Re: [ccp4bb] Semet derivative dying almost immediately in beam

Ah, low resolution experimental phasing. Fun stuff, seems like a lost art these days. Are the crystals large ? Is it possible to do a (continuous helical data) collection? (Manually or if your beamline permits you to). Granted this is anomalous, is it possible to then merge enough partial da

Re: [ccp4bb] Another difficult MR case

First advice - are you sure the images etc are OK? Green lights are not as useful as detailed analysis. I like the CCP4I2 report - it provides enough information to dig down for problems... Again - do try SIMBAD or similar is very sensible. But Beta sheet structures are a pain! As was noted your

Re: [ccp4bb] Semet derivative dying almost immediately in beam

Their web page indicates they’re running a 315, so there are limits on useful low dose data collection. If you can get to a beamline with a pixel array detector and mount your samples carefully you’ll probably get more from low dose methods. The key thing with this is minimising background from

Re: [ccp4bb] Semet derivative dying almost immediately in beam

ALS 822. I tried as low as 0.2 sec exposure but it didn't seem to help much. Kimberly Stanek Postdoctoral Researcher, Goulding Lab Co-chair, UCI Postdoctoral Association University of California, Irvine Natural Science I, Room 2302 (949) 824-0014 From: James Holto

Re: [ccp4bb] Another difficult MR case

EPMR is also a good alternative for finding multiple placements per ASU. If a reasonable packing MR solution can be found and there is significant NCS, then DM followed by NCS enhanced automated model building from initial MR phases can do wonders. Improvement goes as the square root of NCS number

Re: [ccp4bb] Another difficult MR case

Sorry forgot to mention, if you go down the impurities route, there is SAUC to check for similar unit cells in the PDB http://iterate.sourceforge.net/sauc/ And there used to be Nearest Cell but my phone can't find that one anymore ;- Sent from Yahoo Mail on Android On Thu, 29 Aug 2019 at 18:

Re: [ccp4bb] Semet derivative dying almost immediately in beam

What exposure time are you using?  And which beamline? -James Holton MAD Scientist On 8/29/2019 10:26 AM, Kimberly Stanek wrote: Hi folks, We have a protein that we have been trying to solve the structure of for a while now but so far haven't been able to get any diffraction better than ~4.5

[ccp4bb] Beamtime at upgraded CHESS

Having completed a major upgrade, CHESS (Cornell High Energy Synchrotron Source) is accepting proposals for beamtime. Of most interest to this community: BioSAXS station (formerly G1) - on-site or mail-in BioSAXS, featuring: * 7-14 KeV, standard beam size 250x200 micron, smaller beam available.

Re: [ccp4bb] Another difficult MR case

It would be useful to know the number of molecules per asymmetric unit and the sequence similarity of the search model and target. There is always Molrep to try which is good at NCS ;- Sent from Yahoo Mail on Android On Thu, 29 Aug 2019 at 18:30, David Briggs wrote: #yiv8743831735 #yiv87

[ccp4bb] Semet derivative dying almost immediately in beam

Hi folks, We have a protein that we have been trying to solve the structure of for a while now but so far haven't been able to get any diffraction better than ~4.5A. I was able to collect a full 360 degrees of data and index, but MR is failing so we have turned to de novo phasing. Recently we

Re: [ccp4bb] Another difficult MR case

Following on from Ivan's suggestion, SIMBAD might he worth a shot. https://journals.iucr.org/d/issues/2018/07/00/rr5159/ The other thing you might try is handing the MR phases to the density modifying and autobuilding program of your choice, increasing the number of cycles by $arbitarylargenumb

Re: [ccp4bb] SeMet data

The dose rate at ALS 5.0.2 should be about 100 kGy/s with standard settings.  Lindsey?  What was your exposure time?  Was the crystal bigger than the beam?  You need these two bits of information to do a rough estimate of dose per image.  Without this information any strategy is just a wild g

Re: [ccp4bb] Another difficult MR case

Are you *sure* there's no translational NCS ? For example your first molecular replacement solution out of Phenix shows EULER 293.6 27.7 288.7 FRAC -0.02 0.02 0.02 (that's "first molecule at origin in P1") and EULER 294.0 27.9 288.8 FRAC -0.37 0.02 0.02 which is essentially the sa

Re: [ccp4bb] Another difficult MR case

Hi Napo, Apart from other things possible (wrong space group is often the culprit, but it seems like not your case), I would consider a possibility of crystallizing a different protein than expected. see "Protein purification and crystallization artifacts: The tale usually not told" https:/

[ccp4bb] Another difficult MR case

Deal all, Sorry for the long post. I have a data set obtained from a crystal produced after incubating a protease with a protein which is mostly composed by an antiparallel beta sheet. I have tried numerous approaches to solve it, and failed. Molecular replacement using Phaser, and the protease or

Re: [ccp4bb] REGISTRATION OPEN: Engineering Recombinant Proteins: London, Nov 4-5

Hi This is a reminder that the 'early-bird’ registration deadline (4 Sep) is approaching: https://www.eventsforce.net/biochemsoc/frontend/reg/thome.csp?pageID=31653&eventID=71 There will also be opportunitie

Re: [ccp4bb] AW: [bruker-axs] cbf to sfrm

Dear Holger, thanks a lot for the prompt reaction! This will be very useful, in particular in case of proper twins. I look forward to the update, Tim On Thursday, August 29, 2019 11:32:00 AM CEST bruker-...@lists.wisc.edu wrote: > Dear Tim, > > > > Thanks for having brought the bug to our a

Re: [ccp4bb] Rescuing CCP4i2 projects after a loss of CCP4 installation

Dear Jan, The first thing I would do is make sure your CCP4 installation is up to date. Then open a shell/terminal and set up your CCP4 environment in the normal way. Make sure CCP4i2 is not running. Then type: sh $CCP4/share/ccp4i2/bin/reconstructDB A window should appear which lets you sel

[ccp4bb] Rescuing CCP4i2 projects after a loss of CCP4 installation

Dear all, I recently switched most of my work to the "new" CCP4i2 GUI and project management. However, I now had to reinstall my computer and I can't find a way to import ccp4i2 projects back into my fresh CCP4 installation. If I use the "Import" project button, it seems to expect compressed