[ccp4bb] Postdoctoral position at Exeter
Please find a vacancy for a postdoctoral position available at Exeter to work on an exciting multidisciplinary EU grant called 'Hotzyme' Details can be found at http://admin.exeter.ac.uk/personnel/jobs.php?action=jobareaid=4jid=5163 Professor Jenny Littlechild Professor Jenny Littlechild Prof. Biological Chemistry Director Exeter Biocatalysis Centre Henry Wellcome Building for Biocatalysis Stocker Road Exeter EX4 4QD, UK Tel: 44 (0) 1392 263468 Fax: 44 (0) 1392 263489 Email: j.a.littlech...@exeter.ac.ukmailto:j.a.littlech...@exeter.ac.uk www.exeter.ac.uk/bioscienceshttp://www.exeter.ac.uk/biosciences http://centres.exeter.ac.uk/biocatalysis
[ccp4bb] x-ray sensitive dye?
Does anyone know of a water soluble dye that changes color upon exposure to x-rays? Preferably from clear to a dark color. Must work in the liquid state (non-frozen... so color centers are out). Doesn't matter if it is organic or inorganic. Thanks Richard Gillilan MacCHESS Cornell University Ithaca, NY
[ccp4bb] xds question
Dear ccp4bb, I am quite a fan of XDS and have just upgraded to the latest version. Normally, to assess the quality of my data, I look at the tables in CORRECT.LP and especially the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = 0.0 AS FUNCTION OF RESOLUTION. However in my latest run I only get a single table for all the data i.e. for signal/noise = -3.0. Is there a command I can put in my XDS.INP that will give me all the other tables or has the CORRECT.LP logfile been altered in the most recent version of XDS? (FYI my xds.inp obtained from the ESRF last week is copied below) Thanks, Simon !=== File Automaticaly generated by mxCuBE !=== X-Ray data collected at: ESRF_ID14-1 !=== Detector type: ADSC Quantum Q210 !=== Date: Fri Feb 04 03:39:09 2011 !=== User comments: JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !JOB= DEFPIX XPLAN INTEGRATE CORRECT DATA_RANGE= 1 190 SPOT_RANGE= 1 20 SPOT_RANGE= 1 4 !SPOT_RANGE= 187 190 BACKGROUND_RANGE= 1 4 SECONDS=60 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 6 STRONG_PIXEL= 6.0 OSCILLATION_RANGE= 1.000 STARTING_ANGLE= 0.000 STARTING_FRAME= 1 X-RAY_WAVELENGTH= 0.93340 NAME_TEMPLATE_OF_DATA_FRAMES= ./data/sk1_1_???.img !STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10 !TOTAL_SPINDLE_ROTATION_RANGES= 60 180 10 DETECTOR_DISTANCE= 298.55 DETECTOR= ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ORGX= 1014.79ORGY= 1029.10 NX= 2048 NY= 2048 QX= 0.10200 QY= 0.10200 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 7000 3 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ROTATION_AXIS= 1.0 0.0 0.0 INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0 FRACTION_OF_POLARIZATION= 0.98 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !== Default value recommended !AIR= 0.00026895 SPACE_GROUP_NUMBER= 0 UNIT_CELL_CONSTANTS= 0 0 0 0 0 0 INCLUDE_RESOLUTION_RANGE= 50.0 2.4 RESOLUTION_SHELLS= 15.0 8.0 4.0 3.0 2.8 2.6 2.5 2.4 FRIEDEL'S_LAW= FALSE !FRIEDEL'S_LAW= TRUE TRUSTED_REGION= 0 1.40 REFINE(INTEGRATE)= BEAM ORIENTATION CELL !== Default value recommended !DELPHI= 3.000 MAXIMUM_NUMBER_OF_PROCESSORS= 16 !MAXIMUM_NUMBER_OF_JOBS= 16
Re: [ccp4bb] xds question
Dear Simon, I don't know how to change the output written to the log-file (maybe with the TEST-card), but I wonder why you don't want to look at all of your data but only those with I/sigI 0? XDS reports all reflections with I/sigI -3 for a good reason. Cheers, Tim On Tue, Feb 08, 2011 at 12:17:35PM +, Simon Kolstoe wrote: Dear ccp4bb, I am quite a fan of XDS and have just upgraded to the latest version. Normally, to assess the quality of my data, I look at the tables in CORRECT.LP and especially the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = 0.0 AS FUNCTION OF RESOLUTION. However in my latest run I only get a single table for all the data i.e. for signal/noise = -3.0. Is there a command I can put in my XDS.INP that will give me all the other tables or has the CORRECT.LP logfile been altered in the most recent version of XDS? (FYI my xds.inp obtained from the ESRF last week is copied below) Thanks, Simon !=== File Automaticaly generated by mxCuBE !=== X-Ray data collected at: ESRF_ID14-1 !=== Detector type: ADSC Quantum Q210 !=== Date: Fri Feb 04 03:39:09 2011 !=== User comments: JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !JOB= DEFPIX XPLAN INTEGRATE CORRECT DATA_RANGE= 1 190 SPOT_RANGE= 1 20 SPOT_RANGE= 1 4 !SPOT_RANGE= 187 190 BACKGROUND_RANGE= 1 4 SECONDS=60 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 6 STRONG_PIXEL= 6.0 OSCILLATION_RANGE= 1.000 STARTING_ANGLE= 0.000 STARTING_FRAME= 1 X-RAY_WAVELENGTH= 0.93340 NAME_TEMPLATE_OF_DATA_FRAMES= ./data/sk1_1_???.img !STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10 !TOTAL_SPINDLE_ROTATION_RANGES= 60 180 10 DETECTOR_DISTANCE= 298.55 DETECTOR= ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ORGX= 1014.79ORGY= 1029.10 NX= 2048 NY= 2048 QX= 0.10200 QY= 0.10200 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 7000 3 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ROTATION_AXIS= 1.0 0.0 0.0 INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0 FRACTION_OF_POLARIZATION= 0.98 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !== Default value recommended !AIR= 0.00026895 SPACE_GROUP_NUMBER= 0 UNIT_CELL_CONSTANTS= 0 0 0 0 0 0 INCLUDE_RESOLUTION_RANGE= 50.0 2.4 RESOLUTION_SHELLS= 15.0 8.0 4.0 3.0 2.8 2.6 2.5 2.4 FRIEDEL'S_LAW= FALSE !FRIEDEL'S_LAW= TRUE TRUSTED_REGION= 0 1.40 REFINE(INTEGRATE)= BEAM ORIENTATION CELL !== Default value recommended !DELPHI= 3.000 MAXIMUM_NUMBER_OF_PROCESSORS= 16 !MAXIMUM_NUMBER_OF_JOBS= 16 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] Crystal Imaging Instruments?
