- phenixbb - phenix-online.org

fix atoms during refinement
by CPMAS Chen 10 Nov '14

10 Nov '14

Dear All Phenix Users, Is there a way to fix certain atoms position during refinement? I have some heavy atoms identified with MR-SAD, but when I build the whole molecule and have phenix to refine its position, the heavy atom's position is shifted from the anomalous signal. Therefore I would like to have these heavy atoms positions fixed during refinement. Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Ringer
by Ivan IVANOV 09 Nov '14

09 Nov '14

Dear All, I am trying to use ringer with a model I have. I followed the tutorial for Calmodulin and it worked very well for my protein. (http://bl831.als.lbl.gov/ringer/ringer/Tutorial/tutorial.htm). Now I have all files sigma vs chi angles for the residues I want and also the list of peaks identified above the sigma cutoff I selected. I am struggling to analyse the outputs as it is shown on the calmodulin exemple. I found this website (http://bl831.als.lbl.gov/ringer/ringer/Documentation/ringerManual.htm#Userp…) which is explaining very briefly how to plot all different conformation vs chi angles and how to show all selected amino acid conformation in the electron density (4.4 Plotting Accessory). I have to admit that this is not straigthforward for me to plot all outputs in a comprehensive way. Does anyone of you have a script to run with ringer outputs and get the final figures as it is shown on both websites ?? Kind regards, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: ivanov(a)embl.fr Url: http://www.embl.fr

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"Femtosecond crystallography of membrane proteins in lipidic cubic phase (LCP)” Webinar
by Angela Criswell 04 Nov '14

04 Nov '14

Dear colleagues, I would like to draw your attention to an upcoming free, educational webinar to be presented by Dr. Wei Liu titled “Femtosecond crystallography of membrane proteins in lipidic cubic phase (LCP).” Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins, structural studies remain difficult. Wei’s presentation will describe the use of serial femtosecond crystallography of membrane proteins in LCP and how this approach holds promise to interrogate this difficult, yet important, class of proteins. This webinar is scheduled to occur on Thursday, November 13th at 11:00 AM CST (9:00 AM PST / 5:00 PM GMT). You can find an abstract and registration link for this webinar at: http://www.rigaku.com/webinars. We hope you will join us for the event. Best regards, Angela Criswell -- Angela Criswell VP, Life Science X-ray Products Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 77381 USA Ph: +1 281 362 2300 ext. 216 Fax: +1 281 364 3628 Email: angela.criswell(a)rigaku.com URL: http://www.rigaku.com Subscribe to Rigaku eNewsletters<http://www.rigaku.com/subscribe>

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green ball in aspartate
by Murpholino Peligro 30 Oct '14

30 Oct '14

Hi Everybody. Does anybody knows what could this be? Blue map at 1rmsd Green and red map at 3.5 rmsd Purple map (FEM map) at 1rmsd Conditions 100mM sodium acetate, NaCl 10% w/v, cryo=glycerol 30 % v/v; protein is hen egg white lysozyme (usual condition, usual protein and ohh..almost forget it.. ascorbic acid at 0.5 M) A water molecule overlaps with the oxygen atom (OD1) of the aspartate residue. So it is not a water molecule. Any ideas? (In coot -> validate-> difference map peaks and holes-> its the only one at 7.7 rmsd) Thanks

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[ot]: nedit on Mac 10.10 yosemite
by Sebastiano Pasqualato 29 Oct '14

29 Oct '14

Hi folks, sorry for the off-topic and slightly ‘demodée’ question, but, since I updated to Yosemite on my Mac, "nedit" does not work any more. Here’s the error message: Seba@host041:~> nedit dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib Referenced from: /Applications/nedit/nedit Reason: image not found Trace/BPT trap: 5 Seba@host041:~> Anybody knows if there is a fix for that? Thanks in advance, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit

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Fwd: Postdoc position in acoustic crystal preparation and high throughput screening at NSLS II
by Nathaniel Echols 28 Oct '14

