Dear Ed, Thanks so much for the suggestion about REFMAC but I seemed to have found out the issue. The positive density on Met sulfurs and backbone carbonyls and amide NHs does not appear when I calculate a "normal" sigmaa weighted mFo-dFc map. The positive density was appearing only when I checked the kicked map option. So the "extra" density seems to be due to generating kicked maps. Sorry about the confusion related to the sigma level. Just meant that the positive density was not insignificant in the kicked mFo-dFc maps. Density was visible on these specific areas starting around 3.5-4.0 sigma and visible in several places contoured up to 8 sigma. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________ On Dec 20, 2010, at 12:00 PM, [email protected] wrote:

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Today's Topics:

1. ADP restraints - distance power, average power, etc (Joseph Noel) 2. Re: ADP restraints - distance power, average power, etc (Ralf W. Grosse-Kunstleve) 3. Re: ADP restraints - distance power, average power, etc (Pavel Afonine) 4. Secondary structure restraints - where to specify file using GUI? (Luke Rice) 5. Re: Secondary structure restraints - where to specify file using GUI? (Nathaniel Echols) 6. Re: ADP restraints - distance power, average power, etc (Joseph Noel) 7. Re: ADP restraints - distance power, average power, etc (Joseph Noel) 8. Re: ADP restraints - distance power, average power, etc (Ed Pozharski) 9. Re: Secondary structure restraints - where to specify file using GUI? (Luke Rice)

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Message: 1 Date: Sun, 19 Dec 2010 12:58:43 -0800 From: Joseph Noel To: [email protected] Subject: [phenixbb] ADP restraints - distance power, average power, etc Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii"

Hi All,

I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?

I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.

Thanks!

Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA

Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected]

Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________