[ccp4bb] job opening „Computational Chemist” at Proteros, Martinsried
Dear All, Can I draw your attention to this job vacancy at Proteros: We are looking for a Computational Chemist (m/f). The main responsibilities are: - Modeling support for structure-based lead generation projects, - Virtual screening of small molecule libraries within hit identification programs - Advancement of our in-house computational chemistry platform For details please see: http://www.proteros.de/downloads/Computational_Chemist.pdf Best regards Stephan
[ccp4bb] Beamtime @ SLS
=== SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS === Proposal application deadline: Wednesday, February 15, 2012 Periods: May 1, 2012 - August 31, 2012 (Normal / Test proposals) May 1, 2012 - April 30, 2014 (Long-term proposals) Proposal submission: http://www.psi.ch/sls/px-beamlines-call-for-proposals Travel support: http://www.psi.ch/useroffice/eu-support-programmes PSI DUO application for iphone: http://itunes.apple.com/ch/app/psi-duo/id375328818?mt=8 What's New? - X06SA High-resolution diffractometer: PILATUS detector runs two times faster (25 Hz) - X06SA Micro-diffractometer: Triple aperture (5, 10, and 20 microns) with one mouse click exchange - X06DA PILATUS 2M (60 Hz) - the fastest detector for protein crystallography - X06DA Multi-axis goniometer (PRIGO) - X06DA In-situ X-ray diffraction screening for any SBS format plate - X10SA Single crystal spectroscopy (UV-Vis, fluorescence and Raman), but no open call for this period (see details below). X06SA Beamline features (http://www.psi.ch/sls/pxi/pxi) - Undulator beamline with flux of 2x10^12 photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - Focused beam size and divergency: HRD - 85x10 microns and 0.35x0.06 mrad; MD2 - 25x5 microns and 0.5x0.4 mrad - PILATUS 6M pixel detector at the High Resolution Diffractometer, allowing continuous, fine phi-sliced data acquisition (25 frames per second) with 20 bit dynamic range (see http://pilatus.web.psi.ch/ or www.dectris.com for further information) - MAR225 CCD at Micro-Diffractometer MD2, allowing data collection with a focussed beam size of 25 x 5 micrometers, and smaller beam size with triple-aperture assembly ( 5 x 5, 10 x 10, 20 x 20 micrometer). X06DA Beamline features (http://www.psi.ch/sls/pxiii/pxiii) - Super-bending magnet beamline with flux of 5x10¹¹ photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - Focused beam size and divergency: 80x45 microns and 2x0.5 mrad (with possibility to reduce horizontal divergency to 0.4 mrad) - Mini-hutch design for fast manual mounting - PILATUS 2M (60 Hz, 450 um Si sensor) - Multi-axis goniometer (PRIGO) for crystal re-orentation - In-situ X-ray diffraction screening (with any SBS format plate) available during users shifts (R. Bingel-Erlenmeyer, et al., Crystal Growth Design 2011, 11, 916) X10SA Beamline features (http://www.psi.ch/sls/pxii/pxii) - Undulator beamline with flux of 2x10^12 photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 20 keV (2.07 - 0.62 Å) - Focused beam size and divergency: 50x10 microns and 0.6x0.1 mrad - In-situ on-axis single crystal UV-Vis, fluorescence, Raman and Resonance Raman microspectrophotometer (http://www.psi.ch/sls/pxii/spectrolab) - PILATUS 6M pixel detector Note: beamtime for single crystal spectroscopy is very limited in this call period due to a scheduled diffractometer upgrade. Best regards, The MX group at SLS __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://www.psi.ch/sls/ Phone: +41 56 310 4175 Fax: +41 56 310 5292
[ccp4bb] Freezing crystal
Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
Re: [ccp4bb] Freezing crystal
Hi Theresa, Once I had crystals in 3.5 M Amm. Sulfate. I used Paraffin oil and Paraton-N-oil (in 1:1 ratio). I also used 30% Xylatol. Best, Vineet On Sun, Feb 5, 2012 at 5:49 PM, Theresa H. Hsu theresah...@live.com wrote: Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
Re: [ccp4bb] Freezing crystal
Hi Theresa, Try glycerol at 10 % with 5 % increments up to 30 % v/v. You may also be able to attain protection by increasing the ammonium sulfate concentration along with incremental glycerol approach. Crystallization of RNA/protein complexes by Garber and colleagues (Acta Cryst. (2002). D58, 1664-1669) reported using 25% - 30% (w/v) of glucose for cryoprotection with ethanol, MPD, PEG, ethylene glycol, sucrose not being found suitable with concentrated ammonium sulphate. May also want to consider sodium malonate and DMSO along with the already suggested Paratone-N/Paraffin Oil blends. DMSO: http://www.bio.brandeis.edu/publications/bi035849h.pdf Sodium malonate: http://journals.iucr.org/d/issues/2003/12/00/fw5004/fw5004.pdf Take Care, Sean Seaver P212121 http://store.p212121.com/
Re: [ccp4bb] off-topic:schematic representations for secondary structure
