[ccp4bb] Rice vs Sim vs ACNSFD
Dear All, I am unsure about the likelihood function nomenclature. I have seen the Sim function called the Rice function, and aIso have read the acentric conditional normalized structure factor distribution (ACNSFD) called the Rice function (the centric conditional normalized structure factor distribution consistently seems to be the Woolfson distribution). Looking at both the Sim and ACNSFD, they look like the pdf in figure 6 of Rice ( who interestingly, attributes the function to a Mr Bennett in some unpublished work. So I guess Rice made the Race). So believe that a) both the Sim distribution and the ACNSFD are A Rice function, not THE Rice function. Agreeable? b) is there a proper name for the ACNSFD or generally for the acentric conditional structure factor distribution? Thx, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com b...@ruppweb.org http://www.ruppweb.org/ - Die Wissenschaft und die Wissenschafter werden von Angst regiert - Angst vor der öffentlichen Meinung, Angst vor religiöser Intoleranz, vor politischem Druck und vor allem Angst vor Heuchelei und Vorurteilen. William Masters und Virginia Johnson, 1970 -
Re: [ccp4bb] Rice vs Sim vs ACNSFD
Hi Bernhard Oh dear we're getting into naming issues again!! I'm not clear what's the distinction you're making between 'A Rice function' and 'THE Rice function' since my understanding was that there was only one form of Rice distribution, i.e. the one defined here: http://en.wikipedia.org/wiki/Rice_distribution . As for the 'Sim function', one problem seems to be that crystallographers appear to have used this to mean two different things: 1) the PDF of the *(complex) structure factor*, which is really just a 2-D Gaussian, and 2) the PDF of the *(real) structure amplitude*, which is the Rice distribution, and which is the result of integrating out of the phase (which gives the I0 component of the Rice distribution) from the structure factor distribution. I don't have Sim's original paper to hand so I don't know know how he defined it, or even whether he ever called his function a 'Rice function'. However it would seem more logical to call the integrated (Rice) form of Sim's function 'the Sim distribution' and not use this term to mean the 2-D Gaussian. As for ACNSFD CCNSFD, I'm not clear what you mean, could you be more specific, in particular do you mean the *structure amplitude* distributions? Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: 09 April 2009 07:06 To: CCP4BB@jiscmail.ac.uk Subject: Rice vs Sim vs ACNSFD Dear All, I am unsure about the likelihood function nomenclature. I have seen the Sim function called the Rice function, and aIso have read the acentric conditional normalized structure factor distribution (ACNSFD) called the Rice function (the centric conditional normalized structure factor distribution consistently seems to be the Woolfson distribution). Looking at both the Sim and ACNSFD, they look like the pdf in figure 6 of Rice ( who interestingly, attributes the function to a Mr Bennett in 'some unpublished work'. So I guess Rice made the Race). So believe that a) both the Sim distribution and the ACNSFD are A Rice function, not THE Rice function. Agreeable? b) is there a proper name for the ACNSFD or generally for the acentric conditional structure factor distribution? Thx, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com b...@ruppweb.org http://www.ruppweb.org/ - Die Wissenschaft und die Wissenschafter werden von Angst regiert - Angst vor der öffentlichen Meinung, Angst vor religiöser Intoleranz, vor politischem Druck und vor allem Angst vor Heuchelei und Vorurteilen. William Masters und Virginia Johnson, 1970 - Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] CAD on multi-record file
Dear all, (apologies for those being tired of similar questions...) I have tried using CAD on an unscaled MTZ from Mosflm. All I wanted to do was to change crystal name, dataset name and project name. This is what I got: - BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: CAD version 6.1 : 20/01/09## ### User: unknown Run date: 9/ 4/2009 Run time: 16:20:40 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Data line--- TITLE Changing crystal, dataset and project names Data line--- LABIN FILE_NUMBER 1 ALL Data line--- DPNAME FILE_NUMBER 1 New New NONISO Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01 Data line--- END No CTYP lines input for file: 1 Indices output even if all data items flagged missing Warning, NOT all LABOUT data lines given OPENED INPUT MTZ FILE Logical Name: HKLIN1 Filename: exp_01/in1_MS_1_001.mtz * Title: Untitled * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 New New New 81.6000 81.6000 33.6000 90. 90. 120. 