[ccp4bb] XSCALE!!! ERROR

Dear All; I am trying to to xsale several data sets together, but it gives an error of !!! ERROR !!! INSUFFICIENT NUMBER OF COMMON STRONG REFLECTIONS. PROGRAM IS UNABLE TO PRODUCE A SCALED DATA SET. resolution of data sets is ranged from 3.25 to 5A Any suggestion will be highly e

Re: [ccp4bb] cryo protection

Hi Len; I was having exactly the same problem with my crystals, but when we grow the crystals in presence of increasing concentration of Glycerol and MPD starting from 0.5 to 10%. The crystal doesn't appear after 3% of Glycerol or MPD but the one which appear in 2.5 to 3 % were much resistant to c

[ccp4bb] Structure Refinment problem

Dear all; I have a structure at 3.3A resolution of about 140kDa protein containing eight domains, in tetragonal space group.I also have the structure of most of the individual domains.I almost refined the structure in all the possible space groups, the best space group at the moment are the P42 wi

Re: [ccp4bb] per-residue RMSD calculation for homologous structure

Dear Dhiraj; Please try the following web site http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html Here you will find a number of option for structure base sequence alignment no matter what is the similarity of your structures. Regarding the RMSD of every residues you can find this option

[ccp4bb] Structure based and motif based sequence alignment

Dear All; I have structures of two protein one full-length while the other truncated at the c-terminus(one from prokaryote while the other from eukaryotes). Now I want to do the sequence alignment of these two proteins from all species in such a way that the structure based sequence remain constan

Re: [ccp4bb] Structure based and motif based sequence alignment

Frederic wrote: > Muhammed bashir Khan wrote: >> Dear All; >> >> I have structures of two protein one full-length while the other >> truncated >> at the c-terminus(one from prokaryote while the other from eukaryotes). >> Now I want to do the sequence alignment of

Re: [ccp4bb] glycerol

Hi Ray; In case of my protein 5%-10% of glycerol help to increase the solubility both of the soluble domain as well as the trans-membrane domain,improve crystal quality dramatically and even prevent radiation damage to some extent. Best of luck Bashir On Thu, March 10, 2011 23:04, Ray Brown w

[ccp4bb] Molecular Replacement

Dear All; We have solved a crystal structrure of protein at 1.8 A. I have now another crystal of the same protein in aother unit cell,for the new crystal type resolution is 3.6 A but when I use our structure as a seach model It does't give any solution. Any suggestion would be highly appreciated.

[ccp4bb] R merge and R init

Dear All; I have a crystal structure collected on in house X-ray facility from Bruker using Xprep. I submitted the paper but the reviewer ask for the R merge. As I can't access to the computer at the moment its crashed out. But I have the prp file which have the R init values. My question is!!! 1

[ccp4bb] Crystals Soaking in Divalent metals salts.

Dear all; I am working with protein which are supposed to be bound with Magnesium and Cobalt metals.I have now its crystals which are diffracting quite nicely.I want to know the Magnesium and Cobalt binding residues in the target protein. When I add magnesium or Cobalt salts to protein solution

[ccp4bb] Solvent accessible regions of the channel (Pore)

Dear all; Can anybody help me how I can make the solvent accessible surface(inside) of the channel(pore)by pymol, or by any other programme. Thanks in Advance -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna B

[ccp4bb] Structure Based Sequence Alignment

Dear All; Can some body tell me a website for structure based sequence alignment, which can also pin point the similar and identical residues in different colors. regards Bashir -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of

[ccp4bb] Membrane Protein Crystal Optimization

Hi all; I have crystal of membrane protein (110 kDa) in several different conditions. I optimized several of them and tested it for their diffraction. It does not goes behind 10A at CLS and SSRL. The protein is purified by two steps nickel and gel filtration. The crystal grow very fast and reach

Re: [ccp4bb] HKL2000 Display

Waterman wrote: >> Hi Muhammed, >> >> It looks a lot to me like denzo thinks your detector has a larger >> image size than the actual number of elements in the array. However, I >> don't use denzo so I'm not commenting from experience. >> >> Cheer

[ccp4bb] MR_ROSETTA

Hi All; Could some body explain why I am getting the error message when running MR-Rosetta. Message is " Sorry cannot locate a binary starting with mr_protocol.default' in the directory /home/phenix/rosetta_2014.34.57213_bundle/main/source/bin I just download it and locate it in the preferences,

[ccp4bb] Molecular Replacement

Hi All; I have a native data set of membrane protein at 3.8A. I nearly use all the options for Molrep. I would like to ask, is some body has some special strategy which can work for difficult Molrep Thanks you in Advance Bashir -- Muhammad Bashir Khan *

Re: [ccp4bb] Crystal Optimization

Dear All, Thanks alot for your valuable suggestion.I hope I will find out the solution now. As far as to giveup is out of question Thanks once agin Regards; Bashir On Wed, July 11, 2012 05:25, Tuhin Bhowmick wrote: > Dear Muhammad, > > I had a similar case, and the crystals could indeed b

[ccp4bb] Structure Refinement

Dear All I have a data at 2.75A. I process it in Space group P3121, using HKL3000. Run a molrep,find three molecule in a unit cell. I am trying to refine it with phenix, the R and R-free stuck at 34 and 41 respectively. Crystal: The crystal seems multiple thin plates and I tried to freeze the pos