 |
 |
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: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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"<[log in to unmask]> >> To: [log in to unmask] >> 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 > > [log in to unmask] > > > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.11 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFPXl8gUxlJ7aRr7hoRAnKIAKC9BiLuWTo8j/NOUkKee1FlcOSULACggsPw > uFJo7bCPaZ2mJ/LQcsxkDKU= > =Wzko > -----END PGP SIGNATURE----- >