28 Oct '14

---------- Forwarded message ---------- From: "Soares, Alexei" <soares(a)bnl.gov> To: "CCP4BB(a)JISCMAIL.AC.UK" <CCP4BB(a)jiscmail.ac.uk>, "cnsbb(a)yahoogroups.com" <cnsbb(a)yahoogroups.com>, "pdb-l(a)rcsb.org" <pdb-l(a)rcsb.org>, " phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org>, " x-plor(a)net.bio.net" <x-plor(a)magpie.bio.indiana.edu>, "xtal-log(a)net.bio.net" <xtal-log(a)magpie.bio.indiana.edu> Cc: Date: Tue, 28 Oct 2014 14:44:30 +0000 Subject: Postdoc position in acoustic crystal preparation and high throughput screening at NSLS II *Postdoctoral Research Associate – Macromolecular Crystal Preparation for NSLS-II* *2-year Term Position* *BNL Overview:* Brookhaven National Laboratory is a nonprofit research and development institution whose purpose is to advance ideas and knowledge through a multidisciplinary program of basic and applied research. *Project Overview:* A postdoctoral position is available to develop new crystal-preparation technologies to advance the use of serial macromolecular crystallography (MX) at NSLS-II. This new synchrotron will soon begin operation at Brookhaven National Laboratory. The individual will develop technologies for crystallization, drug discovery, and crystal handling to make serial crystallography possible, using various technologies, including acoustic droplet ejection (ADE). The project will provide the capability for experimenters to employ nanoliter quantities of material to produce specimens for diffraction studies with a large number of discrete experiments in a small area. This will exploit the micro-beam capabilities of NSLS-II MX beamlines; both room temperature and cryogenic serial crystallography strategies will be explored. High-throughput screening will be used for different types of structural biology projects (crystallization conditions, fragment binding, etc). The individual will work closely with a broad technology-development team. Our team members have different areas of expertise, from 3D labware design to research on medically relevant expressed proteins. No experience with ADE is necessary. *Essential Duties and Responsibilities:* The successful candidate will assist in the development and implementation of procedures and computer algorithms that leverage the Echo 550 instrument for macromolecular crystallography applications for serial crystallography applications in the few-nanoliter regime. The candidate will also develop novel technologies as well as improve existing technologies, and will have opportunities to participate in other related projects in a large and diverse group. *Required Knowledge, Skills and Abilities:* - Ph.D. in an appropriate chemistry, biology, or physics discipline; structural biology, crystallography, or a related field will have preference - Demonstrated experience (preferably including publications) in innovative experimentation and/or methods development with crystallography or drug discovery - Experience with conventional crystallization, and familiarity with micro crystallization and handling of micro crystals will be valuable - Experience in computer programming - The candidate must have a demonstrated ability to work with a team. *Other Information:* BNL policy states that Research Associate appointments may be made to those who have received their doctoral degrees within the past five years. *Please apply to Job # 137 on our jobs website:* *http://www.bnl.gov/HR/careers/ <http://www.bnl.gov/HR/careers/> * At Brookhaven National Laboratory we believe that a comprehensive employee benefits program is an important and meaningful part of the compensation employees receive. Our benefits program includes but is not limited to: - Medical Plans - Vacation - Holidays - Dental Plans - Life Insurance - 401(k) Plan - On-site Child Development Center, Swimming Pool, Weight room Tennis Courts, and many other employee perks and benefits.

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R/R free reported values
by Cedric 28 Oct '14

28 Oct '14

Hi Phenix and CCP4 community, (sorry for the cross posting). I was looking at a PDB file. The http://www.rcsb.org/ website page gives the following values: R-Value: 0.103 (work) R-Free: 0.134 The actual PDB file gives the following: R :0.110 FREE R VALUE : 0.170 I was wondering why the difference. The structure is 1.0A resolution 2CWS. Thank you, ____________________________________________________________ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more!

