[ccp4bb] New xds-gui XDSAPP V1.0 update release

we would hereby like to announce the update release of the XDS-GUI XDSAPP V1.0. This version presents a major update of the current XDSAPP software (Krug et al., 2012). XDSAPP is an expert system for the interactive and fully automatic data processing using XDS (Kabsch et al., 2010). The

[ccp4bb] Wilson plot of TRUNCATE

Dear All, Recently, I have used TRANCATE to process some data. There is a Wilson plot table in its log file. The first column of table is resolution, the second is ln(I/I_th). And the third column is named Best. I want to know what mean the best. Is it the theoretical estimate of Wilson plot?

[ccp4bb] New ligand

Hello, we have a structure with a novel ligand. I used to use LIG for new ligands but now that is taken in the PDB by 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE. Any suggestions for a generic name that is not already used? thanks and best wishes, Louise

Re: [ccp4bb] New ligand

Hi Louise, You can go through the mon_lib_list.cif file of the CCP4 dictionary to get a name that is free (e.g. A97). It would be nice is a certain name would be reserved for this by the PDB. LIG was a good candidate, but it's gone just like other nice options (XXX, ZZZ, 000). Cheers, Robbie

Re: [ccp4bb] keep ligand conformation

Garib kindly sorted out this problem and external harmonic works well for ligands now. He said that the next ccp4 update will include this version of refmac (5.8.0070 or later). Thanks again for your help. Best, Koji Dear all, I tried to keep a conformation of a ligand during refinement

Re: [ccp4bb] Wilson plot of TRUNCATE

The Best column gives Wilson plot values obtained according to this reference: From the Arp/Warp page: We have implemented an expected Wilson plot derived by Popov Bourenkov (2003) On 26 February 2014 10:04, Tao Zhang zhang...@cryst.iphy.ac.cn wrote: Dear All, Recently, I have used

[ccp4bb] Off Topic: Equipment Available.

Hi All. We have a Rigaku R-AXIS IV detector and controller which we would like to donate to create some space at our core facility. The equipment should be in good working order but hasn't been used in about 18 months. It is currently located at the Beth Israel Deaconess Medical Center in

Re: [ccp4bb] New ligand

Hi Louise, for internal use the name of your ligand does not matter as long as you have a .cif file describing the restraints. I am not sure about the behavior of refmac, but in phenix the presence of a defined name in a .cif file takes precedence over any duplicate entry in your monomer

Re: [ccp4bb] New ligand

Carsten, Phenix does do this a little differently and yes it ignores existing ligands (which I like). CCP4 comes with is own library of existing ligand cif files from the pdb which coot also uses. The best way is to try and find a unique code to call your new ligand. That way you can have some

[ccp4bb] Protein behaves as dimers in 2M NaCl and as high oligomers with 300mM NaCl

Hello everyone! I have run into a problem in a 55kD recombinant human protein crystallization (expressed in E.Coil). The purity is pretty good. However, it behaves as high oligomers in the buffer with 300mM NaCl and behaves as dimers with a little high oligomers in the buffer with 2000mM (2M)