0.92000 * Number of Columns = 18 * Number of Reflections = 40898 * Missing value set to NaN in input mtz file * Number of Batches = 100 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS * Column Types : H H H Y B J Q J Q R R R R R R I I R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 81.6000 81.6000 33.6000 90. 90. 120. * Resolution Range : 0.001090.32315 ( 30.345 - 1.759 A ) * Sort Order : 0 0 0 0 0 * Space group = 'H3' (number 146) File 1 is a multi-record MTZ file. Inputting a multi-record file to CAD is an unmitigated disaster! Please use MTZUTILS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- CAD: Input file is unmerged MTZ file. CAD: Input file is unmerged MTZ file. Times: User: 0.1s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- So it would appear that CAD is no good for this sort of files. What should I use, then? I have tried looking into mtzutils, but I don't see how to do it. Anyone for help? J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page:
[ccp4bb] Schering-Plough Research Institute Postdoctoral Fellowships in the USA
Schering-Plough is an innovation-driven, science-centred global health care company. Through our investment in biopharmaceutical research, development and manufacturing we create therapies that help save and improve lives of people around the world. In recognition of the central role of organic synthesis, analytical, biostructural and computational chemistry in drug discovery, Schering-Plough Research Institute (SPRI) has established a Fellowship programme to support outstanding Ph.D. students in these areas with strong interest in biomedicine who wish to pursue their postdoctoral research at a University in the United States. The Fellowship is designed to provide support for up to two years at an annual $50,000 stipend to cover travel and maintenance costs. The programme is open to the final year Ph.D. students of organic synthesis, analytical, biostructural or computational chemistry at a credited university in the United Kingdom or The Netherlands. Applicants should provide a CV, a synopsis of their PhD research, a letter of recommendation from their PhD supervisor, a concise summary of their proposed postdoctoral research and a conditional letter of acceptance from their postdoctoral supervisor. Proposals will be reviewed by a panel of scientists from SPRI research centres in Scotland and The Netherlands. The short-listed applicants will be invited to present their proposals in early spring, and awards will be made available for studies starting in autumn 2009. Enquires and applications should be submitted by e-mail or in writing to: Applicants from the UK USA Postdoctoral Fellowship Programme HR Department Schering-Plough Research Institute Newhouse, Motherwell, ML1 5SH Scotland, UK e-mail: researchj...@spcorp.com Applicants from The Netherlands USA Postdoctoral Fellowship Programme Schering-Plough Research Institute 5340 BH Oss, P.O. Box 20 The Netherlands e-mail: sandra.schoenmake...@spcorp.com Closing date for applications is 15th May 2009. Shortlisted applicants will be contacted by 15th June 2009. -- *Xavier Fradera* Senior Scientist Computational Medicinal Chemistry Tel: +44 (0) 637263 xavier.frad...@spcorp.com Schering-Plough Research Institute Newhouse Motherwell ML1 5SH United Kingdom www.schering-plough.com
Re: [ccp4bb] CAD on multi-record file
Hi James, This isn't a direct answer to your question, but you can assign these on the Scala command line input, thus: name run 1 project AUTOMATIC crystal DEFAULT dataset WAVE1 name run 2 project AUTOMATIC crystal DEFAULT dataset WAVE2 I am assuming that this would be your next step anyhow. Best wishes, Graeme 2009/4/9 James Foadi james_fo...@yahoo.co.uk: Dear all, (apologies for those being tired of similar questions...) I have tried using CAD on an unscaled MTZ from Mosflm. All I wanted to do was to change crystal name, dataset name and project name. This is what I got: - BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: CAD version 6.1 : 20/01/09## ### User: unknown Run date: 9/ 4/2009 Run time: 16:20:40 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Data line--- TITLE Changing crystal, dataset and project names Data line--- LABIN FILE_NUMBER 1 ALL Data line--- DPNAME FILE_NUMBER 1 New New NONISO Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01 Data line--- END No CTYP lines input for file: 1 Indices output even if all data items flagged missing Warning, NOT all LABOUT data lines given OPENED INPUT MTZ FILE Logical Name: HKLIN1 Filename: exp_01/in1_MS_1_001.mtz * Title: Untitled * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 New New New 81.6000 81.6000 33.6000 90. 90. 120. 0.92000 * Number of Columns = 18 * Number of Reflections = 40898 * Missing value set to NaN in input mtz file * Number of Batches = 100 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS * Column Types : H H H Y B J Q J Q R R R R R R I I R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 81.6000 81.6000 33.6000 90. 