- phenixbb - phenix-online.org

handling of alternate conformations
by Ulrich Baumann 16 Jul '07

16 Jul '07

Dear Phenix experts, we encounter the following "problem" when trying to refine alternating conformations: we have a complex with 4 chemically different polypeptide chains in the asymmetric unit, composition A3B3CD. For chains C and D we see additional density, which appears to belong to three alternating conformations which can be thought as rigid-body motions (for the whole chains C and D, let's call these conformers 1,2 and 3, but we label them conventionally in the file with the prefix A,B,and C) with roughly estimated occupancies of about 0.3, 0.3 and 0.4 (we can really see most of them). A and B have no visible alternating conformations (occupancies set to 1.0). From the atom count it appears that phenix reads in three conformers called A,B and C with A: A3B3C(1)D(1), B: A3B3C(2)D(2) and C: A3B3C(3)D(3). Phenix.refine says it has these 3 conformers: conformer A A:2700 atoms, conformer B:2700 atoms, common with A 2100, conformer C:2700 atoms, common with A 2100, common with B 2100. Refinement yields an R/Rfree of about 0.210/0.325. If we treat the three conformers of polypeptide chains C and D as independent chains with occupancy each 1.0 (this is possible 'cos there are no repulsive contacts between them, fortunately), we get R/Rfree of 0.243/0.291 and phenix applies NCS restraints to all chains. The resolution is about 2.9 A. We use phenix.refine from the CCI_APPS, version 2007-03-26-1903, SUSE Linux. My questions is: is the difference due to the lack of NCS between conformers or are the occupancies mistreated somwhow? I am asking because I would not consider the whole A3B3C(x)D(x) particle as a conformer but only chains C and D ...... Is there a possibility to apply NCS restraints to conformers? Many thanks in advance, Ulrich

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How to keep a custom bond planar ?
by Coincon Mathieu 16 Jul '07

16 Jul '07

Hi, I defined a bond (and angles) between my ligand and the NZ of a lysine in a file (bond.def). ..-C2-.. | -CE-NZ = C1-C3-.... This is a double bond. Everything work good except for the planarity of the lysine's atoms. For the bond I wrote in my bond.def: bond { action = *add atom_selection_1 = chain D and resname LIG and name C2 atom_selection_2 = chain A and resname LYS and resid 66 and name NZ distance_ideal = 1.340 sigma = 0.02 } For an angle: angle { action = *add atom_selection_1 = chain D and resname LIG and name C3 atom_selection_2 = chain D and resname LIG and name C2 atom_selection_3 = chain A and resname LYS and resid 66 and name NZ angle_ideal = 120.000 sigma = 3 } How can I define a plan or some dihedral ?? Or as in the ligand .cif I defined a plan LIG plan-2 C1 0.020 LIG plan-2 C2 0.020 LIG plan-2 C3 0.020 I could add the atoms NZ and CE of the lysine to the plan-2. Thanks by advance. And by the way phenix (with coot) is GREAT (I did my apo-enzyme in four days !!!!) -------- Mathieu Coicon PhD Student Biochimie Universite de Montreal (+1)514-343-6111 #5352

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Phaser
by john kryst 13 Jul '07

13 Jul '07

Hi all !!! Is it possible to fix one domain and search for the second one in phaser !!! What are the keywords to use for that. I have a protein with two domains. It i give both the domains together it is not finding the solution. If i give only one domain it is giving the solution and the R and Rfee is 28 and 33. But it is not finding the second one. Thanks in advance for your suggestions.. regards John

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Refinement use of Friedel pairs
by Mark A Saper 11 Jul '07

11 Jul '07

I am refining a structure containing SeMet with data collected at peak wavelength. Provided I give the f' and f'', will phenix.refine calculate F+ and F- structure factors and use the provided FOBS+ and FOBS- ? CNS does this. Refmac only uses f' and I get >6 sigma Fo-Fc peaks on the Se. Thanks for your help. _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

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setting resolution for 2 datasets in AutoSol
by Thomas C. Terwilliger 10 Jul '07