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difference between phenix.mrage and phenix.MRage?
by Murpholino Peligro 27 Oct '14

27 Oct '14

? Thanks

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Cacodylate won't stay in place
by Kgosisejo, Oarabile 27 Oct '14

27 Oct '14

Hello all, I am trying to fit cacodylate ion in my model using Coot but it does not stay where I put it. The molecule breaks apart and some of its components attach to the peptide residues. Due to this, phenix.refine would not accept this as the input for refinement. Is there a way I can make cacodylate ion stay in its electron density and refine my structure with cacodylate ion? I appreciate your help! Best Regards, Oarabile M. Kgosisejo o.kgosisejo(a)usask.ca

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help on MIR dataset
by Ni, Fengyun 25 Oct '14

25 Oct '14

Hi everyone, I am working on a MIR dataset: one native data, three EMTS soaked data at different concentration, one PbAc2 data. My initial trial with phenix autosol did not give positive solutions. I hope I could get some information from all of you. I index and integrate the data in Mosflm and possible group is P3, though the Pointless said the most possible is P3121. But for now, I only tried P3 at different resolutions for the reason that a potential MR solution (below 20% identities, TFZ=7.1) was found in P31 space group. If P3121 is the real space group, the space is too crowed to fit my molecules unless they have some unexpected symmetry. For the difference among dataset in P3 space group, the output from SCALEIT of CCP4 gives as follows, RMS differences|RMSiso RMSano ---------------------------------------- FP-hg |172.30 22.50 FP-hg2 |159.20 24.07 FP-hg3 |85.08 27.92 FP-pb |31.15 24.55 The native data's resolution cutoff is 3.2 A, and 3.2/3.8/3.5 for different EMTS data, 3.5 for Pb data.I did notice some radiation damage for EMTS (Hg) data (large negative B-factors in SCALA), but not for Pb data. And the anomalous signal only extend to 5.6 and 4.5 A for EMTS and Pb data, respectively, as indicated by phenix.xtriage. These are all the possible heavy atom data we could obtain. So i tried all of them in phenix.autosol. The input is like follows, autosol { seq_file = ../seq.dat crystal_info { solvent_fraction = 0.62 #determined from matthews coefficient to assure "reasonable" content in asymmetric unit. } native { data = nat.mtz } deriv { data = hg1.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = hg2.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = hg3.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = pb.mtz atom_type = Pb inano = noinano *inano anoonly lambda = 0.94640 } model_building { build = False #my structure is DNA/protein complex, so i choose to stop the building process. } } I tried at different resolutions, 3.6/4.0/4.4/4.8/5.2/5.6/6.0 A. One solution was given based on Pb data at 4.8 A with following statistics, Solution # 6 BAYES-CC: 59.7 +/- 17.2 (2SD) Dataset #4 FOM: 0.24 Score type: SKEW CORR_RMS NCS_OVERLAP Raw scores: 0.31 0.69 0.00 100x EST OF CC: 59.74 17.55 31.25 Refined heavy atom sites (fractional): X Y Z xyz 0.033 0.020 0.538 xyz 0.417 0.217 0.113 xyz 0.041 0.010 0.721 The statistics is almost the same for its inverse, and i read from the output that the statistics for phasing other Hg datasets are very low (BAYES-CC is lower than 20) based on the above solution. The resulting map does not make much sense yet. Sorry for the long post. Any suggestion is welcome. Thank you very much! Fengyun

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pdb deposition
by Sneha Rangarajan 24 Oct '14

24 Oct '14

Hi everyone, For a 1.9A dataset, here are my statistics- Rfactors: 22/26 Ramachandran favored: 90.60% Ramachandran outliers: 2.17% Rotamer outliers: 4% Clashscore: 8 Bonds: 0.007 Angles: 1.2 I have tried a couple of things to refine it further but nothing seems to improve all the parameters. My question is what is an acceptable Rfactor at this resolution for deposition in pdb? Thanks, Sneha

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how to refine everything except n residues in phenix.refine?
by Murpholino Peligro 22 Oct '14

22 Oct '14

Hi everybody! Everytime when I (within coot) do "real space refine" two arginines that have two alternate conformations ..(interacting by hydrogen bonds); and then phenix.refine everything, both conformers move away. Therefore, when I open my mtz and pdb files from phenix.refine in coot, I'll have green blobs where there should be guanidium groups. Can I tell phenix.refine not to move only those two residues? It should be something like the following lines in the eff file? sites { individual = None torsion_angles = None rigid_body = None remove_selection=resid 45 remove_selection=resid 68 } Thank you very much

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Electrostatic potential map/Delphi/PDB2PQR
by Ivan IVANOV 21 Oct '14

