creating a symmetric tetramer from a PDB file for a monomer?
Dear Chimera creators: Could you please let me know whether it is possible to create a tetramer structure with 4-fold symmetry from a PDB file for a monomer? Specifically, I want to create a structure of a voltage-gated K channel which has 4 monomers surrounding a central pore symmetrically, beginning with the PDB file for a monomer. There is no 'transformation matrix' in the PDB file to allow me to create the tetramer easily. Thank you very much for your help!
Gea-Ny Tseng
Hello Gea-Ny, The Chimera features that generate multimers (the tools Unit Cell and Multiscale Models) all use matrix information in the PDB file. Multiscale Models uses BIOMT, MTRIX, SMTRY, and/or CRYST1 records, and Unit Cell uses MTRIX, SMTRY, and/or CRYST1.
It sounds like you don't have any of those in your PDB file.
You could either (A) figure out what information should be in such a matrix line and edit it into your file before using one of the Chimera tools, or (B) open four copies of your monomer and try to position them by hand. If you know what the axis of rotation should be, you can use Constrained Move (Tools... Movement... Constrained Move in recent versions) to define and use an axis of rotation. http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ constrained/constrained.html
Neither of these is very easy, but I don't know of any way to automatically position the monomers without the matrix information. It sounds like BIOMT (REMARK 350) records would be the most appropriate. Even with an appropriate example, you would still have to change the values.
REMARK 350 is described at the PDB web site (you have to scroll down to get to the description of REMARK 350): http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_31.html
Here is an example from 1fav (threefold): REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.81900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 17.90950 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.02016 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Sep 6, 2005, at 12:53 PM, gtseng@mail2.vcu.edu wrote:
Dear Chimera creators: Could you please let me know whether it is possible to create a tetramer structure with 4-fold symmetry from a PDB file for a monomer? Specifically, I want to create a structure of a voltage-gated K channel which has 4 monomers surrounding a central pore symmetrically, beginning with the PDB file for a monomer. There is no 'transformation matrix' in the PDB file to allow me to create the tetramer easily. Thank you very much for your help!
Gea-Ny Tseng _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Gea-Ny,
Elaine's comments are right. But there might be an easier way to generate the potassium channel tetramer. If the tetramer appears in the crystal from which the monomer structure was obtained you can use the Chimera Unit Cell or Multiscale tools to get it. Generating the unit cell only requires the CRYST1 PDB record, a one line record describing the crystal symmetry group and unit cell parameters. That line appears in all files from the PDB web site. If the tetramer is not found in the crystal then it may be a non-trivial task to determine the correct 4 matrices to build a tetramer from a monomer.
If your K channel monomer is deposited at the PDB I can investigate if you send me the PDB identifier.
Sorry for the delayed reply. I was on vacation and at a workshop the past week and a half.
Tom
participants (3)
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Elaine Meng -
gtsengļ¼ mail2.vcu.edu -
Thomas Goddard