10 Jul '07

Hi Luca, It's easiest to do this in 2 steps: 1a. You can set the resolution separately for each dataset in the AutoSol Wizard. In the GUI, just go through each dataset and set the overall resolution to your desired values as you go. Ignore the density modification and building that occurs in this run. 1b. Then you'll get an output exptl_fobs_phases_freeR_flags_2.mtz or equivalent that is phased to the resolution you specified, but that has all the data (with no phases) to higher resolution. 2. Now run the AutoBuild wizard, and set the resolution to your high-resolution limit. That should use the phases you generated, and include the high-res data for density modification and refinement. Equivalently, you can run AutoSol at low resolution then run AutoBuild at higher resolution by supplying an input_hires_file with the hires data. A key point here is that the building in AutoSol is just a preliminary build...the building in AutoBuild is the real thing. You can also run 2 datasets and set the resolution for each in a script. Here is a script to read in 2 SAD datasets and solve them together as one, setting the resolution of phasing to 3 A for the first and 2.9 for the second, cat two_datasets.inp input_seq_file seq.dat resolution 2.9 # Resolution expt_type sad input_file_list se.sca ############## NEW DATASET ################ run_list start # run "start" method. run_list read_another_dataset # starting a new dataset here resolution 3.1 # Resolution input_file_list br.sca Let me know if that does not do it! -Tom T >> From: lp212(a)mole.bio.cam.ac.uk >> Date: July 9, 2007 3:38:28 PM PDT >> To: phenixbb(a)phenix-online.org >> Subject: script for Zn and Se phasing >> Hi, >> I have collected two peak datasets on two different crystals, for a protein that contains zinc: >> 1. peak dataset at the Zn edge (lambda=1.285A, 2.5A reso) >> 2. peak dataset at the Se edge (lambda=0.98A, 2.8A reso) >> The protein has 2 Zn and 11 SeMet, and 4/au. When I input both >> datasets in the AutoSol GUI, Hyss finds correctly 8/8 Zn sites, and ~34/44 Se sites, but only when I cut back the resolution (4.2A for Zn, and 4.7A for Se). What I can't figure out is how to tell the Autosol GUI to use a low-res cutoff for finding the sites, and then use all the data for model building. Could someone please explain how to do this in the GUI, or send me a script? >> Thanks a lot! Apologies if this is trivial... >> Luca >

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Re: [phenixbb] depositing phenix-refined coordinates
by Ralf W. Grosse-Kunstleve 05 Jul '07

05 Jul '07

Hi Enrico, > However, I would be very grateful if someone could point me to the topic > already posted in the message below by Dr. Scott few days ago, > exactly at: > "a quick description for depositing phenix-refined coordinates?", > though the full message contained very interesting points I would > love to hear about We don't have a dedicated deposition tool yet, sorry. But we are actively working with the PDB on this. In the meantime, the .pdb files produced by phenix.refine are the best starting point. > (I also performed refinement by refmac/phenix, and observed kind of a > similar trend for those numbers). It may be because we are reporting mean deviations instead of root-mean-square deviations. This is kind of an oversight on our part and will be changed in the next version. Ralf

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CCI-Apps Verisons vs. Phenix Versions
by Schubert, Carsten [PRDUS] 05 Jul '07

05 Jul '07

Hi, Quick question about versions of CCI-Apps as standalones and in phenix. How does once decide which version of the CCI-Apps is more current? I have not looked in depth, but is there a equivalent build tag for the CCI-Apps in phenix as the one for the CCI-Apps. Currently I am assuming that the CCI-Apps are alway more up to date, but that may not hold true for the upcoming phenix 1.3 release. Thanks Carsten

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some general refine questions
by William Scott 05 Jul '07

05 Jul '07

Hi folks: With the helpful advice of the phenix crew, I've re-refined 2goz, an entry in the pdb in which I used refmac5 the first time around. There was a small error in the pdb: One nucleotide (C8 in chain A) was rotated 180 degrees about the glycosylic bond from where it should have been. The net result is one oxygen atom was in the wrong place in the structure, and this was apparent within the difference Fourier. After I rotated the base and re-refined in refmac, the Rfactor and other stats remained essentially unchanged (so this fix has nothing to do with the following): My refinement results in Refmac: REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.241 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1503 ; 0.009 ; 0.021 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2331 ; 1.676 ; 3.000 Then I refined in phenix. I get REMARK Final: r_work = 0.1737 r_free = 0.2224 bonds = 0.003 angles = 0.745 So the working and free R factor are both lower, and the geometry is substantially tighter. If I relax the weights in phenix, even to get rms bonds of around 0.006, the free-R goes up, which tells me this is not something I am justified in doing. Phil Evans once told me that anything tighter than about 0.01 (conservatively) was science-fiction, in that this is within the error of the idealized libraries for bond lengths. Other people have asked me about this too, and I didn't know how to reply. Is bonds = 0.003 angles = 0.745 realistic, or have I done something wrong? Even if I do structure idealization in Refmac, I can't get the rms bonds below about 0.005 (and my understanding is that it uses the same monomer library). Why is the weight multiplied by 0.5 by default? Since changing that to 1.0 slightly increases freeR, I assume it is the default for some reason. All the best, Bill PS: Could someone point me to a quick description for depositing phenix-refined coordinates? (The latest phenix installer seems to have omitted the docs.) William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott

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Re: [phenixbb] sugar links in phenix.refine
by Ralf W. Grosse-Kunstleve 04 Jul '07

04 Jul '07

Almost, but you need a separate scope (thing between braces) for each link, e.g.: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 900 residue_selection_2 = chain A and resname ASN and resid 329 } refinement.pdb_interpretation.apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } Or alternatively: refinement.pdb_interpretation { apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 900 residue_selection_2 = chain A and resname ASN and resid 329 } apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } } Ralf

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Re: [phenixbb] Multivariate Z score L-test
by Claudia Scotti 29 Jun '07

29 Jun '07

Thank you so much. I'll try all the space groups and see what happens. Many thanks again, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ---------------------------------------- > Date: Fri, 29 Jun 2007 07:35:22 -0700 > From: PHZwart(a)lbl.gov > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Multivariate Z score L-test > > Hi Claudia, > > This could indicate that tyour data is actually P 2 1 1, P 1 2 1 or P > 1 1 2 or P 21 1 1, P 1 21 1, P 1 1 21. Try processing that data in > those spacegroups and see if that makes any difference. You might end > up havig to refine your structure in all spacegroups to find out which > possibility is the best. > > It could also indicate that the quality of your data is not very good, > either due to suboptimal data processing or because of bad diffraction > (or both). > > HTH > > Peter > > > 2007/6/29, Claudia Scotti : > > > > Dear List, > > > > I'm only at my third structure (a scFv antibody fragment) and I'm disturbing about a dataset that is giving problems at the refinement stage: it gets stuck at about Rcryst= 0.36 and Rfree=0.44. > > > > I've tried data processing with several softwares (Mosflm, XDS, Denzo) and the result is consistently P222, unit cell 69x79x90, 90, 90, 90. The data are anisotropic, with limits at 2.3 and 2.8 A. I cut the data at 3.0 A. > > Matthews coefficient suggests two molecules per asu. > > No NCS is detected by self-rotation and a native Patterson detects a small peak (10% of origin peak) at 0.19, 0.34, 0.5. > > MR using several softwares (AmoRe, Molrep and Phaser) and several models all agree that the best space group is P21212, though the systematic absences are not perfectly consistent. > > > > When refining, refinement gets stuck as I mentioned above. > > > > I've run Phenix x-triage and the results include this line (see below): "It could be worthwhile considering reprocessing the data". I was wondering if the Multivariate Z score L-test: 6.305 might suggest how to reprocess the data. > > > > Sorry for the probably trivial question and for probably missing important data. > > > > Thanks a lot for any help and suggestions, > > > > Claudia > > > > ------------------------------------------------------------------------------- > > Twinning and intensity statistics summary (acentric data): > > > > Statistics independent of twin laws > > - /^2 : 1.827 > > - ^2/ : 0.838 > > - : 0.649 > > - , : 0.417, 0.242 > > Multivariate Z score L-test: 6.305 > > The multivariate Z score is a quality measure of the given > > spread in intensities. Good to reasonable data is expected > > to have a Z score lower than 3.5. > > Large values can indicate twinning, but small values do not > > neccesarily exclude it. > > > > > > No (pseudo)merohedral twin laws were found. > > > > > > Patterson analyses > > - Largest peak height : 11.094 > > (correpsonding p value : 1.080e-01) > > > > > > The largest off-origin peak in the Patterson function is 11.09% of the > > height of the origin peak. No significant pseudotranslation is detected. > > > > The results of the L-test indicate that the intensity statistics > > are significantly different then is expected from good to reasonable, > > untwinned data. > > As there are no twin laws possible given the crystal symmetry, there could be > > a number of reasons for the departure of the intensity statistics from normality. > > Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems > > as well as bad data quality might be possible reasons. > > It could be worthwhile considering reprocessing the data. > > ----------------------------------------------------------------------------------------------- > > > > Claudia Scotti > > Dipartimento di Medicina Sperimentale > > Sezione di Patologia Generale > > Universita' di Pavia > > Piazza Botta, 10 > > 27100 Pavia > > Italia > > Tel. 0039 0382 986335/8/1 > > Facs 0039 0382 303673 > > > > _________________________________________________________________ > > Express yourself instantly with MSN Messenger! Download today it's FREE! > > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb _________________________________________________________________ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TX…

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