Hi, Which crystal imaging system do you use, if any? Are you satisfied with the software available to run it? This information would help set priorities for future development of xtalPiMS, so I would be grateful for replies. xtalPiMS currently supports Formulatrix instruments, and I am currently adding support for ThermoElectron (Rhombix). regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 https://www.pims-lims.org/ Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD
Re: [ccp4bb] x-ray sensitive dye?
Hi Richard, I assume you want to track down which parts of a crystal you already have exposed ? I think dithionite leads to brown colouring of the protein after/during exposure. At least we've observed frequently that some ingredients in our crystals turn brown over time and you could clearly see where the beam hit. I don't know how applicable this would be for small beamsizes and a couple of images, but for whole datasets it would work. James Holton probably has a build-it-yourself solution to this I expect. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Feb 8, 2011, at 6:32 AM, Richard Edward Gillilan wrote: Does anyone know of a water soluble dye that changes color upon exposure to x-rays? Preferably from clear to a dark color. Must work in the liquid state (non-frozen... so color centers are out). Doesn't matter if it is organic or inorganic. Thanks Richard Gillilan MacCHESS Cornell University Ithaca, NY
Re: [ccp4bb] xds question
Hi Tim, could you write a bit more about this cutoff. I've been using the 0 cutoff for the longest time as it seemed to be much more stringent to report. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Feb 8, 2011, at 7:45 AM, Tim Gruene wrote: Dear Simon, I don't know how to change the output written to the log-file (maybe with the TEST-card), but I wonder why you don't want to look at all of your data but only those with I/sigI 0? XDS reports all reflections with I/sigI -3 for a good reason. Cheers, Tim On Tue, Feb 08, 2011 at 12:17:35PM +, Simon Kolstoe wrote: Dear ccp4bb, I am quite a fan of XDS and have just upgraded to the latest version. Normally, to assess the quality of my data, I look at the tables in CORRECT.LP and especially the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = 0.0 AS FUNCTION OF RESOLUTION. However in my latest run I only get a single table for all the data i.e. for signal/noise = -3.0. Is there a command I can put in my XDS.INP that will give me all the other tables or has the CORRECT.LP logfile been altered in the most recent version of XDS? (FYI my xds.inp obtained from the ESRF last week is copied below) Thanks, Simon !=== File Automaticaly generated by mxCuBE !=== X-Ray data collected at: ESRF_ID14-1 !=== Detector type: ADSC Quantum Q210 !=== Date: Fri Feb 04 03:39:09 2011 !=== User comments: JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !JOB= DEFPIX XPLAN INTEGRATE CORRECT DATA_RANGE= 1 190 SPOT_RANGE= 1 20 SPOT_RANGE= 1 4 !SPOT_RANGE= 187 190 BACKGROUND_RANGE= 1 4 SECONDS=60 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 6 STRONG_PIXEL= 6.0 OSCILLATION_RANGE= 1.000 STARTING_ANGLE= 0.000 STARTING_FRAME= 1 X-RAY_WAVELENGTH= 0.93340 NAME_TEMPLATE_OF_DATA_FRAMES= ./data/sk1_1_???.img !STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10 !TOTAL_SPINDLE_ROTATION_RANGES= 60 180 10 DETECTOR_DISTANCE= 298.55 DETECTOR= ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ORGX= 1014.79ORGY= 1029.10 NX= 2048 NY= 2048 QX= 0.10200 QY= 0.10200 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 7000 3 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ROTATION_AXIS= 1.0 0.0 0.0 INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0 FRACTION_OF_POLARIZATION= 0.98 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !== Default value recommended !AIR= 0.00026895 SPACE_GROUP_NUMBER= 0 UNIT_CELL_CONSTANTS= 0 0 0 0 0 0 INCLUDE_RESOLUTION_RANGE= 50.0 2.4 RESOLUTION_SHELLS= 15.0 8.0 4.0 3.0 2.8 2.6 2.5 2.4 FRIEDEL'S_LAW= FALSE !FRIEDEL'S_LAW= TRUE TRUSTED_REGION= 0 1.40 REFINE(INTEGRATE)= BEAM ORIENTATION CELL !== Default value recommended !DELPHI= 3.000 MAXIMUM_NUMBER_OF_PROCESSORS= 16 !MAXIMUM_NUMBER_OF_JOBS= 16 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
Re: [ccp4bb] xds question
Hello Juergen, since sigma is always positive, a negative I/sigI means that the measured intensity is negative, hence I would refer you to the truncate reference On the treatment of negative intensity observations by S. French and K. Wilson, Acta Cryst (1978) A34, 517-525. Why exactly -3 is chosen as a cut-off I cannot say, though, but it's better than 0 as cut-off, if I am not mistaken. Cheers, Tim On Tue, Feb 08, 2011 at 08:33:13AM -0500, Bosch, Juergen wrote: Hi Tim, could you write a bit more about this cutoff. I've been using the 0 cutoff for the longest time as it seemed to be much more stringent to report. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Feb 8, 2011, at 7:45 AM, Tim Gruene wrote: Dear Simon, I don't know how to change the output written to the log-file (maybe with the TEST-card), but I wonder why you don't want to look at all of your data but only those with I/sigI 0? XDS reports all reflections with I/sigI -3 for a good reason. Cheers, Tim On Tue, Feb 08, 2011 at 12:17:35PM +, Simon Kolstoe wrote: Dear ccp4bb, I am quite a fan of XDS and have just upgraded to the latest version. Normally, to assess the quality of my data, I look at the tables in CORRECT.LP and especially the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = 0.0 AS FUNCTION OF RESOLUTION. However in my latest run I only get a single table for all the data i.e. for signal/noise = -3.0. Is there a command I can put in my XDS.INP that will give me all the other tables or has the CORRECT.LP logfile been altered in the most recent version of XDS? (FYI my xds.inp obtained from the ESRF last week is copied below) Thanks, Simon !=== File Automaticaly generated by mxCuBE !=== X-Ray data collected at: ESRF_ID14-1 !=== Detector type: ADSC Quantum Q210 !=== Date: Fri Feb 04 03:39:09 2011 !=== User comments: JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !JOB= DEFPIX XPLAN INTEGRATE CORRECT DATA_RANGE= 1 190 SPOT_RANGE= 1 20 SPOT_RANGE= 1 4 !SPOT_RANGE= 187 190 BACKGROUND_RANGE= 1 4 SECONDS=60 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 6 STRONG_PIXEL= 6.0 OSCILLATION_RANGE= 1.000 STARTING_ANGLE= 0.000 STARTING_FRAME= 1 X-RAY_WAVELENGTH= 0.93340 NAME_TEMPLATE_OF_DATA_FRAMES= ./data/sk1_1_???.img !STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10 !TOTAL_SPINDLE_ROTATION_RANGES= 60 180 10 DETECTOR_DISTANCE= 298.55 DETECTOR= ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ORGX= 1014.79ORGY= 1029.10 NX= 2048 NY= 2048 QX= 0.10200 QY= 0.10200 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 7000 3 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ROTATION_AXIS= 1.0 0.0 0.0 INCIDENT_BEAM_DIRECTION= 0.0 0.0 1.0 FRACTION_OF_POLARIZATION= 0.98 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !== Default value recommended !AIR= 0.00026895 SPACE_GROUP_NUMBER= 0 UNIT_CELL_CONSTANTS= 0 0 0 0 0 0 INCLUDE_RESOLUTION_RANGE= 50.0 2.4 RESOLUTION_SHELLS= 15.0 8.0 4.0 3.0 2.8 2.6 2.5 2.4 FRIEDEL'S_LAW= FALSE !FRIEDEL'S_LAW= TRUE TRUSTED_REGION= 0 1.40 REFINE(INTEGRATE)= BEAM ORIENTATION CELL !== Default value recommended !DELPHI= 3.000 MAXIMUM_NUMBER_OF_PROCESSORS= 16 !MAXIMUM_NUMBER_OF_JOBS= 16 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Crystal Imaging Instruments?
Chris-- We use the Formulatrix Rock Imager are quite satisfied with it. Thanks! Annie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Chris Morris Sent: Tuesday, February 08, 2011 8:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystal Imaging Instruments? Hi, Which crystal imaging system do you use, if any? Are you satisfied with the software available to run it? This information would help set priorities for future development of xtalPiMS, so I would be grateful for replies. xtalPiMS currently supports Formulatrix instruments, and I am currently adding support for ThermoElectron (Rhombix). regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 https://www.pims-lims.org/ Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD
Re: [ccp4bb] xds question
Hi, I've pasted below the reasons from Dan Gewirth and the HKL2000 manual authors for having a -3 sigma cutoff... I'll add briefly that if you assume the weak data has a Gaussian distribution around zero a -3 sigma cutoff allows you to record ~99.8% of the data. -bob SIGMA CUTOFF Cutoff for rejecting measurements on input. Default = -3.0. Be very careful if you increase this. What is the rationale for using sigma cutoff -3.0 in SCALEPACK? Wouldn't you want to reject all negative intensities? Why shouldn't you use a sigma cutoff 1.0 or zero? The answer to these questions is as follows: The best estimate of I may be negative, due to background subtraction and background fluctuation. Negative measurements typically represent random fluctuations in the detector's response to an X-ray signal. If a measurement is highly negative (= -3[[sigma]]) than it may be more likely the result of a mistake, rather than just random fluctuation. If one eliminates negative fluctuations, but not the positive ones before averaging, the result will be highly biased. In SCALEPACK, sigma cutoff is applied before averaging. If one rejects all negative intensities before averaging a number of things would happen: 1. The averaged intensity would always be positive; 2. For totally random data with redundancy 8, in a shell where there was no signal, , there would be on average 4 positive measurements, with average intensity one sigma. This is because the negative measurements had been thrown out. So the average of the four remaining measurements would be about 2 sigma! This would look like a resolution shell with a meaningful signal; 3. R-merge would be always less than the R-merge with negative measurements included; 4. A SIGMA CUTOFF of 1 would improve R-merge even more, by excluding even more valid measurements. Why should this worry you? Exclusion of valid measurements will deteriorate the final data set. One may notice an inverse relationship between R-merge and data quality as a function of sigma cutoff. So much for using R-merge as any criterion of success. Even the best (averaged) estimate of intensity may be negative. How to use negative I estimates in subsequent phasing and refinement steps is a separate story. The author of SCALEPACK suggests the following: 1. You should never convert I into F. 2. You should square Fcalc and compare it to I. Most, but not all of the crystallography programs do not do this. That is life. In the absence of the proper treatment one can do approximations. One of them is provided by French and also by French and Wilson. An implementation of their ideas is in the CCP4 program TRUNCATE. A very simplified and somewhat imprecise implementation of TRUNCATE is this: if I [[sigma]](I), F=sqrt(I) if I [[sigma]](I), F=sqrt([[sigma]](I)) format SIGMA CUTOFF value default -3 example SIGMA CUTOFF -2.5 referenced from: http://www.hkl-xray.com/hkl_web1/hkl/Scalepack_Keywords.html
Re: [ccp4bb] coot command cannot be located in phenix
Hi, make sure you have Coot installed. Coot is not part of Phenix. This may be useful: http://www.phenix-online.org/download/other.html http://www.phenix-online.org/documentation/coot.htm Pavel. On Mon, Feb 7, 2011 at 4:52 PM, LISA science...@gmail.com wrote: Hi all, I installed phenix1.7 on my mac osx 10.6. But I cannot open coot in this phenix.When I press coot, it said coot command cannot be located. How to fix this problem? Thank. Lisa
Re: [ccp4bb] xds question
Hi, oh, I'm also surprised people seem to use something else than '-3' as the cutoff, i.e. are throwing away data. This, obviously, brings into new light all the discussions (which I definitely don't wish to restart) on the 'cutoff values' in R(sym) and I/sI which you use to determine the 'resolution limit'...and gives one more thing for referees to think about/require when looking at Table 1. I am sure most of them, and the readers, take it for granted that no data were thrown out before calculating those numbers...and sure, the effects of actually using those data might occasionally be more severe than a drop of, say, 1% in the apparent overall R(sym) or an increase in I/sI. Petri On Feb 8, 2011, at 3:07 PM, Robert Immormino wrote: Hi, I've pasted below the reasons from Dan Gewirth and the HKL2000 manual authors for having a -3 sigma cutoff... I'll add briefly that if you assume the weak data has a Gaussian distribution around zero a -3 sigma cutoff allows you to record ~99.8% of the data. -bob SIGMA CUTOFF Cutoff for rejecting measurements on input. Default = -3.0. Be very careful if you increase this. What is the rationale for using sigma cutoff -3.0 in SCALEPACK? Wouldn't you want to reject all negative intensities? Why shouldn't you use a sigma cutoff 1.0 or zero? The answer to these questions is as follows: The best estimate of I may be negative, due to background subtraction and background fluctuation. Negative measurements typically represent random fluctuations in the detector's response to an X-ray signal. If a measurement is highly negative (= -3[[sigma]]) than it may be more likely the result of a mistake, rather than just random fluctuation. If one eliminates negative fluctuations, but not the positive ones before averaging, the result will be highly biased. In SCALEPACK, sigma cutoff is applied before averaging. If one rejects all negative intensities before averaging a number of things would happen: 1. The averaged intensity would always be positive; 2. For totally random data with redundancy 8, in a shell where there was no signal, , there would be on average 4 positive measurements, with average intensity one sigma. This is because the negative measurements had been thrown out. So the average of the four remaining measurements would be about 2 sigma! This would look like a resolution shell with a meaningful signal; 3. R-merge would be always less than the R-merge with negative measurements included; 4. A SIGMA CUTOFF of 1 would improve R-merge even more, by excluding even more valid measurements. Why should this worry you? Exclusion of valid measurements will deteriorate the final data set. One may notice an inverse relationship between R-merge and data quality as a function of sigma cutoff. So much for using R-merge as any criterion of success. Even the best (averaged) estimate of intensity may be negative. How to use negative I estimates in subsequent phasing and refinement steps is a separate story. The author of SCALEPACK suggests the following: 1. You should never convert I into F. 2. You should square Fcalc and compare it to I. Most, but not all of the crystallography programs do not do this. That is life. In the absence of the proper treatment one can do approximations. One of them is provided by French and also by French and Wilson. An implementation of their ideas is in the CCP4 program TRUNCATE. A very simplified and somewhat imprecise implementation of TRUNCATE is this: if I [[sigma]](I), F=sqrt(I) if I [[sigma]](I), F=sqrt([[sigma]](I)) formatSIGMA CUTOFF value default -3 example SIGMA CUTOFF -2.5 referenced from: http://www.hkl-xray.com/hkl_web1/hkl/Scalepack_Keywords.html --- Petri Kursula, PhD Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland) Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).
