[ccp4bb] Call for MX-beamtime at HZB-BESSY II, Berlin, period: July/2010 - June/2011, Deadline: March 1. 2010
Next MX-proposal application deadline: March 1, 2010 See: http://www.bessy.de/boat/ We kindly request new MX-proposals for beamtime applications for the next beamtime period. In order to apply for beamtime, please register at the HZB on-line access tool BOAT (http://www.bessy.de/boat/) and submit a new beamtime application proposal. HZB provides beamtime at the MX-beamlines 14.1 and 14.2. The requested beamtime is granted based on the reviewed proposal and reports from previous research activities at BESSY II. Results from previous projects stated in the Experimental Reports will affect the chances for future beamtimes significantly. Please make sure to include them if available. Experimental setup: BL14.1 setup: - Photonflux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position (0.1-20 sec exposure time per frame) - User defined beam shaping from 30µm-100µm diameter possible - MX-225 X-ray detector, 92mm-720mm max. distance from the sample - Microdiffractometer (MD2) with Mini-kappa goniometer MK3 (STAC controlled) - Automatic sample changer (CATS), 90 sample storage capacity (SPINE-Pin EMBL sample magazine compatibility) - 96-well crystallization plate scanning (test phase) - Dedicated eight-core XEON-CPU server, with fibre channel SAN up-link data processing environment - EDNA installed and available - Common MX software installed including HKL2000, XDS, IMOSFLM, CCP4, Phenix, SHELXC-E, etc. - Automated data processing with ixds and xdsi available - Remotely controlled cryo-shutter for crystal annealing - Bruker AXS X-Flash XRF detector We are offering the hard- and software environment for carrying out UVRIP experiments at BL14.1. For further information, please visit: http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/beamlines/bl14-1/hardware/uvrip_en.html BL14.2 setup: - Photonflux: 2x10¹¹ Phot/sx100mAx0.05%BW at sample position (0.1-20 sec exposure time per frame) - MX-225 X-ray detector, 45mm-380mm distance from the sample, 30 deg 2-Theta possible - mardtb goniometer installed - Dedicated eight-core XEON-CPU server, with fibre channel SAN up-link data processing environment - EDNA installed and available - Common MX software installed including HKL2000, XDS, IMOSFLM, CCP4, Phenix, SHELXC-E, etc. - Automated data processing with ixds and xdsi available - Remotely controlled cryo-shutter for crystal annealing - Bruker AXS X-Flash XRF detector - Pressure chamber for noble gas derivatization (Xe, Kr available upon request) - Ultra high performance stereo microscope Leica M205A, 20-255x zoom, 8 Mpixel CCD-camera Please visit our web page www.helmholtz-berlin.de/bessy-mx to gain updated information about our experimental setup and other requirements. Uwe Mueller, Manfred Weiss and the HZB BESSY-MX group -- Dr. Uwe Mueller Makromolekulare Kristallographie (BESSY-MX) / Group leader Elektronenspeicherring BESSY II Albert-Einstein-Str. 15, D-12489 Berlin, Germany Fon: +49 30 6392 4974 Fax: +49 30 6392 4975 url: http://www.helmholtz-berlin.de/bessy-mx u...@bessy.de http://www.helmholtz-berlin.de/bessy-mx%3Ewww.helmholtz-berlin.de/bessy-mx%3C/a%3E%3Cbr%3E%0A%0Aemail:%3Cbr%3E%0A%3Ca%20href= u...@helmholtz-berlin.de mailto:u...@helmholtz-berlin.de /Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Hahn-Meitner-Platz 1, 14109 Berlin Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583 /
[ccp4bb] fermentation seed
Dear All We perform fermentation using e.coli clone to obtain recombinant protein. our batch size is 20 L we perform seeeding in two phase i,.e cryovial to seed 1 then to seed 2 and then in fermentation broth. seed 2 is 10% of fermentation broth, and seed1 is 10% of seed 2. incubate each for 10 - 12 hrs. Seed media is LB media and fermentation media is complex media with vitamins I just want to know is there a requirement for two seed, cant we just go from seed 1 to fermentation broth to reduce the passage of bacterial cell. thanks and regards
[ccp4bb] Alignment of AU?
