Re: [ccp4bb] 1st NJUST/CCP4 Crystallography School Announcement
Dear Eva I checked the application information on the Web page and can only find the information below: Thank you for your interest in the 2015 CCP4/APS Summer School. The application system for the 2015 school is now closed. The 2016 workshop will be advertised towards the end of 2015. Best Robert 2015-05-27 9:53 GMT+08:00 易军 yi...@njust.edu.cn: Dear All, We are pleased to announce the first CCP4 Chinese crystallographic school at Nanjing University of Science and Technology (NJUST), in the city of Nanjing, China. All details can be found at http://www.ccp4.ac.uk/schools/china-2015/index.php Title:NJUST/CCP4 school: From data processing to structure refinement and beyond Dates: September 13 to September 20, 2015. Site: Nanjing University of Science and Technology, Nanjing, China The school will cover many modern crystallographic software packages including CCP4, XDS and SHELX, taught by authors and other experts. It will be organized in three sections – lectures, tutorials and hands-on trouble-shooting. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during the school. Application information: The application deadline is Friday August 7th. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/china-2015/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations for hotel accommodation close to NJUST. The likely total cost for lodging and meals will be in the region of 2500 RMBs. We hope to see you at the school, Eva, Charles and Ronan Jun (Eva) Yi Department of Biological Engineering Nanjing University of Science and Technology 200 Xiao Ling Wei Street, Building# 364 Nanjing, Jiangsu Province 210094 P. R. China Email: yi...@njust.edu.cn
Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor
Thanks so much. XDS program is a very good example for multi-core cpu processing. I love it. I also have a macbook. Though a notebook, it often runs CCP4 program more quickly than on desktop computer. The programs, for example refmac5, seem to use multi-core on OSX and single core on linux. Is that mean CCP4 runs more efficiently on OSX than linux? Best Chang 2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chang, this is hardly a matter of configuration but a question of programming (meaning you cannot change it unless you modify the source code and recompile). You can run a program of which you know it is parallelised, e.g. XDS, shelxl, shelxd, and check with the command 'top' that your %CPU is about 400%. You can also get the program i7z for more detailed information about the status of your CPUs. Phaser is parallelised, but I dare say it is rather an exception within the ccp4 suite. So all you can do is encourage the developers of cpu-demanding programs to spend time on parallelising their code - XDS is one of the most impressive examples of how much this can be worth in the context of acceptance and propagation. Best, Tim On 12/17/2013 02:51 AM, Chang Qing wrote: Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSsBQ+UxlJ7aRr7hoRAk2wAJ9MauWFkWoiW34xYGJVVPpFTD1NTQCgiNdY +h052qPU7DNQoRlZOGg75Os= =oema -END PGP SIGNATURE-
Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor
Dear Tim Yes, it is just my impression. I don't know how to test it. As now most of computers have multi-core CPU, I really hope CCP4 programs can be paralleled. Thank you so much for answering my questions. All my best Chang 2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chang, Without being aware of the various means to parallelise a computer program I would be surprised if refmac5 was parallelised for MacOSX but not for Linux, although I am sure Garib would correct me if I was wrong. Maybe you only have the impression that refmac5 uses several cores on MacOSX? Regards, Tim On 12/17/2013 01:05 PM, Chang Qing wrote: Thanks so much. XDS program is a very good example for multi-core cpu processing. I love it. I also have a macbook. Though a notebook, it often runs CCP4 program more quickly than on desktop computer. The programs, for example refmac5, seem to use multi-core on OSX and single core on linux. Is that mean CCP4 runs more efficiently on OSX than linux? Best Chang 2013/12/17 Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Chang, this is hardly a matter of configuration but a question of programming (meaning you cannot change it unless you modify the source code and recompile). You can run a program of which you know it is parallelised, e.g. XDS, shelxl, shelxd, and check with the command 'top' that your %CPU is about 400%. You can also get the program i7z for more detailed information about the status of your CPUs. Phaser is parallelised, but I dare say it is rather an exception within the ccp4 suite. So all you can do is encourage the developers of cpu-demanding programs to spend time on parallelising their code - XDS is one of the most impressive examples of how much this can be worth in the context of acceptance and propagation. Best, Tim On 12/17/2013 02:51 AM, Chang Qing wrote: Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSsEI+UxlJ7aRr7hoRAiIiAKDCWKpTFw1nin+BCAdXW7cLMjKq7QCg7EU3 MiuWuXad/KGgBLd6Q8aN0W0= =RiQ5 -END PGP SIGNATURE-
[ccp4bb] How to config CPU to run ccp4 with multi-processor
Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang
[ccp4bb] How to config CPU to run ccp4 with multi-processor
Dear all I just installed CCP4 6.4 on Ubuntu 12.1. The program can work. I found it just used 1 processor instead of 4( Intel i5) for data solving. Does anyone know how to config CPU so that all processors can be used. Thanks Chang
Re: [ccp4bb] How to start my XDS journey after HKL2000?
