an arbitrary rot/transl matrix, but that doesn't
mean there isn't one. From the command line you would use pdbset to generate
rotated/translated molecules. Then merge them all into one file.
IFF your helix makes exactly one turn in an integral number of steps like
2,3,4,6, or 12, you could re-define your space group as say P6 with the Z axis
equal to the translation for for complete rotation, Then the copies would be
symm-related and could be generated easily in coot.
On 06/10/2018 11:15 PM, [email protected] wrote:
Dear all,
this is my first thread here, and I am not sure this topic was discussed or
not, please tell me if it was.
Coot I thought is originally for density map of crystal, it can work on the
cryo-em map too. I have a cryo-em map of helical filament and try to build a
model. I can build a model based on the monomer, but I am not sure how to
generate the copies based on the symmetry. I think the key problem is how to
determine the rotation center which based on the map, then the roation center
together with the known helical parameters can do it.
suppose we got the rotation center, how to implement these operations in Coot?
Certainly, there is a stuipd way which I already did, that is to copy the
refined monomer multiple times and fit them all together, later were refined
using the Phenix.
another way is try to edit the pdb file directly. rotate and tranlate the
monomer, later change the chain ID.
But I want to do it simplely in Coot, could it possible?
Best Wishes,
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Yao-Wang Li
School of Life Science, Tsinghua University
Room 255, New Biology Building, Beijing, China, 100084
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