Re: [ccp4bb] Highest shell standards

This is a good point - I had thought that D would be very low for an incomplete shell, but that doesnt seem to be true.. Garib - what do you think? Eleanor Petrus H Zwart wrote: I typically process my data to a maximum I/sig near 1, and completeness in the highest resolution shell to 50% or

Re: [ccp4bb] How to subtract one electron density map from another

Qing Xie wrote: Hi, I'm trying to get the difference map by subtracting the native electron density map from the complex electron density map. MAPMASK has a function of ADD/MULT, but I don't know how to use it? Any other ways to attack this problem in real space? Thanks in advance, Qing

[ccp4bb] CCLRC changes it's name

Dear All, Apologies, this is not MX related, but is important, especially if you are an industrial user. From the 1st April 2007, CCLRC will be an ex Research Council. It is merging with PPARC and becoming Science Technologies Research Council (STFC). CCLRC will remain a legal entity

Re: [ccp4bb] CCLRC changes it's name

Oops (and not object orientated programming either) Science and Technology Facilities Council (STFC) Charles On 23 Mar 2007, at 11:56, Charles Ballard wrote: Dear All, Apologies, this is not MX related, but is important, especially if you are an industrial user. From the 1st April 2007,

Re: [ccp4bb] Highest shell standards

I seem to recall this being discussed at some point. For the difference electron density map, there clearly isn't a downside to loss of reflections, i.e., the coefficients in the map generation are formally zero for Fo-Fc (which all the scaling, weight, sigma-A bits in there). If the phases are

[ccp4bb] F(+) and F(-) to F(mean) ??

Dear all, I have anomalous data from CNS and I have converted them in CCP4 format with 'cns2mtz' (from Kevin Cowtan). But there are F(+) and F(-) columns, and I would like use DM which need Fmean only. Is there an utility in CCP4 which converts F+ and F- to Fmean ? I have tried mtzMADmod but my

Re: [ccp4bb] Highest shell standards

I don't understand why should D be low for an incomplete shell? According to Randy's tutorial: D includes effects of: difference in position or scattering factor missing atoms difference in overall scale or B-factor i.e. all kinds of error in the SF model, but this is surely uncorrelated with

[ccp4bb] Job opportunity at the Structural Genomics Consortium

A great opportunity is on offer to work on one of the most exciting areas of structural biology - that of integral membrane proteins with a focus on ion channels and transporters. Position Title: Postdoctoral Scientist - Membrane Receptor Signalling Group Grade: Salary scale for

Re: [ccp4bb] change the B-factor for a residue

Below is a horrible hack awk script which patches a file of scores into a PDB file. I'm sure these a nicer way of doing this! Phil Is there a program in CCP4 with a command to change the B-factor of a single residue? I checked the documentation for pdbset and it seems to assign B-factors

Re: [ccp4bb] Nature policy update regarding source code

Hi, I believe such requirements concern only Nature Methods rather than Nature by and large. Regards, Nadir Mrabet Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy

[ccp4bb] change the B-factor for a residue

Is there a program in CCP4 with a command to change the B-factor of a single residue? I checked the documentation for pdbset and it seems to assign B-factors only for the whole molecule. What I'd like to do is plot a given residue property in a graphic software using the color by b-factor

Re: [ccp4bb] change the B-factor for a residue

--- Juergen Bosch [EMAIL PROTECTED] escreveu: How about Coot ? Click the residue you want to change and hit Resdiue Property. That's how I used to do it, but things start to become boring when one needs to do it with more than one pdb file with about 200 residues each. Does coot accept some

[ccp4bb] CXDI workshop at the APS

Dear Colleague, A workshop on coherent x-ray diffractive imaging in biology and nanoscience will be held at the 2007 APS Users Meeting. This emerging technique offers an approach to understanding biological systems that complements crystallography, EM, and solution x-ray scattering by its

[ccp4bb] Inclusion body

Dear All, I got enclusion body in many cases when I tried to express human proteins in E coli. I would like some suggestions on how to go about it. I would also like to try co-expression of GroEL/GroES or DnaJ/DnaK, and would like to know where to get the plasmids. Any help or comments would be

Re: [ccp4bb] Inclusion body

Hi Weijun, you can get a kit from Takara (chaperone kit #3340) which has five different chaperone plasmids (combinations of various chaperone). It worked for me assofar that I could express huge amounts of the chaperones, but my target protein was either not expressed at all any more (seems as if

Re: [ccp4bb] Inclusion body

Weijun, There are literally hundreds of options you can pursue - obviously a comprehensive and detailed list of suggestions would not fit in a little email (in fact they don't all fit into a one-volume book). It would be helpful to narrow things down a bit - for starters, for one or two cases

Re: [ccp4bb] Inclusion body

Dear Weijun Have a look at our REFOLD database - there are some examples of chaperone assisted refolding as well as many protocols for refolding of disulphide-rich proteins http://refold.med.monash.edu.au good luck ashley On 24/03/2007, at 12:23 PM, [EMAIL PROTECTED] wrote: Hi Weijun,

Re: [ccp4bb] Expression hosts (was:Inclusion body)

As has been suggested, you can try other hosts - for instance Gram positive bacteria (Bacillus megaterium is an interesting host as are other bacilli, especially if your protein is secreted), other Gram negative bacteria (Pseudomonas for instance), Can anyone comment on availability of Archaea