Re: [ccp4bb] output individual redundancies
No M/ISYM is different it's the symmetry number plus a full or partial flag. Ed. You could count them from the unmerged output as you say, or I could make you a special version of SCALA or Aimless maybe next week Phil Sent from my iPhone On 14 Jul 2011, at 23:15, Ethan Merritt merr...@u.washington.edu wrote: On Thursday, July 14, 2011 02:55:26 pm Ed Pozharski wrote: I am looking for a way to output redundancy per individual reflection, preferably for scala but if that is not possible then maybe for scalepack. If you read the unmerged file from scalepack into ccp4 using combat, it creates a data column with label M/ISYM that I think is what you are asking for. You can use the Import Unmerged Data (Combat) tab in the ccp4i GUI. Ethan From my (admittedly quick) look at the scala manual it seems that I can use something like UNMERGED output option to exclude outliers and then would need to write a bit of code to calculate the redundancies. But I hope that I missed something and there is a secret keyword that would add redundancies to the merged mtz file. Cheers, Ed. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] output individual redundancies
Hi Ed, I was recently looking for that value myself, but couldn't find it. I suppose (at some point) it may be useful information to deposit. If something is a mean value, it is nice to know how many individual values were used to construct that mean. Unfortunately, there doesn't seem to be a cif token for that. Cheers, Robbie Date: Fri, 15 Jul 2011 09:26:39 +0100 From: p...@mrc-lmb.cam.ac.uk Subject: Re: [ccp4bb] output individual redundancies To: CCP4BB@JISCMAIL.AC.UK No M/ISYM is different it's the symmetry number plus a full or partial flag. Ed. You could count them from the unmerged output as you say, or I could make you a special version of SCALA or Aimless maybe next week Phil Sent from my iPhone On 14 Jul 2011, at 23:15, Ethan Merritt merr...@u.washington.edu wrote: On Thursday, July 14, 2011 02:55:26 pm Ed Pozharski wrote: I am looking for a way to output redundancy per individual reflection, preferably for scala but if that is not possible then maybe for scalepack. If you read the unmerged file from scalepack into ccp4 using combat, it creates a data column with label M/ISYM that I think is what you are asking for. You can use the Import Unmerged Data (Combat) tab in the ccp4i GUI. Ethan From my (admittedly quick) look at the scala manual it seems that I can use something like UNMERGED output option to exclude outliers and then would need to write a bit of code to calculate the redundancies. But I hope that I missed something and there is a secret keyword that would add redundancies to the merged mtz file. Cheers, Ed. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] hkl2map on Mac OSX 10.6
Just a hint: Subshels do not always use aliases, so put shelx etc. in your path e.g. in /usr/local/bin Am 15.07.11 11:40, schrieb Sebastiano Pasqualato: Hi all, has anybody managed to have hkl2map running on an intel-based Mac? I have downloaded and installed the shelx programs, which I have aliased in my .bashrc, and will run from the command line. I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that does open hkl2map windows. However, when type hkl2map, I get this: ... Any ideas on how to solve the problem? Thanks a lot in advance, best, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 -- Joachim Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] hkl2map on Mac OSX 10.6
I only managed to get it working using zsh. All other shells were giving me errors. Ciao R. On 15 Jul 2011, at 10:40, Sebastiano Pasqualato wrote: Hi all, has anybody managed to have hkl2map running on an intel-based Mac? I have downloaded and installed the shelx programs, which I have aliased in my .bashrc, and will run from the command line. I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that does open hkl2map windows. However, when type hkl2map, I get this: Screen shot 2011-07-15 at 11.39.22 AM.png Any ideas on how to solve the problem? Thanks a lot in advance, best, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk
Re: [ccp4bb] hkl2map on Mac OSX 10.6
thanks Joachim. thanks Luca, the path hint was successful. I have added the lines : export SHELXPATH=~/xtal/shelx_intelmac export PATH=$PATH:$SHELXPATH to my .bashrc, rather than adding the aliases, and now hkl2map find the shelx executables. (it does complain that I don't have xfit, but I guess that's not a big deal) Thanks again, ciao, s On Jul 15, 2011, at 11:44 AM, Joachim Reichelt wrote: Just a hint: Subshels do not always use aliases, so put shelx etc. in your path e.g. in /usr/local/bin Am 15.07.11 11:40, schrieb Sebastiano Pasqualato: Hi all, has anybody managed to have hkl2map running on an intel-based Mac? I have downloaded and installed the shelx programs, which I have aliased in my .bashrc, and will run from the command line. I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that does open hkl2map windows. However, when type hkl2map, I get this: ... Any ideas on how to solve the problem? Thanks a lot in advance, best, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 -- Joachim Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990
