Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
Good morning Colin (from this side of the pond), I never liked the word redundancy. Multiplicity is a however a good word for multiple measurements. So, Ethan, what does someone in the USA say when made redundant ie out of a job? Surely not that they are now a useful surplus for the US economy of the future? Re benefits of multiple measurements I would add:- Any time dependent related variations such as :- X-ray beam rapid variations; Crystal movements; Variations in cold stream flow; ?? ?? More esoterically perhaps extinction for very strong reflections in bigger crystal cases with longer Xray wavelengths. This would be data sets where multiple crystals are needed. This however I don't think affects more than a handful of reflections. Just my two UK pennies worth, John Prof John R Helliwell DSc On 14 May 2013, at 21:58, Colin Nave colin.n...@diamond.ac.uk wrote: Yes, a good summary. The use of the term redundancy (real or otherwise!) in crystallography is potentially misleading as the normal usages means superfluous/ surplus to requirements. The closest usage I can find from elsewhere is in information theory where it is applied for purposes of error detection when communicating over a noisy channel. Seems similar to the crystallographic use. The more relevant point is what sort of errors would be mitigated by having different paths through the crystal. The obvious ones are absorption errors and errors in detector calibration. Inverse beam methods can mitigate these by ensuring the systematic errors are similar for the reflections being compared. However, my interpretation of the Acta D59 paper is that it is accepted that systematic errors are present and, by making multiple measurements under different conditions, the effect of these systematic errors will be minimised. Can anyone suggest other sources of error which would be mitigated by having different paths through the crystal. I don't think radiation damage (mentioned by several people) is one. Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 14 May 2013 14:23 To: ccp4bb Subject: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity? George points out that the quote I referred to did not make it to the BB -- here we go, read below and learn, it is a most succinct summary. phx Original Message Subject: Re: [ccp4bb] reference for true multiplicity? Date: Tue, 14 May 2013 09:25:22 +0100 From: Frank von Delft frank.vonde...@sgc.ox.ac.ukmailto:%3cfrank.vonde...@sgc.ox.ac.uk%3e To: George Sheldrick gshe...@shelx.uni-ac.gwdg.demailto:gshe...@shelx.uni-ac.gwdg.de Thanks! It's the Acta D59 p688 I was thinking of - start of discussion: The results presented here show that it is possible to solve protein structures using the anomalous scattering from native S atoms measured on a laboratory instrument in a careful but relatively routine manner, provided that a sufficiently high real redundancy is obtained (ranging from 16 to 44 in these experiments). Real redundancy implies measurement of equivalent or identical re¯ections with different paths through the crystal, not just repeated measurements; this is expedited by high crystal symmetry and by the use of a three-circle (or ) goniometer. Wise words... phx On 14/05/2013 08:06, George Sheldrick wrote: Dear Frank, We did extensive testing of this approach at the beginning of this millenium - see Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea. Best wishes, George On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead: Anybody know a (the) reference where it was showed that the best SAD data is obtained by collecting multiple revolutions at different crystal offsets (kappa settings)? It's axiomatic now (I hope!), but I remember seeing someone actually show this. I thought Sheldrick early tweens, but PubMed is not being useful. (Oh dear, this will unleash references from the 60s, won't it.) phx -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light
Re: [ccp4bb] Refmac error
Dear colleagues, I have the same problems as Peer Mittl once had. Was this solved and what was the solution? Running arpWarp the job terminates with the message: Refmac_5.7.0032: Open failed: File: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif However the mon_lib_list.cif is readable to my user? [x_marmo@triolith3 CCP4]$ more /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif global_ _lib_name mon_lib _lib_version 5.39 _lib_update06/11/12 #- Here is the output of the ls -l command suggested by Tim Gruene [x_marmo@triolith3 CCP4]$ ls -l /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif -rw-r--r-- 1 raber nsc 1078257 May 15 08:15 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif At the end of the warpNtrace logfile is the following information: [x_marmo@triolith3 CCP4]$ tail -22 /home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log B value outliers 10.000 NCS outliers 20.000 --- Input file :arp_0.pdb_start Size of lib_com.fh(bytes) : 118100416 Open failed: Unit: 7, File: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif (logical: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif) BFONT COLOR=#FF!--SUMMARY_BEGIN-- Refmac_5.7.0032: Open failed: File: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif Times: User: 0.3s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 *** Look for error message in the file: /home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log [x_marmo@triolith3 CCP4]$ What is wrong here? Best regards, Martin
Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
