Re: [ccp4bb]: measure circumference

[Richard Gillilan <reg8@cornell.edu>]

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This is an interesting problem that my XTM Crystal Modules
package might be able to handle.  XTM is a set of add-on
molecular modelling and crystallography modules
for the free, open-source visualization package OpenDX (www.opendx.org)
I haven't formally announced their availability mainly because I have no 
time
or funding to support external users. If you are interested, I might be 
able to
try a quick experiment however. My suggestion would be to intersect a
molecular surface with a plane and measure the circumference of the
resulting curves using the Measure module. The complication is that 
molecular
surfaces contain internal cavities. You would have to get rid of them by 
either
choosing a large solvent probe radius or some other method.

For those who are interested in trying something different,
XTM can be downloaded from bridgedec.chess.cornell.edu via anonymous
ftp.  There is some basic support for viewing and indexing 
crystallographic data via DPS,
but the package's main use is molecular modeling. You can download some 
of the movies
I have made with it from my web site 
(www.staff.chess.cornell.edu/~richard). Most recently
using it to process SAXS data. Readers for CCD images,  CNS-style 
electron density maps
and coordinate formats (pdb, mol2) are available. The package requires 
OpenDX (www.opendx.org), which is a separate installation.  
Alternatively, XTM is available on CD by Visualization and Imagery 
Solutions Inc. (www.vizsolutions.com) as part of their well-maintained 
OpenDX distro. The package runs on Linux, MacOS X, Windows (untested), 
DEC, SGI and other Unix platforms.  I'll put out a more complete 
official announcement sometime this Fall when the code goes up on
public CVS.

Richard Gillilan
MacCHESS, Cornell


>> Jianghai Zhu wrote:
>>>
>>> ***  For details on how to be removed from this list visit the  ***
>>> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>>>
>>> Ok, my dimer is not a perfect sphere. Let's say I want to wrap a rope
>>> around my protein in a certain orientation. What word should I use 
>>> for that
>>> distance instead of circumference? And which program can measure that
>>> distance?
>>>
>