Hi everybody, I have a question concerning a sequence alignment with the sequences of my 4 molecules in the AU. Unfortunately I found out that the sequences of the 4 monomers do not match exactly. I used the program moleman and it showed me the different numbers of atoms for the monomers. I know in Coot there is a sequence view button, but I can't see the differing residues. The number of residues matches, so I think the mistakes happened when I mutated loops etc. for building and refining. Thanks in advance for any suggestions, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
Re: [ccp4bb] Alignment of AU?
Katja Schleider wrote: Hi everybody, I have a question concerning a sequence alignment with the sequences of my 4 molecules in the AU. Unfortunately I found out that the sequences of the 4 monomers do not match exactly. I used the program moleman and it showed me the different numbers of atoms for the monomers. I know in Coot there is a sequence view button, but I can't see the differing residues. The number of residues matches, so I think the mistakes happened when I mutated loops etc. for building and refining. Thanks in advance for any suggestions, Katja Validate - Align vs PIR ... that's what I would do using Coot.
Re: [ccp4bb] slow coot in mac 10.6
rui wrote: Hi, Dear All, I have a mac 10.4 with 4GB memory, I thought it should be pretty fast. However when I run coot, it's kind of slow. Even when I push the space key to go to next residue, I can feel it is really walking to the next residue. Is this normal or something maybe not set up correct? I wonder how feasible it is to do modeling in laptop. Sorry for the dumb question, but I just want to get a sense how fast it should be, so that I can have things fixed. About - On Line Docs - Slow - Search ...works for me. Otherwise: http://www.biop.ox.ac.uk/coot/doc/chapters/user-manual_8.html#SEC199 Or search the coot mailing list archive yourself. Here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912L=COOTD=0P=42829 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912L=COOTP=R4009 https://www.jiscmail.ac.uk/cgi-bin/webadmin?S2=COOTq=slows=f=a=b= Or search majorgroove yourself: http://www.majorgroove.org/questions/99/why-has-my-coot-gone-slow Or Edit - Preferences - Smooth Recentering - Number of Steps - 10 Also the Coot Spin Test page may be of interest http://www.biop.ox.ac.uk/coot/spin-test.html Paul.
[ccp4bb] Displaying electron density in PYMOL
Hi, I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1. file…….open ……..pdb and map files. I can see these two objects on the right column. 2. Then I selected the waters for which I want to display the electron density and created an object named ‘wat’ 3. In the command line I wrote ‘isomesh mesh1, 3fo2fc.map, 1.0, wat, carve=1.6’ and it creates an object ‘mesh1’ that shows the electron density of some of the waters (not all) selected in ‘wat’. I tried with other sigma levels, but the problem persists. I could not understand why for some waters electron density did not show up in PYMOL, but it does in COOT. I also noticed the same problem remains for part of this molecule, not just for some waters. I checked the pdb file, which looks fine and have the standard format. Does anyone have any idea, what’s going wrong? Thanks… Raja Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/
Re: [ccp4bb] Displaying electron density in PYMOL
On Wed, Feb 10, 2010 at 12:16 PM, Raja Dey deyra...@yahoo.co.in wrote: I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1. file…….open ……..pdb and map files. I can see these two objects on the right column. 2. Then I selected the waters for which I want to display the electron density and created an object named ‘wat’ 3. In the command line I wrote ‘isomesh mesh1, 3fo2fc.map, 1.0, wat, carve=1.6’ and it creates an object ‘mesh1’ that shows the electron density of some of the waters (not all) selected in ‘wat’. I tried with other sigma levels, but the problem persists. I could not understand why for some waters electron density did not show up in PYMOL, but it does in COOT. I also noticed the same problem remains for part of this molecule, not just for some waters. I checked the pdb file, which looks fine and have the standard format. Does anyone have any idea, what’s going wrong? What format is the map? If it's in XPLOR format, this is probably the source of the problem - it lacks symmetry information and only covers a pre-determined portion of the unit cell. Try leaving out everything after the sigma level when you run the 'isomesh' command, and you'll get some idea of the coverage. PS. There is a PyMOL mailing list too: https://lists.sourceforge.net/lists/listinfo/pymol-users -Nat
Re: [ccp4bb] Displaying electron density in PYMOL
