[ccp4bb] Warren Obituary

2009-12-04 Thread Bernhard Rupp
To the Warren Memorial raffle donators: Thank you for your support and please read the obituary accessible from my site. http://www.ruppweb.org/Garland/Warren_raffle.htm Thx,BR - Bernhard Rupp US National Academy of Sciences Committe

Re: [ccp4bb] Electron density improvement with resolution graphic

2009-12-04 Thread Bernhard Rupp
This could be useful: http://www.ruppweb.org/Xray/resolution.html BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Brad Bennett Sent: Friday, December 04, 2009 5:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Electron density improvement with resolution graphi

Re: [ccp4bb] Electron density improvement with resolution graphic

2009-12-04 Thread Jonathan Winger
James Holton has a great little movie showing how electron density changes with decreasing resolution: http://ucxray.berkeley.edu/~jamesh/movies/resolution.mpeg Jon On Dec 4, 2009, at 5:37 PM, Jim Fairman wrote: You can find one here on the Cambridge X-ray crystallography course website:

Re: [ccp4bb] Electron density improvement with resolution graphic

2009-12-04 Thread Jim Fairman
You can find one here on the Cambridge X-ray crystallography course website: http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html On Fri, Dec 4, 2009 at 8:25 PM, Brad Bennett wrote: > Hi all- > I recall seeing a long time ago a figure which showed the progressive > improvement of

[ccp4bb] Electron density improvement with resolution graphic

2009-12-04 Thread Brad Bennett
Hi all- I recall seeing a long time ago a figure which showed the progressive improvement of electron density as one increases resolution, say from 6 to 3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing the ability to model side chains of alpha helices at higher resolution

[ccp4bb] LG announces 3D display

2009-12-04 Thread David J. Schuller
http://www.pcworld.com/article/183644/lg_announces_3d_high_definition_lcd_displays.html "LG Announces 3D High Definition LCD Displays" 23", "full HD" (which I think means 1920 x 1080) No mention of connectors or ports, No mention of compatibility with existing products (e.g. nVidia 3D Vision) "No

[ccp4bb] postdoc position in Cambridge

2009-12-04 Thread Matthew Higgins
A Medical Research Council funded post doctoral position is available to work with Dr Matt Higgins in the Cambridge University Department of Biochemistry on the structural biology and biochemistry of malarial cell surface proteins. This will involve the production and characterisation of malari

[ccp4bb] Structural Biologist - permanent position in Central London

2009-12-04 Thread Andrew Turnbull
Structural Biologist - permanent position Central London, UK Cancer Research Technology (CRT) is a specialist oncology company which advances discoveries arising from Cancer Research UK and other prestigious oncology focused organizations into potential therapies for the benefit of cancer pati

Re: [ccp4bb] Refining residues as rigid bodies

2009-12-04 Thread Pavel Afonine
You can do it in phenix.refine. The prototype is: for trial in trials: phenix.refine model.pdb data.mtz main.random_seed=random_value modify_start_model.adp.shake=true output.prefix=str(random_value) where each refinement will start with the original B-factors that are shaken by a certain v

[ccp4bb] Postdoctoral position at the Goethe University Frankfurt- Institute of Biochemistry

2009-12-04 Thread pos
Post-doc Position at the Institute of Biochemistry at the Goethe University Frankfurt, Germany I am looking for an experienced crystallographer at the post-doctoral level with interest to work on structures of membrane transport machineries, in particular multidrug efflux proteins. The lab is

Re: [ccp4bb] PLEASE I NEED YOUR HELP.

2009-12-04 Thread Sanishvili, Ruslan
Best story I've heard on scamming the scammers appeared on BBC some years ago. Fortunately, it was easy to find it. Take a look at http://news.bbc.co.uk/2/hi/africa/3887493.stm Enjoy, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439

Re: [ccp4bb] How to reduce free-R factor

2009-12-04 Thread Lionel Mourey
Lionel Mourey Institut de Pharmacologie et de Biologie Structurale CNRS - Université de Toulouse 205 route de Narbonne 31077 Toulouse France Tél : 05 61 17 54 36 Mobile : 06 73 50 95 51 Fax : 05 61 17 59 94 E-mail : lionel dot mourey at ipbs dot fr - Message d'origine - De: Pankaj Chauha

Re: [ccp4bb] Memory allocation error in phaser - Mac os

2009-12-04 Thread Vellieux Frederic
Hi Subbu, Vaguely rings a bell. From years ago. Try the command "limit" in tcsh or csh (I think it's ulimit in bash, don't use bash myself). [Mac OS X is a Unix system (BSD) so it should be similar if not identical]. I get here on a Linux box: limit (followed by carriage return) cputime