Re: [ccp4bb] hkl2map on Mac OSX 10.6
works fine in bash for me On Jul 15, 2011, at 5:51 AM, Steiner, Roberto wrote: I only managed to get it working using zsh. All other shells were giving me errors. Ciao R. On 15 Jul 2011, at 10:40, Sebastiano Pasqualato wrote: Hi all, has anybody managed to have hkl2map running on an intel-based Mac? I have downloaded and installed the shelx programs, which I have aliased in my .bashrc, and will run from the command line. I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that does open hkl2map windows. However, when type hkl2map, I get this: Screen shot 2011-07-15 at 11.39.22 AM.png Any ideas on how to solve the problem? Thanks a lot in advance, best, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk .. 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: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] hkl2map on Mac OSX 10.6
and in tcsh for me... On 15 Jul 2011, at 14:48, Bosch, Juergen wrote: works fine in bash for me On Jul 15, 2011, at 5:51 AM, Steiner, Roberto wrote: I only managed to get it working using zsh. All other shells were giving me errors. Ciao R. On 15 Jul 2011, at 10:40, Sebastiano Pasqualato wrote: Hi all, has anybody managed to have hkl2map running on an intel-based Mac? I have downloaded and installed the shelx programs, which I have aliased in my .bashrc, and will run from the command line. I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that does open hkl2map windows. However, when type hkl2map, I get this: Screen shot 2011-07-15 at 11.39.22 AM.png Any ideas on how to solve the problem? Thanks a lot in advance, best, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.uk .. 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: +1-410-955-3655 http://web.mac.com/bosch_lab/ Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011
[ccp4bb] Pymol question
Hi, I'm a little stuck with a Pymol script. I'd like to represent my protein with fancy helices and B-sheets, and in a looped domain I want to show a few residues, but only the side chains. In my script I tried using set cartoon_side_chain_helper, on, HISA on the selection of residues I want to show, but I still get the rest of the side chain displayed. In the script window I can see that it loads this command, but it does not seem to lead to what I want. I'm using Pymol 1.4, so I suppose it is recent enough for this script to work. Below is a section of my script. Help will be gratefully appreciated. Chris B xxx SCRIPT xxx load gpV-trimer.pdb, gpVabc center gpVabc #util.ss gpVabc hide everything, gpVabc create VA, (gpVabc//A/6:211/) alter VA//A/45:47/, ss='S' #show ribbon, A #set ribbon_width=8, ecr20e set cartoon_fancy_helices=1, VA show cartoon, VA #set cartoon_transparency=0.7, VA #set cartoon_rect_length=0.75, VA color salmon, VA #hide everything, (VA//A/128:211/) create HISA, (gpVabc//A/197,199/) show sticks, HISA set cartoon_side_chain_helper=1, HISA color gray40, (HISA and elem C) color red, (HISA and elem O) color blue, (HISA and elem N) color yellow, (HISA and elem S) set stick_radius=0.20, HISA #hide everything, HISA -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
Re: [ccp4bb] Pymol question
Hi Christopher, I saw your script and there's many ways to the same destination. Here's how my brain thinks: load A.pdb hide everything, A show cartoon, A [cmds for whatever else I like: fancy helices etc. etc.] Option 1: show sticks, A and resi 197-199 Option 2: And if you hate that the backbone CA sticks out in an ugly manner say for resi 197 on the cartoon, then do: hide sticks, A and resi 197 and resn CA (...or even just...) hide sticks, A and and resn CA (made hide CA you don't want...) Hope this helps. Raji On Fri, Jul 15, 2011 at 9:52 AM, Christopher Browning christopher.brown...@epfl.ch wrote: Hi, I'm a little stuck with a Pymol script. I'd like to represent my protein with fancy helices and B-sheets, and in a looped domain I want to show a few residues, but only the side chains. In my script I tried using set cartoon_side_chain_helper, on, HISA on the selection of residues I want to show, but I still get the rest of the side chain displayed. In the script window I can see that it loads this command, but it does not seem to lead to what I want. I'm using Pymol 1.4, so I suppose it is recent enough for this script to work. Below is a section of my script. Help will be gratefully appreciated. Chris B xxx SCRIPT xxx load gpV-trimer.pdb, gpVabc center gpVabc #util.ss gpVabc hide everything, gpVabc create VA, (gpVabc//A/6:211/) alter VA//A/45:47/, ss='S' #show ribbon, A #set ribbon_width=8, ecr20e set cartoon_fancy_helices=1, VA show cartoon, VA #set cartoon_transparency=0.7, VA #set cartoon_rect_length=0.75, VA color salmon, VA #hide everything, (VA//A/128:211/) create HISA, (gpVabc//A/197,199/) show sticks, HISA set cartoon_side_chain_helper=1, HISA color gray40, (HISA and elem C) color red, (HISA and elem O) color blue, (HISA and elem N) color yellow, (HISA and elem S) set stick_radius=0.20, HISA #hide everything, HISA -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40 -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] Pymol question
