Re: [ccp4bb] Matthews coeff. from model
rwcontents xyzin my.pdb Eleanor It will not be able to guess the number og H atoms associated with the RNA so the answer will be a bit out. Eleanor On Mar 12 2012, 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. -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] Matthews coeff. from model
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" 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 -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-
Re: [ccp4bb] Matthews coeff. from model
-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" > 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 -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-
Re: [ccp4bb] Matthews coeff. from model
Is there a difference in the psv between DNA and RNA? I assumed (possibly incorrectly) that they would be very close if not exactly the same? Is mattprob more applicable to protein-DNA complexes than Protein-RNA complexes? Thanks for the insight, Mike - Original Message - From: "Bernhard Rupp (Hofkristallrat a.D.)" To: "Michael Thompson" , CCP4BB@JISCMAIL.AC.UK Sent: Monday, March 12, 2012 12:48:42 PM GMT -08:00 US/Canada Pacific Subject: RE: [ccp4bb] Matthews coeff. from model > 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" 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 -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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. >> > - -- 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/ iD8DBQFPXjthUxlJ7aRr7hoRAqPSAJ0Zr7H/Zt0w8TnaJvHsc5g5mZbZngCcCTEC inwbgapeZ+O0jfc20pMVS/M= =0cVz -END PGP SIGNATURE- -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] Matthews coeff. from model
> 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" 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 -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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. >> > - -- 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/ iD8DBQFPXjthUxlJ7aRr7hoRAqPSAJ0Zr7H/Zt0w8TnaJvHsc5g5mZbZngCcCTEC inwbgapeZ+O0jfc20pMVS/M= =0cVz -END PGP SIGNATURE- -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] Matthews coeff. from model
James, For a detailed analysis of Matthews coefficients (Matthews probabilities), you can use this web-based tool: http://www.ruppweb.org/Mattprob/ There is a pull-down menu to select the sample type, and one choice is "protein-DNA complex." Perhaps someone can correct me if I'm wrong, but I can't imagine the results would be very different for protein-DNA vs. protein-RNA. Also, if you already have a crystallographic model, as you say you do, then you know how many molecules are in the ASU and you could calculate it by hand : Vm = (volume of unit cell)/(molecular weight of all unit cell contents) Good luck, Mike - Original Message - From: "Tim Gruene" 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 -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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. >> > - -- 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/ iD8DBQFPXjthUxlJ7aRr7hoRAqPSAJ0Zr7H/Zt0w8TnaJvHsc5g5mZbZngCcCTEC inwbgapeZ+O0jfc20pMVS/M= =0cVz -END PGP SIGNATURE- -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] Matthews coeff. from model
... or rwcontents ? -- Ian On 12 March 2012 17:35, 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. > >
Re: [ccp4bb] Matthews coeff. from model
matthews_coef ? -- Ian On 12 March 2012 17:35, 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. > >
Re: [ccp4bb] Matthews coeff. from model
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 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. >> > - -- 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/ iD8DBQFPXjthUxlJ7aRr7hoRAqPSAJ0Zr7H/Zt0w8TnaJvHsc5g5mZbZngCcCTEC inwbgapeZ+O0jfc20pMVS/M= =0cVz -END PGP SIGNATURE-
Re: [ccp4bb] Matthews coeff. from model
Dear CCP4bbers, > > Is there any tool to calculate the Matthews coefficient from a > crystallographic model of RNA-protein complex? > > Thanking you. > James. >
