Re: [ccp4bb] B-iso vs. B-aniso

Dear Yuri, Why do you think you need 36 reflections per atom when atoms with anisotropic B-factors only have 9 parameters? You can get away with much fewer in many cases especially if you have good restraints. As Ethan points out, a drop in R-free after adding many parameters may be misleading.

Re: [ccp4bb] B-iso vs. B-aniso

On Monday, September 17, 2012 11:31:53 am Yuri Pompeu wrote: > Dear community, > > The protein model I am refining has 400 amino acids (3320 atoms). > Some real quick calculations tell me that to properly refine it > anisotropically, I would need 119,520 observations. Given my unit-cell > dimens

Re: [ccp4bb] B-iso vs. B-aniso

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear, 1.24A resolution is reasonable for anisotropic refinement - including restraints you have more observations than the number of reflections, so just doing the calculation does not give a concise answer! You should try and see if the refinement i

[ccp4bb] B-iso vs. B-aniso

Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set.

[ccp4bb] Beamline scientist position at SSRL

The Structural Molecular Biology (SMB) Group of Stanford Synchrotron Radiation Lightsource (SSRL, a Directorate of SLAC) has an opening for a Beam Line Scientist. This position will participate in a large user support team that provides expert technical & methodological support for scientific

[ccp4bb] problem with phenix refine and non bonded interactions

I am using Phenix 1.8-1069. I am having a problem with phenix refine terminating with an error message. I added several solvent molecules, MPD and bicarbonate in Coot, and ran Phenix ReadySet to generate restraints for them and applied those restraints to all future jobs in that project. When I try

[ccp4bb] CCP4 Study Weekend 2012

The CCP4 Study Weekend (3 - 5 January 2013) East Midlands Conference Centre, University of Nottingham Thursday 3 - MX User Meeting Friday 4 / Saturday 5 - CCP4 Study Weekend "Molecular Replacements" We cordially invite you to participate in this year's Study Weekend at the the East Midlands

Re: [ccp4bb] imosflm background definition

Hi Andreas, The simple answer to this is that you do NOT attempt to redefine the background. Providing the additional spots shown in your image belong to the same lattice, mosflm will automatically exclude pixels from adjacent spots when doing the background plane fi

[ccp4bb] imosflm background definition

Hi all, I'm integrating data from a crystal with a fairly long axis. In iMosflm (1.0.7), the background definition is so generous that plenty of pixels from adjacent peaks are included (see attached). Can someone tell me how I redefine the background to be tighter around the spots? Thanks.

[ccp4bb] Postdoc position in X-ray crystallography

A Postdoctoral (or senior postdoc) Research Associate position in Protein X-ray crystallography is available in the Song laboratory at Baylor College of Medicine, which is one of the top medical schools in the US (* http://www.bcm.edu/about*/). The successful candidate is expected to have a strong

Re: [ccp4bb] mosflm and dectris pilatus

Dear Bhupesh, The first thing is to check that you are using the latest version of mosflm (7.0.9, 14th May 2012). If you are using this version, then please send me more details of the problem and ideally some images. Best wishes, Andrew On 17 Sep 2012, at 09:

Re: [ccp4bb] Series termination effect calculation.

Tim, Correct, but take care that 's' in Niu's program is 2.sin(theta)/lambda whereas in exp(-Bs^2) it is just sin(theta)/lambda (as it is in the usual expression for f(s)). Cheers -- Ian On 17 September 2012 10:24, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Ja

Re: [ccp4bb] Series termination effect calculation.

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear James et al., so to summarise, the answer to Niu's question is that he must add a factor of e^(-Bs^2) to the formula of Cromer/Mann and then adjust the value of B until it matches the inset. Given that you claim rho=0.025e/A^3 (I assume for 1/dma

[ccp4bb] mosflm and dectris pilatus

Dear all We have recently collected data at XRD1 beamline at Sincrotrone Trieste on a Dectris Pilatus detector. We are unable to integrate the images in mosflm, which keeps crashing with some error: e.g. "profile_fitted_partials" or "b_slope" or some such! (indexing seems to work ok). Any

Re: [ccp4bb] Series termination effect calculation.

Le Lundi 17 Septembre 2012 08:32 CEST, James Holton a écrit Hello May I add a few words after the thorough comments by James. I lmay be easier to consider series termination in real space as follows. The effect of series termination in 3D on rho(r) is of convoluting the exact rho(r) with the "