mdff for EM map with helical symmetry and the asymmetric unit is dimer

From: Zhang Yan (yanzhang_at_moon.ibp.ac.cn)
Date: Thu Jan 17 2019 - 21:28:37 CST

Hi,
I have another question about my MDFF job: How can I deal with the helical symmetry data with asymmetric unit is dimer? Is it necessary for me to merge the two chains in dimer as one chain? I have to prepare the set_symmetry.tcl file. Say I have 9 dimers or 9 asymmetric units in my EM map. How many segname I have to set in the set_symmetry.tcl, 9 or 18? The current way I used is merging each dimer as one chain, and set the segname in the set_symmetry.tcl 9. Any suggestion is welcome.
Thanks a lot.
Yan

The following is my set_symmetry.tcl file:
set selall [atomselect top all]
$selall set occupancy 0
$selall set beta 0
set sel [atomselect top "name CA"]
$sel set occupancy 1
set sel1 [atomselect top "(segname P1) and name CA"]
$sel1 set beta 1
set sel2 [atomselect top "(segname P2) and name CA"]
$sel2 set beta 2
set sel3 [atomselect top "(segname P3) and name CA"]
$sel3 set beta 3
set sel4 [atomselect top "(segname P4) and name CA"]
$sel4 set beta 4
set sel5 [atomselect top "(segname P5) and name CA"]
$sel5 set beta 5
set sel6 [atomselect top "(segname P6) and name CA"]
$sel6 set beta 6
set sel7 [atomselect top "(segname P7) and name CA"]
$sel7 set beta 7
set sel8 [atomselect top "(segname P8) and name CA"]
$sel8 set beta 8
set sel9 [atomselect top "(segname P8) and name CA"]
$sel8 set beta 9
$selall writepdb helix-symmetry.pdb

’Ň—ř
Yan Zhang£¨
Associate Professor£¨
Institute of Biophysics,
Chinese Academy of Sciences

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