- phenixbb - phenix-online.org

(no subject)
by John Pascal 03 Dec '09

03 Dec '09

Hello, I am looking for advice on how to best refine the structure of a complex that has one component that can adopt two completely different conformations (a DNA duplex). I can model both conformations and set occupancies to 0.5, and try to constrain_group their occupancies, but in phenix.refine the two conformations are interpreted as major clashes. Thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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P32 twin or p3221?
by lauren 03 Dec '09

03 Dec '09

Hi everyone, I have a dimmer protein diffract to 1.6 A resolution. After processing the data, the Linear R-fac was 0.26/0.038 (last/all), the data quality seems good. This data can be processed to P3 or P321 with the R-fac almost the same After that, I used Bales to do the MR, two solutions were found in P32 (dimmer) and one in P32 21 (monomer) Then, I refine the structure using phenix.refine in both P32 and P32 21 sets, but the R/Rfree stopped at 0.19/0.25 and never goes down. Rfree 25% seems a little bit too high for a 1.6 resolution data. However, if I treat the P32 data as a twin (with twin law h,-h-k,-l ), the R/Rfree can down to 0.12/0.18. I use P3 to run the phenix.xtriage (see bellows), it looks like the L-test says it is not a twin data. So, I am wondering is it a twin data or not? The results are as follow. "Twinning and intensity statistics summary (acentric data): --------------------------------------------------------------------------- Statistics independent of twin laws - <I^2>/<I>^2 : 2.105 - <F>^2/<F^2> : 0.773 - <|E^2-1|> : 0.757 - <|L|>, <L^2>: 0.508, 0.344 Multivariate Z score L-test: 2.013 Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.484 | -0.003 | 0.022 | 0.022 | | h,-h-k,-l | M | 0.026 | 0.454 | 0.479 | 0.478 | | -k,-h,-l | M | 0.507 | -0.004 | 0.026 | 0.022 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 8.386 (corresponding p value : 0.29163) The largest off-origin peak in the Patterson function is 8.39% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. Even though no twinning is suspected, it might be worthwhile carrying out a refinement using a dedicated twin target anyway, as twinned structures with low twin fractions are difficult to distinguish from non-twinned structures. The correlation between the intensities related by the twin law h,-h-k,-l with an estimated twin fraction of 0.45 % is most likely due to an NCS axis parallel to the twin axis. This can be verified by supplying calculated data as well." Thanks! Lauren

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High B Factors
by Miles Pufall 03 Dec '09

03 Dec '09

Hello All - I am working on a kinase:inhibitor complex with some interesting properties. First, it is a long, thin unit cell (45x45x300) that has highly anisotropic B-factors (60 in two dimensions and 35 in the other according to xtriage). We had a fair amount of trouble collecting data for these complexes due to somewhat high mosaicity (1.5) and overlap trouble, mostly due to the long unit cell. As a result, although we get diffraction out to ~2.3 A with good signal (I/sigma of 3), the completeness is only OK - dropping off from a high of 95% around 3.5 A pretty much linearly to 75% at 2.3. As a result, the maps look only OK for 2.3A data, but clearly show the interactions between the inhibitor and the kinase that we are looking to define. In that sense, the experiment worked just fine. That said, the structure looks pretty good, although about 1/3 shows poor density for sidechains, which I wouldn't expect at this resolution. But as I put the finishing touches on the structure a couple of things have worried me - first, there is consistently a larger than average gap between R and Rfree (Typically in the R~22 and Rfree~29). This, according to Polygon, is within the range of reported structures, so I think that's OK. What is odd is that despite having an average B caluclated from the reflection of ~50, the average B after refinement is ~80, which is very much on the high end of what has been reported. I have played around a lot with the wxc/wxu balance, and although this can change the Rs and tends to tighten the geometry perhaps inappropriately (rms bond ~0.003, rms angle ~0.7), the B factors stay very high. My question is, should I worry about this? And if so, what can you recommend trying. As usual, I'm happy to provide data if it help elucidate the problem. Thanks in advance - M Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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Atom Selection for Conformers
by John Pascal 02 Dec '09

02 Dec '09

Hello, What is the syntax for selecting one conformer of a residue? for example, if there are two arginine alternate conformations labeled A and B, how do you select just one of them. Thanks. Best Regards, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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phenix server upgrade
by Ralf W. Grosse-Kunstleve 01 Dec '09

01 Dec '09

Over the weekend we've moved the phenix web server and mailing list to new hardware. If you notice any problems with the web content, the downloads, or the mailing list, please let us know. Ralf