Hi, everyone Now I can get collect result after setting ORGX and ORGY to 1024. Thank Manfred for his help. Thank everyone who helped me. Best regard Chang 2012/10/29 Manfred S. Weiss manfred.we...@helmholtz-berlin.de: The same is true for the third data. I would suggest the following. Examine the images and try to see where the origin is. If you cannot figure this out, set ORGX and ORGY both to 1024, which is the exact center of the detector. And then try again and send me the IDXREF.LP Best wishes Manfred On 29.10.2012 08:35, Chang Qing wrote: 2012/10/29 Chang Qing robie0...@gmail.com: 2012/10/29 Chang Qing robie0...@gmail.com: Thank you very much. I will send you the files through three mail. 2012/10/29 Manfred S. Weiss manfred.we...@helmholtz-berlin.de: Thank you very much. I think this is a trivial error, but I will have to investigate a little bit. Can you also send me the files IDXREF.LP and FRAME.cbf for the three data sets processed with XDS? Of course I will treat your data in confidence. With best wishes Manfred On 29.10.2012 07:54, Chang Qing wrote: 2012/10/29 Chang Qing robie0...@gmail.com: 2012/10/29 Chang Qing robie0...@gmail.com: Dear Manfred Thank you very much. I think I cannot answer your questions in detail. As I am a clinical doctor indeed, I don't know some principles in detail. I will send you all log file. Mail will be separated in three. First letter, data is collected in spring8(41xu), and can get correct result. Second and third letter, date is collected in KEK(nw12a), and space group are wrong. As my data is not publication yet, would you please keep it secret? Thank you very much. As I use macbook, XDSAPP cannot be installed on it. 2012/10/29 Manfred S. Weiss manfred.we...@helmholtz-berlin.de: Dear Chang, there is something seriously wrong with this data. It is possible that the lattice is mis-indexed. Which images did you use for indexing. In contrast to HKL2000, which indexes based on a Fourier analysis of just one images, XDS indexes based on differences vector and needs at least a few (10) images, better would be two slices of 10 images 90 degrees apart. Which XDS tutorial have you followed? Have you tried any of the automatic versions of XDS, such as XDSAPP which we are developing in our lab? Where were the data collected? If you send me some more information about your data I will help you process them using XDS. With best regards Manfred On 29.10.2012 06:03, Chang Qing wrote: And CORRECT file 2012/10/29 Chang Qing robie0...@gmail.com: Here, I show some information about my data and input files of XDS. Wavelength (A) 1. Raster size (mm) 0.10240 (default) Raster size (mm) 0.10240 (default) Film width (mm) 209.72 (default) Film length (mm) 209.72 (default) Record length (pixels) 2048 (default) Number of records 2048 (default) Top limit of useful data 0. (default) Left limit of useful data 0. (default) spots rejected when pixel overflow at value : 65500.0 pixels rejected at value: 0 Oscillation starts at 0. Oscillation range 1. Lattice type: primitive Orientation axis 1 (vertical plane) 1*h 0*k 0*l (default) Orientation axis 2 (spindle) 0*h 0*k 1*l (default) Mosaicity 0.3 CrysZ (beam) axis 0. (default) CrysY (vertical) axis 0. (default) CrysX (spindle) axis 0. (default) unit cell parameters not entered Detector (mis)orientation angles: CassZ (beam) axis 0. CassY (vertical) axis 0. CassX (spindle) axis 0. Detector 2 theta 0. Detector rotation 90.000 (default) Flat detector (default) Detector to crystal distance 166.20 X beam104.80 Y beam105.10 Beam polarization 0.99000 Detector absorption 100.00 (default) Air absorption length 860.00 (default) Crossfire y 0. Crossfire x 0. Crossfire xy 0. Horizontal box size 3.6864 Vertical box size3.6864 2012/10/29 Zhijie Li zhijie...@utoronto.ca: BTW, did you supply XDS with correct beamline/detector information in your input file? Have you compared these information with your HKL2000 site file? If you show us the input file and the HKL2000 site file it might be helpful. -- From: Chang Qing robie0...@gmail.com Sent: Monday, October 29, 2012 12:06 AM To: Zhijie Li zhijie...@utoronto.ca Subject: Re: [ccp4bb] How to start my XDS journey after HKL2000? There were no obvious error messages after XDS. Just, the result of space group was wrong. I can not solve structure through wrong space group. Quality of data is very good. I thought I could get correct result even parameters were in default as recommended
Re: [ccp4bb] How to start my XDS journey after HKL2000?