21 Oct '14

Dear All, I am facing a problem. I have a protein-RNA complex at 2A resolution I refined using TLS in Phenix. Now in the pdb file I have ANISOU line for every atom and probably many other errors. This is the reason I am not able to run Delphi or PDB2PQR to create potential electrostatic map. I removed already all water molecules and all heteratoms and ANISOU lines and RNA molecule. The program creating the phi file for the potentials does not work at all. Do you know any server which can correct any errors in the pdb file in order to run properly the program to create electrostatic map ?? Thanks a lot, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: ivanov(a)embl.fr Url: http://www.embl.fr

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An old (?) tutorial?
by Bryan Lepore 21 Oct '14

21 Oct '14

Greetings - On the public webpage, there used to be an outstanding text tutorial under the phenix.refine link (I think!) that described the attachment of prosthetic groups and such to protein, I think using NAG (or was it something else...). It had all the commands for inclusion in the .def. and of course I can't find it now on the public site. Should I look in the local docs of an old release? -Bryan

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Phenix Table 1 discrepancy
by Rich Grey 20 Oct '14

20 Oct '14

I'm preparing Table 1 for a structure I have recently solved. I chose to compare the Table 1 Phenix produces to the data found in the PDB file and the log file from my last refinement in Phenix. I see discrepancies between the data for the highest resolution bin's R-factors, including what resolution data that bin contains. In addition, the number of reflections used in refinement is different (although only by about 5, so not a large difference). The PDB file appears to match the log file, and the overall Rwork and Rfree agree for all. Does anyone know where the Table 1 program in Phenix pulls these values from why I may be seeing these differences? Thank You. -Rich

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anomalous signal
by Matteo Colombo 20 Oct '14

20 Oct '14

Hello, I was wondering if the f'' determined by XANES experiment is quantitatively significant and if it can be contributed by two different anomalous scatterers. For example in my protein I know that Co and Zn are present. In theory, at Zn absorption edge, I have a contribution from Co too. If I perform a XANES experiment to determine Zn absorption edge and I obtain a f'' of 5.87, does this value correspond to only Zn signal or to a sum of Zn+Co? Thanks a lot Matteo -- Matteo Colombo PhD Groupe Extremophile et grands assemblages moléculaire Institut de Biologie Structurale 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9

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phenix error
by Ivan IVANOV 17 Oct '14

17 Oct '14

Dear all, I have an error appearing in phenix. I think it is a problem of my pdb file. I do not know how to change it. Error: residue.id_str(suppress_segid=false):segid is not unique: pdbres=ATP C 1 "segid= "O" Does anyone can help me?? Where is the mistake and how to solve it ?? Kind regards, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: ivanov(a)embl.fr Url: http://www.embl.fr

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Re: [phenixbb] COOT and default dictionary
by Yazan Abbas 16 Oct '14

16 Oct '14

Hi, I was trying to troubleshoot this and it seems to be a problem related to the FEM map only. When I open my FEM.mtz and do RSR in coot it works well if I choose the 2mFoDfc map but not the FEM map. I'm still not sure why it stopped working since coot was behaving normally just yesterday. Maybe it had something to do with the cif file I tried to import earlier (see previous message). Yazan PS I'm replying to my previously sent message, I hope it ends up in the same thread... On Thu, Oct 16, 2014 at 11:41 AM, Yazan Abbas <yazan.abbas(a)mail.mcgill.ca> wrote: > Hi, > > I am encountering a problem with coot real space refinement (RSR). > Basically when I try to fit any residues using RSR the atoms come apart and > fit into the center of the density, possibly because it is not reading in > any geometry restraints. This happens for examples when I am opening my > FEM .mtz map (either manually or 'open in coot' via phenix). > > The only times coot RSR behaves normally is when I load it via phenix > after running phenix refine, or when I open coot via the command line and > auto-open an mtz (the same one generated by phenix refine). Also, fetching > a pdb and map via EDA/PDBredo still allows me to use RSR. > > When I encountered the problem I tried to reinstall coot 0.8 stable and > also tried to install the latest pre (0.8.1-5404), and upgraded to phenix > 1.9-1692. My coot installation comes from the stand alone packages of the > Scott lab website. > > The only thing I can think of as having caused this is when I was trying > to fit an unusual ligand into my density, I used phenix elbow to generate a > cif file and then loaded that into coot (--> import cif dictionary). > Shortly afterwards coot gave up on real space refinement under most > circumstances. > > Have I somehow replaced a default dictionary file? > > Thanks, > > Yazan > > > -- > PhD Candidate > Dr. Bhushan Nagar Lab > McGill University > Tel: (514)-398-7271 > http://bhushan-nagar.lab.mcgill.ca/ > -- PhD Candidate Dr. Bhushan Nagar Lab McGill University Tel: (514)-398-7271 http://bhushan-nagar.lab.mcgill.ca/

