Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

I agree completely! The higher resolution data is determined entirely by the atoms with low B factor. If fact, the Wilson B plots I've seen have a distinct curve to them -- They are not straight lines. As one looks to higher and higher resolution the curve gets shallower and shallower. You

Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

Hi Edward This is because taking a naive straight arithmetic average of the B factors as all the programs do is nonsense! To simplify your argument say we have just 2 atoms with B = 10 and 1000. What's the average B? Answer: not 505 but very close to 10 because the atom with B=1000 most likely

Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

What if you have one domain with many B-factors aroun 70 and above, and another domain with B-factors around 20? The atoms with high B-factor will make essentially no contribution to the intensty of spots beyond 3 A, and so have no effect on the slope of the Wilson plot byond that. But they

Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

Le Mardi 12 Mars 2019 19:55 CET, Dale Tronrud a écrit: Dale Good to have the opportunity of going back to the crystallography of the fifties in these post-modern times... There is an essential argumentation that should be recalled. The only reason for the fact that one ignores low-resolution

Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

> I do not believe comparing the average B to the Wilson B has any > utility at all. > > Dale Tronrud There are not many times that reading a CCP4bb posting makes me laugh out loud, but this one made my day. Thanks! Diana ** Diana R. Tomchick

Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

The numeric average of the B factors of the atoms in your model only roughly corresponds to the calculation of the Wilson B. While I always expect the average B to be larger than the Wilson B, how much larger depends on many factors, making it a fairly useless criteria for judging the

[ccp4bb] acceptable difference between Average B-factor and Wilson B

Dear CCP4bb community, The average B-factor (calculated from model) of my protein is 65, whereas the Wilson B is 52. I have read in this BB that "it is expected that average B does not deviate strongly from the Wilson B". How I can evaluate if the difference calculated for my data is

Re: [ccp4bb] Protein modeling issue

Yes you are absolutely right. I believe the problem is the difficulty of fitting valine, leucine and isoleucine rotomers and sidechains to what are essentially "blobs" of map density. Refinement has a hard time with this. I guess we have to stick with the experimental density. Best Ray

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Re: [ccp4bb] Refmac5 refinement question

Hi Ray, Not necessarily close to 1.00 but rather 1.00 or lower. Cheers, Robbie -Original Message- From: Raymond Brown [mailto:ray-br...@att.net] Sent: Tuesday, March 12, 2019 15:56 To: Robbie Joosten Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac5 refinement question Hi

Re: [ccp4bb] Refmac5 refinement question

Hi Robbie, Thank you for your very clear explanation and suggestions. Am I right in thinking that what this means is that the zBOND and zANGLE values in Refmac5 refinement should be made to be close to 1.000? Best Ray On Tue, 3/12/19, Robbie

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Re: [ccp4bb] 3D

Dear all, I do agree with Paul: VR is just perspective images that don't give you a stereoscopic view and is hence poorer. This being said it is possible to build a structure in mono: all you need is to have enough and the right projections in the plane... I started 20 years ago using side

Re: [ccp4bb] Refmac5 refinement question

Hi Ray, This is how I see it: Because different bond length and angle target tolerances/sigmas you cannot compare them on an absolute scale. What is less likely? A two 0.020A deviation in the CD1-CG in PHE or a the same deviation in the CD1-CG bond in LEU. If you think they are equally likely,

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