[ccp4bb] Memory allocation error in phaser - Mac os

2009-12-04 Thread Narayanan Ramasubbu
Dear All: How to increase the memory size (?) to avoid the following error? *** * Information from CCP4Interface script *** The program run with command:

[ccp4bb] Positions available in Membrane Protein Structural Biology

2009-12-04 Thread Said Eshaghi (Vg Assoc Prof)
The School of Biological Sciences at Nanyang Technological University in Singapore is seeking outstanding scientists for functional and structural studies of integral membrane proteins. The School hosts a number of research groups specialized in working with membrane proteins using methodologies

Re: [ccp4bb] Minimum hardware requirement of Mac OSX for CCP4

2009-12-04 Thread William G. Scott
Hi Sergei: No. That is the real beauty of it. It is completely passive. In fact I am using it now just as a regular display hooked into my laptop. It comes with a pair of glasses that are essentially identical to the ones they give away in 3D movie theaters. You start up the program,

[ccp4bb] Post-Doctroal position

2009-12-04 Thread santiago ramon
An opening for a Post-doctoral position is available starting January 15th in the Structural Basis of Genome Integrity Group at the Spanish National Cancer Research Centre in Madrid (CNIO). The ideal candidate should have a PhD in structural biology, biochemistry or a related field and should

Re: [ccp4bb] Map averaging question

2009-12-04 Thread Kevin Cowtan
Simon Kolstoe wrote: 1. Can the map averaging function in coot cope with averaging across twenty monomers Yup. Just tries it with 1c9s (22-fold ncs) The 'all' button is handy for turning off the 19 maps you aren't interested in, then turning on the one you are. The averaged density will

Re: [ccp4bb] Map averaging question

2009-12-04 Thread Vellieux Frederic
Simon Kolstoe wrote: Hi, I have 20 identical monomers in my asu of a 2.5A structure. We have previously model built all twenty monomers and used strict NCS in the refinement, however I would like to compare this with the maps generated by building one monomer into an averaged map and then r

[ccp4bb] Map averaging question

2009-12-04 Thread Simon Kolstoe
Hi, I have 20 identical monomers in my asu of a 2.5A structure. We have previously model built all twenty monomers and used strict NCS in the refinement, however I would like to compare this with the maps generated by building one monomer into an averaged map and then replicating it nineteen ti

Re: [ccp4bb] Bad geometry for alt. conformation refined in Refmac5

2009-12-04 Thread Kay Diederichs
Ian Tickle schrieb: Before you all go away and install the latest Intel compilers to fix this bug - don't bother! We just installed the latest version (ifort 11.3) and it has the same bug! We plan to file a bug report with Intel. Ian, I just checked my older versions of ifort: ifort 11.0.0

Re: [ccp4bb] Bad geometry for alt. conformation refined in Refmac5

2009-12-04 Thread Kay Diederichs
Ian, I cannot reproduce that bug on my x86_64 CentOS 5.4 system: di...@turn29:-/tmp% cat temp.f90 CHARACTER A(2)*2 DATA A/2*'.A'/ CALL CA(A) STOP 1 END SUBROUTINE CA(A) CHARACTER A(2)*2 DO 1 I=1,2 ! With given data, the condition "A(I)(2:).NE.

[ccp4bb] HKL2000 def.site file for ID14-4

2009-12-04 Thread raz zarivach
Dear CCP4 members Can anyone please send me a  HKL2000 def.site file for ESRF ID14-4? Thanks Raz ‎    Raz Zarivach, Ph.D. Department of Life Sciences and the NIBN Ben-Gurion University of the Negev POB 653 Zip code 84105 Beer-Sheva Israel H

Re: [ccp4bb] PLEASE I NEED YOUR HELP.

2009-12-04 Thread Partha Chakrabarti
He needs to be refined in dual space with different weights and gradients.. (whip round and spam reporting). Considering the space time anomaly.. Ming Zhou is stuck in Nigeria, speaking English but no physics.. and it is not even 1st April.. If you wish, you can report such emails to ab...@hotmai

Re: [ccp4bb] PLEASE I NEED YOUR HELP.

2009-12-04 Thread Bernhard Rupp
Try unrestrained refinement first. BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ming Zhou Sent: Friday, December 04, 2009 12:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [Bulk] [ccp4bb] PLEASE I NEED YOUR HELP. Dear, How are you today? May this emergency appeal fin