90. 120. * Resolution Range : 0.00109 0.32315 ( 30.345 - 1.759 A ) * Sort Order : 0 0 0 0 0 * Space group = 'H3' (number 146) File 1 is a multi-record MTZ file. Inputting a multi-record file to CAD is an unmitigated disaster! Please use MTZUTILS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- CAD: Input file is unmerged MTZ file. CAD: Input file is unmerged MTZ file. Times: User: 0.1s System: 0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- So it would appear that CAD is no good for this sort of files. What should I use, then? I have tried looking into mtzutils, but I don't see how to do it. Anyone for help? J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page:
Re: [ccp4bb] CAD on multi-record file
Don't use CAD. Use REBATCH. -James Holton MAD Scientist James Foadi wrote: Dear all, (apologies for those being tired of similar questions...) I have tried using CAD on an unscaled MTZ from Mosflm. All I wanted to do was to change crystal name, dataset name and project name. This is what I got: - BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: CAD version 6.1 : 20/01/09## ### User: unknown Run date: 9/ 4/2009 Run time: 16:20:40 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Data line--- TITLE Changing crystal, dataset and project names Data line--- LABIN FILE_NUMBER 1 ALL Data line--- DPNAME FILE_NUMBER 1 New New NONISO Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01 Data line--- END No CTYP lines input for file: 1 Indices output even if all data items flagged missing Warning, NOT all LABOUT data lines given OPENED INPUT MTZ FILE Logical Name: HKLIN1 Filename: exp_01/in1_MS_1_001.mtz * Title: Untitled * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 New New New 81.6000 81.6000 33.6000 90. 90. 120. 0.92000 * Number of Columns = 18 * Number of Reflections = 40898 * Missing value set to NaN in input mtz file * Number of Batches = 100 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS * Column Types : H H H Y B J Q J Q R R R R R R I I R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 81.6000 81.6000 33.6000 90. 90. 120. * Resolution Range : 0.001090.32315 ( 30.345 - 1.759 A ) * Sort Order : 0 0 0 0 0 * Space group = 'H3' (number 146) File 1 is a multi-record MTZ file. Inputting a multi-record file to CAD is an unmitigated disaster! Please use MTZUTILS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- CAD: Input file is unmerged MTZ file. CAD: Input file is unmerged MTZ file. Times: User: 0.1s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- So it would appear that CAD is no good for this sort of files. What should I use, then? I have tried looking into mtzutils, but I don't see how to do it. Anyone for help? J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page:
Re: [ccp4bb] Rice vs Sim vs ACNSFD
Dear Ian, distinction you're making between 'A Rice function' and 'THE Rice function' since my understanding was that there was only one form of Rice distribution, i.e. the one defined here: http://en.wikipedia.org/wiki/Rice_distribution . The same distinction seems common for the Gauss ND - we say that some normal distribution is A Gauss function, not THE Gauss function and 2) the PDF of the *(real) structure amplitude*, which is the Rice distribution, and which is the result of integrating out of the phase (which gives the I0 component of the Rice distribution) from the structure factor distribution. The integrated-out real distribution with I0 seems to be the one that appears in the majority of the Sim papers. He probably never called it a Rice function, because his first derivation of that formula probably parallels the 1954 'Mathematical analysis of random noise', but there are references to earlier talks of Rice in it. However it would seem more logical to call the integrated (Rice) form of Sim's function 'the Sim distribution' and not use this term to mean the 2-D Gaussian. That seems logical. As for ACNSFD CCNSFD, I'm not clear what you mean, Integrated form of Sim/Rice distribution and Woolfson distribution, expressed in normalized structure factor amplitudes. Fits your defs. do you mean the *structure amplitude* distributions? Ah - payback for the obsoleting of the structure amplitudes Yes, all clear. Thx! And thx again to Dominika for copying the Rice article (a 180 pp book part, actually) Cheers BR
[ccp4bb] Domain rotation axis reprentation
