Re: [ccp4bb] selenomethionine contact

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 wrote: > Hi -- I have a case in which I have a refined structure

[ccp4bb] selenomethionine contact

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 thi

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Re: [ccp4bb] changing residue numbering in Coot

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 Moll

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

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 t

Re: [ccp4bb] Sc calculation

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

Re: [ccp4bb] changing residue numbering in Coot

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

[ccp4bb] changing residue numbering in Coot

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 numb

Re: [ccp4bb] Kd's in Crystals

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 ---