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green ball in aspartate
by Murpholino Peligro 31 Oct '14

31 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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