Re: [ccp4bb] data collection

Any reciprocal lattice point (relp) not in the blind region will cross the Ewald sphere twice. This is because it follows a closed circular path that passes through a closed surface. Must be one "in" and one "out". However, even in P1 there is always a Friedel mate, and that is "symmetry equ

[ccp4bb] data collection

Hi All, I wish to confirm that when we collect native dataset 0-360 for a protein crystal (P1 space group) , the redundancy could very well be >2 since many reciprocal points cross Ewald sphere twice, right ? Thanks a lot. John

Re: [ccp4bb] Coot "File Save Coordinates"

Hi Raji, Yeah, this can be frustrating. I had a related problem a few years ago. The following thread may be informative: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=COOT&P=R2679&1=COOT&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 As Antony points out, it's a problem with X11 as imp

Re: [ccp4bb] Coot "File Save Coordinates"

Thanks for pointing that out. -Raji On Mon, Aug 15, 2011 at 4:29 PM, Antony Oliver wrote: > If you're running Coot on a Mac - it's also unfortunately a > well-documented "feature", something to do with Apple's implementation of > X11. > > > Sent from my iPhone > > On 15 Aug 2011, at 21:25, "Raji

Re: [ccp4bb] Coot "File Save Coordinates"

If you're running Coot on a Mac - it's also unfortunately a well-documented "feature", something to do with Apple's implementation of X11. Sent from my iPhone On 15 Aug 2011, at 21:25, "Raji Edayathumangalam" mailto:r...@brandeis.edu>> wrote: Thanks Mischa and Juergen. That was probably my mo

Re: [ccp4bb] Coot "File Save Coordinates"

Thanks Mischa and Juergen. That was probably my most ridiculous post to the CCP4BB!! I found the pop-up dialog box hiding behind all my zillion windows. Now why the pop-up window would not pop up actively on top of all other windows is a question for another time. Nevertheless, your replies helped

Re: [ccp4bb] Coot "File Save Coordinates"

Have you moved your primary window away ? I mean just in case the pop up window opened behind the actual scene window. Jürgen On Aug 15, 2011, at 3:54 PM, Raji Edayathumangalam wrote: Hi Folks, Apologies for a non-CCP4 question. I am trying to write our coordinates following SSM superposition

[ccp4bb] Coot "File Save Coordinates"

Hi Folks, Apologies for a non-CCP4 question. I am trying to write our coordinates following SSM superposition using the File Save Coordinates option in Coot. But if I click the "Select Filename" button, nothing happens. I thought I would get an option to pick a filename and specify what I want my

Re: [ccp4bb] Another paper & structure retracted

A bit of praise for Ptolemy's integrity, however, is that he didn't fudge the equant circle issue (I am not sure whether others maybe knew about it previously, actually). That was really the monkey wrench in the whole theory, and without that, probably we would still be geocentric. It would have be

Re: [ccp4bb] HOLE & CHANNEL

Oliver Smart is now with Global Phasing and HOLE is supported by/available from the Sansom lab at Oxford: http://hole.biop.ox.ac.uk/hole Quoting "Hargreaves, David" : Dear CCP4, I'm looking for the authors of the programs (listed below). I want to analyse our crystal systems and would lik

Re: [ccp4bb] Protein crosslinking before crystallization

Hi Opher, I have a project where a protein was made 'cysless' and selective cysteines were introduced to allow for directed crosslinking using MTS and aldrithiol activated reagents (see Toronto Research Company and Pierce for a range of reagents of different lengths). A side product of these cr

[ccp4bb] HOLE & CHANNEL

Dear CCP4, I'm looking for the authors of the programs (listed below). I want to analyse our crystal systems and would like to use these algorithms. However, I'm not convinced the addresses on the papers are current. Does anybody know how to contact the authors or of any other programs that exist

Re: [ccp4bb] Protein crosslinking before crystallization

I found this paper to be very helpful for a similar experiment. "Elucidation of the mechanism and end products of glutaraldehyde cross-linking reaction by x-ray structure analysis". Wine et al. Biotechnology & Engineering, Vol. 98, No. 3, October 15, 2007. -CCP4 bulletin board wrote: ---

Re: [ccp4bb] Protein crosslinking before crystallization

Hi Opher, I seem to recall some old papers in which glutarldehyde was used (in the RESERVOIR only) in order to promote crystallization of proteins with suspected inter-domain flexibility. Unfortunately, I don't have specific references in mind. Cheers, Boa

[ccp4bb] Protein crosslinking before crystallization

Hi all Does anyone have experience or insights on intramolecular crosslinking of proteins before crystallization? The idea is to lock a felxible (multidomain) protein into a restricted conformation. Thanks, Opher

[ccp4bb] PDRA vacancy at Diamond Microfocus MX beamline

Dear All, I'd like to draw your attention to a PDRA vacancy at Diamond Light Source to work as part of the I24 Microfocus MX beamline team. Please visit http://www.diamond.ac.uk/Home/Jobs/Current/DIA0630-TH.html for more details or contact Gwyndaf Evans (gwyndaf.ev...@diamond.ac.uk

Re: [ccp4bb] "Truncate style Wilson plot"?

ctruncate style Wilson plot is the old form log / ) I believe "Wilson plot estimated B factor" is am Arp_Warp style plot where ) is replaced by a more sophisticated estimate of expecting scattering. You will have to look at a Arp_warp publication for details.. Eleanor On 08/11/2011 07:4

Re: [ccp4bb] Another paper & structure retracted

On Thu, 2011-08-11 at 14:33 -0600, Maia Cherney wrote: > Even great scientists sometimes published papers > with wrong analysis. Absolutely (although I am not sure how high crimes and misdemeanors of Henry VIII absolve more petty criminals of responsibility): http://www.amazon.com/Claudius-Ptol

[ccp4bb] Coot for Virtalis Immersive VR Display System

Hi All, We now have access to a rather nice Virtalis Immersive VR Display System with an InterSense Tracking handset. Virtalis provides a version of Pymol that's been modified to use the InterSense Tracking library which is quite fun. Do you know of anybody who has already done a modified Coot

Re: [ccp4bb] PyMol plugin

On 08/15/2011 12:15 AM, Yuri Pompeu wrote: ... I then installed cctbx+Python bundle from http://cci.lbl.gov/cctbx_build/ and sourced it. I still get the same result in PyMol though.. Does anyone know what to do? You need to launch PyMOL with the python executable that was installed by cctbx.