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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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