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R-factor difference between phenix and sftools
by Simon Jenni 13 Oct '14

13 Oct '14

Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors are: Final R-work = 0.3221, R-free = 0.3638 phenix.cc_star agrees: phenix.cc_star com_001.pdb com_001.mtz \ f_obs_labels="F-obs,SIGF-obs" \ f_model_labels="F-model,PHIF-model" \ unmerged_data="xscale.hkl" r_work: 0.322 r_free: 0.364 so does phenix.model_vs_data: phenix.model_vs_data com_001.pdb com_001.mtz r_work : 0.3221 r_free : 0.3638 sigma_cutoff : None However, when I calculate the R-factors with sftools, I get a discrepancy between the phenix and sftools results: sftools << eof read com_001_f_model.mtz Y select col R_FREE_FLAGS > 0 correl col FOBS FMODEL select invert correl col FOBS FMODEL quit Y eof R-work: 33.6 R-free: 38.1 Does anyone perhaps know what causes this difference? With best regards, Simon PS: The structure is in spacegroup P212121 with strong pseudocentering tNCS (dimer in the asymmetric unit, native Patterson peak at 0.500 0.500 0.497). No indication for a P21 twin (L-test and refinement in P21 with twin law), not higher symmetry spacegroup I222 (alternating strong and weak reflections are visible in the diffraction patterns, resolved structural differences in the two protomers of the dimer). Two datasets from different beamlines. As might be expected, the R-factors after refinement are unusually high (e.g. 28/35 [conventional resolution cutoff at 3.1 A], 32/36 with Kay's CC cufoff at 2.6 A). I wanted to compare refinements between different programs to see how they cope with the unexpected bimodal amplitude distribution.

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ligand fitting
by Sneha Rangarajan 13 Oct '14

13 Oct '14

Hello everyone, I have a question about ligand fitting into density. At this point my maps look quite good with decent density for the peptide (ligand)[Rfactprs 26/31]. I tried using ligandfit by giving it the pdb and mtz of the ligand free model along with peptide.pdb (peptide stripped from a pdb where it was complexed with a homologous protein). However the output was a ligand.pdb file with a CC of 0.49. I am not sure how to interpret this. Does this mean it could not find the density for the ligand? Is there a better way to fit the peptide into density? Thanks, S From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Sneha Rangarajan Sent: Wednesday, October 08, 2014 10:30 AM To: Nathaniel Echols Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] (no subject) This was a great idea. My Rfactors after a second round of autobuild are now 25/32. I think it might be getting there afterall ☺ S From: Nathaniel Echols [mailto:[email protected]] Sent: Friday, October 03, 2014 3:08 PM To: Sneha Rangarajan Cc: Pavel Afonine; phenixbb(a)phenix-online.org<mailto:[email protected]> Subject: Re: [phenixbb] (no subject) On Fri, Oct 3, 2014 at 11:58 AM, Sneha Rangarajan <rsneha(a)umd.edu<mailto:[email protected]>> wrote: I did another round of refinement with default settings (XYZ,realsp, IndB and occ) with and without weight optimization. Without weight opt, the Rfactors are 23/36 with RMSbonds-0.0108 and RMSangles-1.750 One idea would be to run AutoBuild again. I've seen cases before where it didn't converge using the default settings, and feeding a previous result back into the program for a second run produced significantly better models. It might help get rid of the overfitting. -Nat

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Re: [phenixbb] R-factor difference between phenix and sftools
by Ed Pozharski 13 Oct '14

