Re: [ccp4bb] Summary - Valid to stop Refmac after TLS refinement?

Bernhard Rupp wrote: People also felt that the RMSD bond/angle of 0.016/1.6 was still a little high. This was subject of a discussion before on the board and I still don't understand it: If I recall correctly, even in highly accurate and precise small molecule structures, the rmsd of corresp

Re: [ccp4bb] Strange behavior in R32

Hi Dan, In hexagonal R32 setting there is translational crystallographic symmetry leading to systematic absences. If you think Xtal 5 is basically the same but with slightly different packing that break the symmetry then you will have pseudo-translational symmetry leading to one set of very s

Re: [ccp4bb] Summary - Valid to stop Refmac after TLS refinement?

>People also felt that the RMSD bond/angle of 0.016/1.6 was still a little high. This was subject of a discussion before on the board and I still don't understand it: If I recall correctly, even in highly accurate and precise small molecule structures, the rmsd of corresponding bonds and angles

[ccp4bb] Strange behavior in R32

Dear Friends, I have some crystals of a small RNA in sg R32 that exhibit some bizzare behaviors and fail to give phasing solutions. I am hoping someone out there might be able to lend some insight. All crystals come out of the same condition and look the same morphologically but, for reasons unkno

Re: [ccp4bb] cryo was:bigger size - > better diffraction?

for cryoprotection just drag it through paratone-N (put next to your crystal drop) and you dont have to worry about ill effects on the crystal (usually). this will cut down the long road with cryoprotectant search to minimal. (..not sure if this had anything to do with the original topic, but sinc

Re: [ccp4bb] bigger size - > better diffraction?

A small comment: crystals that do not diffract well at R.T. can still diffract well when frozen. There are several reasons for this, including: * poor stability of crystal once the drop is open to the air * crystal has low tolerance for handling (capillary mount can be challenging and cause mor

Re: [ccp4bb] bigger size - > better diffraction?

For room temperature testing, it is much easuier to use a cryoloop enclosed in a capillary (with some mother liqour at the top) or the plastic tubes supplied by MiTeGen as per the method detailed in: Skrzypczak-Jankun, E., Bianchet, M. A., Amzel, L. M. and Funk Jr., M. O. (1996). /Acta Cryst./

Re: [ccp4bb] bigger size - > better diffraction?

The first thing to try before going down the long road of fussing with cryo is to take a shot at room temp. and see how your crystal diffracts in general. It is true it may be a cryo problem, but if the non cryo protected crystals do not diffract then why would one expect the cryo protecte

Re: [ccp4bb] bigger size - > better diffraction?

Streak seeding all your trays should give you a better handle on nucleation. You might be too high in protein or precipitant w/o the seeding, hence the showering and rare nice crystals. Varying cryos, or cryo concentrations, or how the cryo is added can help a lot. Try 5 or 6 different cryos at 3

Re: [ccp4bb] bigger size - > better diffraction?

Hello Jenny, 0.2 Rmerge may be an indication of incorrectly assigned SG or perhaps a misindexing by one, etc. Check what happens if you reprocess in P4. For a 10kDa protein, your unit cell is kind of large - depending of course on the symmetry, the higher obviusly the better. I would bet that you

[ccp4bb] Detwinning

I am working with crystals with apparent I422 space group but it may be actually I4. Twinning analysis shows twinning fraction of 0.46. I tried to detwin the anomalous data in CCP4. Just to check the files were read and written properly, I wrote the detwinned data in ascii. The numbers look stra

[ccp4bb] New crystal screening analysis web server...

Hi all, I've recently set up a web server to help in the initial crystal screening process, and thought it might be useful for other people too. It allows one to point-and-click to catalog and analyze the results of initial screens to help see what your protein does and doesn’t like, as well a

[ccp4bb] Scientist and intern positions open in crystallization group

We have two positions open in our crystallization group, one for a scientist and one for an intern. Please use our website to apply: http://www.sgxpharma.com/careers/opportunities.php Shane Atwell Associate Director, Crystallization SGX Pharmaceuticals 10505 Roselle Street San Diego, CA 92121

Re: [ccp4bb] Summary - Valid to stop Refmac after TLS refinement?

Hello, Thanks very much to all who replied with thoughts and suggestions. The consensus was that my interpretation was not correct, and it is not valid to stop Refmac after TLS refinement. People also felt that the RMSD bond/angle of 0.016/1.6 was still a little high. Phenix.refine was sugg

[ccp4bb] CNS query

Dear All, I have been experimenting with resolution limits in CNS in order to simulate a low resolution scenario. I increase the high resolution till there are thrice the reflections as number of atoms in the structure. Most of the times this works but sometimes CNS aborts with this message: ---

[ccp4bb] POSTDOCTORAL POSITION IN PROTEIN COMPLEX CRISTALLOGRAPHY

POSTDOCTORAL POSITION IN PROTEIN COMPLEX CRYSTALLOGRAPHY Applications are invited for a postdoctoral position in Prof. Miquel Coll’s group at the Institute of Research in Biomedicine / Institut de Biologia Molecular de Barcelona (CSIC) to work on the structural characterization of protein comple

Re: [ccp4bb] bigger size - > better diffraction?

oh, One thing forgot to mention is that I actually collected data in house ( about 70 frames ), the completness is high ( 98%) but the Rmerge is high ( 0.2 ), what does this suggest? On 4/4/07, Jenny <[EMAIL PROTECTED]> wrote: Hi, All, I got a crystal that diffracts at 3.3A in house.The crystal

[ccp4bb] bigger size - > better diffraction?

Hi, All, I got a crystal that diffracts at 3.3A in house.The crystal size is about 0.2mm* 0.1mm * 0.2mm. At first I thought the size is fine,but it turns out the smaller ones diffract worse.I guess the reason is that the cell unit is really big (126.292 126.292 134.904 p4212, pretty big for

[ccp4bb] EBSA/BBS Eurobiophysics Congress, London, July 2007

The 6th EUROBIOPHYSICS CONGRESS will take place in London, from 14 - 18 July 2007. http://www.eurobiophysics.org There are just 10 days left for abstract registration (deadline 14th April), and ~60 short oral presentations are still to be selected from the abstracts, which cover 26 themes.

Re: [ccp4bb] truncate error on x86_64

Hi Daniele I recently made a change in truncate (added cumulative distribution for twinned intensities), however I'm not sure whether 6.0.2 incorporates that change. I've not seen either of the problems you report before, all I can suggest is you re-compile truncate with the debug (-g switch),

[ccp4bb] question about structure analysis

Hi everybody I have a question about soluble structures analysis. I've been working on a heme protein who presents two isomers. These isomers can only be detected by NMR and its ratio varies among organisms. My goal is to explain how the isomer ratio is modulated and why o

[ccp4bb] truncate error on x86_64

Dear all, i installed ccp4 6.0.2 on an amd64 machine running Ubuntu 6.10, 64bit version. Everything is running fine except a problem i have with truncate. At the beginning it failed giving a "segmentation violation" error which i overcame using "ulimit -s unlimited". Now I got another error (qui

[ccp4bb] Crystallization position, 25793BR, Novartis Pharma, Basel (Switzerland)

Please apply via the web. Do not email replies to me. A global healthcare leader, Novartis has one of the most exciting product pipelines in the industry today. A pipeline of innovative medicines brought to life by diverse, talented, performance driven people. All of which makes us the most r