[ccp4bb] contour level for cryoEM deposition: coot vs chimera

Dear all, I am depositing my first cryoEM structure and I am facing the following problem concerning the contour level of the map. Briefly, where do I find the value for the contour level to associate to the uploaded map in Coot? Long story: I worked with coot and I am happy with my map when I se

Re: [ccp4bb] metal coordination at low resolution - restraints

the program that generates these >> > restraints to CCP4 though. >> > >> > Cheers, >> > Robbie >> > >> > >> > >> >

[ccp4bb] metal coordination at low resolution - restraints

Dear all, quickly: is there a way to restrain metal coordination geometry (even angles) in refmac? I am refining a low resolution structure (3.3A) with 2 zinc binding sites. I am pretty sure about metal position (strong anomalous signal) and what are the residues involved in coordination since I

[ccp4bb] space group from direct space coordinates

Dear all, that's probably a trivial problem but I couldn't solve it and I need some suggestions. I have (for curious people, below I explain why) a file with periodic coordinates, ie the content of "many" contiguous unit cells whose asymmetric unit is a point. Can you suggest a program able to defi

Re: [ccp4bb] Problems in crystallization

Why don't you try batch under oil? 2012/11/7 Eva Bligt-Lindén > Dear ccp4 users, > > I have a problem in the crystallization of my target protein. Whenever I > set up a vapour diffusion experiment, either hanging or sitting drops, the > drops spread out. The surface tension is completely lost in

Re: [ccp4bb] cryo for high salt crystal

Hi Min, I agree with Christian Roth, try malonate at high concentration, 2.8 molar is enough. I suggest to adjust the pH to about the value of your xtallization condition. To avoyd salt xtals formation, humidify the environment, some wet paper around the drop can do the job! cheers anna 2012/7/1

Re: [ccp4bb] saxs on xtals

Thanks to all again! Find below my answers/comments to all your replies. Colin Nave, I'll certainly collect higher resolution dataset to look for more diagnostic rings. Apo-ferritin xtallizes in the same conditions with the same cell (I know it from literature), I'll measure it too, to look for di

[ccp4bb] saxs on xtals

Dear all, I'd like some suggestions/opinions about the sense of an experiment proposed by a collaborator expert in saxs. In few words, he wants to collect SAXS data on a suspension of protein xtals to investigate "low resolution periodicity" of the xtal (more details below). The experiment requires

Re: [ccp4bb] B average lower than Wilson

be other causes for limited resolution? Anna Il giorno 05 marzo 2012 16:56, H. Raaijmakers ha scritto: > Anna, > > Did you use TLS refinement, and are looking at the residual B? > then use tlsanl to add the tls contribution. > > cheers, > > Hans > > anna anna schreef:

[ccp4bb] B average lower than Wilson

Dear all, I hope you can help me! I solved a structure at 3.0 A res and everything is quite satisfactory, my only concern is the discrepancy between the B factor from Wilson plot (58.8 A^2) and the average B (36.9). It seems strange, usually the opposite occurs... What does it mean? Which may be th