As a general principle, I would always run MR searches in all 8 P2x2x2x space groups just to get some controls, if you haven't done it already. Trivial to do in Phaser Phil On 8 Feb 2011, at 17:49, Francis E Reyes wrote: Hi all I have a case of a dataset that indexed, integrated, and scaled well in P 21 21 21 (55.6410 81.6493 147.1294 90. 90. 90.) . The data has an Mn(i/sd) of 2.1 at 3.5 A with a Rpim of about 0.398 at the highest resolution shell (3.49-3.58). Analysis with phenix.xtriage warns of pseudotranslational symmetry (26% of origin). x y zheight p-value(height) ( 0.500, 0.000, 0.233 ) : 26.344 (2.681e-03) ( 0.000, 0.338, 0.000 ) :5.380 (8.476e-01) If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space groupoperator unit cell of reference setting C 2 2 21 (b-1/4,c-1/4,2*a) x+1/2, y, z+1/4 (73.64, 55.47, 81.46, 90.00, 90.00, 90.00) From what I've read about pseudo c-centering via pseudotranslational symmetry, the problem exhibits itself with alternating weak and strong reflections at low resolution, but become consistent at high resolution. Inspection of the h+k parity groups via truncate does not show this behavior . Despite the fact the data was collected at the anomalous peak, I do not observe any anomalous signal (DelAnom correlation between half-sets is 0.013 for all data). Using a reasonably complete model (80%) I searched for two molecules in the ASU in space group P 21 21 21 and obtained a solution at TFZ=22.1 for two molecules related solely by a translation. However the electron density maps (after rigid body refinement) are not great (or maybe my expectations are too high). I am encouraged by the fact the density is weak for a region of the model which should have a different conformation, while strong density is maintained for the rest of the molecule. Is this the proper way to approach pseudotranslation (i.e. is there any reason to believe that the solution obtained by MR is not the correct solution?). Is the space group determined? (i.e. does the pseudo c-centering affect pointless's ability to analyze the systematic absences?). Is the lack of a pattern of alternating weak/strong reflections normal (would observing this behavior be dependent on the crystal orientation) ? any advice would be greatly appreciated! (especially from those who have had a case like this before) F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[ccp4bb] 1st Annual CLS Mx Data Collection School
The Canadian Macromolecular Crystallography Facility (CMCF) is pleased to introduce an intensive 5-day hands-on data collection school at the Canadian Light Source (CLS) synchrotron. The School will take place May 16 - 20, 2011. Participants will attend a series of lectures and be actively engaged in macromolecular crystallography (Mx) data collection at CMCF beamlines. Completing the school will be an essential step to making use of the beamlines remotely and will better equip participants to effectively collect diffraction data on-site. Additionally, this year’s special topic will be an in-depth look at the use of PHENIX for data analysis and structure solution with invited speaker Dr. Paul Adams. Participants should have a basic grounding in crystallography prior to attending the course. Application deadline is March 1, 2011. Please visit the CMCF website for more information and application form at http://cmcf.lightsource.ca/school
[ccp4bb] Post-Doctoral position available at Queen's University, Kingston, Ontario, Canada
Subject: Post-Doctoral position available at Queen's University, Kingston, Ontario, Canada Project Description: A postdoctoral position is available immediately for structure-function studies of cytoskeletal motor proteins in human and agricultural fungal pathogens in the Department of Biochemistry at Queen's University. Projects investigating the structural basis of secondary metabolite biosynthesis and biofilm generation in these organisms are also available. For these studies, combined approaches in molecular biology, biochemistry, biophysics and X-ray crystallography are employed. The laboratory is fully equipped with all the required infrastructure and in-house X-ray crystallography instrumentation. We also have full access to several synchrotron beamlines in APS, CHESS, and NSLS. Qualifications: The position requires a Ph.D. degree with experience in protein purification, crystallization and successful structure determination. How to Apply: Interested candidates should send a CV and names and contact information for 3 references by email to: John S. Allingham (Email: allin...@queensu.ca) Assistant Professor Tier 2 Canada Research Chair in Structural Biology Department of Biochemistry Botterell Hall Queen's University 18 Stuart St., Rm 641 Kingston, ON K7L 3N6 Canada Phone: (613) 533-3137 Fax: (613) 533-2022 For more information, please visit http://meds.queensu.ca/biochem/biochemistry_faculty?id=36
Re: [ccp4bb] quality homology model
Hi Susy, Before going into details: you have to get the alignment right. After that, you may look into packing quality and geometry of your models. Regarding the parameters you are interested in: I talked to a guy from the Sali lab (Modeller) about quality assessment of homology models. He recommends to compare the gromos or anolea profiles per residue (or whatever packing score your software uses) to the template. In case there is gap: pay attention to the alignment! Regarding cut-off values (what's ok and what not) you may want to look into published work on your modeling software and/or contact the authors directly. Another way to look at model quality, and maybe more significant, is to check geometry (clashes, rotamers, bond angles etc.). You could use MolProbity for that. The supplementary material of the following article contains a good example (Table S1) on the evaluation of a trimer interface: http://www.ncbi.nlm.nih.gov/pubmed/20457942 Good luck! Oliv On 02/07/11 01:13, Susy Rao wrote: Dear Community, I have a question regarding protein model quality for introduction of point mutations which should increase solibity/stability of my protein of interest. I plan to do homology models so that I can check the most promising amino acids. Which quality/resolution of the model do I need? Which parameters would you check (gromos, anolea), and what would you use as cut-off values? At the moment I thought, that it could be interesting to model a homologue of my protein and check the RMSDs with the crystal structure. Maybe you know some good literature, describing this? Thank you Susy -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eid...@blur.compbio.ucsf.edu
[ccp4bb] N-terminal sequencing
