[3dem] density threshold calculator

Michael Radermacher mraderma at uvm.edu
Wed May 18 08:57:14 PDT 2011


Just a remark, when using a program that determines the threshold  
given a specific volume, one must not forget that, depending on  
resolution, the true molecule envelope may enclose a larger volume  
than defined by the molecular mass. A smaller volume may also be  
possible, but I have never observed this.

Michael



Quoting Carlos Oscar Sánchez Sorzano <coss at cnb.csic.es>:

> Dear Joanna,
>
> you may find useful the program xmipp_volume_segment
> (http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Segment). If you need to
> incorporate it into your own program, the source code is accessible.
>
> Kind regards, Carlos Oscar
>
> On 17/05/2011 16:57, Joanna Kasprzak wrote:
>> Hi,
>>
>> Could you please tell me is is possible to calculate a density threshold
>> value
>> for a particular complex volume?
>>
>> Eg. Complex A has a volume of 120 000 A3 and I want to know a density
>> threshold value of a density map which will describe me a shape
>> corresponding to
>> this volume?
>>
>> Ideally I would like to find a method/algorithm easy to
>> implement/incorporate with my computer program?
>>
>> Looking forward to hearing from you. Thanks for any help in advance!
>>
>> best regads,
>>
>> Joanna
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>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>
>
> -- 
> ------------------------------------------------------------------------
> Carlos Oscar Sánchez Sorzano                  e-mail:   coss at cnb.csic.es
> Biocomputing unit                             http://biocomp.cnb.csic.es
> National Center of Biotechnology (CSIC)
> c/Darwin, 3
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-- 
Michael Radermacher, Ph.D., Prof.
University of Vermont
Dept. Molecular Physiology and Biophysics
HSRF 120 / 149 Beaumont Ave
Burlington, VT 05405
USA

Tel: + 802 656-4834
Fax: + 802 656-0747



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