Re: [ccp4bb] Chiral volume outliers SO4

2012-07-15 Thread Dale Tronrud
On 7/13/2012 1:58 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I am surprised by the discussion about chiraliy of an utterly centrosymmetric molecule. Shouldn't the four Oxygen atoms be at least from a QM point-of-view to indistinguishable? What reason is there

[ccp4bb] crosslinking protein by non-natural amino acids

2012-07-15 Thread Jan Rashid Umar
Dear All, I am interested in cross-linking of a protein molecule with a complex (isolated). The protein is expressed recombinantly from E.coli and we are would like to precisely map the residues involved in interaction. So far, all other crosslinking methods (targeting amines etc.) have not

Re: [ccp4bb] Chiral volume outliers SO4

2012-07-15 Thread Ethan Merritt
On Sunday, 15 July 2012, Dale Tronrud wrote: There are good reasons for maintaining order in this human-induced numbering scheme. A common operation is to superimpose two molecules and calculate the rmsd of the positional differences. This calculation is not useful when the Val CG1 and

Re: [ccp4bb] strict structure based alignment

2012-07-15 Thread Eric Pettersen
On Jul 13, 2012, at 4:00 PM, Christian Roth wrote: I want align a couple or protein structures by secondary structure matching to one target and want get a kind of aminoacid alignment file e.g. what residue fit the other, without adjustments due to sequence based alignments. I tried

[ccp4bb] Heme incorporation in expressed protein

2012-07-15 Thread Biswajit Pal
Dear all, Sorry for non-crystallography related question. We are trying to express an eukaryotic heme protein in E. coli. We are able to express it in soluble form. When we use 5-Aminolevulinic Acid, E. coli becomes brown. However, after cell lysis the soluble protein contains no heme and the