13 Oct '14

To be fair, I made the same mistake initially, but the question is about calculating Rs with sftools using output mtz from phenix.refine, not sfcheck. Thusly, bulk solvent explanation does not seem to apply. My other theory (impossible to check without actual data) was that phenix.refine outlier reflection rejection makes the difference here, although it's surprising if effect is so noticeable. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Pavel Afonine <pafonine(a)lbl.gov> </div><div>Date:10/13/2014 2:21 PM (GMT-05:00) </div><div>To: Tim Gruene <tg(a)shelx.uni-ac.gwdg.de>, phenixbb(a)phenix-online.org </div><div>Subject: Re: [phenixbb] R-factor difference between phenix and sftools </div><div> </div>Thanks Tim, yes missed this one! Hi Simon, the differences in R-factors you observe are most likely because we use improved bulk-solvent modeling and overall scaling procedure. This is described here: Bulk-solvent and overall scaling revisited: faster calculations, improved results. Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A. Acta Cryst. D69, 625-34 (2013). Specifically, Figures 3-4 in this paper make your observations very expectable. Other contributions to differences are discussed here: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 43, 677-685 (2010). Pavel On 10/13/14 11:10 AM, Tim Gruene wrote: Dear Simon, I found this a very puzzling observation and given the high throughput of this board, it is likewise puzzling you have not received a reply yet - or have you? Best regards, Tim On 10/12/2014 08:25 PM, Simon Jenni wrote: Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors are: Final R-work = 0.3221, R-free = 0.3638 phenix.cc_star agrees: phenix.cc_star com_001.pdb com_001.mtz \ f_obs_labels="F-obs,SIGF-obs" \ f_model_labels="F-model,PHIF-model" \ unmerged_data="xscale.hkl" r_work: 0.322 r_free: 0.364 so does phenix.model_vs_data: phenix.model_vs_data com_001.pdb com_001.mtz r_work : 0.3221 r_free : 0.3638 sigma_cutoff : None However, when I calculate the R-factors with sftools, I get a discrepancy between the phenix and sftools results: sftools << eof read com_001_f_model.mtz Y select col R_FREE_FLAGS > 0 correl col FOBS FMODEL select invert correl col FOBS FMODEL quit Y eof R-work: 33.6 R-free: 38.1 Does anyone perhaps know what causes this difference? With best regards, Simon PS: The structure is in spacegroup P212121 with strong pseudocentering tNCS (dimer in the asymmetric unit, native Patterson peak at 0.500 0.500 0.497). No indication for a P21 twin (L-test and refinement in P21 with twin law), not higher symmetry spacegroup I222 (alternating strong and weak reflections are visible in the diffraction patterns, resolved structural differences in the two protomers of the dimer). Two datasets from different beamlines. As might be expected, the R-factors after refinement are unusually high (e.g. 28/35 [conventional resolution cutoff at 3.1 A], 32/36 with Kay's CC cufoff at 2.6 A). I wanted to compare refinements between different programs to see how they cope with the unexpected bimodal amplitude distribution. _______________________________________________ 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

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Refine three alternate conformations of residues and two loop confirmations.
by AMIT 13 Oct '14

13 Oct '14

Hi All, I am unable to refine three alternate conformations of a residue provided in PDB file prefixed before resname as A,B and C in Phenix dev-1370. When I make it two alternate conformations it runs OK. Also I am not able to refine two loop confirmations, the refinement somehow puts both in the major 2Fo-Fc map peak and makes the almost same, even though the starting loop has different trace.Turning off siulated annealing or making temp. lower or just doing 1 cycle is not doing any good. Any suggestions will be helpful. Thanks, Amit. ------------------------------------------------------- AMIT DAS, Ph.D. PRESENT ---- BUILDING 8600, MS-6460 BIOLOGY AND SOFT MATTER DIVISION P O BOX 2008 OAK RIDGE NATIONAL LABORATORY 1 BETHEL VALLEY ROAD OAK RIDGE, TN 37831-6460 U.S.A. PROTEIN CRYSTALLOGRAPHY SOLID STATE PHYSICS DIVISION BARC, TROMBAY, MUMBAI-400085. INDIA. --------------------------------------------------------

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Test
by Paul Adams 11 Oct '14

11 Oct '14

-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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anomalous difference map
by CPMAS Chen 10 Oct '14

