Re: [ccp4bb] Poor diffraction of eukaryotic membrane protein crystals

Hi Damon, In case your target oligomerizes to produce an assembly larger than 100 kDa, you may try to use the 100 kDa MWCO concentrator which will not only allow the detergent monomers to pass through, but also the micelles for most detergents used for membrane proteins. The 50 kDa one wil

[ccp4bb] Poor diffraction of eukaryotic membrane protein crystals

Dear CCP4bb, I am attempting to crystallise a 25kDa membrane protein of eukaryotic origin. We have obtained crystals of the protein (with and without a potential ligand). However crystal quality is poor, as exposure at room temperature and cryo-protected conditions have given diffraction as

[ccp4bb] Postdoctoral positions at CSHL

POSTDOCTORAL POSITIONS in STRUCTURAL BIOLOGY at COLD SPRING HARBOR LABORATORY Applications are invited for postdoctoral positions in Structural Biology at Cold Spring Harbor Laboratory to work on complexes involved in gene expression and silencing, or replication. Please see our web page for mo

Re: [ccp4bb] song CRT Multiscan E540 monitor for stereo view

See http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo first. The xorg.conf file must be configured correctly to enable stereo. Roger Rowlett Eric Liu wrote: Hi All, I would like to explore if anybody had experience using song CRT multiscan E540 monitor for stereo view? I

Re: [ccp4bb] song CRT Multiscan E540 monitor for stereo view

Hi Eric, I use a Sony Mutiscan E530. I'm not sure of the difference in specifications, but I posted my xorg.conf file here, which works under Ubuntu 8.10 in stereo for Coot & O. http://82.239.206.16/xorg.conf HTH, Mark 2009/2/4 Eric Liu : > Hi All, > > I would like to explore if an

Re: [ccp4bb] PHENIX & BSS refinement

Hi Miguel, there are limits and they are applied to total B-factor: - minimal Biso should be positive; - anisotropic ADP matrix is always enforced to be positive definite. Pavel. Thanks, it is clear now. I have a last concern, though. Does phenix impose minimal values to the refined ADPs? I

Re: [ccp4bb] PHENIX & BSS refinement

Hi Pavel, Thanks, it is clear now. I have a last concern, though. Does phenix impose minimal values to the refined ADPs? I guess it does not, for I have found nothing like that in the documentation. But, if it does so, are they imposed to the individual B-factors or the B-overall is also ta

[ccp4bb] song CRT Multiscan E540 monitor for stereo view

Hi All, I would like to explore if anybody had experience using song CRT multiscan E540 monitor for stereo view? I connected the monitor to our linux machine (Red Hat Enterprise 5.0). When I launch coot, I don't see a stereo view of the structure. Do I need to do some kind of configuration in orde

Re: [ccp4bb] PHENIX & BSS refinement

Hi Miguel, Right, but why this happens only in the final bss step ? Why not in the first one? It's arbitrary: one can do it every macro-cycle as well. The main idea is to have a total B-factor in ATOM records written out to a PDB file. I have noticed the behaviour described by José when I r

Re: [ccp4bb] ccp4 6.1.0 with macbookpro

Dear Choel: This is probably my fault I think, not ccp4's. I'll look into it as soon as I get a chance (which means after I teach this afternoon). Sorry for this. Briefly, check the ownership/permissions on ~/.CCP4 and if needed change it so you have write permissions. Bill On Feb 3,

Re: [ccp4bb] PHENIX & BSS refinement

Hi Pavel, We have also seen that the B factor jumps up in this last step (see bellow). Is anybody aware of this? This is because the trace of overall anisotropic scale matrix is added to atomic B-factors and subtracted from that matrix. This is exactly what CNS does (at least version 1

Re: [ccp4bb] problem with ccp4 6.1.0 installation

Dear Witek, On some systems we have found that there can be a problem with the CCP4 distributed version of Graphviz which is used to display the graphical view of the project. This is caused by a missing font package. It looks as if this has caused the error you see. To fix it we suggest that

Re: [ccp4bb] To identify specific type of interaction

How about PISA? That's what it's designed for. http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Andreas Kadhirvel Saraboji wrote: Dear all, Is there any program/server to identify all occurrences of specific type of interaction between molecules in crystal structures, whether they are w

[ccp4bb] To identify specific type of interaction

Dear all, Is there any program/server to identify all occurrences of specific type of interaction between molecules in crystal structures, whether they are within the same asymmetric unit or between symmetry-related molecules? I am interested in particular in interactions in which anti-parallel b

[ccp4bb] MX-beamtime at BESSY-Berlin, period: July/2009 - June/2010, Deadline March 1, 2009

Next MX-proposal application deadline: March 1, 2009 See: http://www.bessy.de/boat/www/ We kindly request new MX-proposals for beamtime applications for the next beamtime period. In order to apply for beamtime, please register at the BESSY on-line access tool "BOAT" (http://www.bessy.de/boat/ww

Re: [ccp4bb] X-ray photon correlation length

Hi James, Am 03.02.2009 um 17:38 schrieb James Holton: Hey Dirk, You're wrong. ;) okay, thanks a lot! ;-) The remarkable part of this is that the integrated spot intensity (photons) is essentially invariant with how you divide up the unit cells into mosaic domains. Well, okay, if N=1,

Re: [ccp4bb] Obtaining relationships between two cross rotation solutions?

I presume theta1 theta2theta3 are eulerian angles? When theta2 ~ 0, you can onlyy define theta1+theta2 so solution 1 is effectively the identity; theta1+theta3 = 360 (ie 0) theta2~0. theta3 not defined - that generates the identity matrix. When theta2 ~ 180, you can onlyy define theta1-t