Hi all Sorry for partially off topic query I am working with a multidomain protein. which is present in closed and open conforamtion because of the motion in the domains of the protein. I would like to describe the roation angle of the different domains of the protein and the direction of the domain motion of my structure as a pictorial representation. I know the rotation angles and the direction of motion. My major problem is the represtion in picture with arrows and shaft with the cartoon diagram. I donot know which program can do this. could it be possible with any model represtation tools. I know that Dyndom can do everything, but here again i am not aware with the represetion of the domain motion with arrows and shaft. i would appreciate the suggestions. Thanks in advance Peter
Re: [ccp4bb] Rice vs Sim vs ACNSFD
Actually, on more digging, there seems to be a publication of the Mathematical Analysis of Random Noise, by Rice already in 1944/45 http://www.ieee.org/web/aboutus/history_center/biography/rices.html No idea of Rice and Sim were aware of each other's work. Best, BR
Re: [ccp4bb] CAD on multi-record file
or Pointless On 9 Apr 2009, at 18:09, James Holton wrote: Don't use CAD. Use REBATCH. -James Holton MAD Scientist James Foadi wrote: Dear all, (apologies for those being tired of similar questions...) I have tried using CAD on an unscaled MTZ from Mosflm. All I wanted to do was to change crystal name, dataset name and project name. This is what I got: - BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: CAD version 6.1 : 20/01/09## ### User: unknown Run date: 9/ 4/2009 Run time: 16:20:40 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Data line--- TITLE Changing crystal, dataset and project names Data line--- LABIN FILE_NUMBER 1 ALL Data line--- DPNAME FILE_NUMBER 1 New New NONISO Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01 Data line--- END No CTYP lines input for file: 1 Indices output even if all data items flagged missing Warning, NOT all LABOUT data lines given OPENED INPUT MTZ FILE Logical Name: HKLIN1 Filename: exp_01/ in1_MS_1_001.mtz * Title: Untitled * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 New New New 81.6000 81.6000 33.6000 90. 90. 120. 0.92000 * Number of Columns = 18 * Number of Reflections = 40898 * Missing value set to NaN in input mtz file * Number of Batches = 100 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS * Column Types : H H H Y B J Q J Q R R R R R R I I R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 81.6000 81.6000 33.6000 90. 90. 120. * Resolution Range : 0.001090.32315 ( 30.345 - 1.759 A ) * Sort Order : 0 0 0 0 0 * Space group = 'H3' (number 146) File 1 is a multi-record MTZ file. Inputting a multi-record file to CAD is an unmitigated disaster! Please use MTZUTILS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- CAD: Input file is unmerged MTZ file. CAD: Input file is unmerged MTZ file. Times: User: 0.1s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- So it would appear that CAD is no good for this sort of files. What should I use, then? I have tried looking into mtzutils, but I don't see how to do it. Anyone for help? J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page:
Re: [ccp4bb] Domain rotation axis reprentation
If you have the arrow defined by GLY CA coordinates which is created from DynDom then you can use the script on the following link to define an axis in PyMOL and change the color or thickness as you want. Define the position of the axis using two of the GLY CA coordinates found along the arrow line from DynDom. http://pymolwiki.org/index.php/Symmetry_Axis The script is the copyright of Matthew O'Meara and Xavier Ambroggio 2007. Quoting peter hudson peter.hudson.pe...@gmail.com: Hi all Sorry for partially off topic query I am working with a multidomain protein. which is present in closed and open conforamtion because of the motion in the domains of the protein. I would like to describe the roation angle of the different domains of the protein and the direction of the domain motion of my structure as a pictorial representation. I know the rotation angles and the direction of motion. My major problem is the represtion in picture with arrows and shaft with the cartoon diagram. I donot know which program can do this. could it be possible with any model represtation tools. I know that Dyndom can do everything, but here again i am not aware with the represetion of the domain motion with arrows and shaft. i would appreciate the suggestions. Thanks in advance Peter -- Michael Oldham Home: 3035 Courthouse Drive West Apt. 2B West Lafayette, IN 47906 (502) 210 0274 Work: 915 W. State Street West Lafayette, IN 47907 office: 765-494-9510 lab: 765-494-0299
Re: [ccp4bb] CAD on multi-record file
Many thanks for all your answers! It appears that using REBATCH is the best option for me, as I'm not planning on using SCALA (or POINTLESS) on this unmerged file. Keywords were as follows (for those who might be interested): TITLE Change Project, crystals and datasets name_ change batch numbers BATCH 1 TO 100 PNAME NONISO XNAME Insulin_01 DNAME Dataset_01 END Best wishes, J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk