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Re: [phenixbb] sigma cutoff
by Kay Diederichs 30 Nov '09

30 Nov '09

> > > Hi, > > According to the Phenix manual, phenix.refine uses no sigma cutoff by > default. Since I haven't changed this manually, why do I see in my pdb > file MIN(FOBS/SIGMA_FOBS) 1.340? > > Thanks for help, > Karolina > > This one I can answer because I asked myself the same question recently. The answer is that Phenix does not impose any sigma cutoff, but rather your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . You can verify this for yourself by going through your reflection file, line by line, and calculating Fobs/Sigma_Fobs for each reflection. You will find that all your reflections have a Fobs/Sigma_Fobs larger or equal to 1.34 . So it has nothing to with phenix; phenix just reports a property of your data. An easier way than doing it "manually" is using CCP4 sftools for calculating a new column "ratio", writing out the resulting MTZ file, and looking at this with mtzdmp. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

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Re: [phenixbb] Confused by the output from Phenix autobuild jobs
by Thomas C. Terwilliger 30 Nov '09

30 Nov '09

Hi Serah, You are right that the coefficients that you want for a difference map are not present in the overall_best_refine_map_coeffs.mtz file. The coefficients in that file (labelled FP PHIM) are the same as 2FOFCWT PH2FOFCWT from the refinement output, but there are no difference map coefficients. I will change this. In the meantime, I would do this after the end of autobuild: phenix.refine AutoBuild_run_1_/overall_best.pdb \ AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz and then you will have your map coefficients. >> I'm still wondering about the overall_best_*.* outputs - are these the >> really final output, or do we go for cycle_best_3.* series? The overall_best_xxx files are copied from the cycle_best_xxx files which are copied from the original files, all of which are in the TEMP0/ subdirectory. Thanks for pointing out that the difference coefficients are not present in the autobuild map file. I will fix the output to have the original refinement map file available. All the best, Tom T

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alternate conformation
by subhash bihani 25 Nov '09

25 Nov '09

Hi, I am refining a structure with ligand in alternate conformations. I tried giving them A and B, it worked. but I feel that this doesnot make interactions between alternate conformations absolutely zero. Is there any command in phenix similar to Igroup statement in CNS which can be used for such cases. Regards subhash -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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R-free rules
by Bryan W. Lepore 25 Nov '09

25 Nov '09

in the phenix.reflection_file_editor gui not sure i understand this: [x] Extend existing R-free array(s) ... [R-free flags generation] <--+ | | | | +-if this is checked, then do NOT check "Generate R-free flags" in here ... because "extend" is not the same as "generate", right? ... and thanks for the help before. -bryan

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Age Concern edition of the Computing Commission and Teaching Commission newsletter
by Ralf W. Grosse-Kunstleve 24 Nov '09

24 Nov '09

Posted on behalf of Lachlan Cranswick: The Computing Commission and Teaching Commission has produced a joint November 2009 newsletter on the theme of "Age Concern", which deals with issue concerning "the slow march towards retirement of the major generation of crystallographic programmers", as further explained by David Watkin within the newsletter. http://www.iucr.org/resources/commissions/crystallographic-computing/newsle… or via http://www.iucr.org/resources/commissions/crystallographic-teaching/newslet… --------------------------- This issue's articles include : - the latest background and information from the UK based EPSRC funded Age Concern Project. - history and science within the Caltech based CRYRM single crystal suite; DIMS - Direct methods In Multidimensional Space software; Crunch 1.5 Direct Methods Software; the Glasgow based GX single crystal suite; the Italian based CAOS structure refinement software; Ton Spek's Platon; and a list of programs archived at Armel Le Bail's Crystallography Source Code Museum. - experience in conversion of large crystallographic Fortran-77 to C++; as well as the place of the Quick and Dirty Crystallographic Computer Program - Historical group photographs from some of the Crystallographic Computing and Teaching School of the 1970's. - Archived manuals and source code from the above mentioned software. - Teaching material of Isabella L. Karle, as she presented at the 1978 Erice School on Direct Methods for Solving Crystal Structures - A reprint of the The Analytical Theory of Point Systems (1923) by J. D. Bernal (1901-1971) Further Computing Commission newsletters are intended on theme of Age Concern : capturing the history and the crystallographic science behind past and present Small Molecule, Powder Diffraction, Protein and other crystallographic software. Submissions on this topic are welcome and encouraged. - Lachlan Cranswick ( lachlan.cranswick(a)nrc.gc.ca )

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