Hi, Sorry for non-crystallography related questions. I am seeking protein N-terminal sequencing service. However, the facilities I have worked with previously (Michigan state and UCSD) were both closed. Does anyone know any companies or core facilities that can do this? Thanks, Junyu --- Junyu Xiao, Ph.D. University of California, San Diego Leichtag Room 283 9500 Gilman Drive, 0721 La Jolla, CA 92093-0721 Lab phone: 858-822-0684
Re: [ccp4bb] xds question
Hi Simon, I've put my answer into the XDSwiki article FAQ http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/FAQ#why_do_the_latest_XDS.2FXSCALE_versions_only_give_a_single_table.2C_with_I.2Fsigma.3E.3D-3_cutoff.3F because I was asked this privately a couple of times, after this was changed for the May 2010 version. In short, the table describes the data that are written out by XDS/XSCALE, and giving more than one table obscures this fact and tends to confuse users (which table should I use? - the -3 sigma cutoff table - then why are there the others?). Others have already mentioned in this thread that SCALEPACK uses the same cutoff of -3 sigma. I'm not sure about the cutoff in MOSFLM/SCALA. I do realize now that some people have been using the tables for deciding on a suitable resolution cutoff. With a bit of scripting, this can be overcome - pls ask me by email. hope that helps, Kay Am 08.02.2011 20:58, schrieb Simon Kolstoe: Dear ccp4bb, I am quite a fan of XDS and have just upgraded to the latest version. Normally, to assess the quality of my data, I look at the tables in CORRECT.LP and especially the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = 0.0 AS FUNCTION OF RESOLUTION. However in my latest run I only get a single table for all the data i.e. for signal/noise = -3.0. Is there a command I can put in my XDS.INP that will give me all the other tables or has the CORRECT.LP logfile been altered in the most recent version of XDS? (FYI my xds.inp obtained from the ESRF last week is copied below) Thanks, Simon
Re: [ccp4bb] N-terminal sequencing
A colleague here has had good results with the facility at Iowa state: http://www.biotech.iastate.edu/service_facilities/protein.html If you just want to identify the protein, mass spec may be cheaper. The same place will do that, or we have had excellent results with http://www.appliedbiomics.com/ If you need to confirm N-term construct, Edman degradation is probably still more cost effective. Junyu Xiao wrote: Hi, Sorry for non-crystallography related questions. I am seeking protein N-terminal sequencing service. However, the facilities I have worked with previously (Michigan state and UCSD) were both closed. Does anyone know any companies or core facilities that can do this? Thanks, Junyu --- Junyu Xiao, Ph.D. University of California, San Diego Leichtag Room 283 9500 Gilman Drive, 0721 La Jolla, CA 92093-0721 Lab phone: 858-822-0684
Re: [ccp4bb] xds question
On Tue, Feb 8, 2011 at 7:17 AM, Simon Kolstoe s.kols...@ucl.ac.uk wrote: XDS [...] signal/noise = -3.0. i'd be interested to know if there is an equivalent in scala... perhaps 'REJECT 6 ALL -8' -Bryan
Re: [ccp4bb] N-terminal sequencing
We have used Alphalyse (http://www.alphalyse.com/picknpost.html). Dan
Re: [ccp4bb] xds question
No cutoffs in Scala Phil On 8 Feb 2011, at 20:13, Kay Diederichs wrote: Hi Simon, I've put my answer into the XDSwiki article FAQ http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/FAQ#why_do_the_latest_XDS.2FXSCALE_versions_only_give_a_single_table.2C_with_I.2Fsigma.3E.3D-3_cutoff.3F because I was asked this privately a couple of times, after this was changed for the May 2010 version. In short, the table describes the data that are written out by XDS/XSCALE, and giving more than one table obscures this fact and tends to confuse users (which table should I use? - the -3 sigma cutoff table - then why are there the others?). Others have already mentioned in this thread that SCALEPACK uses the same cutoff of -3 sigma. I'm not sure about the cutoff in MOSFLM/SCALA. I do realize now that some people have been using the tables for deciding on a suitable resolution cutoff. With a bit of scripting, this can be overcome - pls ask me by email. hope that helps, Kay Am 08.02.2011 20:58, schrieb Simon Kolstoe: Dear ccp4bb, I am quite a fan of XDS and have just upgraded to the latest version. Normally, to assess the quality of my data, I look at the tables in CORRECT.LP and especially the table SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = 0.0 AS FUNCTION OF RESOLUTION. However in my latest run I only get a single table for all the data i.e. for signal/noise = -3.0. Is there a command I can put in my XDS.INP that will give me all the other tables or has the CORRECT.LP logfile been altered in the most recent version of XDS? (FYI my xds.inp obtained from the ESRF last week is copied below) Thanks, Simon
[ccp4bb] Postdoctoral position at the University of Washington - Seattle
A postdoctoral position is available in the group of Ethan Merritt to work on the structure-based design and development of drugs targeting disease caused by eukaryotic parasites. This project combines crystal structure determination done in the Merritt Lab with synthetic chemistry and biological assays against the target parasites carried out by collaborating UW groups. The current focus of the project is to further develop a set of lead compounds that we have determined to have nanomolar activity against Toxoplasma and Cryptosporidium. Our goal is to modify these lead compounds to optimize their efficacy against the target parasites while maintaining their non-toxicity in humans. We hope over the next several years to bring these compounds to the point of initial clinical trials. Crystallographic work will include structure determination of homologous proteins from related parasites, which may allow us to expand the project to target additional diseases. Two recent papers from this project provide additional information: Ojo et al., Nature Structural Molecular Biology 17:602 (2010) Murphy et al., ACS Med. Chem. Letters 1:331 (2010) The Merritt Lab is part of the Biomolecular Structure Center (BMSC) at the University of Washington School of Medicine. The BMSC provides a collaborative environment that brings together crystallographers, computational chemists, and synthetic chemists. We also collaborate closely with UW groups in the departments of Chemistry, Global Health, and Tropical Medicine. Email inquiries and applications to merr...@u.washington.edu. Please enclose a CV, a summary of research interests and previous crystallographic experience, and contact information for three people who might provide a reference letter or recommendation. -- Ethan A Merritt Department of Biochemistry Biomolecular Structure Center, Mailstop 357742 University of Washington, Seattle 98195, USA
