VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sat Sep 20 2014 - 03:17:42 CDT

Hi Brian,

You've input the matrices correctly, and the positions of each monomer are coming out correct... just in different unit cells. To be honest, I don't know enough crystallography to know why the operators are written out that way, but that's how it is.

To check this for yourself, set your PBC box to the dimensions of the unit cell by entering

pbc set {33.95 33.95 74.82} -all -molid top

and then in the Graphical Representations box click the Periodic tab and check all the checkboxes.

So you're most of the way there - all you have to do now is work out the translations to bring them all back to the same unit cell.

Cheers,

Tristan

Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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On 20 Sep 2014, at 3:05 am, "Bennion, Brian" <Bennion1_at_llnl.gov<mailto:Bennion1_at_llnl.gov>> wrote:

Hello,

I posted a similar question a few years back and was directed to the mono2poly tcl script.

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19379.html

I would like to add onto this discussion as recent work forced my to look at this again.

Using the mono2Poly script appears to work as written for expanding out the structure of the asymmetric unit to the biologically relevant assembly.

Now, if i wanted to recreate the unit cell I should be able to use the same type of matrix operations with the symtry records in the pdb file as found in the remarks 290 section. The unit cell has dimensions 33.95 33.95 74.82.

Initially I just modified the mono2poly.tcl to search for the symtry string to populate the matrices. In my case I was using 2FDN which has a single chain in the asymmetric unit but is a 8mer in the unit cell. So there are 8 symtry operations found by mono2poly.
The resulting structure of the unit cell is wrong.

So I try it by hand and entered a few of the symtry operations into matrices sym[1-8] and used the $all move $sym[1-8] commands to update the coordinates.

example:
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 37.41000

set sym8 {{0.0 -1.0 0.0 0.0 } { -1.0 0.0 0.0 0.0} { 0.0 0.0 -1.0 37.41 } { 0.0 0.0 0.0 1.0 }}

I was only able to replicate what the mono2poly script had done previously.
Attached is an image that compares what chimera outputs and what the mono2poly script outputs.

Did I create the matrices incorrectly?

Brian

<unitCellCalcs.png>