Re: [ccp4bb] Space group problem

Hello Rain Field, I third Felix and Craig, there is nothing unusual about the statistics table you present. The data look pretty good and I would assume P6_something and integrate further than 3.1A. Regards, Tim On 05/07/2014 08:16 PM, wrote: > additional info: > If I let xds go through, it wil

Re: [ccp4bb] Space group problem

It is definitely P6 or P3 with a twinning about the unique axis. The differences in merging statistics between P2 P3 and P6 are not very significant in my opinion. On May 7, 2014, at 1:16 PM, wrote: > additional info: > If I let xds go through, it will choose P6. actually pointless suggest

Re: [ccp4bb] Space group problem

I thought there was a theoretical Rmeas number for I/sigma=2 that is around 50%? In my case, the Rmeas is much higher. Before, we reported P62(4) and got rejected. I'll just change a journal. Hopefully reviewer will not be too picky about that. Thanks to everyone!

Re: [ccp4bb] Space group problem

Your symmetry is of family P6. There is no dramatic difference between 7.8% and 9.3% of Rmerge Go with pointless, wave reviewer nonsense. BTW reviewer of what journal he is? Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnol

Re: [ccp4bb] Space group problem

additional info: If I let xds go through, it will choose P6. actually pointless suggest P62/P64. The thing is the Rmeas and Rmerge are significantly higher for P2/P3/P6 than P1, especially the highest shell. That indicates those higher symmetry ones are not the choice, it that right? (Actually, th

[ccp4bb] Space group problem

Hi all, I have a 360 degree data set collect on home beam. I used XDS to integrate the frames in P1. I progressively merge the data from P1 to P2 or P1 to P3 in XDS and attach the log below. The cell looks like P3 and pointless suggest P6. But the Rmerge and Rmeas are much higher than normal at

Re: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Ed, I guess it depends on what 'successfully' means. The large correlation implies quite an error margin, and I find an occupancy range of +/- 0.2 - 0.3 quite a lot, although this impression may vary depending on what you are discussing w.r.t. the

Re: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

On 05/07/2014 10:52 AM, Tim Gruene wrote: At 2.5A resolution (the resolution this thread is about) But maps ae not made "at 2.5 A" but from say 30A to 2.5 A. In principle (i.e. if the 0,0,0 reflection were used), the effect of diminishing the amplitude of high resolution terms is not to decrea

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Herman, you provided a nice pictorial explanation of the term 'correlation'. I'll leave it to you to run the experiment - I spent a couple of weeks on this project because the separation is quite tricky. Apologies for being sloppy, I referred to

Re: [ccp4bb] Increase in Rfee as the number of cycles increase, using Refmac

Hi Amit Most likely nothing is going wrong. Your final Rfree looks quite respectable for 2.8 Ang. data. It's meaningless to compare the Rfree at the beginning of a refinement with that at the end. Rfree is only meaningful if the refinement has converged. So it is valid to compare the Rfree at

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

Dear Tim, As I see it, the issue is not how good the overall correlation is, but whether the differences in distribution of the electrons (narrow vs. broader) will show up in difference maps, which often show up at the edge of the ion. To make such calculations, I would calculate a difference m

[ccp4bb] Increase in Rfee as the number of cycles increase, using Refmac

Hello, I have a 2.8 angstrom structure of a protein ligand complex. The R/R free before adding the ligand was 0.21614/0.27760 and after adding the ligand, the R/Rfree is 0.2030/0.2691. . However while refining the structure by Refmac 5, I see a decrease in R factor but an increase in R free as num

[ccp4bb] LAST DAY TO REGISTER: SBGrid/NE-CAT Computing School

We're in the final stages of planning for our June Computing School and *registration will close on Friday. *Join us in June for our data processing workshop followed by Phenix and Schrodinger/BioLuminate workshops. *Register Here

Re: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 P.S.: For clarity, I meant to say 'calculate' (with full-matrix refinement) instead of 'collect'. Tim On 05/07/2014 04:52 PM, Tim Gruene wrote: > Dear Bernhard, > > I just happen to collect the correlation between ADP and occupancy > for a publicati

Re: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Bernhard, I just happen to collect the correlation between ADP and occupancy for a publication I am involved in. At 1.5A (!) resolution, the correlation for a single ion between both figures is greater than 90% - there is certainly not a clear d

Re: [ccp4bb] SOS from last century!

Many thanks to Tim and Nat for, respectively, answering both questions fully, and to Ethan Merritt for subsequent help!! Charlie On May 6, 2014, at 1:24 PM, Tim Gruene wrote: > Dear Charlie, > > I still use molscript quite a bit, it is not so old fashioned as you > might think. Raster3D is eve

Re: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

>the negative difference density surrounding your metal ion shows that the >lower occupancy could not be fudged by a higher B-factor Because there is a clear difference between high B-factor and low occupancy: High B factor attenuates high resolution scattering most, while lower occupancy just e

Re: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

Don't forget, metals with their many electrons behave a lot better in refinement than light (CNOS) atoms, because scattering goes as square of number electrons. So you ought to get good behaviour even for joint occupancy and B-factor refinement even at quite rubbish resolutions. On 07/05/201

[ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy

Dear Chris, In my experience, modern refinement program manage quite well to deconvolute occupancy and B-factor. In your case the negative difference density surrounding your metal ion shows that the lower occupancy could not be fudged by a higher B-factor. I would just refine occupancy and B-f

[ccp4bb] CCP4-6.4.0 Update 014

Dear CCP4 Users An update for the CCP4-6.4.0 series has just been released, consisting of the following changes * refmac5: 5.8.0071, fix for peptide planarity * buccaneer: version 1.6 with new MR modes and user interface * pointless: version 1.9.8, fixes for multilattice and output in qtrview * a

[ccp4bb] AW: SOS from last century!

It can be done with pymol: In the box in the lower left corner is an item "selecting residues". By clicking on "residues" you can change it to "atoms" or "C-alphas" When you now click on the appropriate active site atoms, you can select the alpha carbons and a "(sele)" item appears. In the "(sel

Re: [ccp4bb] Crystals Disappearing Overnight

I tried microbatch and the crystals are not stable. They dissolve overnight. I also have reproducibility issue. Can this be due to poor stability of adenosine? Best Maria On Monday, May 5, 2014, Bob Cudney wrote: > Try the microbatch first to see if the problem is related to ionic strength. >

Re: [ccp4bb] SOS from last century!

Hi Charlie, From molscript 2.1.2 you can directly create png, jpeg or gif also, default being postscript file. At least it is working in linux. I am not sure in iMac. Just type molscript -h. It should give the options... HTH -Karthik On 5/6/2014 10:45 PM, Carter, Charlie wrote: I need help