Hi Chris, set cartoon_side_chain_helper=1, HISA should be set cartoon_side_chain_helper=1 That setting cannot yet be applied just to a specific set of atoms: it's a global setting. This is something we should add to our to-do list. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] hkl2map on Mac OSX 10.6
...and in zsh for me r On 15 Jul 2011, at 14:56, Harry Powell wrote: and in tcsh for me... On 15 Jul 2011, at 14:48, Bosch, Juergen wrote: works fine in bash for me On Jul 15, 2011, at 5:51 AM, Steiner, Roberto wrote: I only managed to get it working using zsh. All other shells were giving me errors. Ciao R. On 15 Jul 2011, at 10:40, Sebastiano Pasqualato wrote: Hi all, has anybody managed to have hkl2map running on an intel-based Mac? I have downloaded and installed the shelx programs, which I have aliased in my .bashrc, and will run from the command line. I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that does open hkl2map windows. However, when type hkl2map, I get this: Screen shot 2011-07-15 at 11.39.22 AM.png Any ideas on how to solve the problem? Thanks a lot in advance, best, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk .. 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: +1-410-955-3655 http://web.mac.com/bosch_lab/ Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011 Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk
Re: [ccp4bb] hkl2map on Mac OSX 10.6
does it work on Windows ? Just curious, because I will hit this roadblock soon. Jürgen On Jul 15, 2011, at 10:37 AM, Steiner, Roberto wrote: ...and in zsh for me r On 15 Jul 2011, at 14:56, Harry Powell wrote: and in tcsh for me... On 15 Jul 2011, at 14:48, Bosch, Juergen wrote: works fine in bash for me On Jul 15, 2011, at 5:51 AM, Steiner, Roberto wrote: I only managed to get it working using zsh. All other shells were giving me errors. Ciao R. On 15 Jul 2011, at 10:40, Sebastiano Pasqualato wrote: Hi all, has anybody managed to have hkl2map running on an intel-based Mac? I have downloaded and installed the shelx programs, which I have aliased in my .bashrc, and will run from the command line. I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that does open hkl2map windows. However, when type hkl2map, I get this: Screen shot 2011-07-15 at 11.39.22 AM.png Any ideas on how to solve the problem? Thanks a lot in advance, best, s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990 Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk .. 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: +1-410-955-3655 http://web.mac.com/bosch_lab/ Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011 Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk .. 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: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] output individual redundancies
On Fri, 2011-07-15 at 09:26 +0100, Phil Evans wrote: Ed. You could count them from the unmerged output as you say, or I could make you a special version of SCALA or Aimless maybe next week Phil, that would be fantastic! Hope there is broader interest in such option (beyond Robbie and myself). I'll try unmerged output in the meantime. Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] output individual redundancies
At the risk of asking a question to which I should already know the answer: do partials count as redundancy? That is, in SCALA, is the number of observations the number of recorded spots? Or is it the number of recorded spots after adding partials? If it is the latter, what happens if you collect more than 360 degrees of data? Does the second pass through a given unmerged hkl index count as more partials or is it now somehow upgraded to an independent observation? Then again, in Eastern English the word redundancy has a negative connotation, and the output of SCALA actually uses the word multiplicity. I wonder if that makes unmerged partials redundant? -James Holton MAD Scientist On 7/15/2011 8:09 AM, Ed Pozharski wrote: On Fri, 2011-07-15 at 09:26 +0100, Phil Evans wrote: Ed. You could count them from the unmerged output as you say, or I could make you a special version of SCALA or Aimless maybe next week Phil, that would be fantastic! Hope there is broader interest in such option (beyond Robbie and myself). I'll try unmerged output in the meantime. Ed.