Here, I show some information about my data and input files of XDS. Wavelength (A) 1. Raster size (mm) 0.10240 (default) Raster size (mm) 0.10240 (default) Film width (mm) 209.72 (default) Film length (mm) 209.72 (default) Record length (pixels) 2048 (default) Number of records 2048 (default) Top limit of useful data 0. (default) Left limit of useful data 0. (default) spots rejected when pixel overflow at value : 65500.0 pixels rejected at value: 0 Oscillation starts at 0. Oscillation range 1. Lattice type: primitive Orientation axis 1 (vertical plane) 1*h 0*k 0*l (default) Orientation axis 2 (spindle) 0*h 0*k 1*l (default) Mosaicity 0.3 CrysZ (beam) axis 0. (default) CrysY (vertical) axis 0. (default) CrysX (spindle) axis 0. (default) unit cell parameters not entered Detector (mis)orientation angles: CassZ (beam) axis 0. CassY (vertical) axis 0. CassX (spindle) axis 0. Detector 2 theta 0. Detector rotation 90.000 (default) Flat detector (default) Detector to crystal distance 166.20 X beam104.80 Y beam105.10 Beam polarization 0.99000 Detector absorption 100.00 (default) Air absorption length 860.00 (default) Crossfire y 0. Crossfire x 0. Crossfire xy 0. Horizontal box size 3.6864 Vertical box size3.6864 2012/10/29 Zhijie Li zhijie...@utoronto.ca: BTW, did you supply XDS with correct beamline/detector information in your input file? Have you compared these information with your HKL2000 site file? If you show us the input file and the HKL2000 site file it might be helpful. -- From: Chang Qing robie0...@gmail.com Sent: Monday, October 29, 2012 12:06 AM To: Zhijie Li zhijie...@utoronto.ca Subject: Re: [ccp4bb] How to start my XDS journey after HKL2000? There were no obvious error messages after XDS. Just, the result of space group was wrong. I can not solve structure through wrong space group. Quality of data is very good. I thought I could get correct result even parameters were in default as recommended in tutorial. I was confused so much. 2012/10/29 Zhijie Li zhijie...@utoronto.ca: You had better also include some error message. -- From: Chang Qing robie0...@gmail.com Sent: Sunday, October 28, 2012 10:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to start my XDS journey after HKL2000? Hi all Now, I am studying XDS. I have 2 sets of data, which can correctly treated by HKL2000 and the results are very good. I followed the tutorial of XDS, but got wrong space group. Inputing the correct space group was helpless. Results of pointless were also wrong, and I can not pass scala. Can someone give me some recommendation? Thanks. Chang XDS.INP Description: Binary data
Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image
Hi, Thanks for answering my question. I think I'd better provide more informations. These four images were taken from one crystals. The distance of image1-2 is 250mm, and image3-4 is 100mm. I checked more than 10 crystals and results were similar. The spots look very large. The lowest resolution is about 6A. As my protein can hydrolyze ATP, so protein buffer with 5mM of ATP. There is 0.2M of MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl can improve quality of crystals. I also setup control, in which target protein was not added, and could get nothing in it. I don't think it is a protein crystal. But salt spot should not be so large. And the rings are not just ice-ring. As I got crystal first in hampton crystal screen kit with MgCl2, TrisHCl and PEG4,000, there are only rings in images from 5-6A to about 3A. 2012/10/12 THOMPSON Andrew andrew.thomp...@synchrotron-soleil.fr: Hi Chang No mention of the resolution limit / oscillation range (I think I can see an ice ring, so I would guess 2.5 A?), but it looks like salt to me, with some weaker satellite peaks that may be something weird like an incommensurate phase. Did you try to index? Cheers Andy De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre 2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange diffraction image Hi, everyone: I just got some strange diffraction images from crystals with triangular pyramid shape. I think this should not be protein diffraction. I never saw so strange images like this. Does anyone know what it is? Is it a kind of salt diffraction? Thank you very much Chang