While it's hard to argue with Wikipedia (since it's 100% reliable, etc etc...), here is my two ha'porth. By the way, in the next paragraph read multiply as the adverb and not the verb. It's hard to find real evidence for this, but my thought was that the use of redundant in cases like this is a short-hand way of saying multiply redundant - the system where multiple systems are installed which are individually truly redundant. Multiple redundancy is particularly popular in critically important systems like manned spacecraft. In a RAID system, of course, each redundant disk is truly redundant - if a single disk fails, your data are still there (you just have to think about getting a replacement hard drive). My guess is that people have just dropped the multiply bit and carried on with the redundant. There are plenty of other examples around, e.g. in the UK we talk about football while dropping the Association or Rugby (depending on the shape of your ball); in the States they shudder at both of these (in Australia I understand they have a game where they drop the football and just call their own version Aussie Rules, while many people across the Globe are happy to drop the Football altogether and call the Beautiful Game Soccer. We also (as crystallographers all around the world, not just on both sides of the pond) talk about freezing our crystals and collecting reflections. Both are wrong, but our peers understand what we mean. On 14 May 2013, at Tue14 May 23:25, Ethan Merritt wrote: On Tuesday, May 14, 2013 01:58:06 pm Colin Nave wrote: The use of the term redundancy (real or otherwise!) in crystallography is potentially misleading as the normal usages means superfluous/ surplus to requirements. That may be true in the UK, but on this side of the pond redundancy normally refers to ensuring a safety margin by having more of whatever than is strictly needed for functionality, so that even if some of the whatsits fail you have enough remaining to go on with. The use of the term in crystallography is perfectly normal to American ears. Here's a definition from Wikipedia redundancy is the duplication of critical components or functions of a system with the intention of increasing reliability of the system... just another tidbit of cross-pond difference in language. Ethan The closest usage I can find from elsewhere is in information theory where it is applied for purposes of error detection when communicating over a noisy channel. Seems similar to the crystallographic use. The more relevant point is what sort of errors would be mitigated by having different paths through the crystal. The obvious ones are absorption errors and errors in detector calibration. Inverse beam methods can mitigate these by ensuring the systematic errors are similar for the reflections being compared. However, my interpretation of the Acta D59 paper is that it is accepted that systematic errors are present and, by making multiple measurements under different conditions, the effect of these systematic errors will be minimised. Can anyone suggest other sources of error which would be mitigated by having different paths through the crystal. I don't think radiation damage (mentioned by several people) is one. Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 14 May 2013 14:23 To: ccp4bb Subject: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity? George points out that the quote I referred to did not make it to the BB -- here we go, read below and learn, it is a most succinct summary. phx Original Message Subject: Re: [ccp4bb] reference for true multiplicity? Date: Tue, 14 May 2013 09:25:22 +0100 From: Frank von Delft frank.vonde...@sgc.ox.ac.ukmailto:% 3cfrank.vonde...@sgc.ox.ac.uk%3e To: George Sheldrick gshe...@shelx.uni- AC.GWDG.DEmailto:gshe...@shelx.uni-ac.gwdg.de Thanks! It's the Acta D59 p688 I was thinking of - start of discussion: The results presented here show that it is possible to solve protein structures using the anomalous scattering from native S atoms measured on a laboratory instrument in a careful but relatively routine manner, provided that a sufficiently high real redundancy is obtained (ranging from 16 to 44 in these experiments). Real redundancy implies measurement of equivalent or identical re�ections with different paths through the crystal, not just repeated measurements; this is expedited by high crystal symmetry and by the use of a three-circle (or ) goniometer. Wise words... phx On 14/05/2013 08:06, George Sheldrick wrote: Dear Frank, We did extensive testing of this approach at the beginning of this millenium - see Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea. Best wishes, George On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm
Re: [ccp4bb] Refmac error
Thanks Alexander, I got the solution #2 below as well from my colleague Johan Raber :) Cheers, Martin solution #2 ## Hi Martin, A colleague of mine suggested this could be a known OS bug related to opening files on a read-only mounted file system (such as /software on Triolith). We have a workaround for this until that bug is fixed by RedHat. Please try to do: $ export LD_PRELOAD=/software/tools/ldpreload/openrocrwrap/libopenrocrwrapsilent.so before running CCP4i again, and tell us if this fixed the problem. /Johan -Original Message- From: Alexander Batyuk [mailto:bat...@bioc.uzh.ch] Sent: den 15 maj 2013 10:34 To: Martin Moche Subject: Re: [ccp4bb] Refmac error Dear Martin, I think we solved it by changing the file's permissions (for mon_lib_list.cif) to rwxrwxrwx Best wishes, Alex On 15 May 2013, at 10:25, Martin Moche martin.mo...