Re: [ccp4bb] X-ray photon correlation length

Dear James, what an interesting discussion! Am 30.01.2009 um 19:42 schrieb James Holton: ... I think the coherence length is related to how TWO different photons can interfere with each other, and this is a rare event indeed. It has nothing to do with x-ray diffraction as we know it. No

[ccp4bb] correlation length - reloaded

Thanks Colin, Yours is one of several lessons I have received on coherence and optics in the past few days. I do appreciate all effort and the input. However, as I mentioned before I am a biologist and I don't so much care about the fundamental nature of the universe as I do about how it

Re: [ccp4bb] difficult MAD dataset

Hello - Sorry if some of my suggestions are redundant since I jumped in late in this thread. A couple of additional comments after struggling with a similar albeit not identical case. With a pseudo translation vector like that the SG could be any of the 8 orthorhombic SGs; P222 P21 22

[ccp4bb] PHENIX BSS refinement

We have seen that the recent versions of phenix (1.3) the structure refinement ends with a bulk solvent correction step, something I found quite unusual (absent in other refinement programs and in older versions of phenix, 1.24.1). We have also seen that the B factor jumps up in this last step

Re: [ccp4bb] difficult MAD dataset

Chi2 is unusually high at lower resolution (Chi2 is 3 from 3.5A as shown below) and there is a relatively high percentage of rejections (1.5 %). Chi^2 in Scalepack *must* be adjusted by changing the expected errors to be about 1. Until then, I would not reject reflections. Only

[ccp4bb] putting in methionines for SeMet crystals

Dear All, I have a 9-kDa protein that crystallizes well. Since there is no structural homologue for this molecule, I intend to make Se-Met derivative of the protein. The molecule has no Met/Cys residues in its sequence. I wanted to know where in the sequence should I mutate, so that the

Re: [ccp4bb] putting in methionines for SeMet crystals

Hey Amit, as your protein is tiny, maybe you can calculate a molecular replacement model as described in Acta Cryst. (2009). D65, 169–175. This might take longer than engineering a few methionines, though. I'd mutate leucines. Andreas amit sharma wrote: Dear All, I have a 9-kDa

Re: [ccp4bb] correlation length - reloaded

Re my previous post of this title: Harry Greenblatt just pointed out that I should have said that it is the reciprocal cell edges a* and b* that are non-equivalent in P4, not the real-space cell edges a and b. Hope that didn't confuse too many people. -James Holton MAD Scientist

Re: [ccp4bb] PHENIX BSS refinement

Hi Jose, We have seen that the recent versions of phenix (1.3) the structure refinement ends with a bulk solvent correction step, something I found quite unusual (absent in other refinement programs and in older versions of phenix, 1.24.1). - the software is evolving and gets better over

[ccp4bb] Obtaining relationships between two cross rotation solutions?

I have trouble with visualizing things in three dimensions so I'm trying to figure out the relationship between two cross rotation functions (given as theta1, theta2, theta3). Is there a program or webapp that'll tell me whether two rotation solutions are related by a

Re: [ccp4bb] putting in methionines for SeMet crystals

Hi Amit, Based on the original analysis of M. Dayhoff (PAM matrix, Dayhoff substitution probability, Dayhoff, et. al 1978), introduction of Leu-Met would be the best choice for production of Se-Met derivatized protein. It would be best to consider a multiple sequence alignment of

[ccp4bb] TeachSG workshop Expertise in Macromolecular Structure Refinement in Prague April 3-4

A two-day workshop focused on both the basics and the current development in macromolecular single crystal structure refinement techniques will be held in Prague on April 3-4 2009. The workshop is organized within the TeachSG project of the EC (tightly connected with the project

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

I forgot to mention that I think the only fail-safe direct approach will involve converting both rotations into quaternions, subtracting (inv(A)*B) said quaternions, then converting the difference into an axis-angle pair. James On Feb 3, 2009, at 9:47 AM, Francis E Reyes wrote: I have

[ccp4bb] 'Sticky Crystals' on ccp4-wiki

Dear colleagues, I have just deposited an entry on the ccp4-wiki that summarizes input/ideas on dealing with 'sticky crystals'. Please feel free to edit it further as necessary. http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Crystals#Crystal _handling best wishes Savvas

[ccp4bb] problem with ccp4 6.1.0 installation

Hello, After installation I tried Graphical View of Project and I got: dotgraph_render: error: graph 1.000 5.861 0.528 node Job1 0.472 0.264 0.945 0.500 1: autoSHARP\nautoSHARP filled box black #9DD05B node Job2 1.667 0.264 0.945 0.500 2: autoSHARP\nautoSHARP filled box black #9DD05B