Re: [ccp4bb] NCS and manual building

2008-11-28 Thread Jens T. Kaiser
MAIN does that for ages (n_molecules->generate_others). Also, the new COOT can do that (look in the - rather cluttered - treasure chest 'Extensions'->'NCS'->'Copy NCS chain') HTH -j. On Wednesday 26 November 2008 00:25:12 Prakash Rucktooa wrote: > Dear Olga, > > I have also encountered the sam

Re: [ccp4bb] soft white paraffin

2008-11-28 Thread Jens T. Kaiser
I switched to mineral oil (same as for pcr). You can apply it either with a 1mL pipet tip or with use a glass vial with the same diameter as the linbro wells as a stamp. This is much nicer as round cover slips do self-center and opening is gentler on the slips, too. HTH, Jens On Thursday 27 N

Re: [ccp4bb] RNA Torsion Angle Measurement Error

2008-11-28 Thread Ethan A Merritt
On Friday 28 November 2008, Donnie Berkholz wrote: > On 16:04 Fri 28 Nov , Ethan A Merritt wrote: > > On Friday 28 November 2008, Ben Akiyama wrote: > > > I am measuring and comparing torsion angles in several solved > > > crystal structures of RNA helices using AMIGOS. I was wondering if > >

Re: [ccp4bb] RNA Torsion Angle Measurement Error

2008-11-28 Thread Donnie Berkholz
On 16:04 Fri 28 Nov , Ethan A Merritt wrote: > On Friday 28 November 2008, Ben Akiyama wrote: > > I am measuring and comparing torsion angles in several solved > > crystal structures of RNA helices using AMIGOS. I was wondering if > > anyone knows of a program that can give me an idea of the

Re: [ccp4bb] RNA Torsion Angle Measurement Error

2008-11-28 Thread Ethan A Merritt
On Friday 28 November 2008, Ben Akiyama wrote: > Hi Everyone, > > I am measuring and comparing torsion angles in several solved crystal > structures of RNA helices using AMIGOS. I was wondering if anyone knows > of a program that can give me an idea of the error in these measurements > based on

[ccp4bb] RNA Torsion Angle Measurement Error

2008-11-28 Thread Ben Akiyama
Hi Everyone, I am measuring and comparing torsion angles in several solved crystal structures of RNA helices using AMIGOS. I was wondering if anyone knows of a program that can give me an idea of the error in these measurements based on coordinate error, b-factors, etc. Thanks, Ben Akiyama

Re: [ccp4bb] Program to fill unitcell randomly

2008-11-28 Thread Ethan A Merritt
On Friday 28 November 2008, Mueller, Juergen-Joachim wrote: > > Dear all, > does anybody know a program to > fill an unit cell a,b,c randomly by an arbitrary number > of spheres (atoms)? First you would need to define "random". Uniform density throughout the lattice? Uniform distribution of nei

[ccp4bb] Program to fill unitcell randomly

2008-11-28 Thread Mueller, Juergen-Joachim
Dear all, does anybody know a program to fill an unit cell a,b,c randomly by an arbitrary number of spheres (atoms)? Thank you for help, Juergen

[ccp4bb] Monochromator Stabilization

2008-11-28 Thread Lucas Sanfelici
Hello All! Does anyone know if is there available in the market some sort of all-in-one device capable of keeping the crystals of a double crystal monochromator tunned? I've contacted colleagues around the globe who have similar systems running, but none of them were able to indicate me some co

[ccp4bb] ccp4 6.1

2008-11-28 Thread Charles Ballard
Well, we were gearing up for a release tomorrow, but a major problem with mmdb has come to light. We are moving to fix this and get binaries on the ftp site. So please hold off until it is announced. Charles Ballard CCP4

[ccp4bb] Postdoctoral Position in Crystallography

2008-11-28 Thread Jose Casasnovas
We are seeking an experienced protein crystallographer interested in the study of cell and virus glycoproteins to join our group at the Centro Nacional de Biotecnología (Spanish Research Council) Madrid, Spain ( http://150.244.80.11/content/research/macromolecular/interactions/index.php?l=0). Ap

Re: [ccp4bb] Co-crystallization

2008-11-28 Thread Kontopidis George
Very long soaking time will also help. In your question why the binding kinetics was so slow Here are some explanations Diffusion Rate depends from solution viscosity, size of the molecule that moves in this solution and the pores it has to go through. The binding kinetics in the crystals are usua

Re: [ccp4bb] Co-crystallization

2008-11-28 Thread Joern Krausze
Dear Priya, How long did you soak your crystals? I had a similar problem. When I tried to co-crystallize my protein with its substrate (5 mM) I never got any substrate bound. I tried soaking with higher concentration (up to 50 mM) and this didn't work either. The crystals were infinitely stab

Re: [ccp4bb] CCP4 6.1 release date? (again)

2008-11-28 Thread Martyn Winn
Their presence there signifies that we are in the final stages of testing the downloads However we are still finding problems, hence no announcement. If you take from here, most things will work most of the time. However, they are definitely not supported, and we won't take time out from prep

[ccp4bb] Randomly filled unit cell

2008-11-28 Thread Mueller, Juergen-Joachim
Dear all, does anybody know a program to fill an unit cell a,b,c randomly by an arbitrary number of spheres (atoms)? Thank you for help, Juergen

Re: [ccp4bb] Co-crystallization

2008-11-28 Thread Kontopidis George
What is the solubility of substrate? Try analogues with higher solubility. The 2mM may not be 2mM in the solution! The fact that you added there does not mean that it goes to the solution. If solubility is indeed high and Ki/[solubility]>1 you should be able to see some density in the binding s

[ccp4bb] BSG Winter Meeting

2008-11-28 Thread R. J. Lewis
hi there all just a final reminder about the BSG BCA winter meeting on tuesday 16th december. i need to finalise numbers with the caterers soon, so please can you register, (or failing that just send me an email), by friday 5th december. many thanks. http://conferences.ncl.ac.uk/BCA_BSG_Winter_2