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<p>Hi Ashok,</p>
<p>Chimera experts may be able to explain you how to calculate coiled-coil radius in the Chimera, nonetheless<span style="font-family: Arial,Helvetica,sans-serif;">, for our purposes we have recently used the program TWISTER (<span style="font-size: 9pt;">Strelkov,
S. V. & Burkhard, P. (2002). </span><span style="font-size: 9pt;">J. Struct. Biol.
</span><span style="font-size: 9pt;">137</span><span style="font-size: 9pt;">, 54–64.</span>) that analyzes various coiled-coil parameters including coiled-coil radius from the pdb coordinate file. You may want to give it a try, it is very easy to use. We summarized
our results in the form of table that you can find i<span style="font-family: Arial,Helvetica,sans-serif;">n the published article Bhardwaj, A., Casjens, SR., Cingolani, G.
<em></em>Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography (2014)
<span role="menubar"><a role="menuitem" href="http://www.ncbi.nlm.nih.gov/pubmed/24531468#" title="Acta crystallographica. Section D, Biological crystallography.">Acta Crystallogr D Biol Crystallogr.</a></span> 2014 Feb;70(Pt 2):342-53.</span></span></p>
<p><span style="font-family: Arial,Helvetica,sans-serif;">You can request the program TWISTER from Sergei V. Strelkov, sergei.strelkov@pharm.kuleuven.be</span></p>
<p><br>
</p>
<p>From TWISTER documentation;</p>
<p><br>
</p>
Program TWISTER (2006 version)<br>
<br>
AUTHOR<br>
Sergei V. Strelkov <br>
e-mail: sergei.strelkov@pharm.kuleuven.be<br>
<br>
PURPOSE<br>
The program TWISTER is designed to analyse the local geometry of coiled-coil (cc) structures. With the three-dimensional coordinates on input, TWISTER first traces the alpha-helical axes and then the cc axis. Thereafter the local cc parameters are determined
as a function of residue number. In addition, heptad positions are assigned based on structural criteria. The current version of the program is designed to analyse
<br>
parallel coiled coils with residue numbering in different chains being in register; however, see a note on antiparallel / out-of-register coiled coils below.<br>
<br>
REFERENCE<br>
Strelkov, S.V., and Burkhard, P. (2002) Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation. J. Struct. Biol. 137, 54-64. Please consult this publication for full description of program function
and definitions.<br>
<br>
DISTRIBUTION<br>
The program executables can be obtained from the author on request. The program is written in standard C programming language.
<br>
<br>
SUPPORTED PLATFORMS<br>
1. Linux: Use the executable tw2006_linux_exe.<br>
2. Windows: You must install the free unix emulator cygwin <br>
(www.cygwin.com) first. Make sure that you have installed <br>
the tcsh shell (available in cygwin but not installed by default). <br>
Then use the tw2006_cygwin_exe.<br>
3. OSX: The current executable tw2006_osx_exe is outdated and<br>
will only run under older versions of OSX.<br>
4. SGI IRIX: Use tw2006_sgi_exe.<br>
<br>
USAGE<br>
Please use a short shell script (see twister_example.sh) to run the program, as running the program directly from command line may not work on all platforms. A sample output from this script with the GCN4 zipper trimer is provided in subdirectory /example.
Please edit this example script according to your needs.<br>
<br>
Input is a standard PDB format coordinate file. It is sufficient to input the C-alpha coordinates only. Within the shell script, the user has to specify which part of the structure to analyse (e.g. residues 101 to 151 of chains A, B and C if these form a triple-stranded
coiled coil). There are two output files. The first one is a log file that contains a table of geometrical parameters versus residue number. In addition, average values of each parameter over all residues and their standard deviations are output. The log
file can be piped into the program XLOGGRAPH which is part of the CCP4 package to produce plots from the tables. Alternatively, any other graphing software can be used. The second output file includes the coordinates of all alpha-helix axes and of the cc axis.