Re: [ccp4bb] Fwd: [ccp4bb] RE : [ccp4bb] Strange diffraction image
Dear Nicolas ATP crystals is a reasonable answer. Thank you very much. Best regard Chang 2012/10/12 Nicolas Foos nicolas.f...@afmb.univ-mrs.fr: Dear Chang, i have seen ATP diffraction, it's not very different of your image. Maybe you have only ATP in your crystals? Best regard Nicolas Le 12/10/12 14:56, Chang Qing a écrit : Dear Tim I think your explanation is logical. But I tried ADP as ligand first and got crystals and diffraction. ATP in additive kit was found to improve the quality of crystals from cluster to single crystal. CsCl can go on improving the quality and finally I got crystals like this. Is it possible that I get some strange crystals such as CsMgCl3 or something else? Best regard Chang -- Forwarded message -- From: Tim Gruene t...@shelx.uni-ac.gwdg.de Date: 2012/10/12 Subject: Re: [ccp4bb] RE : [ccp4bb] Strange diffraction image To: Chang Qing robie0...@gmail.com 抄送： CCP4BB@jiscmail.ac.uk -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chang, What makes you think spots from salt crystals should not be as large? You have got an ordinary small molecule crystal (or probably a cluster of them) in the beam, with a unit cell somewhat bigger than that of ice judging by the extra real ice rings you've got. Hydrolysis of ATP and Mg2+ present - it's probably (Mg)3(PO4)2- it is very unsoluble http://en.wikipedia.org/wiki/Solubility_table. Best, Tim On 10/12/2012 09:29 AM, Chang Qing wrote: Hi, Thanks for answering my question. I think I'd better provide more informations. These four images were taken from one crystals. The distance of image1-2 is 250mm, and image3-4 is 100mm. I checked more than 10 crystals and results were similar. The spots look very large. The lowest resolution is about 6A. As my protein can hydrolyze ATP, so protein buffer with 5mM of ATP. There is 0.2M of MgCl2 in precipitant buffer with PH7.0. 0.06M of CsCl can improve quality of crystals. I also setup control, in which target protein was not added, and could get nothing in it. I don't think it is a protein crystal. But salt spot should not be so large. And the rings are not just ice-ring. As I got crystal first in hampton crystal screen kit with MgCl2, TrisHCl and PEG4,000, there are only rings in images from 5-6A to about 3A. 2012/10/12 THOMPSON Andrew andrew.thomp...@synchrotron-soleil.fr: Hi Chang No mention of the resolution limit / oscillation range (I think I can see an ice ring, so I would guess 2.5 A?), but it looks like salt to me, with some weaker satellite peaks that may be something weird like an incommensurate phase. Did you try to index? Cheers Andy De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Chang Qing [robie0...@gmail.com] Date d'envoi : vendredi 12 octobre 2012 08:11 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Strange diffraction image Hi, everyone: I just got some strange diffraction images from crystals with triangular pyramid shape. I think this should not be protein diffraction. I never saw so strange images like this. Does anyone know what it is? Is it a kind of salt diffraction? Thank you very much Chang - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQeAheUxlJ7aRr7hoRAibDAJ9yAfiSwNmh8R4tGwUIwFEZno2qWACfStCM y+xKb+FGGglmv8lTL9Ej8ZQ= =ub/P -END PGP SIGNATURE-