[ccp4bb] Detaching crystals from glass cover slides
Hi all, I have crystals growing by the hanging-drop method, using 24-well VDX plates and Hampton Research siliconized glass cover slides. Most crystals are attached to the cover slide, and I am having difficulties detaching the crystals (using a cryoloop) without breaking them. There are few smaller crystals floating in the drop, and they diffract X-rays pretty well (clean spots, ~3.5A resolution using RAXIS). However, I would like to try the bigger ones, because they may diffract to a higher resolution. Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru
Re: [ccp4bb] Detaching crystals from glass cover slides
Hi Wataru: I hope all is well. For the ones you already have grown, try very gently prying them off with a wedge-shaped needle. If you can grow more, try using a very thin smooth layer of vacuum grease, and apply the drop to that. I managed to get RNA crystals to grow that way that otherwise irreversibly adhered to the surface. All the best, Bill On Feb 8, 2011, at 6:06 PM, Wataru Kagawa wrote: Hi all, I have crystals growing by the hanging-drop method, using 24-well VDX plates and Hampton Research siliconized glass cover slides. Most crystals are attached to the cover slide, and I am having difficulties detaching the crystals (using a cryoloop) without breaking them. There are few smaller crystals floating in the drop, and they diffract X-rays pretty well (clean spots, ~3.5A resolution using RAXIS). However, I would like to try the bigger ones, because they may diffract to a higher resolution. Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru
Re: [ccp4bb] Detaching crystals from glass cover slides
Dear Wataru-san: I understand the problem and sometimes I also faced the same difficulties. One likely suggestion to pick up the crystal is here: 1. Hold the cover-glass in hand (the drop should be facing bottom side as in the hanging drop setup) 2. Adjust the microscope to see the crystals (bottomside) and decide which one you are going to pick-up (keep in mind that you are going to use cryo-loop, so you need enough space between the cover glass and bottom of the microscope) [please look at the attachements for quick understanding] 3. Use the cryoloop from the bottom of the coverglass and pick the crystals. moving the crystals might be easier... all the best. With regards, Kumarevel -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@jiscmail.ac.uk] On Behalf Of Wataru Kagawa Sent: Wednesday, February 09, 2011 11:06 AM To: CCP4BB@jiscmail.ac.uk Subject: [ccp4bb] Detaching crystals from glass cover slides Hi all, I have crystals growing by the hanging-drop method, using 24-well VDX plates and Hampton Research siliconized glass cover slides. Most crystals are attached to the cover slide, and I am having difficulties detaching the crystals (using a cryoloop) without breaking them. There are few smaller crystals floating in the drop, and they diffract X-rays pretty well (clean spots, ~3.5A resolution using RAXIS). However, I would like to try the bigger ones, because they may diffract to a higher resolution. Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru cryoloop.ppt Description: MS-Powerpoint presentation
Re: [ccp4bb] Detaching crystals from glass cover slides
Have you tried seeding ? And another suggestion, if the small ones already diffract to 3.5 Å on a home source, why don't you try to go to a synchrotron ? Big is also not always better, they might freeze worse than your small ones or might have growth artifacts etc. If you take several huge crystals and touch them gently with e.g. a hair from a Unicorn* then let it sit and recover you might get lucky. Jürgen * can be replaced by any stronger hair of your preference e.g. pot-bellied pig, horse, cats anything that's a bit more sturdy or simply the Microtools from HR - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Feb 8, 2011, at 9:06 PM, Wataru Kagawa wrote: Hi all, I have crystals growing by the hanging-drop method, using 24-well VDX plates and Hampton Research siliconized glass cover slides. Most crystals are attached to the cover slide, and I am having difficulties detaching the crystals (using a cryoloop) without breaking them. There are few smaller crystals floating in the drop, and they diffract X-rays pretty well (clean spots, ~3.5A resolution using RAXIS). However, I would like to try the bigger ones, because they may diffract to a higher resolution. Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru
Re: [ccp4bb] quality homology model
Dear Susy, You describe two things: making a homology model and designing mutants. As Oliv pointed out, the first step is getting the alignment right. Even with a multiple sequence alignment and knowledge of the template that can be quite difficult. You may need to make several models for alternative alignments. When validating your model, packing is IMO the most useful thing to look at. Rosetta-holes is very good at finding poor models. What_check also has very good packing analysis and also flags unsatisfied hydrogen bond donors/acceptors which may help a lot. There are also some compound scores such as the MolProbity score and Q-mean which may help you to find the best model from a set. The quality of the template is also important. Get the best template or use more than one. If the sequence identity isn't too low you should also use templates from pdb_redo. They helped (a lot?) in the previous CASP. If you want to analyse single mutants you can try to work from simple principles such as minimizing the loss of torsional freedom of the main and side chain (entropy) or optimizing the gain of water entropy when the protein folds. Also minimising the loss of hydrogen bonds upon folding is quite useful. Just don't expect miracles. Cheers, Robbie Joosten Date: Tue, 8 Feb 2011 10:52:09 -0800 From: eid...@blur.compbio.ucsf.edu Subject: Re: [ccp4bb] quality homology model To: CCP4BB@JISCMAIL.AC.UK Hi Susy, Before going into details: you have to get the alignment right. After that, you may look into packing quality and geometry of your models. Regarding the parameters you are interested in: I talked to a guy from the Sali lab (Modeller) about quality assessment of homology models. He recommends to compare the gromos or anolea profiles per residue (or whatever packing score your software uses) to the template. In case there is gap: pay attention to the alignment! Regarding cut-off values (what's ok and what not) you may want to look into published work on your modeling software and/or contact the authors directly. Another way to look at model quality, and maybe more significant, is to check geometry (clashes, rotamers, bond angles etc.). You could use MolProbity for that. The supplementary material of the following article contains a good example (Table S1) on the evaluation of a trimer interface: http://www.ncbi.nlm.nih.gov/pubmed/20457942 Good luck! Oliv On 02/07/11 01:13, Susy Rao wrote: Dear Community, I have a question regarding protein model quality for introduction of point mutations which should increase solibity/stability of my protein of interest. I plan to do homology models so that I can check the most promising amino acids. Which quality/resolution of the model do I need? Which parameters would you check (gromos, anolea), and what would you use as cut-off values? At the moment I thought, that it could be interesting to model a homologue of my protein and check the RMSDs with the crystal structure. Maybe you know some good literature, describing this? Thank you Susy -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eid...@blur.compbio.ucsf.edu
