July 2011 - phenixbb - phenix-online.org

Summer X-rays at the NSLS
by Robert Sweet 12 Jul '11

12 Jul '11

Summer X-rays at the NSLS The PXRR operates five beamlines at the NSLS: http://www.px.nsls.bnl.gov/. Two of these are the undulator beamlines X25 and X29. The dipole beamlines X12-B and X12-C are available, and are very effective for conventional crystallography. There are efficient ALS-Style Automounters available -- 8400 crystals mounted in the last 12 months. Also, at beamline X26-C, we have a unique-in-the-US station for combined x-ray diffraction and single-crystal optical spectroscopies: http://www.px.nsls.bnl.gov/x26c/x26c_info.html Notice also our world-leading Mail-In crystallography program: http://www.px.nsls.bnl.gov/Mailin.html You may request access to any of these here: http://www.px.nsls.bnl.gov/beamtime_requests.html, and can look at the schedules for all five here: http://www.px.nsls.bnl.gov/ Stay tuned for the announcement in December of RapiData, our annual course in rapid data collection and structure solving: http://www.bnl.gov/rapidata/ Bob Sweet ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

11 19

significant figures in reporting Rfree
by Jennifer Weinreich 12 Jul '11

12 Jul '11

Hi. I am wondering what is the common practice with respect to how many significant figures should be used for reporting Rfree at different resolution? Should we always use all 4 figures that are reported by the program? Thank you, Jenn

4 4

How to rebuild a molecular only‏
by dingding830106＠sina.com 09 Jul '11

09 Jul '11

Dear All, There are 8 moleculars in an asymmetry unit, but only one molecular should be rebulit, what can I do ? Thanks a lot! Wei Feng

2 1

Re: [phenixbb] Elbow and smiles to make CO coordinates
by Yarrow Madrona 09 Jul '11

09 Jul '11

Thanks! Didn't realize it was so easy. > For getting carbon monoxide coordinates: In coot, go to File > Get > Monomer... > Type in "CMO" and click OK. > > A carbon monoxide molecule will po up in the middle of the window > (provided everything is set up correctly). > > If you are trying to fit an electron density, place that density in the > middle of the window before you retrieve the ligand. > > Hope that helps. > > Cheers! > MM > > On Jul 8, 2011, at 1:41 PM, Yarrow Madrona wrote: > >> >> Hi, >> >> I am trying to use Elbow and smiles to generate carbon monoxide >> coordinates. I thought it would be easy enough. I made two waters in >> coot >> and changed the the oxygens to C and O and set the distance around 1.13 >> angstrom. Saved these coordinates as a PDB. I then used this in Elbow >> but >> it gives me a methyl group. Not sure what is going on. Any help would >> be >> appreciated. Thank you! >> >> -Yarrow >> >> -- >> Yarrow Madrona >> >> Graduate Student >> Molecular Biology and Biochemistry Dept. >> University of California, Irvine >> Natural Sciences I, Rm 2403 >> Irvine, CA 92697 >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

1 0

Elbow and smiles to make CO coordinates
by Yarrow Madrona 09 Jul '11

09 Jul '11

Hi, I am trying to use Elbow and smiles to generate carbon monoxide coordinates. I thought it would be easy enough. I made two waters in coot and changed the the oxygens to C and O and set the distance around 1.13 angstrom. Saved these coordinates as a PDB. I then used this in Elbow but it gives me a methyl group. Not sure what is going on. Any help would be appreciated. Thank you! -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

3 2

AutoSol question
by Laurie Betts 08 Jul '11

08 Jul '11

If I want to run Autosol with a set of previously determined heavy atom positions (seleno-Met protein) that I might have edited, and NOT search for any more sites, just use those sites for phasing and density modification and model building, I can't seem to find in any of the parameter buttons a way to do this - every time I try it seems to just re-run hyss and find the same sites again. It seems to find multiple Se sites on top of each other that are closer than the minimum distance I specified in the input. Thanks LAurie Betts

2 1

NCS Question
by Yuri 08 Jul '11

08 Jul '11

Dear PHENIX community, Could someone please point me toward a good paper on NCS? Cheers, -- Yuri Pompeu

3 2

SA omit map
by Tjaard Pijning 07 Jul '11

07 Jul '11

Hi, I would like to generate an SA-omit Fo-Fc map for a ligand bound to protein. Using the GUI I selected the AutoBuild-Create Omit Map module and set the following : - data.mtz - protein.pdb (no ligand, no solvent) = start model - ligand.pdb (just ligand) = omit map atoms - omit map type = simulated annealing - omit region = omit around pdb The resulting map (/OMIT/resolve_composite_map.mtz) shows density for both the protein and the ligand. When I feed this into the CCP4 module FFT to generate an nF1-mF2 map (with n=1 and m=1) I still get density for both the protein and ligand. However I need only the ligand Fo-Fc density. What is the right way to do this ? Thanks, Tjaard Ing. Tjaard Pijning Research Assistant Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85

4 6

Re: [phenixbb] phenix.mr_rosetta: Inconsistent query numbering
by Thomas C. Terwilliger 06 Jul '11

06 Jul '11

Hi Pietro, There is something that phenix.mr_model_preparation cannot read in Japanin.hhr (attached): phenix.mr_model_preparation Japanin.hhr gives the same error. I'll copy Gabor Bunkoczi and see if he can help with this. All the best, Tom T >> Dear all, >> >> my run of phenix.mr_rosetta stops with: >> >> ******************* ERROR ENDING *************** >> Inconsistent query numbering >> >> ******************* ERROR ENDING *************** >> >> I attach script and logfiles. >> >> Any suggestions? >> >> Thanks >> >> Pietro >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

3 2

Validation question: R-factor (all) and # of unique reflections (all)
by Young-Jin Cho 06 Jul '11

06 Jul '11

Hi everyone, While I am trying to deposit, I am faced with several things that I am not sure: FYI. I am in the <Refinement Statistics> section (Auto Dep Input Tool) in the PDB bank. Most values are came from pdb file that was made from phenix.refine but it asks me "R-factor (all)" that satisfy the limits established by high & low resolution cut off and "number of unique reflections (all)". My simple question is if phenix has those kind of information, if so where I can find them. Another question is if I changed water (deletion or changed occupancy) based on 'precheck', should I run phenix.refine again to get R/Rfree values in correct? I am not sure if these are captured by PDB automatically or not. (seemingly they do like that at this point but not 100% sure yet.) With many thanks~ Young-Jin

4 3