Re: [ccp4bb] MX Frontiers at the One Micron Scale

Not to worry- close inspection of the legalese shows that it is the _USES_ of the system that may be intercepted, monitored etc; not the _USERS_. Of course if by monitoring your _USE_ they discover a good reason why you the _USER_ should be intercepted, apprehended, and prosecuted, then all bets

Re: [ccp4bb] sharp beam focus and radiation damage?

Richard A paper from some time back which describes this is Increased resolution data from a large unit cell crystal collected at a third-generation synchrotron X-ray source Authors: W R Wikoff, W Schildkamp, J E Johnson Acta crystallographica. Section D, 56(Pt 7):890-3. By focusing the bending m

[ccp4bb] Migrating R-Free flags across space groups.

I have an R-free set for R32, I want to try scaling the data into say R3 or C2. How does one keep the R-free flags consistent? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

Re: [ccp4bb] Molecular Replacement of a small peptide

I've had good luck using Phaser on test cases like that, but haven't had access to a case that was previously unsolved. But in principle it should work, if the model is good enough. It sounds like you've thought about the resolution already, so this is probably redundant. Anyway, the defa

[ccp4bb] MX Frontiers at the One Micron Scale

(ignore previous posting) Meeting Notice: Early registration deadline: June 30th We invite you to participate in a workshop entitled 'MX Frontiers at the One Micron Scale' which we are organizing at Brookhaven National Laboratory for July 23 and 24, 2009. If you examine the workshop's agenda

[ccp4bb] MX Frontiers at the One Micron Scale

Meeting Notice: Early registration deadline: June 30th We invite you to participate in a workshop entitled 'MX Frontiers at the One Micron Scale' which we are organizing at Brookhaven National Laboratory for July 23 and 24, 2009. If you examine the workshop's agenda on its website at http://ww

Re: [ccp4bb] Phantom Crystals

V. Nagarajan wrote: Is there some sort of consensus on what properties make a crystal diffract well or poorly? For example, solvent content is assumed to be critical. Assumed? Yes. Critical? No. Bernhard Rupp will probably jump on me for this, but there are plenty of high solvent content cryst

[ccp4bb] sharp beam focus and radiation damage?

I know that sometimes people like to defocus the x-ray beam at the sample so that the intensity profile is not sharply peaked. I think the rationale is that the sharp peak will cause damage, but contribute few photons to the overall diffraction pattern. Does anyone know of a reference where

Re: [ccp4bb] Phantom Crystals

We do see these from time to time with users, but nobody pays attention to them. It once happened to us a number of years ago. They were perfectly good looking lysozyme crystals treated with heavy metal soak. They diffracted fine when fresh, but failed to diffract at all after a couple mon

Re: [ccp4bb] Molecular Replacement of a small peptide

Have you tried acorn in ccp4? I've had it work well at this resolution, especially if the protein/peptide has some alpha helical content. We used acorn to solve a small cro protein that we couldn't get molecular replacement to work with by using a 5-residue ideal poly-ala helix as the starting m

[ccp4bb] FW: Molecular Replacement of a small peptide

I should have added we are currently getting licenses for direct methods software but right now I do not have that option. Allen From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Sickmier, Allen Sent: Friday, June 19, 2009 9:27 AM To: CCP4BB@

[ccp4bb] refmac autoweight

Dear All, In absence to an authoritative answer, I'd like to repost my question. I guess that the overwhelming majority of routine users will use this auto-weight, and it be nice to know what happens there. 1) is there an authoritative description somewhere on the site what refmac precisely does

[ccp4bb] Molecular Replacement of a small peptide

I am trying to do molecular replacement on a small peptide (less than 40 AA) and have not had any success using phaser. Are there any tricks or better programs for really small peptides? The data is great 1.1 A, ~35% solvent, and two molecules in the ASU. I have tried all the standard stuff, cha

[ccp4bb] Phase Comparison

I want to compare my experimental resolve phases (before final refinement) to my model(PDB) phases. I have tried to compare the model phases vs. experimental phases using: Sfall (to ensure I have the appropriate PHI columns) -> Cad (for merging mtz files) -> Phase comparison (Clipper utilities).

Re: [ccp4bb] off topic

Hi Kien, You may also want to try to wash your column with elution buffer (without reducing agents), equilibrate it with binding buffer (plus reducing agents) and then bind your protein. In the case of HisTrap columns (a pre-packed, Ni(II) resin column), this procedure is recommended if y

[ccp4bb] Clues to (perfect) twinning from the density map?

Hi all I know of a lot of reports that attempt to diagnose twinning from intensity distributions, however, are there reports that diagnosed (perfect) twinning from density maps? Strange unmodeled/modeled density? This is coming from a point of view that a perfectly twinned structure can

Re: [ccp4bb] off topic

Hi Kien, DTT coordinates very nicely the Ni(II) on the column. However the DTT-Ni(II) is prone to oxidation which gives almost immediately Ni(III) which causes the brownish colour. As Jürgen pointed out TCEP chelates only weakly Ni(II) and is a better choice. Also beta-mercapto-ethanol does n

Re: [ccp4bb] off topic

Jürgen Bosch schrieb: Try TCEP as it does not interfere with the NiNTA resin whereas DTT does. But why do you care if your column is brown or not - can you elute your protein ? Are there other metal ions e.g. iron which bind to your resin perhaps ? Jürgen On 19 Jun 2009, at 02:25, Kn Ly wrote

Re: [ccp4bb] off topic

Try TCEP as it does not interfere with the NiNTA resin whereas DTT does. But why do you care if your column is brown or not - can you elute your protein ? Are there other metal ions e.g. iron which bind to your resin perhaps ? Jürgen On 19 Jun 2009, at 02:25, Kn Ly wrote: Hello everyone, I

[ccp4bb] Integration of highly anisotropic data

Dear all, I have a data set which is highly anisotropic (3.5-4A in one direction and 2A in the other) and huge amount of scattering in some rotation ranges. I know there is the anisotropic correction server which I can use to do scaling to the weaker data and get it into a kind-of isotropic

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