@ki.se wrote: Dear colleagues, I have the same problems as Peer Mittl once had. Was this solved and what was the solution? Running arpWarp the job terminates with the message: Refmac_5.7.0032: Open failed: File: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif However the mon_lib_list.cif is readable to my user? [x_marmo@triolith3 CCP4]$ more /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif global_ _lib_name mon_lib _lib_version 5.39 _lib_update06/11/12 #- Here is the output of the ls -l command suggested by Tim Gruene [x_marmo@triolith3 CCP4]$ ls -l /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif -rw-r--r-- 1 raber nsc 1078257 May 15 08:15 /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif At the end of the warpNtrace logfile is the following information: [x_marmo@triolith3 CCP4]$ tail -22 /home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log B value outliers 10.000 NCS outliers 20.000 --- Input file :arp_0.pdb_start Size of lib_com.fh(bytes) : 118100416 Open failed: Unit: 7, File: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif (logical: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif) BFONT COLOR=#FF!--SUMMARY_BEGIN-- Refmac_5.7.0032: Open failed: File: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif Times: User: 0.3s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: REFMAC5 *** Look for error message in the file: /home/x_marmo/MexR/CCP4/2_warpNtrace_refine.last.log [x_marmo@triolith3 CCP4]$ What is wrong here? Best regards, Martin -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun
Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
One day many years ago, my Ph.D. students all appeared wearing T-shirts with the logo We want more redundancy. They had clearly got the message about how to do sulfur SAD phasing, but were completely unaware of the usual meaning of the word in the UK! George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
Oh – I seemed to have diverted Frank’s thread. Fortunately most languages themselves are highly redundant, with following characters and words being quite predictable. The entropy and redundancy of English language was analysed by Shannon (with the help of his wife) and he obtained figures of about 1 bit per character rather than log base 2 (27), a redundancy of around 75%. I guess this redundancy helps us put things in context. However, in order to avoid future misunderstandings, I would like to suggest that further communications with CCP4BB be done in Latin which I believe has less ambiguity. I hope people will adopt this helpful suggestion. OK – perhaps not a good idea. More relevant to Frank’s question, I was referring to cases where, for a particular reflection, the path of x-rays through the crystal was altered to average out systematic errors. What type of systematic errors would be mitigated by this? There is one potential addition to the list (absorption errors, detector calibration) I produced but it applies to synchrotron sources rather than the type of x-ray source used in the Acta D paper. I will let others have a think before suggesting it. Colin
[ccp4bb] Abstract submission deadline for BSR2013 is approaching!
** *11th International Conference: Biology and Synchrotron Radiation (BSR) 8-11 September 2013, EMBL Hamburg, Germany * ** *Abstract submission deadline is approaching! http://www.embl-hamburg.de/training/events/2013/BSR13-01/registration/?utm_source=eventmailingutm_medium=E-Mailutm_content=bsr13-04utm_campaign=bsr*** *Join us in Hamburg, Germany for BSR 2013!* Scientists at all possible career levels are invited to this meeting*. *Check out our preliminary programme http://www.embl-hamburg.de/training/events/2013/BSR13-01/programme/index.html?utm_source=eventmailingutm_medium=E-Mailutm_content=bsr13-04utm_campaign=bsr to learn more! *Young researchers *are highly welcome to apply for a travel grant http://www.bsr2013.org/BSR13-01/info/index.html from the International Union of Crystallography when registering. *Present your work! ** *Selected talks and poster sessions provide great opportunities for participants to present their work. Unique *networking opportunities* are also available to meet colleagues, friends and future collaboration partners from all over the world. *Discover the city of Hamburg! ** *BSR 2013 includes asocial programme http://www.bsr2013.org/BSR13-01/attractions/index.html with boat trips and day and night excursions. Accompanying persons will enjoy special rates! A tour of DESY's http://www.bsr2013.org/BSR13-01/desy/index.html?utm_source=eventmailingutm_medium=E-Mailutm_content=bsr13-04utm_campaign=bsr most impressive research infrastructures - including PETRA, FLASH and the future X-FEL -- is included in the registration fee. *Dates at a glance:* ·*Registration and abstract submission: 1 June 2013* ·Registration without abstract: 1 August 2013 Take a look at the updated BSR webpage (www.bsr2013.org http://www.bsr2013.org) for more information and to register. *CONTACT* diah.yulia...@embl.de mailto:diah.yulia...@embl.de?subject=I%20would%20like%20to%20have%20information%20about%2011th%20International%20Conference%20on%20Biology%20and%20Synchrotron%20Radiation%20%28BSR%29 Alternatively, contact us on the event facebook page http://de-de.facebook.com/events/332259356868854/?utm_source=eventmailingutm_medium=E-Mailutm_content=bsr13-04utm_campaign=bsr
Re: [ccp4bb] deleted font settings for ccp4i--how to have ccp4i use Ubuntu fonts
