My memory is not as good as it used to be, but I think that I indeed got
the number of 140 cubic Angstroms per amino-acid from Kevin. It has
worked fine ever since, and is how hkl2map calculates the solvent
content for proteins.
George
On 12.03.2012 21:40, Tim Gruene wrote:
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The number 380A^3/base I gave results from a decent number of nucleic
acids-only PDB files I once analysed with the 'volume' program from
ccp4. I cannot think of an application where knowing the solvent content
must be known to more than 1%, so I bet this number is fine for any such
purposes.
I got the number 140A^3/a.a. from George Sheldrick who told me where he
got this number from, but I do not remember for sure - it could be Kevin
Cowtan, but George may update my memory in order to pay proper credit.
Cheers,
Tim
On 03/12/2012 08:48 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
I can't imagine the results would be very different for protein-DNA vs.
protein-RNA.
The reason protein-nucleic acids is an extra category in mattprob is largely
due to poorer statistics
resulting from limited sample size and hence no reliable resolution dependence
can be computed.
In addition the partial specific volumes for protein (0.74 cm3/g) and nucleic
acids (0.50 cm3/g) are
different, so an exact calculation needs to consider their ratio to obtain the
correct psv estimate
BR
----- Original Message -----
From: "Tim Gruene"<t...@shelx.uni-ac.gwdg.de>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, March 12, 2012 11:07:29 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] Matthews coeff. from model
Dear James,
I do not know such a tool, but you can use 140A^3/a.a. and 380A^3/base to
calculate the solvent content by hand.
Regards,
Tim
On 03/12/2012 06:35 PM, james09 pruza wrote:
Dear CCP4bbers,
Is there any tool to calculate the Matthews coefficient from a
crystallographic model of RNA-protein complex?
Thanking you.
James.
- --
Michael C. Thompson
Graduate Student
Biochemistry& Molecular Biology Division
Department of Chemistry& Biochemistry
University of California, Los Angeles
mi...@chem.ucla.edu
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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