Re: [ccp4bb] ctruncate

There are two known issues with ctruncate: one with the anisotropic correction and one with the fitting of as a function of resolution. The first is easily addressed - try turning off the anisotropy correction. That may solve the problem. Ricardo Aparicio wrote: Dear all, For the same inpu

Re: [ccp4bb] write out unmerged Scalepack file in HKL2000

Hi Alexandra, Sure.  Go to the Macros tab and add "no merge original index" during scaling window. Cheers, Scott * Scott T. R. Walsh, Ph.D. Assistant Professor Center for Advanced Research in Biotechnology University of Maryland Biotechno

[ccp4bb] write out unmerged Scalepack file in HKL2000

Hi all: Is there a way to write out UNMERGED Scalepack files from HKL2000 ? In the older days of Scalepack, I remember you could have a NO MERGE in the script, but what about the newer HKL2000? If there is a way , well, I could not find it... Thanks a lot, Alex Alexandra M. Deaconescu

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

I say deposit it both ways, someone needs to start keeping those computational chemists on their toes.

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

P6122 or P6522 make sure you get it right, otherwise the SpaceGroupPolicePatrol will get you :-) Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore,

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

William G. Scott wrote: On Sep 8, 2009, at 4:29 PM, Ezra Peisach wrote: If you want to gamble - go w/ P6122... Data from the PDB indicates that there are 1.5x as many proteins w/ P6122 vs P6522... So if you believe in the overall anisotropy of the universe (neglecting the weak interaction)

[ccp4bb] Postdoctoral fellowship in Stockholm

Postdoctoral fellowship in functional studies of membrane-bound enzymes Opening for a postdoctoral research fellow to join the Structural Biology group at the Division of Glycoscience, KTH Biotechnology (Royal Institute of Technology), Stockholm, Sweden. We are looking for an highly motivated,

[ccp4bb] AW: [ccp4bb] Ignoring DFIX instructions in the refinement (SHELX)

Dear Sergii, >refinement I checked a structure in Coot and all atoms of these 3 molecules >were separated from each other and on much bigger distances then in DFIX >instruction In the header, you have set the connectivity to zero for residues 4001 to 4288. CONN 0 O_4001 > O_4288 This is also a

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

On Sep 8, 2009, at 4:29 PM, Ezra Peisach wrote: If you want to gamble - go w/ P6122... Data from the PDB indicates that there are 1.5x as many proteins w/ P6122 vs P6522... So if you believe in the overall anisotropy of the universe (neglecting the weak interaction), it is time for some mo

[ccp4bb] ctruncate

Dear all, For the same input in a ccp4i (v .2.0.4) Scala (v. 3.3.9) job I have obtained the following: with CTRUNCATE (v. 1.0.01) == Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. Low

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

Thanks for all the replies. I guess there's no easy way to distinguish between the two space groups before obtaining an electron density map. Cheers. Rafael. Eleanor Dodson wrote: Rafael Couñago wrote: Hi, I am in doubt between the enamtiomorph space groups, p6522 and p6122. Is there

Re: [ccp4bb] Help with improving these crystals

Hi One of the easiest things to try is in-situ proteolysis - chymotrypsin (1:1000 or so, we add 1ul of a 1mg/ml solution of chymotrypsin in H20 to about 100ul of protein solution) is the classic - mix the protease with the protein and then set up as normal. Of course you can try other protease

Re: [ccp4bb] Off topic: Purification steps

Dear Ronaldo! I think this should be very straight forward, Generally, after Ni-column protein can be digested with TEV (1:50, or 1:100 ratio) either at room temperature or at 4C depending on the stability of the protein. I had tried this at room temperature, overnight cleavage at 1:100 (TEV: Subs

Re: [ccp4bb] Help with improving these crystals

Beyond improvement via 'chemical' means, I would heartily recommend mutagenesis for crystal packing improvement. I would be glad to help you with the latter if you're interested. Artem > Dear All: > We have been struggling to improve the crystals shown in the attachment. > These crystals form fro

Re: [ccp4bb] Help with improving these crystals

Have you tried microseeding or macroseeding? The original crystals for my Ph D project only diffracted to ~8 angstroms. Microseeding gave crystals that eventually diffracted to ~2.0. Here are two refs that might be useful: Bergfors, T. (2003). "Seeds to crystals." J Struct Biol 142(1): 66-76.

[ccp4bb] Team Leader Position at EMBL, Hamburg Unit

Dear All, there is a job vacancy at the EMBL Hamburg for the following position: *Team Leader Computational Infrastructures and Applications* EMBL is building an integrated facility in structural biology at the new PETRA-3 synchrotron ring at DESY, Hamburg, Germany. The optical properties of PET

[ccp4bb] Purified Membrane Protein Samples for CrystalJet

We are developing a prototype inkjet based crystal screening platform (NIH SBIR funded). Details regarding the system are posted here: http://www.microfab.com/equipment/pdf/CrystalJet_Handout_rev3.pdf I'm looking for purified membrane protein samples to further validate the system. Please let m

Re: [ccp4bb] Off topic: Purification steps

Hi Ronaldo, We immediately desalt after His-Trap (desalting column connected in series) into an Imidazol free and low salt buffer and digest with 1:50 to 1:100 TEV:substrate ratios (w:w) at RT or in the cold room (time often a compromise between protein precipitation and completion of the cut)

[ccp4bb] Off topic: Purification steps

Dear CCP4bb users (this is an off-topic question), We have a few proteins being expressed as HIS-TAG_(TEV_cleavage_site)_PROTEIN and we are about to initiate the purification steps. We have already used the HiTrap-Chelating columns from GE for the first purification step (affinity chromatography)

[ccp4bb] Postdoc position in drug discovery - King's College London

A 2+ year industry funded post-doctoral research assistant position suitable for an experienced protein crystallographer is available at King's College London. The project in the laboratory of Andrew Beavil and Brian Sutton involves structure based drug discovery for the inhibition of an important

[ccp4bb] Postdoc position at GlaxoSmithKline

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Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

Rafael Couñago wrote: Hi, I am in doubt between the enamtiomorph space groups, p6522 and p6122. Is there a way to distinguish the correct one in the absence of a molecular replacement model? Cheers. Rafael. No is the short answer.. If you have heavy atom data with anomalous scattering yo

Re: [ccp4bb] purchasing heavy atom clusters

Hi Engin, On Tue, Sep 08, 2009 at 04:06:20PM -0700, Engin Ozkan wrote: ... > On a related point, I would appreciate any pointers, especially on > software like shelx, sharp, solve, and mlphare, on treating clusters at > resolutions where the heavy atoms are not resolved (at 6A or worse). > U

[ccp4bb] Postdoc Positions in Structural Biology at Astex Therapeutics

Career Opportunities at Astex - September 2009 Astex Therapeutics Ltd, based in Cambridge, UK, was founded 10 years ago and is a world-leading biotechnology company that has pioneered fragment-based drug discovery (FBDD) platform to discover and develop medicines in areas of unmet medical need. A