Re: [ccp4bb] Hydrophobic hotspots

Hi Hugh, Waltz is an excellent web-server to give very good results on amyloidogenic regions based on sequence stretches (correlate the regions with hydrophobic patches by hydropathy plot obtained from Expassy-Protscale). Aggrescan and PASTA are two other reliable servers for the same kind of

[ccp4bb] Hydrophobic hotspots

Hi all, can anyone recommend a program for identifying hydrophobic (aggregation) hotspots using either the amino acid sequence and/or structural data. Thanks in advance for your help Hugh Ps. Have tried aggrescan but would like to try a few others and compare, ideally a more structural based

Re: [ccp4bb] About weighting factor settings in new ccp4i2

The simple matrix weighting option (x-ray/restraints weight) is under main refinement option and set automatically. Change that to manually and you can put the value in if you want to avoid too many keywords. There is even an option in advanced parameters to run several quick refinements to

[ccp4bb] Trainee/student, undergraduate or master student Student internship

Job ID 213766BR Position Title Master Student Division NIBR Business Unit CBT - NIBR Country Switzerland Work Location Basel Company/Legal Entity Novartis Pharma AG Functional Area Interns/Students on Novartis Payroll Job Type Full Time Employment Type Internship Job Description Trainee/student,

Re: [ccp4bb] resolution limits

Andrew, phenix.refine may not use reflection-outliers (Read, R. J. (1999). Acta Cryst. D55, 1759–1764.). Typically this is just a few reflections. If you have a good reason to disable this, then use xray_data.outliers_rejection=false. P.S.: There is Phenix mailing list for Phenix-related

[ccp4bb] Software Engineer / Bioinformatician position at PDBe

We are looking for a bioinformatician to integrate value-added information on enzymes and catalytic binding sites with the PDB structure data and make it available programmatically and via PDBe website. The work will involve close collaboration with the Thornton research group and with UniProt

Re: [ccp4bb] resolution limits

Hi Eleanor, what you say is of course true, particularly in the case of the 1st dataset where probably the indices go down to 52 Ang. but the measurements only start at 36 Ang. But still it's hard to see how for the 2nd dataset, if the low res cut-off of the indices and/or measurements is 57

Re: [ccp4bb] resolution limits

The resolution limits of the measured data are not changed but your output file must contain all possible h k l even if there is no observations for the lowest resolution ones.. dont worry about it! Eleanor On 26 July 2017 at 08:36, Andrew Marshall wrote: >

[ccp4bb] Postdoc position in ubiquitin signaling

Postdoc Position Structural Mechanisms of Ubiquitin Ligases in Cancer A postdoc position is available in the lab of Sonja Lorenz at the Rudolf Virchow Center for Experimental Biomedicine, Würzburg, Germany. The Lorenz lab explores the molecular mechanisms of ubiquitin ligases and their

[ccp4bb] resolution limits

Dear crystallographers, I have two datasets that were merged/scaled using ccp4's aimless, with resolution ranges of 52-1.7 and 57-1.9. However, upon refinement, the resolution range used by phenix.refine is 36-1.7 for one and 104-1.9 for the other. 1) Why does phenix.refine change the low