Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

I find Lothar's comments regarding H and RSRZ excellent! I would think of it as a pretty much bug report. I hope developers at that end listen. This goes very well in line with Phoebe's comment earlier today. Pavel On Mon, Nov 28, 2016 at 2:51 PM, Dale Tronrud wrote: >

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

On 11/28/2016 12:52 PM, esse...@helix.nih.gov wrote: >> I found that one can get RSRZ to go way down by loosening the geometry >> restraints. The result is a crappy structure and I don't recommend doing >> that, but it does get all the atoms crammed into some sort of density. > > Your

[ccp4bb] sorry for spamming

Dear all, sorry for spamming your mail boxes - there is a bug in our system. Best regards, Sacha

Re: [ccp4bb] wavelet application in CCP4

Dear Charles, if you are interested in applications of wavelets to macromolecular crystallography problems, you may look also at a slightly earlier publication by Vladimir Lunin in Acta Cryst (2000) A56, 73-84 "Fixed-scale wavelet-type approximation of periodic density distributions."

Re: [ccp4bb] wavelet application in CCP4

Dear Charles, if you are interested in applications of wavelets to macromolecular crystallography, you may look also at a slightly earlier publication by Vladimir Lunin Acta Cryst. (2000). A56, 73-84

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

> I found that one can get RSRZ to go way down by loosening the geometry > restraints. The result is a crappy structure and I don't recommend doing > that, but it does get all the atoms crammed into some sort of density. Your observation is quite interesting. I can add this: when we were

[ccp4bb] Need suggestions on Mac Pro and accessories for structural biology work

Dear CCP4 community, I am posting to get your suggestions on a Mac Pro system for structural biology and not entertainment. Any comments will be appreciated. Please feel free to send off line messages if you prefer. My target is a Mac Pro with 8-12 cores and Dual AMD FirePro D700 GPUs. I will

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

On Mon, Nov 28, 2016 at 10:17 AM, Phoebe A. Rice wrote: > RSRZ, in my most humble of opinions, seems like one of those statistics > that is far more useful in theory than reality. > Can't agree more! Pavel

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

I found that one can get RSRZ to go way down by loosening the geometry restraints. The result is a crappy structure and I don't recommend doing that, but it does get all the atoms crammed into some sort of density. RSRZ, in my most humble of opinions, seems like one of those statistics that is

Re: [ccp4bb] wavelet application in CCP4

Dear Charles, if you are interested in applications of wavelets to macromolecular crystallography, you may look also at a slightly earlier publication by Vladimir Lunin Acta Cryst. (2000). A56, 73-84

Re: [ccp4bb] wavelet application in CCP4

Hi Phase extension, albeit at high (rather than low) resolution (and I don't think it uses wavelets) has been more recently popularised in the various implementations of the "free lunch algorithm". Otherwise that might be a good place to start looking. Harry -- Dr Harry Powell Chairman of

Re: [ccp4bb] wavelet application in CCP4

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Peter Main is retired. Julie works on different stuff now. I'm not aware of any application aside what Julie implemented at the

[ccp4bb] wavelet application in CCP4

Dear, All I happen to see this paper, Low-resolution phase extension using wavelet analysis. Main P 1, Wilson J However, I did

Re: [ccp4bb] Density for an unknown ligand

Dear Wei, I am not sure which molecule this density corresponds to but I think you should also consider the possibility of a molecule that can be fitted in the density but is in fact at a special position meaning that the axis of symmetry passes through the center of the molecule leading to

Re: [ccp4bb] Density for an unknown ligand

Dear Wei, I think Prem’s suggestion that the molecule is on a symmetry axis is right. There are 2 images in those that you have sent that show a two fold rotation axis within the missing density, so I think the density corresponds to two molecules. - possibly something like PMSF? Did you

[ccp4bb] CCP4 Study Weekend 2017 - EMS back up

Dear all Registration for the CCP4 Study Weekend 2017 is now back online at https://eventbooking.stfc.ac.uk/news-events/ccp4-study-weekend-2017-344 . There are now approx. 30 places available. Payment can also be made by credit card through EMS by logging into your account at