Re: [ccp4bb] quality homology model
Dear Susy, You describe two things: making a homology model and designing mutants. As Oliv pointed out, the first step is getting the alignment right. Even with a multiple sequence alignment and knowledge of the template that can be quite difficult. You may need to make several models for alternative alignments. When validating your model, packing is IMO the most useful thing to look at. Rosetta-holes is very good at finding poor models. What_check also has very good packing analysis and also flags unsatisfied hydrogen bond donors/acceptors which may help a lot. There are also some compound scores such as the MolProbity score and Q-mean which may help you to find the best model from a set. The quality of the template is also important. Get the best template or use more than one. If the sequence identity isn't too low you should also use templates from pdb_redo. They helped (a lot?) in the previous CASP. If you want to analyse single mutants you can try to work from simple principles such as minimizing the loss of torsional freedom of the main and side chain (entropy) or optimizing the gain of water entropy when the protein folds. Also minimising the loss of hydrogen bonds upon folding is quite useful. Just don't expect miracles. Cheers, Robbie Joosten Date: Tue, 8 Feb 2011 10:52:09 -0800 From: eid...@blur.compbio.ucsf.edu Subject: Re: [ccp4bb] quality homology model To: CCP4BB@JISCMAIL.AC.UK Hi Susy, Before going into details: you have to get the alignment right. After that, you may look into packing quality and geometry of your models. Regarding the parameters you are interested in: I talked to a guy from the Sali lab (Modeller) about quality assessment of homology models. He recommends to compare the gromos or anolea profiles per residue (or whatever packing score your software uses) to the template. In case there is gap: pay attention to the alignment! Regarding cut-off values (what's ok and what not) you may want to look into published work on your modeling software and/or contact the authors directly. Another way to look at model quality, and maybe more significant, is to check geometry (clashes, rotamers, bond angles etc.). You could use MolProbity for that. The supplementary material of the following article contains a good example (Table S1) on the evaluation of a trimer interface: http://www.ncbi.nlm.nih.gov/pubmed/20457942 Good luck! Oliv On 02/07/11 01:13, Susy Rao wrote: Dear Community, I have a question regarding protein model quality for introduction of point mutations which should increase solibity/stability of my protein of interest. I plan to do homology models so that I can check the most promising amino acids. Which quality/resolution of the model do I need? Which parameters would you check (gromos, anolea), and what would you use as cut-off values? At the moment I thought, that it could be interesting to model a homologue of my protein and check the RMSDs with the crystal structure. Maybe you know some good literature, describing this? Thank you Susy -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eid...@blur.compbio.ucsf.edu
[ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday
I see in the news that Ken Olsen has died. Although he was not a crystallographer I think we should stop for a moment to remember the profound impact the company that this man founded had on our field. My first experience in a crystallography lab was as an undergraduate in M. Sundaralingam's lab in Madison Wisconsin. While I never had the opportunity to use them, his two diffractometers were controlled by the ubiquitous PDP-8 computers. I had more experience with his main computer, which was either a PDP-11/34 or 35 (Ethan help me out!). This was connected to a Vector General graphics display running software called UWVG. Having the least stature in the lab I got the midnight to 4am time slot for model building. The computer took about 10 minutes to compute and contour each block of map, covering about three residues. While waiting I would crawl under the DECwriter and nap. The computer would stop rattling when the map was up and that would wake me. When I joined the Matthews lab in Oregon they had a VAX 11/780. What an amazing machine! It had 1 MB of RAM and could run a million instructions in a second. It only took 48 hours to run a cycle of refinement with PROLSQ, that is, if no one else used the computer. These specs don't sound like much but this computer was really a revolution for computational crystallography. That a single lab could own a computer of such power was unheard of before this. It wasn't just that the computer had so much RAM (We later got it up to its max of 4 MB.) but the advent of virtual memory made program design so much easier. You could simply define an array of 100,000 elements and not have to worry about finding where in memory, mixed in with the operating system, utility programs, and other users' software, you could find an unused block that big. Digital didn't invent virtual memory, but the VAX made it achievable for regular crystallographers. Through most of the 1980's you didn't have to worry about getting your code to run on other computers - Everyone had access to a VAX. In the 1990's DEC came out with the alpha CPU chip which really broke ground for performance. These things screamed when in came to running crystallographic software. In 1999 the lab bought several of the 666 MHz models. It was about four years before Intel came out with a chip that would match these alphas on my crystallography benchmark and they had to be clocked at over 2 GHz to do it. Yes, Digital lost out in the competition of the marketplace, and Ken Olsen was pushed out of the company well before the end. But what a ride it was. What great computers they were and what great science was done on them! Dale Tronrud
