[ccp4bb] Postdoc position at the University of British Columbia, Vancouver, Canada

A postdoctoral position is available for a highly motivated individual in the laboratory of Filip Van Petegem, University of British Columbia (UBC), Department of Biochemistry and Molecular Biology (http://www.biochem.ubc.ca ; http://crg.ubc.ca/VanPetegem/). The postdoctoral fellow will be expecte

Re: [ccp4bb] Running Resolve after Sharp?

As a follow-up: About a week or two ago, SOLOMON worked very well at 2.4A Hg-SAD (1A) phased map for ~1100 amino acids and 6 mercury sites. Almost 70% solvent did help quite a bit, I am sure :) Resolve produced comparable maps that were 'subjectively' slightly less pretty. As a crude measure of '

Re: [ccp4bb] Running Resolve after Sharp?

Dear all, funny, I just gave a talk partly abuot this at the IUCr computing school in Kyoto today. Weird coincidences .. Anyway, to explain things a bit more (although previous posts already did most of it): - FP/SIGFP are the 'native' amplitude and sigma - HLA/HLB/HLC/HLD is the phase probab

Re: [ccp4bb] How best to scale together absolute and Fo-Fc density maps?

Hi David One big problem you have here is that, depending on the low & high resolution cutoffs and the completeness of your X-ray data, there will be Fourier series termination and phase error effects on both the electron density maxima and minima. The effects will be to reduce the peak heights

[ccp4bb] How best to scale together absolute and Fo-Fc density maps?

I've computed an electron density map, on an absolute scale, from the atomic positions of a molecular dynamics simulation. I would like to compare this map, in particular a few peaks in it, to a (sigmaA-weighted) Fo-Fc map, calculated from a randomly-shaken & refined (with a few key atoms at zero o

Re: [ccp4bb] Phaser fails with malloc error

Hello Phil and thanks for your email..I was running a VMware fusion Ubuntu session which was grabbing onto a large chunk of memory ( entirely my fault). I didnt realize that virtualized sessions can divert memory away from even the OS and make it essentially unavailable. I am waiting for my ubunt

[ccp4bb] CCP4 windows installation error: 1603: Error installing Microsoft(R).NET Framework.

Hi, We were trying to install the windows version of new ccp4 but met the following error: 1603: Error installing Microsoft(R).NET Framework. Anyone expeienced similar problem, and how to solve it ? Thanks. Hongmin IMPORTANT NOTICE: This e-mail and any attachments may contain confidential

Re: [ccp4bb] Running Resolve after Sharp?

Yes, I did that recently and it worked although I found SOLOMON maps to be (subjectively) better. You should probably use the 'centroid' phases from the eden.mtz (SHARP gurus might want to correct me :)) Artem > Hi > > Sorry for a mixed up question about two great software. > > Has anybody tried t

[ccp4bb] Phaser fails with malloc error

Hello, I am running phaser from the ccp4 6.0.99 suite on an OSX 10.5.4 Leopard , Mac Pro machine . I get the rather ominous error given below . We have gotten similar malloc errors with large datasets before on this machine. In those cases the same jobs ran fine on regular linux. Thought I would wr

[ccp4bb] GNU-Darwin Package set of Molecules Machine

I am starting to get questions about how the Molecules site was constructed. http://molecules.gnu-darwin.org/ I think that it is a good example of what is possible using GNU-Darwin OS and FOSS, free and open source software. I also thought that GNU-Darwinists and others would be interested in t

Re: [ccp4bb] Running Resolve after Sharp?

Your "native" structure factors and their stand.deviations are named FP and SIGFP in the eden.mtz. Further you need the phases and the figure of merit, PHIB and FOM, also from the edem.mtz. If you want to use some other density modification program the Hendrickson-Lattman coefficients might come ha

Re: [ccp4bb] HKL2MAP

Hi Kristof, On Thu, 21 Aug 2008 17:36:52 +0200, Kristof Van Hecke <[EMAIL PROTECTED]> wrote: > I'm looking to obtain a copy from HKL2MAP..? > Does anyone know who to contact and the correct email address please..? There is a link to it from the CCP4 wiki. I found the link by "googling" hkl2map:

[ccp4bb] HKL2MAP

Dear, I'm looking to obtain a copy from HKL2MAP..? Does anyone know who to contact and the correct email address please..? The email of Thomas Schneider ([EMAIL PROTECTED]) is apparently not working anymore. Many thanks Kristof -- Kristof Van Hecke, PhD

Re: [ccp4bb] Protein concentration

Mark, There are two very easy alternatives. First is the Bradford Coomassie Dye binding assay. You can buy a kit from Biorad at the following link: http://www.bio-rad.com/B2B/BioRad/product/br_category.jsp?BV_SessionID=0349900713.1219329576&BV_EngineID=ccchadeemgdfflfcfngcfkmdhkkdfll.0&c

Re: [ccp4bb] Protein concentration

Mark, A little more information on the protein and need would be nice. Is it a large peptide, a small protein, or a recombinant protein? Do you want real quantitative results or semi quantitative (like BCA, Bradford, or Lowry which can be off by 20% or more relative to the [BSA])? Do y

Re: [ccp4bb] Protein concentration

Often the exact concentration is not so important compared to the ability to establish proportional read-out, ease and reproducibility so that systematic variations and comparisons can be made. For considerations of molar ratios of for example protein:ligand complexes one would often screen

[ccp4bb] postdoctoral positions in protein crystallography available at Bethesda Maryland, USA

Two postdoctoral positions are available at the Department of Biochemistry, Uniformed Services University to perform structural and biochemical research on potential drug target proteins from Mycobacterium tuberculosis. The candidates will be involved in recombinant protein expression and purifica

[ccp4bb] Thermal control

Dear all, We are studying the possibility to control the temperature of our optical hutch room at MX beam line (length ~ 15 m, width ~ 3 m, height ~ 2,2 m). If somebody already had experience in the subject, I would like to know the adopted solution and have a notion of its cost. Thanks. Fern

Re: [ccp4bb] Protein concentration

Dear Mark Most easy way to have relative estimation is to run PAGE of your protein with known proteins of known different concentration so u can have a good relative estimation. but for more accurate estimation u can go for Biochemical methods such as Lowry method or BCA method which are more se

[ccp4bb] Protein concentration

Dear all, I would be glad to hear what (simple) method I should use to determine protein concentrations as accurately as possible. Presently, I'm measuring absorption at 280nm with a nanodrop device. I either have 0 or 1 tryptophan and no activity test. Many thanks in advance! Best regar

[ccp4bb] Running Resolve after Sharp?

Hi Sorry for a mixed up question about two great software. Has anybody tried to use Resolve after sharp / autosharp? i.e., escaping the Solomon step other than handedness determination and doing the density modification (& maybe NCS / building) directly with the sharp output? If so, I would appre

Re: [ccp4bb] Coot and OS X Leopard

Hi Paul, and everyone else who responded, Yes, Bill does provide a standalone version, but this required an X-window update which I was not at the time comfortable doing, as my iMac had been updating itself fairly regularly and I didn't know what I was letting myself in for. The consensus appears