Re: [ccp4bb] Refmac out-put file header information

Dear Mitch, I did not run uniqueify but i have added free-R flags by running xdsconv with extra command line in in-put file GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 Dear Leo, This 94.5% is total completeness of the data. I am pasting below the header information in that PDB file. REMARK 3

Re: [ccp4bb] Refmac out-put file header information

Hi Yusuf, You need to run the uniqueify script to expand the input file to include all possible reflections (observed and missing from your data set). I have not run xdsconv with the GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 However, generally after running xdsconv without that command, it is

Re: [ccp4bb] Refmac out-put file header information

Hi Mitch, When i checked carefully again log files. I came to know that, when i used xdsconv then only the total completeness have been changed from 95% to 100%. Before xdsconv all log-files have original 95%. Now what should i do?? thanks, yusuf Quoting Miller, Mitchell D. [EMAIL

Re: [ccp4bb] interface

Which brings up something about PISA. If I run PISA on pdb entry 2IE3, which I'm familiar with, I get the following numbers from PISA and CCP4's AREAIMOL (surface areas in Angstrom^2) for the A:C interface. PISA for 2IE3 Automatic A:C interface selection 907.9 (a crystal

Re: [ccp4bb] interface

Phil, I had a follow up conversation regarding this very topic. Here is an excerpt: The following is from Chothia and Janin (1975) Nature, 256:705-708, one of the early articles regarding buried surface area and protein interfaces: The surface area buried in the complex is then defined

[ccp4bb] April fools hand issue solved

Dear crystallographers, although many laughed off one CCP4BB poster's comments several months ago as an April fools' trick (he had proposed that Bijvoet had actually botched the job, as I remember), there is now apparently experimental evidence against that trick: Was Bijvoet right? Sodium

Re: [ccp4bb] interface

The way I look at it; BSA the the total surface area defined within two bisecting 3D curves, interface area is the minimum surface area that can be that can be produced by interpolation between regions at bisect each other. Probably not the best definition. On a side note: can one really use

[ccp4bb] merohedral twinning problem

Dear, Sorry for the off-topic question. I'm facing a (probably) merohedral twinning problem, regarding a small molecule. Using Xprep, I get a Hexagonal P-lattice with cell: 18.014 18.014 22.048 90.00 90.00 120.00 Mean |E*E-1| = 0.902 [expected .968 centrosym and .736 non-centrosym]

[ccp4bb] stereo in coot with RHEL 5

Hi- There seems to be a problem enabling stereo with coot on RHEL 5, which results in the error: CATASTROPHIC ERROR:: in gl_extras no GtkGL widget! WARNING:: switch to hardware_stereo_mode failed I've found mention of this through a google search, but no solution. Has anyone encountered this

Re: [ccp4bb] April fools hand issue solved

Could be a case of modeler bias. Just look at the name of the institute. This is like having a Jessie Helms endowed chair in the therapeutic benefits of tobacco. On Aug 8, 2008, at 8:31 AM, Jacob Keller wrote: Dear crystallographers, although many laughed off one CCP4BB poster's comments

[ccp4bb] map coefficients - origin shift

Dear all, Is there a program, which will shift the origin of a set of mtz map-coefficients by means of a fractional coordinate vector R? Thanks, -Martin -- Martin Laurberg, PhD Noller Laboratory 225 Sinsheimer Laboratories University of California at Santa Cruz CA-95064 Santa Cruz USA