October 2014 - phenixbb - phenix-online.org

how to refine everything except n residues in phenix.refine?
by Murpholino Peligro 23 Oct '14

23 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 22 Oct '14

22 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 22 Oct '14

22 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 21 Oct '14

21 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 21 Oct '14

21 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 17 Oct '14

17 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 14 Oct '14

14 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 14 Oct '14

14 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 14 Oct '14

14 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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