Re: [ccp4bb] Small lysozyme crystals protocol

Hi Jacob, Keep regular drops and run a cat whisker through the drops after 4 - 5 hours. You should have small crystals within 6-10 hrs. If they are still large, use higher protein concentration or precipitant. Kind regards Mathews -Original Message- From: CCP4 bulletin board [mailto:

Re: [ccp4bb] air bubbles in the Bio-Rad Duoflow system

Most likely you have a reasonable pressure differential in some spot - somewhere in the system air bubbles get compressed (and dissolved) under high pressure, then the pressure drops as you reach the column, and the bubbles re-form. This may not happen with water due to lower viscosity or perhaps l

[ccp4bb] Small lysozyme crystals protocol

Dear Crystallogrphers, does anybody here know a protocol to get consistently well-diffracting but smaller, ~50um, cryoprotect(ed/able) lysozyme crystals? Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training P

[ccp4bb] air bubbles in the Bio-Rad Duoflow system

Hello All, I own a Bio-Rad Duoflow system for almost a year. The machine lived up to some of the recommendations I saw on this board. However, there is this annoying problem with air bubbles entering columns and I cannot figure out the source. The system would be free of any air bubbles in th

Re: [ccp4bb] Parameter MAXSAVE exceeded

Dear friends, (for EZRA) On the first hand .cv a cns file writtenout as an output by xdsconv from .hkl as an input file. Am working with a mad dataset collected at two diff wavelenght. sure i will try the other two mentioned by P.H. Zwart and Mitch. thanks On Thu, Jul 3, 2008 at 9:26 PM, Mill

Re: [ccp4bb] Parameter MAXSAVE exceeded

If you have phenix installed, you may also try: phenix.cns_as_mtz cns_file.cv http://www.phenix-online.org/documentation/reflection_file_tools.htm Regards, Debanu. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Miller, Mitchell D. Sent: Thursday, J

Re: [ccp4bb] Parameter MAXSAVE exceeded

You could also try cns2mtz? http://www.ysbl.york.ac.uk/~cowtan/cns2mtz/cns2mtz.html Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ezra Peisach Sent: Thursday, July 03, 2008 11:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Param

Re: [ccp4bb] Parameter MAXSAVE exceeded

I do not know off hand what a .cv file is - unless it is a cns/xplor reflection file. Instead of using f2mtz - try sftools. Ezra Jayashankar wrote: Dear scientists and friends, When I try to convert a .cv file to .mtz by f2mtz I got the following error,what it means ans what should I do to

Re: [ccp4bb] Molecular Dynamics for dummies.

Yes, I was maybe too positive in my reply. Looking more closely, classical MD may not be appropriate here. The better way is QM/MM but that is not quick and dirty. It depends whether the main effect of the mutations is in the geometry of the protein or in the electronic structure of the metal bindi

[ccp4bb] Parameter MAXSAVE exceeded

Dear scientists and friends, When I try to convert a .cv file to .mtz by f2mtz I got the following error,what it means ans what should I do to get rid of it. ''Parameter MAXSAVE exceeded'' -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany

Re: [ccp4bb] Molecular Dynamics for dummies.

Just a word of warning regarding metals in macromolecular simulation. There is no 'good' way of modeling protein-metal interactions in many cases. Some metal ions are very polarizable (Ca 2+ being one example) and the simple mechanics used in protein simulation don't allow for this. Even using a po

Re: [ccp4bb] Molecular Dynamics for dummies.

GROMACS binaries are available for Macs http://www.gromacs.org/content/view/32/100/ Afaic, GROMACS is user-friendly. There are good tutorials, and there is even third-party GUI: http://resal.atspace.com/grogui.htm IMHO, the GUI is not much better than running Gromacs jobs from command line, bu

Re: [ccp4bb] Molecular Dynamics for dummies.

Gromacs www.gromacs.org It is GPL. It can certainly handle metals, although as is always the case, you have to be careful in the choice of force field. It is fairly user friendly (by the standards of that field ;-). Not sure what the situation is for Macs but certainly runs well on Linux. Alter

[ccp4bb] Molecular Dynamics for dummies.

Hi everyone. I have a slightly off topic question I hope someone can help with. I have a structure of a wild type domain, which binds metal ions. Certain mutations in chelating residues cause changes in the apparent affinity for said metal ions. As I have (so far) failed to crystallise the mutan

Re: [ccp4bb] FW: [ccp4bb] .getTwoTheta() in DiffractionImage library

Dear Francois Remacle, One example images for the mar225 is available under: http://www.mx.bessy.de/temp_stuff/mar225_5_theta_1_001.img.bz2 The output for this image using DiffractionImage library looks like this (using the function listed below): DEBUG OUTPUT ===