Thanks Installing those fonts did the trick. sudo apt-get install xfonts-75dpi xfonts-100dpi xfs xfstt Hari On Tue, May 14, 2013 at 9:04 PM, Roger Rowlett rrowl...@colgate.edu wrote: In 12.04LTS I install X-fonts, and font servers e.g., sudo apt-get install xfonts-75dpi xfonts-100dpi xfs xfstt This allows ccp4i to display the fonts I remember. X-fonts are not installed by default in Ubuntu 12.04 and probably 13.04 as well. There may be a more elegant way to customize ccp4i but this works for me and is legible. Roger Rowlett On May 14, 2013 6:49 PM, hari jayaram hari...@gmail.com wrote: After an Ubuntu 13.04 reboot I noticed that all my ccp4i fonts looked very jagged and illegible. The preferences have the font assigned to be -Adobe-Helvetica-Medium-R-Normal--*-120-*-*-*-*-*-* Is there a way to have ccp4i use the Ubuntu fonts ? Thanks for your help Hari
Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
The traditional benefit was in reducing absorbtion errors. This obviously depends on crystal path, and seeing it is hard to model well, one way to mitigate the errors was to average equivalents collected at different settings. The error was still there, but assuming random distribution about the true intensity, averaging helps.. On 15 May 2013 10:20, Colin Nave colin.n...@diamond.ac.uk wrote: Oh – I seemed to have diverted Frank’s thread. Fortunately most languages themselves are highly redundant, with following characters and words being quite predictable. The entropy and redundancy of English language was analysed by Shannon (with the help of his wife) and he obtained figures of about 1 bit per character rather than log base 2 (27), a redundancy of around 75%. I guess this redundancy helps us put things in context. However, in order to avoid future misunderstandings, I would like to suggest that further communications with CCP4BB be done in Latin which I believe has less ambiguity. I hope people will adopt this helpful suggestion. OK – perhaps not a good idea. More relevant to Frank’s question, I was referring to cases where, for a particular reflection, the path of x-rays through the crystal was altered to average out systematic errors. What type of systematic errors would be mitigated by this? There is one potential addition to the list (absorption errors, detector calibration) I produced but it applies to synchrotron sources rather than the type of x-ray source used in the Acta D paper. I will let others have a think before suggesting it. Colin
Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?
Times up! The 3rd case I had in mind was the presence of anisotropy of the anomalous scattering in the presence of a polarised beam. John Helliwell and Pete Dunten suggested this. Dave Waterman identified the general issue with polarisation. All three kept the fun going (as John put it) by just responding to myself. The Templetons and then Schiltz and Bricogne regard this as an opportunity rather than a source of errors. See also the paper by Fanchon and Hendrickson. This leads me to think that there are four ways of handling this sort of issue (or rather among the many ways there are at least four). 1. Pretend these errors don't exist and ignore them. This is maximising the probability of not getting a structure. 2 The pragmatic approach of recognising these errors occur and are difficult to correct. Then devise a data collection and processing strategy where they can be mitigated. This would typically involve a high real redundancy. 3. Developing a model to handle the errors - for example a model for the absorption errors. This is presumably better in principle but suffers from the danger that the model is wrong. 4. Rename the errors as an opportunity - the approach taken by Gerard Bricogne and Marc Schiltz following the Templetons. The latter 3 are all fine and involve selecting an appropriate data collection strategy followed by appropriate data processing. For systematic errors, it is worth considering, for each type, which of the 4 cases above are the most appropriate way of handling them. My present thoughts are Absorption errors - category 2 above. Detector non uniformity - category 3 Anisotropy in a polarised beam - category 4. As understanding evolves one would hope each systematic error would move at least to category 3. I think Felix Frolow is a supporter of category 3 and, by implication, category 4. Apologies for all the quotation marks round errors, redundancy etc. This of course relates to identifying potential transmission errors while communicating in the English (I guess it would also apply to Latin) language. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 15 May 2013 10:21 To: ccp4bb Subject: Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity? Oh – I seemed to have diverted Frank’s thread. Fortunately most languages themselves are highly redundant, with following characters and words being quite predictable. The entropy and redundancy of English language was analysed by Shannon (with the help of his wife) and he obtained figures of about 1 bit per character rather than log base 2 (27), a redundancy of around 75%. I guess this redundancy helps us put things in context. However, in order to avoid future misunderstandings, I would like to suggest that further communications with CCP4BB be done in Latin which I believe has less ambiguity. I hope people will adopt this helpful suggestion. OK – perhaps not a good idea. More relevant to Frank’s question, I was referring to cases where, for a particular reflection, the path of x-rays through the crystal was altered to average out systematic errors. What type of systematic errors would be mitigated by this? There is one potential addition to the list (absorption errors, detector calibration) I produced but it applies to synchrotron sources rather than the type of x-ray source used in the Acta D paper. I will let others have a think before suggesting it. Colin