The axes appear as polypeptide chains containing C-alpha atoms only and can be visualised with any biomolecular graphics software such as RASMOL or PyMol.<br>
<br>
DESCRIPTION OF THE LOG FILE<br>
1. Sequence and heptad assignment <br>
TWISTER assigns the heptad positions on the basis of the <br>
structure. First the a and d positions are assigned based <br>
on their proximity to the cc axis. The residues for which <br>
the heptad position could not be assigned are labelled 'z'.<br>
2. Coiled-coil parameters<br>
These are tabulated for every residue with the exception of <br>
the N- and C-terminal residues. <br>
CC_PHASE: cc phase in degrees relative to zero phase at the <br>
first residue.<br>
CC_RAD: local cc radius in A.<br>
CC_RISE: cc rise per residue (measured along the cc axis).<br>
CC_PIT: local cc pitch calculated as 2Pi*CC_RIS/CC_DANG. <br>
If the local cc geometry is right-handed, the pitch value <br>
is followed by a letter 'R'.<br>
CC_DANG: increment of the cc phase per residue. This is <br>
negative for a left-handed geometry and positive for a <br>
right-handed one.<br>
POS: heptad position.<br>
CR_ANG: the angle (first introduced by F. Crick) which <br>
defines the phase of the Calpha atom relative to the cc <br>
axis.<br>
A_RAD: alpha-helical radius.<br>
A_RIS: alpha-helical rise.<br>
RES/TUR: number of residues per one alpha-helical turn.<br>
A_DANG: increment of the alpha-helical phase per residue.<br>
AXIS_CUR: curvature of the alpha-helical axis in 1/A.<br>
3. Crick angles for residues in a and d positions.<br>
4. A table for XLOGGRAPH.<br>
<br>
A NOTE ON ANTIPARALLEL AND OUT-OF-REGISTER COILED COILS<br>
The current version of the program is designed to work on <br>
parallel coiled coils with residue numbering in all chains <br>
being in register. However, both these limitations can<br>
be overcome by renumbering the side chains manually so that<br>
to bring them into register. In an antiparallel structure, <br>
this would require inverting some chain(s).<br>
Here is an example. Suppose you want to analyse a two-<br>
stranded antiparallel coiled coil consisting of residues A1 <br>
to A20 (downward chain) and B51 to B70(upward chain), with <br>
residues A1 and B70 being in register. Then you have to <br>
renumber chain B so that residue B70 becomes B1, B69 <br>
becomes B2 etc. (renumbering Calphas suffices). Thereafter <br>
run TWISTER as follows: <br>
<br>
~/myprogs/twister/twister << eof > $log<br>
$title $infile $outfile 1 20 A B<br>
eof<br>
<br>
The sequence will be read from the first chain listed, in <br>
this case chain A.<br>
<br>
BUGS AND FURTHER DEVELOPMENT<br>
Please report bugs and send your comments and suggestions <br>
to sergei.strelkov@pharm.kuleuven.be<br>
<br>
<span style="font-family: Arial,Helvetica,sans-serif;"></span>
<p>Hope this helps!</p>
<p>Best,</p>
<p>Anshul Bhardwaj<br>
</p>
<p><em></em><br>
</p>
<p><br>
</p>
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<div style="font-family:Tahoma; font-size:13px"><font color="black" size="2" face="Tahoma"><span dir="ltr" style="font-size:10pt"><font size="2" face="Arial">Anshul Bhardwaj, Ph.D.<br>
Faculty, Department of Biochemistry and Molecular Biology <br>
Manager, Kimmel Cancer Center X-ray Crystallography and Molecular Interactions<br>
Thomas Jefferson University<br>
233 South 10th Street, BLSB suite 822 <br>
Philadelphia, PA 19107<br>
Tel: (215) 503-4587<br>
Anshul.Bhardwaj@Jefferson.edu<br>
http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/bhardwaj.html
<br>
http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.htm</font><br>
</span></font></div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> on behalf of ashok rout <ashok9869@gmail.com><br>
<b>Sent:</b> Sunday, April 20, 2014 3:10 PM<br>
<b>To:</b> chimera-users@cgl.ucsf.edu Mailing List<br>
<b>Subject:</b> [Chimera-users] how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix)</font>
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<div>Hi,<br>
</div>
I have a transmembrane domain of a protein (20 amino acid long, single helix). The NMR derived structure comes out as a coiled-coil trimer. So can you please assists me how to calculate the core diameter of this trimer.<br>
</div>
Regards,<br>
</div>
Ashok<br clear="all">
<br>
-- <br>
<div dir="ltr">
<div>thanks & regards,<br>
</div>
Ashok<br>
</div>
</div>
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