[ccp4bb] Shear number of beta-barrel proteins

Hello everybody, I need some pratical advice for determination of the shear number of my beta-barrel protein. Is there any software tool, which I can use or do I have to determine it by hand? Thanks in advance, Iris ___ Dipl-Biol. Iris Gawarzewski PhD student

Re: [ccp4bb] Twin or underestimation of symmetry

This is a bit puzzling. Sticking to point groups: P3 P6 are sub groups of P6/mmm so data which merges in P6/mmm will always satisfy P3 and P6. And twinning in P3 or P6 will make the data seem to have higher symmetry. Four way twinning is unusual, but possible of course. But if you really have

Re: [ccp4bb] Twin or underestimation of symmetry

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jeffrey, how complete is you model, i.e. what is the ratio between the number of atoms in the PDB file (without solvent/ ligands) and the expected number of atoms as calculated from the sequence? If a substantial part of the molecule is

[ccp4bb] Placing coordinates and mtz reflections file on a common new origin

Hi all, I am trying to get multiple molecular replacement solutions on the same origin. I know this has been asked before, however, in my case I want to stick to CCP4 programmes (I am aware PHENIX can do this). I have tried to get this to work using csymmatch which outputs the origin-shifted

Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster

Dear Sergei, Second point is probably easier to do. An alternative to NFS is sshfs. The advantage is that it uses SSH which is installed by default and configured the same way. If you generate key pairs you can use ssh or sshfs without a password. Check this page below;

Re: [ccp4bb] Twin or underestimation of symmetry

Check the pseudo-precession pics (0kl plane, etc). A rhombohedral crystal that is indexed as P6xx may have seemingly-bizarre systematic absences that could trick one into thinking its P63xx. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf

Re: [ccp4bb] Twin or underestimation of symmetry

The model is essentially 100% identical. The structure is of a point mutant that has already been solved. From: Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Tuesday, July 30, 2013 5:26 AM To: Jeffrey D Brodin Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re:

Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster

Be careful that running data intensive jobs over NFS is super slow (at least an order of magnitude compared to writing things on a local disk). Not only the computation is slow, but you may be slowing down all other users of the cluster too... F. On 07/30/2013 11:28 PM, Adam Ralph wrote: Dear

[ccp4bb] Output of Phaser

Dear all, I am sorry for my new-comer question, but I am not clear what the multiple RFZ, TFZ, PAK and LLG scores belong to after each solution set in the phaser output (eg. .sol) file. My bet is that each of them corresponds to each of the solutions listed below, but I am not sure. Also I know

[ccp4bb] delete reflections with negative peak profile correlation

Hi All, Inspired by the micro diffraction assembly methods (see http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12357.html), I checked one XDS_ASCII.HKL file and found many reflections has negative peak profile correlation. After deleted them and rerun XSCALE, I/sigma is higher