Re: [ccp4bb] Kd's in Crystals

2011-06-28 Thread George Kontopidis
Determination of Kd in crystal using only crystallographic data look at The First Direct Determination of a Ligand Binding Constant in Protein Crystals Wu SY, Dornan J., Kontopidis G., Taylor P., Walkinshaw M.D. Angew Chem Int Ed Engl, 2001, 40, 582-586. George

[ccp4bb] changing residue numbering in Coot

2011-06-28 Thread Katrina L Molland
Hello, I am trying to use Coot to change the numbering of the residues in a PDB file. The structure contains six semi-identical lettered chains, currently described as D through I. For some reason, the feature in coot that should allow me to change them to A-F, as well as change the residue

Re: [ccp4bb] changing residue numbering in Coot

2011-06-28 Thread Paul Emsley
On 28/06/11 12:13, Katrina L Molland wrote: I am trying to use Coot to change the numbering of the residues in a PDB file. The structure contains six semi-identical lettered chains, currently described as D through I. For some reason, the feature in coot that should allow me to change them to

Re: [ccp4bb] Sc calculation

2011-06-28 Thread Mike Lawrence
Hi Fahimeh, what has happened here is that the interface area in the new file is very small, particularly after the periphery is trimmed (see the original paper for how this is defined). For the old file, the area is about 1100 Angs**2, for the new it is about 110 Angs**2. As the log file states,

[ccp4bb] AW: [ccp4bb] changing residue numbering in Coot

2011-06-28 Thread Stefan Gerhardt
Hi, worth to try moleman - %moleman Choose READ_pdb_file - your_pdbfile.pdb Choose AUTO_chain_segid Choose WRITE_pdb_file - out.pdb Or the tedious NEDIT way Open your pdb.file in nedit, mark ONLY the chain ID column - put your cursor before the first X, press [Shift][Ctrl], go the the last X

Re: [ccp4bb] changing residue numbering in Coot

2011-06-28 Thread Tim Gruene
Dear Katie, the menu entry Calculate - Change Chain ID works fine, although in the current version (0.6.1), you cannot use the preselected Whole Chain radio button but have to explicitly tell coot the residue range 'from' - 'to'. Tim On Tue, Jun 28, 2011 at 07:13:56AM -0400, Katrina L Molland

[ccp4bb] Protein scientist position at Syngenta

2011-06-28 Thread Daniel Kloer
Protein Scientist £28,000 - £35,000 + benefits Jealott’s Hill, Bracknell, Berkshire As an independent worker, you will be a part of our Protein Production Team, providing protein expression/purification support in a timely manner across a range of Crop Protection Research projects. This will

[ccp4bb] PhD student position

2011-06-28 Thread Petri Kursula
Dear colleagues, I would appreciate it if you could bring this off-topic opportunity to the attention of any suitable candidates. Petri --- A PhD student position is available in the group of Dr. Petri Kursula, to use neutron scattering methods to study proteins specifically expressed in the

[ccp4bb] Postdoctoral position available

2011-06-28 Thread Brian Mark
POSTDOCTORAL POSITION AVAILABLE Applications are invited for a postdoctoral position to investigate the structural and cellular biology of viral immune evasion tactics and assembly mechanisms of Bunyaviruses, the largest family of negative-strand RNA viruses. The family Bunyaviridae includes

[ccp4bb] selenomethionine contact

2011-06-28 Thread Alexander U. Singer
Hi -- I have a case in which I have a refined structure in which the 'so-far' measured distance between the Se atom of a selenomethionine and its crystallographic neighbouring Se atom (same residue) is 2.9 A, and I see continuous density between the two atoms. Has anyone subscribing to

Re: [ccp4bb] selenomethionine contact

2011-06-28 Thread Jacob Keller
Sounds to me like an artifact of the two-fold (I think there must be one between the two atoms if it is the same residue?). I think things get dicey near the symmetry axes... JPK On Tue, Jun 28, 2011 at 6:25 PM, Alexander U. Singer alexander.sin...@utoronto.ca wrote: Hi -- I have a case in