You have to make sure the asymmetric unit for the maps is the same as for your molecule (which it probably isn't). The easiest way is to extend the map so it covers all the atoms with a few angstrom border. Coot calculates the map on the fly from the mtz file (I am guessing this is the difference) so you don't run into this problem. Raja Dey wrote: Hi, I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1. fileâ¦â¦.open â¦â¦..pdb and map files. I can see these two objects on the right column. 2. Then I selected the waters for which I want to display the electron density and created an object named âwatâ 3. In the command line I wrote âisomesh mesh1, 3fo2fc.map, 1.0, wat, carve=1.6â and it creates an object âmesh1â that shows the electron density of some of the waters (not all) selected in âwatâ. I tried with other sigma levels, but the problem persists. I could not understand why for some waters electron density did not show up in PYMOL, but it does in COOT. I also noticed the same problem remains for part of this molecule, not just for some waters. I checked the pdb file, which looks fine and have the standard format. Does anyone have any idea, whatâs going wrong? Thanks⦠Raja Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/
Re: [ccp4bb] Displaying electron density in PYMOL
How are you creating your map for Pymol? You can find instructions for constructing sensible omit maps using refmac5 and fft in CCP4 here: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac For displaying omit maps in Pymol look here: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps Cheers, Roger Rowlett On 2/10/2010 3:16 PM, Raja Dey wrote: Hi, I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1. file…….open ……..pdb and map files. I can see these two objects on the right column. 2. Then I selected the waters for which I want to display the electron density and created an object named ‘wat’ 3. In the command line I wrote ‘isomesh mesh1, 3fo2fc.map, 1.0, wat, carve=1.6’ and it creates an object ‘mesh1’ that shows the electron density of some of the waters (not all) selected in ‘wat’. I tried with other sigma levels, but the problem persists. I could not understand why for some waters electron density did not show up in PYMOL, but it does in COOT. I also noticed the same problem remains for part of this molecule, not just for some waters. I checked the pdb file, which looks fine and have the standard format. Does anyone have any idea, what’s going wrong? Thanks… Raja Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!.
Re: [ccp4bb] Displaying electron density in PYMOL
Hi Raja, If you are reading in the map saved from coot, it covers just the AU. Most likely the selection that you are trying to show the mesh around in pymol is outside of the AU. The solution is to use FFT to draw maps around your model (it an option in one of the drop down menus in the FFT CCP4i gui) and use these maps in pymol. And don't forget to add the .ccp4 extension to the map files for reading into pymol. hope that solves your problem. Eric __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Thu, 11 Feb 2010, Raja Dey wrote: Hi, I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1. file…….open ……..pdb and map files. I can see these two objects on the right column. 2. Then I selected the waters for which I want to display the electron density and created an object named ‘wat’ 3. In the command line I wrote ‘isomesh mesh1, 3fo2fc.map, 1.0, wat, carve=1.6’ and it creates an object ‘mesh1’ that shows the electron density of some of the waters (not all) selected in ‘wat’. I tried with other sigma levels, but the problem persists. I could not understand why for some waters electron density did not show up in PYMOL, but it does in COOT. I also noticed the same problem remains for part of this molecule, not just for some waters. I checked the pdb file, which looks fine and have the standard format. Does anyone have any idea, what’s going wrong? Thanks… Raja Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!.
Re: [ccp4bb] Displaying electron density in PYMOL
The map was created quite long time ago in cns. I have .cv file only. I am using the same map file both in COOT and PYMOL. I think this a limitation in PYMOL over COOT. Raja From: William G. Scott wgsc...@chemistry.ucsc.edu To: Raja Dey deyra...@yahoo.co.in Cc: ccp4bb@jiscmail.ac.uk Sent: Wed, 10 February, 2010 1:27:38 PM Subject: Re: [ccp4bb] Displaying electron density in PYMOL You have to make sure the asymmetric unit for the maps is the same as for your molecule (which it probably isn't). The easiest way is to extend the map so it covers all the atoms with a few angstrom border. Coot calculates the map on the fly from the mtz file (I am guessing this is the difference) so you don't run into this problem. Raja Dey wrote: Hi, I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1. file…….open ……..pdb and map files. I can see these two objects on the right column. 2. Then I selected the waters for which I want to display the electron density and created an object named ‘wat’ 3. In the command line I wrote ‘isomesh mesh1, 3fo2fc.map, 1.0, wat, carve=1.6’ and it creates an object ‘mesh1’ that shows the electron density of some of the waters (not all) selected in ‘wat’. I tried with other sigma levels, but the problem persists. I could not understand why for some waters electron density did not show up in PYMOL, but it does in COOT. I also noticed the same problem remains for part of this molecule, not just for some waters. I checked the pdb file, which looks fine and have the standard format. Does anyone have any idea, what’s going wrong? Thanks… Raja Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/ Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/
