[3dem] Generate BIOMT

[Matthias Wolf]

Hi Elad,

the BIOMT entry contains the transformation matrix with rotation as quaternions in 3x3 matrix format. The 4th column contains the x,y,z translations.

In the classic program O, you can generate the matrix between copies of subunits in any position using the LSQ_EXPLICIT command - for example, to find the matrix for an atom sequence between identical molecules a and b:

lsq_ex
{first_mol_name}
{second_mol_name}
b1 b427
a1
{return}
MATRIX_NAME
write .LSQ_MATRIX_NAME matrix_b_to_a.mat (3f15.8)

The reference molecule has the identity matrix (all zeroes), so it is not rotated or translated.
The x,y,z translations are on the 4th line.
The origin is (0,0,0).
The tricky part is to get the convention right (signs, order of operations, coord system). This is were checking with O is often helpful.
You can transfer the O-derived matrix directly to the BIOMT lines, but the x,y,z translations must go into the last column instead.
Cryo-EM reconstructions are typically centered not at the corner like for X-ray unit cells, but in the center of the box - must update the map header accordingly. You can do this with Gerard Kleywegth's program MAPMAN (using option translate), or - easier - in chimera by changing the origin to center and saving the map.

The CCP4 program PDBSET is also helpful. It can also invert matrices to generate rotation/translation in opposite direction. Actually, I think you can directly generate the matrices with PDBSET using its SYMGEN option by providing the spacegroup. The matrices should be in the log file. Of course, if you already have the NCS operators in matrix format, you may use them directly for your BIOMT. Always check in chimera or O or COOT if the transformations are correct.

There are probably easier options in one of the cryo-EM programs, like in EMAN2.

   Matthias


On Fri, Mar 20, 2020 at 5:45 PM Elad Binshtein <eladbi at gmail.com> wrote:

> Hi All,
>
> How can I generate the PDB BIOMT remark for my model?
> I have the NCS coordinate and the map symmetry.
>
> Thanks.
>
> --
> ________________________________
> Elad Binshtein, Ph.D.
> Cryo-EM specialist - Senior Scientist
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