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wxu for anisotropic ADP refinement
by Joseph Noel 12 Aug '10

12 Aug '10

Dear Phenix User Community, If one would like to try different weights for anisotropic ADP refinement (ie fixing wxu) should one be focusing on numbers like - wxu = 199.878301 - instead of the usual low numbers such as - wxu = 0.25 - found during isotropic ADP refinement? While optimize X-ray/ADP weight is useful in phenix, I am still getting anistropic ADP values that are a bit outside what one might expect at 1.5 A compared to the PDB. For the latter, I check things using Parvati (http://skuld.bmsc.washington.edu/parvati/). 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: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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difference in estimated error between phenix and refmac
by Ling Qin 12 Aug '10

12 Aug '10

Dear Colleagues, I am refining a 2.15 A structure that was previously refined with refmac by someone else. Without changing anything in the refmac-refined model and using all the default phenix.refine settings, I am getting pretty much the same R and Rfree (from 19.3%/21.7% to 18.9%/21.8%), with an ML estimated error of 0.22 A. In the refmac-refined pdb file, the estimated error is much lower: 0.16 (based on R), 0.144 (based on Rfree), and 0.096 (based on ML). I am using phenix.refine version 1.6_289, but also tried 1.5_2 with the same result. Is there an underlying reason for this difference? Thank you very much for your insightful opinions in advance. Cheers, Ling

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autosol
by Abd Ghani Abd Aziz 12 Aug '10

12 Aug '10

Dear All, Just been trying to run autosol for SAD data with the new phenix (1.6.4-486) on ubuntu, but I get an error message: *********************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked ********************************************************************** xtriage appears to run OK, and I get the same error with unmerged or merged scalepack data. The same files in 1.6-289 (admittedly on OSX) work fine. I wonder if there is a known problem with this version of phenix? Thanks for any suggestions, Ghani

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Disappearing density?
by Kyle Dolan 12 Aug '10

12 Aug '10

Hi all, I attempted to improve the density around a helix and short linker region using an average kick map but it didn't make things look much better. I then tried creating a composite iterative-build omit map from phenix.autobuild, but in this case the electron density around the helix/linker in question largely disappeared! Is there another approach I can use that might improve my maps, or should I start questioning my data? The dataset has >95% completeness to 2.7 A so I am very curious as to why I am missing the backbone now, where before I was only missing the side chain densities. One thing I am wondering is if the problem could have something to do with symmetry; the part of the map I am looking at may be close to a two-fold crystallographic symmetry axis and I have been told that these regions tend to be very noisy and hard to model--comments? Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

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Statistics for pdb deposition
by Elwood A. Mullins 11 Aug '10

11 Aug '10

I apologize if this has already been addressed. I'm trying to deposit a model to the pdb database, but there are a few required values in the Refinement Statistics section that I'm not sure where to find. 1,2) Cut-off sigma (F), Number unique reflections (observed) Looking at the log file, it appears that the cut-off is 0, which results in 330 reflections being rejected. The pdb header, however, lists the number of reflections at a value corresponding to 352 reflections being rejected. Why are these numbers different and which should I report? 3) R-factor (all) R-factor (all) includes both the working and test sets in addition to reflections rejected by the sigma cut-off. Does PHENIX calculate this value? I know R-factor (observed), which includes the working and test sets but not rejected reflections, is calculated. Thanks, Elwood

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elbow: more detailed website : 404
by Lepore, Bryan 11 Aug '10

11 Aug '10

this link : http://www.phenix-online.org/elbow/docs/index_image.html is 404 the link is found on this page : http://www.phenix-online.org/documentation/elbow.htm ... IS there a "more detailed website"? i saw the reel site. -bryan

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Random seeds?
by Joseph Noel 10 Aug '10

10 Aug '10

Hi All, Okay, a fairly mundane question concerning random seeds in Phenix. Obviously they are random but any restrictions on how many digits phenix will accept? Any other restrictions? Are they (it) only used for coordinate refinement or do the random seeds get used for other things as well? I know about hydrogen building but wandering about other refinement protocols and the use of "new" random seeds. I realize some use different random seeds to create slightly different models after refinement. Is it useful to change the number from time to time when going through iterative rounds of re-building and coordinate refinement? What about ADP refinement? Sorry for the mundane questions! 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: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Restraint creation for ligand
by Hermella Woldemdihin 10 Aug '10

10 Aug '10

Hi! I was trying to fit my ligands into my model and density. And I have successfully fitted 2 ligands (same molecule) but my 3rd ligand is different molecule. After fitting my 3rd ligand (with COOT) and merged it with my protein, II created a restraint file with: phenix.elbow my_model_coot-0..pdb --do-all --output=all_ligands It created all_ligand.cif, which I used for in my next refinement with Phenix (GUI). I supplied my density, model and the restraint file and run phenix.refine. Unfortunatate I'm getting this error message when it starts to run phenix.refine and opening COOT window: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 1 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. I have use the same procedure for fitting my first 2 ligands. and it worked. But this time it failed! What do you think I should do? Thanks Hermi

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monomer-dimer
by intekhab alam 10 Aug '10

10 Aug '10

Hi everyone Sorry for some non specific query!!!!! i am working with a protein that shows a dimer in the crystal structure but when i tried to figure out that with standard molecular markers in gel filteration (superdex-200, 24ml column) it turned out to be a monnomer. Native gel analysis after incubating the protein at 20 degree, 37 degree showed more dimer at 20 degree celcius as compared to 37. I tried similar strategy in gel filteration by incubating my protein at various temperature,where a lot of precipitation was observed at 37 degree celcius and after removing the precipitates i run the gel filteration that has 0.5 ml higher elution volume as compared to samples incubated at 20 degree celcius and 4 degree celcius.( Is this significant) Furthermore i have done some experiments in cold room (4 degree) where the elution volume is stuck at a point irrespective of the conditions (as Flow rate, concentration of protein etc) and that is higher than that of the room temperature by 1 ml. Standard moleculr weight markers also show higher elution volume in cold room in comparison to the room temperature by 1 ml. I will be highly obliged if someone suggest some literature or any otherway to do gel filtrtaion so that i can clearly resolve this issue. Also let me know if there is some literature available on effect of temperature on the elution volume of proteins. Thanks in advance -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Phenix reflection statistics
by Lepore, Bryan 07 Aug '10

07 Aug '10

in this table : Overall correlation: 0.901 unused: - 16.7088 [ 0/9 ] bin 1: 16.7088 - 2.0456 [5236/5928] 0.858 bin 2: 2.0456 - 1.6241 [5610/5946] 0.744 bin 3: 1.6241 - 1.4189 [5539/5925] 0.641 bin 4: 1.4189 - 1.2892 [5357/5873] 0.516 bin 5: 1.2892 - 1.1969 [5405/5972] 0.497 bin 6: 1.1969 - 1.1263 [5241/5939] 0.464 bin 7: 1.1263 - 1.0699 [5067/5903] 0.408 bin 8: 1.0699 - 1.0234 [4960/5934] 0.416 bin 9: 1.0234 - 0.9840 [4808/5941] 0.376 bin 10: 0.9840 - 0.9500 [4700/5931] 0.348 unused: 0.9500 - [3339/6874] 0.330 the average CC is 0.508 +/- 0.17 if y is the correlation, and x is bin number, and 0.330 is excluded, that line fits with a CC=-0.941 (therefore R^2=0.885) is the median resolution per bin used for the overall CC? how is "unused" treated? -bryan

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