[ccp4bb]

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[ccp4bb] Post doctoral position in chromatin structural biology at the University of Toronto

A Post-doctoral position in chromatinstructuralbiology is available at the Structural Genomics Consortium, University of Toronto. The Chromatin Biology and Epigenetics Group at the Structural Genomics Consortium (SGC), University of Toronto, aims to characterize chromatin proteins by X-ray cry

Re: [ccp4bb] dark progression of radiation damage

Regarding "striking distances", there might be some shorter range effects with low energy Auger electrons but for all practical purposes I agree with James. The main reason for this message is to ensure the original question raised by James is not forgotten as it is definitely worth resolving.

Re: [ccp4bb] [CCP4] identify a rotation centre: domain rotation

Would this work? Take the rot-trans operator from superpose or lsqman and express the rotation matrix as polar coordinates of rotation axis (and angle about it). Get the rotation axis as direction cosines, which will be a vector along the rotation axis of the matrix. Now take the component of the

Re: [ccp4bb] dark progression of radiation damage

Since "striking distance" is about 3 microns for the primary photoelectron and the largest unit cell in the PDB is ~0.1 microns long, I think that means all bets are off when trying to "connect" energy absorbed by a heavy atom to damage somewhere else in the unit cell. -James Holton MAD Scient

Re: [ccp4bb] dark progression of radiation damage

I understand that absorbed dose increases with presence of heavy atoms, but I don't understand why that should play a role in damaging the crystal, as heavy atoms such as in cacodylate should probably usually not be near enough to protein atoms to cause problems. At 100K, isn't it true that seconda

Re: [ccp4bb] dark progression of radiation damage

Also, cacodylate contains arsenic which is heavy, and thus has a much larger X-ray absorption cross section than do buffers constituted of lighter atoms. There is therefore a bigger dose (Joules/kg of crystal) absorbed with cacodylate in the buffer than there would be without it (and no extra d

Re: [ccp4bb] dark progression of radiation damage

Any cacodylate buffer will cause gas to be produced. One only needs a minute exposure on a modern home lab source to see this happening. I suggest that everyone avoid cacodylate in their crystallization drops that end up being exposed to X-rays. Jim F

Re: [ccp4bb] dark progression of radiation damage

I think I need to clarify couple of things in my recent post about "exploding" crystals during re-mounting by a robot. First, it was a bit over-dramatization - what I meant by "explosion" was actually bubbling often observed when heavily exposed crystal is warmed up. Second, this bubbling was obser

Re: [ccp4bb] negative density in difference map

I assumed that since this topic came up fairly recently, in fact 3 weeks ago (see thread starting from http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg23628.html), it wasn't just a re-run of the same question. Perhaps the original poster could clarify whether we are talking about unexplained

Re: [ccp4bb] negative density in difference map

There may be several reasons. 1) Artefacts (some of them) a) effect of mask: if there are large holes inside molecule and there should be no electron density (for example hydrophobic holes) then in older versions masks would put a constant density there and as a result difference map would

[ccp4bb] Postdoctoral position, institut Pasteur, Paris, France

Postdoctoral position, institut Pasteur, Paris, France Deadline for application: 15th of January 2012. A 3 year postdoctoral position funded by the ERC (European Research Council) is available in the G5 Unit « structural biology of bacterial secretion » (http://www.pasteur.fr/research/sbbs) in

Re: [ccp4bb] negative density in difference map

Sounds like rad dam to me. See Burmeister, W. (2000)."Structural changes in a cryo-cooled protein crystal owing to radiation damage", Acta Cryst. D 56, 328-341. The first sign of a Met loosing its S-CH3 group will be a negative difference peak on the S. -James Holton MAD Scientist On 11/2

Re: [ccp4bb] negative density in difference map

On Wed, Nov 23, 2011 at 7:57 AM, Ian Tickle wrote: > On 23 November 2011 07:54, Careina Edgooms wrote: >> I have a question about a 2F0-Fc difference map that I calculated with >> Refmac. > > On 23 November 2011 15:40, Nat Echols wrote: >> The negative density around Met S could be radiation da

Re: [ccp4bb] negative density in difference map

On 23 November 2011 07:54, Careina Edgooms wrote: > I have a question about a 2F0-Fc difference map that I calculated with Refmac. On 23 November 2011 15:40, Nat Echols wrote: > The negative density around Met S could be radiation damage. But you wouldn't expect to see -ve density in the 2Fo-Fc

Re: [ccp4bb] negative density in difference map

On Tue, Nov 22, 2011 at 11:54 PM, Careina Edgooms wrote: > I have a question about a 2F0-Fc difference map that I calculated with > Refmac. In some instances it gives me negative (red) density around part of > a side chain and no positive density in sight. Furthermore the entire > residue fits wel

Re: [ccp4bb] [CCP4] identify a rotation centre: domain rotation

I guess the rotation centre is approximately the mid point between the two centroids.. But these look surprisingly similar? I would hsave expected after an 8 degree rotation there would be some greater difference.. Eleanor On 11/23/2011 02:45 PM, WENHE ZHONG wrote: Dear members, I would li

[ccp4bb] [CCP4] identify a rotation centre: domain rotation

Dear members, I would like to have your ideas if there is any way to identify a rotation centre of domain in two different states using CCP4 or other program. The situation is: the domain of the protein will rotate between two different states (depending on substrate binding) around 8 degree, and

Re: [ccp4bb] negative density in difference map [SEC=UNCLASSIFIED]

Hi Careina Since my name came up I felt compelled to comment, though I don't have a definitive answer. Over-restraining of B factors is certainly a possibility and could well explain otherwise inexplicable difference density. IMO B factors are generally over-restrained. They are a bit like the

Re: [ccp4bb] negative density in difference map [SEC=UNCLASSIFIED]

I wish I could answer this! One possibility is that the side-chain B values are too tightly restrained - Ian Tickle recommends releasing these somewhat.. Here are the default refmac values. THERMAL FACTORS Weight= 1.00 Main chain bond (1-2 neighbour) 1.5A**2 Main ch

Re: [ccp4bb] crystal orientation during data collection

I would interpret "random" as aimed to be uniformly distributed, or highly diverse,... continuing this chain of definitions and having a precise kappa goniometer in hand, we can easily arrive to a "planned" strategy to follow. Certainly, if you can get only a few frames per xtal - Frank (vD), d

Re: [ccp4bb] negative density in difference map [SEC=UNCLASSIFIED]

Delete (set occupancies to zero) the side chain back to CA. Do a few rounds of refinement and calculate Fo-Fc and examine. It is possible that the side chain is disordered, or ordered in multiple conformations. Compare the density for alternate confonformers against the density for CA.