[ccp4bb] Ph.D. studentship in Durham (UK)
Applications are invited for a fully-funded Ph.D. studentship at the Biophysical Sciences Institute at Durham University (UK). to work on bacterial metal-sensors and their inhibition. Project description The aim is to understand how cells detect different metals. You will (1) purify DNA-binding metal-sensing transcriptional-regulators and generate crystals for structural determinations, (2) test metal-chelating compounds proposed to interfere with metal-binding, metal-sensing, (3) measure metal-affinities of the sensor proteins using small molecule probes. This work will be an integral part of a major research project aiming to extend our understanding of metal-selectivity by these proteins: How is the correct sensor in the set triggered by the correct metal? The supervisory team includes a biologist specialized in the cell biology of metals, a structural biologists experienced in determining structures of bacterial metal sensor proteins and bio-inorganic chemist expert in the synthesis and characterization of small molecule metal-complexes. Further details can be found at: http://www.dur.ac.uk/biosciences/postgrad/current_phd/ Informal inquiries are welcome to nigel.robin...@durham.ac.uk or ehmke.p...@durham.ac.uk
Re: [ccp4bb] output individual redundancies
Summed partials count as one. SCALA doesn't adjust for 360deg, maybe it should as they are not independent. What would you call them? I prefer multiplicity since Elspeth Garman commented if they are redundant why bother measuring them Phil Sent from my iPhone On 15 Jul 2011, at 18:24, James Holton jmhol...@lbl.gov wrote: At the risk of asking a question to which I should already know the answer: do partials count as redundancy? That is, in SCALA, is the number of observations the number of recorded spots? Or is it the number of recorded spots after adding partials? If it is the latter, what happens if you collect more than 360 degrees of data? Does the second pass through a given unmerged hkl index count as more partials or is it now somehow upgraded to an independent observation? Then again, in Eastern English the word redundancy has a negative connotation, and the output of SCALA actually uses the word multiplicity. I wonder if that makes unmerged partials redundant? -James Holton MAD Scientist On 7/15/2011 8:09 AM, Ed Pozharski wrote: On Fri, 2011-07-15 at 09:26 +0100, Phil Evans wrote: Ed. You could count them from the unmerged output as you say, or I could make you a special version of SCALA or Aimless maybe next week Phil, that would be fantastic! Hope there is broader interest in such option (beyond Robbie and myself). I'll try unmerged output in the meantime. Ed.
Re: [ccp4bb] output individual redundancies
Hi, I was wondering if anyone knows what HKL 2000 does? Does it merge all partials and treat it as one, because often times I noticed with increase in partials the redundancy increases. Shya On Fri, Jul 15, 2011 at 1:24 PM, James Holton jmhol...@lbl.gov wrote: At the risk of asking a question to which I should already know the answer: do partials count as redundancy? That is, in SCALA, is the number of observations the number of recorded spots? Or is it the number of recorded spots after adding partials? If it is the latter, what happens if you collect more than 360 degrees of data? Does the second pass through a given unmerged hkl index count as more partials or is it now somehow upgraded to an independent observation? Then again, in Eastern English the word redundancy has a negative connotation, and the output of SCALA actually uses the word multiplicity. I wonder if that makes unmerged partials redundant? -James Holton MAD Scientist On 7/15/2011 8:09 AM, Ed Pozharski wrote: On Fri, 2011-07-15 at 09:26 +0100, Phil Evans wrote: Ed. You could count them from the unmerged output as you say, or I could make you a special version of SCALA or Aimless maybe next week Phil, that would be fantastic! Hope there is broader interest in such option (beyond Robbie and myself). I'll try unmerged output in the meantime. Ed.
Re: [ccp4bb] output individual redundancies
For each observation or measurement, HKL, d*TREK, and all other common programs to my knowledge add up the bits of each relfection from its parts. They do not add parts of of other reflections (even if symmetry-related) into a reflection. Reflections for which only part of the Bragg peak is measured are tossed out. For example, at the beginning and end of a scan there are partial reflections which cannot be made full. (I am aware that one can take a partial measurement and scale it up by the inverse of its so-called partiality to make it into a fake full reflection.) One can use the NO MERGE ORIGINAL INDEX macro of scalepack and output the individual measurements of denzo or HK that have had scale factors applied. This file can be a converted to a d*TREK reflectiion file with SCA2DTREK and then the individual measurements averaged with dtscaleaverage to get statistics such as Rmeas, completeness, reduced ChiSq, multiplicity, and a Table 1 suitable for framing in your Nature paper. The unique reflection list output could have the multiplicity of each unique reflection added pretty trivially if there is a demand for this. Jim _ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Shya Biswas Sent: Friday, July 15, 2011 6:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] output individual redundancies Hi, I was wondering if anyone knows what HKL 2000 does? Does it merge all partials and treat it as one, because often times I noticed with increase in partials the redundancy increases. Shya On Fri, Jul 15, 2011 at 1:24 PM, James Holton jmhol...@lbl.gov wrote: At the risk of asking a question to which I should already know the answer: do partials count as redundancy? That is, in SCALA, is the number of observations the number of recorded spots? Or is it the number of recorded spots after adding partials? If it is the latter, what happens if you collect more than 360 degrees of data? Does the second pass through a given unmerged hkl index count as more partials or is it now somehow upgraded to an independent observation? Then again, in Eastern English the word redundancy has a negative connotation, and the output of SCALA actually uses the word multiplicity. I wonder if that makes unmerged partials redundant? -James Holton MAD Scientist On 7/15/2011 8:09 AM, Ed Pozharski wrote: On Fri, 2011-07-15 at 09:26 +0100, Phil Evans wrote: Ed. You could count them from the unmerged output as you say, or I could make you a special version of SCALA or Aimless maybe next week Phil, that would be fantastic! Hope there is broader interest in such option (beyond Robbie and myself). I'll try unmerged output in the meantime. Ed.
