*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
I omitted to say that the Carugo and Bordo split their analysis into cryo and room temperature. As you hint, the latter are more numerous (873 against 33). But both give effectively zero at 3.5A, though standard error is larger for cryo obviously. At higher resolutions, there are slightly more waters for low temperature, but not a doubling. But this is what people do, not what they can do. Cheers Martyn On Fri, 31 Mar 2006, Bart Hazes wrote: > > A lot of the structures analysed by Carugo and Bordo were done at room > temperature. We and others found that you see about double the number of > waters in cryo-structures and at least in the 1.8 to 0.8 Angstrom range > we didn't see the number increase much, at least not for first shell > waters. I don't know how this holds up at moderate resolution, but at > low resolution it remains in my opinion hard to convincingly prove there > is a water. After all if Carugo and Bordo predict zero waters at 3.5 A > and more recent data suggests there are twice as many at 100K then that > still amounts to zero waters. > > Bart > > PS: other effects of cryo cooling can be found in > Dunlop et al. (2005) Pros and cons of cryocrystallography: should we > also collect a room-temperature data set? Acta Cryst D61, 80-87. > > Martyn Winn wrote: > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > > > The analysis of Carugo and Bordo, Acta Cryst D55, 479 (1999) > > as implemented in the CCP4 program RWCONTENTS, suggests > > that you shouldn't see any waters at 3.5A. > > > > Their analysis was based on PDB structures, so this just > > confirms your own observations. And it is therefore based > > on working practice rather than any explicit justification. > > > > Of course, this is only a guide, and doesn't preclude > > identifying e.g. well-defined conserved water sites. > > > > Cheers > > Martyn > > > > On Thu, 30 Mar 2006, Prem kumar wrote: > > > > > >>*** For details on how to be removed from this list visit the *** > >>*** CCP4 home page http://www.ccp4.ac.uk *** > >> > >> > >>Dear all, > >> > >>I am refining structure at 3.5 A resolution. the > >>protein has 340 residues. CNS water_pick gave me 80 > >>water molecules. out of that ~50 are in resonably good > >>density. when i go through PDBs at this resolution > >>many people didnt add water. my question is, can I add > >>water molecules in this resolution, or upto what > >>resolution. please quote if any reference regarding > >>this case. > >> > >>Thanks in advance! > >> > >>with regards > >>prem > >> > >> > >> > >>====================================================== > >>R. Prem kumar > >>Research Scholar, > >>Department of Biophysics, > >>All India Insitute of Medical Sciences(AIIMS), > >>New Delhi-110029. > >>INDIA > >>Phone: +91-11-26593201, 9810304855 > >>====================================================== > >> > >>__________________________________________________ > >>Do You Yahoo!? > >>Tired of spam? Yahoo! Mail has the best spam protection around > >>http://mail.yahoo.com > >> > > > > > > > > > > ************************************************************************** > > * * > > * Dr. Martyn Winn * > > * * > > * Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND * > > * Tel: +44 1925 603455 E-mail: [EMAIL PROTECTED] (personal) * > > * Fax: +44 1925 603825 E-mail: [EMAIL PROTECTED] (CCP4 problems) > > * > > * URL: http://www.ccp4.ac.uk/martyn/martyn.html * > > ************************************************************************** > > > > > > > -- > > ============================================================================== > > Bart Hazes (Assistant Professor) > Dept. of Medical Microbiology & Immunology > University of Alberta > 1-15 Medical Sciences Building > Edmonton, Alberta > Canada, T6G 2H7 > phone: 1-780-492-0042 > fax: 1-780-492-7521 > > ============================================================================== > ************************************************************************** * * * Dr. Martyn Winn * * * * Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND * * Tel: +44 1925 603455 E-mail: [EMAIL PROTECTED] (personal) * * Fax: +44 1925 603825 E-mail: [EMAIL PROTECTED] (CCP4 problems) * * URL: http://www.ccp4.ac.uk/martyn/martyn.html * **************************************************************************
