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

From: Ryan McGreevy (
Date: Tue Jan 22 2019 - 14:07:55 CST

You should only need to make 9 selections, one for each dimer. However,
make sure your selections are correct, i.e. that "segname P1", etc. are the
actual segnames of the dimers in your structure. If the 'symmetryfile' pdb
is not set up properly, this could result in the simulation hanging at
startup, which you mentioned in another email.

On Thu, Jan 17, 2019 at 10:31 PM Zhang Yan <> wrote:

> 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
> 张艳
> Yan Zhang,
> Associate Professor,
> Institute of Biophysics,
> Chinese Academy of Sciences

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