On 02/04/2012 08:11 PM, Vellieux Frederic wrote: I believe Procheck generates drawings such as those. It generates PostScript files, and if you need to have (eg) jpg files, a PostScript interpreter, screen capture and there you are (Gimp to select only the areas you're interested in) The convert command from the ImageMagick package on Linux can usually deal with any image format conversion. Regards, F. HTH, Fred. WENHE ZHONG wrote: Dear memebers, Thank you all firsit for the helps on my previous post about sequence alignment. They are really useful! Apologize for the off-topic question again. I usually use DSSP method to calculate the secondary structures on my sovled structures. I saw a nice schematic representation for secondary structure from PDB database website (please see the attached figure). Does anyone know whether there is a program to draw these schematics? Thank you. King regards, Wenhe
[ccp4bb] shape complementarity
Dear All, Greetings! Can anybody tell me a method to quantitate shape complementarity between two surfaces? Sc program in CCP4 is not running properly. thanks and regards Deepak
Re: [ccp4bb] Freezing crystal
Hi Theresa, A good place to start when searching for suitable cryo conditions are the tables in these references: Garman, et al. J. Appl. Cryst. (1996). 29, 584-587. McFerrin, et al. J. Appl. Cryst. (2002). 35, 538-545. hope they help and good luck. Eric __ Eric Larson Boehringer Ingelheim Ridgefield, CT Date:Sun, 5 Feb 2012 22:49:25 + From:Theresa H. Hsu theresah...@live.com Subject: Freezing crystal Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
Re: [ccp4bb] shape complementarity
Deepak Thankappan Nair wrote: ~~~ Can anybody tell me a method to quantitate shape complementarity between two surfaces? Sc program in CCP4 is not running properly. thanks and regards Deepak I think SC is THE way to calculate it. If not working in the current release, we should get it fixed. Can you be more specific? For me using ccp4-6.2.0 it runs and gives apparently reasonable output: Mean normal product:surface 2 to surface 1 = 0.419 Median normal product: surface 2 to surface 1 = 0.411 Summary of results: D(A-B) D(B-A) D(A-B)+D(B-A)/2 Mean 1.1681.0571.113 Median 1.1161.0001.058 S(A-B) S(B-A) S(A-B)+S(B-A)/2 Mean 0.3890.4190.404 Median 0.3550.4110.383 Shape complementarity statistic Sc =0.383 _
Re: [ccp4bb] Freezing crystal
if you use oil do direct dry Paratone-N, with paraffin oil is not as good. Li-salts should work also - i would almos imgaine you can freeze directly from so high (NH4)2SO4 conc. but perhaps not. little bit (10%) glycerol probably does it also.. Tommi On Feb 6, 2012, at 12:55 AM, Vineet Gaur wrote: Hi Theresa, Once I had crystals in 3.5 M Amm. Sulfate. I used Paraffin oil and Paraton-N-oil (in 1:1 ratio). I also used 30% Xylatol. Best, Vineet On Sun, Feb 5, 2012 at 5:49 PM, Theresa H. Hsu theresah...@live.com wrote: Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
Re: [ccp4bb] shape complementarity
Deepak Thankappan Nair wrote: Dear Dr. Berry thanks for the mail. maybe the syntax that I provide is not correct. i assume you have to write MOLECULE1 CHAIN A to define the first surface but i get the following error: MOLECULE1 CHAIN A No molecule number given BFONT COLOR=#FF!--SUMMARY_BEGIN-- SC: Syntax: MOLECULEn SC: Syntax: MOLECULEn I think you don't put the in n - just the number. here is an example that runs: sc xyzin temp.pdb eof MOLecule 1 zone C 20 C 379 MOLecule 2 zone R 74 R 196 eof Good luck! eab there are no examples on the ccp4 website any light on this would be very valuable, regards deepak On 2/6/12, Edward A. Berryber...@upstate.edu wrote: Deepak Thankappan Nair wrote: ~~~ Can anybody tell me a method to quantitate shape complementarity between two surfaces? Sc program in CCP4 is not running properly. thanks and regards Deepak I think SC is THE way to calculate it. If not working in the current release, we should get it fixed. Can you be more specific? For me using ccp4-6.2.0 it runs and gives apparently reasonable output: Mean normal product:surface 2 to surface 1 = 0.419 Median normal product: surface 2 to surface 1 = 0.411 Summary of results: D(A-B) D(B-A) D(A-B)+D(B-A)/2 Mean 1.1681.0571.113 Median 1.1161.0001.058 S(A-B) S(B-A) S(A-B)+S(B-A)/2 Mean 0.3890.4190.404 Median 0.3550.4110.383 Shape complementarity statistic Sc =0.383 _
Re: [ccp4bb] Freezing crystal
if your crystals are from 2 M AmSO4 without buffer, try to measure the pH in the drop, if possible. Or if you have plenty of crystals, transfer to 2 M AmSO4 buffered at a wide range of different pHs to see where the crystals are stable, before adding cryoprotectant. In the end, you may need to grow new crystals in the presence of buffer and, if possible, glycerol. The latter could allow direct freezing. Mark On 5 Feb 2012, at 23:49, Theresa H. Hsu wrote: Hi all Is there a list of conditions to be tried *first* for cryoprotectant? My crystals diffract at room temperature capillary but no in 30% PEG 400. Crystals are from 2 M ammonium sulfate. Thank you. Theresa
