[ccp4bb] Open Beamline Scientist Position at XAIRA beamline-Alba Synchrotron

Dear colleagues, A position of Beamline Scientist for the new BL06-XAIRA microfocus Macromolecular Crystallography beamline at the Alba Synchrotron (Barcelona) is currently open. We are seeking a positive, motivated scientist, proficient in macromolecular crystallography methods,

Re: [ccp4bb] RMSD between unaligned structures

James, I wrote a jiffy script for doing this ages ago. http://bl831.als.lbl.gov/~jamesh/pickup/rmsd Please feel free to copy/edit/port and use in whatever you like. It's only a few dozen lines. Reports RMS deviations for all pairs of atoms with the same "name" (columns 12-27 in the PDB

Re: [ccp4bb] to fix angle between ligand and residue atoms

Hi Markus, You can add plenarity restraint to your LINK. You can model it after one of the peptide LINKs in the mon_lib_list.cif file from CCP4. Cheers, Robbie Sent from my Windows 10 phone Van: Markus Heckmann Verzonden: maandag 3 juli 2017 16:46

Re: [ccp4bb] RMSD between unaligned structures

I second the use of LSQMAN. The command for calculating wo aligning appears to be: rmsd_calc (abbreviated rm). http://xray.bmc.uu.se/usf/lsqman_man.html#S59 If you have multiple chains, use the option "chain_mode original" before loading the pdb's to avoid renaming chains:

[ccp4bb] to fix angle between ligand and residue atoms

Dear ccp4-ers, I have a data set at 2.8 A. There is clear *continuous* density for a ligand + residue. I used the LINK record to connect the S-gamma-atom from Cys to C1-atom of ligand OCA. My biochemistry collaborator says that CB-SG-C1-O1 should be approximately planar. However, during

Re: [ccp4bb] RMSD between unaligned structures

Hi James If you have access to a Phenix installation then phenix.find_alt_orig_sym_mate does what you want in one go. It tries to position the two MR structures on the same origin and symmetry site like Csymmatch. Besides computing a score value indicating the quality of the match it also

Re: [ccp4bb] RMSD between unaligned structures

Yes - I wrote something long long ago called compar. It is still there.. you give it XYZIN1 and XYZIN2 and I think it lists all distances somewhere E [ed1@setsuko ~]$ compar ###

Re: [ccp4bb] RMSD between unaligned structures

Hi Eleanor.You do the alignment if you are looking to measure the similarity of two molecules after refinement or the similarity of two molecules in general. When you do this, like you say, you have to carry out some sort of alignment, i.e. you move one of the two structures so to have the

[ccp4bb] Cryo-EM Research Scientist position at Imperial College London & MRC LMS

The MRC LMS & Imperial College is looking for a Cryo-EM research Scientist. Your main role will be to manage the EM requirements of the institute. Electron microscopy has been identified as a key technology at the ICL/LMS to support investigation into epigenetic mechanisms, large molecular

Re: [ccp4bb] RMSD between unaligned structures

Dont understand your Q James.. You have to make sort of alignment to get the RMSD surely? And csymmatch will just apply the symmetry and origin shifts needed for any comparisonn? E On 3 July 2017 at 11:32, Stéphane Duquerroy wrote: > Hi James > LSQMAN can calculate

Re: [ccp4bb] RMSD between unaligned structures

Hi James LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1 range1 mol2 range2 [Ltarget]) Be careful it renames the chain names Stephane --- Duquerroy Stéphane Structural Virology Unit - PASTEUR INSTITUTE 25 rue du

[ccp4bb] RMSD between unaligned structures

Dear ccp4 tribe,this might have been asked before, but I haven't paid enough attention. I'd like to measure the RMSD between two models after molecular replacement. I can force the two models to overlap as much as possible within the symmetry and origin-shift constraints (using CSYMMATCH). But