Re: [ccp4bb] water soluble protein that needs detergent to be stable

I have not dealt myself with this type of protein, but Alex McPherson tested the detergent beta-octylglucoside (at a concentration of 1.5 %, i.e. above the cmc) for the crystallisation of soluble protein and tRNA (1986, J.Biol.Chem 261:1969-75), the detergent did not hampered the crystallisation, a

Re: [ccp4bb] The importance of USING our validation tools

Could such solvent ordering be a byproduct of unusually low solvent content as both of the structures seem to have (1h6w & 1ocy)? Perhaps cryoprotectant did not penetrate the solvent channels, but the crystal maintained its integrity nevertheless? On Aug 28, 2007, at 1:14 AM, Kevin Cowtan

Re: [ccp4bb] Mean phase difference calculation

Hi All, Thanks for your help with this - cphasematch is clearly what I was looking for. For reference, here is the final script: # compute PHI from refined structure - only necessary if these are the # "reference" phases sfall XYZIN 1VRM.pdb HKLIN 13185_free.mtz HKLOUT 1VRM_HKLREF.mtz << eof

Re: [ccp4bb] Mean phase difference calculation

Kevin Does this give the correlation between two (weighted) complex Fs, which is arguably (ref Bricogne) the best measure, as it corresponds to the map correlation but as a function of resolution? Phil On 28 Aug 2007, at 17:22, Kevin Cowtan wrote: Yup. cphasematch It gives unweighted an

[ccp4bb] permanent crystalliser job - AZ Boston

AstraZeneca has a permanent position at our research site in Boston USA for someone interested in doing protein crystallization. The work will be crystallising bacterial proteins for use in antibiotic drug design. The successful candidate will be able to demonstrate predominant interest and trac

[ccp4bb] Why wwPDB and members are doing a poor job.

This is a reply to the below message posted under "[ccp4bb] The importance of USING our validation tool", which is a rather long thread now. This is part of why I claim that wwPDB and its members are doing a bad job. They have worked to systematically remove "general purpose" information that does

[ccp4bb] Rotation function calculation from 2 patterson maps

Hi, I have two patterson maps created from two observed data sets of similar structures. I want to rotate one map against the other and hence to match them to get the corresponding rotation function. Does anyone have experience how I can do that? Raja

Re: [ccp4bb] The importance of USING our validation tools

I would like to mention some other issues now that Ajees et al. has stirred all sorts of discussions. I hope I haven't opened Pandora's box. >From what I have learned around here, very often, there seems to be little >time allowed or allocated to actually learn--a bit beyond the surface--some of

[ccp4bb] High solvent content crystals

This is a reply to the below message posted under "[ccp4bb] The importance of USING our validation tool", which is a rather long thread now. I worked with Lars Pedersen on a rather high (78%) solvent content crystal, 1VKJ. The interesting thing is that there are 3 molecules in the AU, with 2 well-

[ccp4bb] exporting the "NCS found for Chain ... onto Chain ..." map

Dear all, I am trying to export the intermediate maps obtained in coot when obtaining NCS average maps. That is the ones called "NCS found for Chain ... onto Chain ..." When I use the command (export-map imol "name", in linux, or export_map (imol, "name"), in windows, I manage to obtain a map o

[ccp4bb] solving structure of which 70% is known

Hello, I am trying to solve a multi-protein DNA complex structure from a 3.6 A native data set. The target structure is a dimer (95 aa in each monomer) in complex with DNA( 15 base pairs) plus a second protein of 131 aa. The data has been scaled to P6(1)22 sp. gr. and one target structu

[ccp4bb] Question about the percentages of occupancy for dual conformations.

Dear all, If I have a set of high-resolution data in which there is an important residue having apparent dual conformations, my question is: how or where could I test and calculate the percentages of occupancy for the dual conformations? Any suggestion is welcome. Yours, Jian -- Jian Wu Ph.D. St