[ccp4bb] Job offer: Protein Crystallographer (with Ph.D)

PROTEROS is a leading service-provider for the preparation and three-dimensional structural analysis of proteins for structure-guided drug discovery. Our work contributes to fast and rational development of new therapeutic compounds. Since its foundation in 1998, PROTEROS is a continuously growing,

Re: [ccp4bb] PDB format survey?

Joe, I feel that atom serial numbers are particularly important, since they, combined with CONECT records, provide the only semi-standard convention I know of for reliably encoding bond valences information into a PDB file. single bond = bond listed once double bond = bond listed twice triple b

Re: [ccp4bb] SAD: Refine against anomalous data

Thanks for your answer. I guess I did not make it clear. I used the data file for refinement which is also used for phasing (peak_anomalous.hkl). Traditionally, people will reprocess the same set of data for refinement (rescale it in hkl2000 without using the option "anomalous", to yield the non_a

[ccp4bb] SAD: Refine against anomalous data

Dear All. Is there any disadvantage of using the anomalous data set to do refinement? I recently solved a structure using Se-SAD. The anomalous data set was used in refinement with CNS. It gives decent result. Because traditionaly, after phasing we will use the nonanomalous data set in refineme

[ccp4bb] SAD: Refine against anomalous data

Dear All. Is there any disadvantage of using the anomalous data set to do refinement? I recently solved a structure using Se-SAD. The anomalous data set was used in refinement with CNS. It gives decent result. Because traditionaly, after phasing we will use the nonanomalous data set in refinemen

[ccp4bb] adjustable loops, other cryo mounting methods

could anyone comment on the use of these adjustable cryoloops that are out there? could you bend the loop without unmounting from the goniometer? how many times could you adjust it? and has anyone seen cryomounting equipment that is something akin to a capillary mount? i.e., capillary action

Re: [ccp4bb] refmac problem in running arp/warp

Dear Tommi, a) WHAT IS GAMMA?? Gamma is a factor used in the Refmac minimization procedure. In most cases Refmac achieves convergence with gamma = 0.0. In case the program fails to reach convergence with gamma = 0.0, gamma is increased stepwise. This generally facilitates convergence. Regards,

Re: [ccp4bb] PDB format survey?

Edward A. Berry wrote: Ethan A Merritt wrote: On Wednesday 08 August 2007 20:47, Ralf W. Grosse-Kunstleve wrote: Implementations to generate intuitive, maximally backward compatible numbers can be found here: http://cci.lbl.gov/hybrid_36/ From that URL: ATOM 8 SD MET L 48.

Re: [ccp4bb] PDB format survey?

Hi Ethan, > Is that "A" a hexidecimal number, or is it a decimal number > that just happens to have an "A" in front of it? > [A-Z][0-] gives a larger range of values than 5 bytes of hexadecimal, > so I'm guessing it's the former. But the example is not clear. > > (yes I could download and

[ccp4bb] CCP4 web-newsletter 46 (Summer 2007)

Dear developers and users, This is my great pleasure to announce the release of the summer issue of the web-based CCP4 newsletter. I hope all of you will enjoy the reading of these interestings articles. You can find the newsletter and the past issues at www.ccp4.ac.uk/newsletters.php. I wo

Re: [ccp4bb] mr query

The choice of origin is completely arbitrary as far as I can see - any or all of the alternates satisfies an MR search equally well.. Eleanor Kolstoe S.E. wrote: Thanks for the help everyone. I followed Jan's suggestion of running lsqkab which gave a translation vector in fractions of cell ed

Re: [ccp4bb] refmac5 refinement with PEG400

You dont seem to have assigned LIBIN as 1pe.cif - you need to assign your library file - are you using the GUI? Enter 1pe.cif in LIB In slot. Craig McElroy wrote: Hi all, I am trying to refine a structure with a PEG400 molecule using refmac 5.3. I have created the necessary library file and

Re: [ccp4bb] refmac problem in running arp/warp

On Aug 9, 2007, at 15:02, Tommi Kajander wrote: so, a) WHAT IS GAMMA?? gamma is possibly the letter of the greek alphabet that has had most abuse from scientists. http://en.wikipedia.org/wiki/Gamma_%28disambiguation%29 seriously now, I have seen that as well, but never increasing to such

[ccp4bb] refmac problem in running arp/warp

dear all (well experts i suppose), can someone explain what this means (REFMAC): Resolution limits= 19.944 2.600 Number of used reflections = 12652 Percentage observed = 100. Percentage of free reflections = . Overall

[ccp4bb] PhD studentship at University of Groningen, the Netherlands

A position for a PhD student is available at the University of Groningen to study the structure and function of proteins involved in sex pilin biosynthesis. The research will be conducted in the groups of Dr. Thunnissen (Laboratory of Biophysical Chemistry) and Dr. van der Does (Department of M

Re: [ccp4bb] mr query

Thanks for the help everyone. I followed Jan's suggestion of running lsqkab which gave a translation vector in fractions of cell edge of 0.5 0.5 0.5 between the two solutions. I then checked Paul's link to the alternative origins spacegroup page on the ccp4 site and sure enough one of the alternat

Re: [ccp4bb] More than 70 TLS groups

You should be able to change this on its own. In fact, if you get refmac 5.3 from the York site or our prerelease area, then you'll find its been increased to 200. The limit in tlsanl is already a 1000 HTH Martyn On Thu, 2007-08-09 at 12:54 +1000, Craig Morton wrote: > I'm working on a system