Re: [ccp4bb] problem with HKL2000 license

Make sure the command "hostname" returns the same value as it did before the reinstall -- check in the cr_info file that access_prod produces. Almost always, it's that the domain name is either now added or alternatively removed, i.e. that you used to have "machine.some.domain.edu", and not it's

Re: [ccp4bb] NCS-averaged composite omit map?

Use COOT to do NCS averaging then look at the maps of B onto A a well as the averaged one to see where differences might be. Eleanor Paul Paukstelis wrote: I'm working on a 4.5-A structure with 4-fold NCS. I've generated a SA composite omit map and all the protomers look pretty good, but with

Re: [ccp4bb] buried surface area

I use PISA - it tells you lots of things and I think will do this as well http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html You can download your coordinates.. Will need to name subunits A and B or something I think.. Eleanor Gloria Borgstahl wrote: Hello all, What is the easiest way, th

[ccp4bb] Postdoc position in Korea (Samsung Biomedical Research Institute)

Postdoctoral Position - Protein Crystallography Samsung Biomedical Research Institute Sungkyunkwan University School of Medicine Suwon, Korea A post-doctoral position in protein crystallography is immediately available at Sungkyunkwan University School of Medicine/Samsung Biomedical Research

Re: [ccp4bb] weird thing about MR

You say you have only found one of at least 3 copies? Why not continue and find the other 2 before starting refinement? Phaser will do that automatically if you ask for 3 molecules.. Refinement of structural fragments is always tricky.. Eleanor Yi Xue wrote: Dear all: I have a dataset d

[ccp4bb] TFT monitors n stereo

Hi all i have a non CCP4 query. pls tell me how to view stereo images on a TFT monitor. thanx vineet gaur

Re: [ccp4bb] extra high B factor

Dear All: According to your suggestion, I have set the peptide's occupency to 0.5. Two strategies were employed. 1. Direct using Refmac restrained refinement for 10 cycles. The B factor only drops to around 100. R/Rf did not change, either. 2. Direct CNS B-fator refinemen. The B factor drops to a

Re: [ccp4bb] extra high B factor

Well - it is extremely likely that the peptide is partially occupied and the occupancy may well be < 0.5.. But at this resolution you are going to have great difficulty deciding whether you should have Occ=1.0 Occ = 0.5 Occ = 0.33 As your Rfactors show it makes very little difference t

Re: [ccp4bb] extra high B factor

Does anyone know a program can perform the ocupancy refinement? Or we always only refine B factor to reflect the occupancy? Thanks On 4/30/07, Eleanor Dodson <[EMAIL PROTECTED]> wrote: Well - it is extremely likely that the peptide is partially occupied and the occupancy may well be < 0.5..

Re: [ccp4bb] extra high B factor

Shelx can refine occupancies. Arti > Does anyone know a program can perform the ocupancy refinement? > Or we always only refine B factor to reflect the occupancy? > > Thanks > > > On 4/30/07, Eleanor Dodson <[EMAIL PROTECTED]> wrote: >> >> Well - it is extremely likely that the peptide is partially

Re: [ccp4bb] extra high B factor

Dear all, Frankly speaking I am having some doubts about this whole discussion. 1. Apparently, it does not make a difference in R and Rfree whether the peptide is in the structure or not. This does suggest that there is very little (if any) information about the peptide in the data. Righ

Re: [ccp4bb] extra high B factor

Dear Jiamu Du, what were the exact concentrations (Molar values please) of protein and peptide in the co-crystallization experiment? This may help in estimating the (possible) occupancy of your peptide. Jeroen. JDwrote: Does anyone know a program can perform the ocupancy refinement? Or we

[ccp4bb] AW: [ccp4bb] extra high B factor

Dear All, What I read from the email is that the R/Rfree values do not change much if you refine with high occupancy-high B or with low occupancy-low B, which is what one expects with 2.6 Å data. This is something different from leaving out the inhibitor from the refinement. Considering the a

Re: [ccp4bb] extra high B factor

> If you assume atomic B-factors of 100 or larger and > calculate the density, I really can't see how this is possible. Well, I do. The recipe has been published in NSB as a cautionary tale. http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf and there is quite fail-safe away to inves

[ccp4bb] Electron Microscopist Position

Electron Microscopist Researcher and Facility Manager Indiana University in Bloomington (IUB) has a position open for an Electron Microscopist Researcher and Facility Manager. IUB is purchasing a 300 kV FEG TEM designed for both biological and material science applications, including cryo, tom

[ccp4bb] Buried Surface Area - summary

Here was the query.What is the easiest way, these days, to calculate the buried surface area between two subunits of a protein? Here are the software and links received (thank you all):1. 4+ votes for PISA  - This following website is great and does a very nice job of analyzing protein interfaces (