10 Oct '14

Hi, phenix users, A difference map is used to identify whether there is anything not-modeled, say some ligands, ions. Then when I generate anomalous difference map, I should not put the ligand(which contains Br) in the model, right? Or in phenix, after I put the Br-ligand in the model, I should not see the anomalous difference density at the site, right? Could anyone give me a confirmation of this? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Re: [phenixbb] (no subject)
by Sneha Rangarajan 08 Oct '14

08 Oct '14

After running autobuild, the Rfactors were 26/39 (autobuild removed the first 30 residues from the Nter!) but the maps look much better. I ran a quick refinement with default settings and the Rfactors are now 31/39 and can now see the density for my peptide (absent in the model) coming up. I have a few questions- 1) When is a good time to start building the peptide into the density (should I wait until Rfactors improve significantly)? 2) If so, should I be masking the peptide density somehow so that further refinement doesn't flatten out that density? 3) What is a general good strategy for lowering Rfactors? (Esp if the gap between Rwork and Rfree is high..like 28/40 or so)? Thanks a lot, S -----Original Message----- From: Sneha Rangarajan Sent: Wednesday, October 01, 2014 12:54 PM To: 'Paul Adams' Cc: phenixbb(a)phenix-online.org Subject: RE: I think my problem in MR has been one of the chains. Anyway I tried the ideas you suggested and seems like they worked! I used ensembler to create a merged pdb of the problematic chain and used phaser giving both chains as multiple ensembles. It gave me a solution with LLG=474 (highest I have got so far) and TFZ=18.8. I also tried MRage and got a solution with LLG=294. In both these maps, the density for chain1 ("bad chain") is not as good as the other chain but is nonetheless far better than what I have got before. I am currently running autobuild on the solution hoping my Rfactors would be reasonable this time. Thanks a lot for your inputs. They really helped!! S -----Original Message----- From: Paul Adams [mailto:[email protected]] Sent: Tuesday, September 30, 2014 7:51 PM To: Sneha Rangarajan Subject: Re: This likes normal orthorhombic data. In this case I suggest that the most likely issue is the search model (I assume your molecule is fairly small given the unit cell dimensions). I would look at ways to create the best search model using using tools like sculptor and ensembler. You can get Phaser to search for the two domains in the same run but using multiple ensembles. You might also want to try MRage in Phenix, where you can just provide the data file and the sequence and it will try to make the best model and solve the MR problem. On Sep 30, 2014, at 3:32 PM, Sneha Rangarajan <rsneha(a)umd.edu> wrote: > Oh I see. I tried to repeat xtriage with the scala.mtz file and am attaching the log file. > > ________________________________________ > From: Sneha Rangarajan > Sent: Tuesday, September 30, 2014 5:58 PM > To: Paul Adams > Cc: help(a)phenix-online.org > Subject: RE: > > Even i thought so but after i run mosflm and process the data in p21 or p1 and run quicksymm/quickscale it always suggests that the chosen space group is not correct and that it should be p212121. > > I will try looking into Zanuda. Thanks. > > S > ________________________________________ > From: Paul Adams [pdadams(a)lbl.gov] > Sent: Tuesday, September 30, 2014 5:36 PM > To: Sneha Rangarajan > Cc: help(a)phenix-online.org > Subject: Re: > > It looks like your R-merge etc in P222 is very high, what leads you to think this is the correct point group? Can you send the xtriage output for the unmerged P2 data? > > On Sep 30, 2014, at 2:29 PM, Sneha Rangarajan <rsneha(a)umd.edu> wrote: > >> Hi Nat, >> >> I am attaching the Xtriage log file from p222.mtz. >> Would you need anything else (mtz,pdb)? >> >> Thanks, >> Sneha >> <xtriage_237.log> > > -- > Paul Adams > Deputy Division Director, Physical Biosciences Division, Lawrence > Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, > Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, > U.C. Berkeley Vice President for Technology, the Joint BioEnergy > Institute Laboratory Research Manager, ENIGMA Science Focus Area > > Building 64, Room 248 > Building 80, Room 247 > Building 978, Room 4126 > Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul > > Lawrence Berkeley Laboratory > 1 Cyclotron Road > BLDG 64R0121 > Berkeley, CA 94720, USA. > > Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ > 1-510-495-2506 ] > -- > > > > > > > > > > > > > <xtriage_264.log> -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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