[ccp4bb] Harmonic Restraints
Hello, I've been trying to use harmonic restraints in Refmac by creating a .txt file with the following in it: external harmonic residues from 2 H to 4 H external harmonic residues from 17 H to 19 H external harmonic residues from 26 H to 28 H I've used it both with and without the 'sigma' value at the end of each line. Either way restraints do not hold during restrained refinement. These few rotamers which I fix in Coot, validate in Phenix, refine in Refmac, and validate again in Phenix keep getting pushed into areas that are not favored. I would love to hear some ideas as I'm out and this model is otherwise done. Thanks in advance! -Jon Here is the link to harmonic restraints link if anyone is curious: http://www.ccp4.ac.uk/dist/html/refmac5/keywords/keywords_5_5.html#Harmonic
Re: [ccp4bb] Harmonic Restraints
Hi Jon, These few rotamers which I fix in Coot, validate in Phenix, refine in Refmac, and validate again in Phenix keep getting pushed into areas that are not favored. I would love to hear some ideas as I'm out and this model is otherwise done. did you try refining it in Phenix with or without fix_rotamers=True option? This may help. Do these residues have good density (since you say you do validate in Phenix, then you must have the real-space CC computed and listed per residue/atom)? There are plenty of other options to try out, such as changing weights, for example. Or fixing coordinates of specific residues during refinement. You can do it in phenix.refine. If nothing helps, you can send me the data and model files and I will have a closer look - this may help us to improve the software too and help you to resolve this problem. Let me know if you have questions. Pavel.
[ccp4bb] SLS BEAMTIME for PROTEIN CRYSTALLOGRAPHY
=== SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS === Proposal application deadline: Monday, February 15, 2010 Periods: May 1, 2010 - August 31, 2010 ( Normal / Test proposals) May 1, 2010 - April 30, 2012 ( Long-term proposals) Proposal submission: http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls/PX/index.html Travel support: http://sls.web.psi.ch/view.php/users/experiments/eusupport/index.html What's New? - Possibility to combine beamtime at X06SA and X06DA, please indicate your shift requests in the proposal (only one proposal needed on either X06SA or X06DA) - Automatic sample changer (IRELEC CATS) available at all beamlines - X06SA: pilatus 6m pixel detector and micro-diffractometer - X06DA: better focusing 80x45 microns, higher flux 5 x10¹¹ photons/ sec, and in-situ diffraction screening - X10SA: accepting proposal for single crystal UV-Vis and Raman spectroscopy studies X06SA Beamline features: - PILATUS 6M pixel detector available for user operation at High Resolution Diffractometer. Continuous, fine phi-sliced data acquisition (12.5 frames per second) with 20 bit dynamic range, see http://pilatus.web.psi.ch/ or www.dectris.com http://www.dectris.com/ for further information - mar225 CCD installed at Micro-Diffractometer MD2. This MAD- compatible diffractometer allows for data collection with a focussed beam size of 25 x 5 micrometers, and down to 10 x 5 micrometer using an aperture. - Automatic sample changer (IRELEC CATS) with SPINE pucks, vials, and caps (MOLECULAR DIMENSIONS) on HRD. - http://sls.web.psi.ch/view.php/beamlines/px/index.html X06DA Beamline features: - fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - 5x10¹¹ photons/sec at sample position - 80x45 microns focused beam - MAR225 CCD detector - Mini-hutch design for fast manual mounting - Automatic sample changer (IRELEC CATS) with SPINE pucks, vials, and caps (MOLECULAR DIMENSIONS). - In-situ diffraction screening for beta-test users (please contact Rouven Bingle-Erlenmeyer or Vincent Olieric) - http://sls.web.psi.ch/view.php/beamlines/px3/index.html X10SA Beamline features: - limited beamtime available for single crystal UV-Vis and Raman spectroscopy (c.f. R.Owen, et al., JSR, (2009), 16, 173) - PILATUS 6M pixel detector - Automatic sample changer (IRELEC CATS) with SPINE pucks, vials, and caps (MOLECULAR DIMENSIONS) - http://sls.web.psi.ch/view.php/beamlines/px2/index.html Best regards, Meitian Wang, Vincent Olieric, Takashi Tomizaki, Martin Fuchs, Anuschka Pauluhn and Clemens Schulze-Briese __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone: +41 56 310 4175 Fax: +41 56 310 5292
