[ccp4bb] Why the name aimless
Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it
Re: [ccp4bb] Why the name aimless
Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it
Re: [ccp4bb] Why the name aimless
Occasionally given to losing extremities. is that a good thing? Andreas On 02/05/2013 11:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto.
Re: [ccp4bb] Why the name aimless
Entirely appropriate for data processing! and Aimless is clearly some sort of optimisation program :-) Phil On 2 May 2013, at 11:31, Andreas Förster docandr...@gmail.com wrote: Occasionally given to losing extremities. is that a good thing? Andreas On 02/05/2013 11:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto.
Re: [ccp4bb] Why the name aimless
I think Phil saw something nasty in the woodshed ... HTH Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto Battistutta Sent: 02 May 2013 11:07 To: ccp4bb Subject: [ccp4bb] Why the name aimless Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it -- Scanned by iCritical.
Re: [ccp4bb] Why the name aimless
I thought it was just a logical pun progression from pointless to aimless. Perhaps the next program will be useless? DISCLAIMER: This is intended as a JOKE... I FULLY appreciate and use the wonderful programs generated by Phil. Just in case I unintentionally start yet another CCP4bb flame-a-thon. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On May 2, 2013, at 11:23 AM, Martyn Winn wrote: I think Phil saw something nasty in the woodshed ... HTH Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto Battistutta Sent: 02 May 2013 11:07 To: ccp4bb Subject: [ccp4bb] Why the name aimless Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it -- Scanned by iCritical.
Re: [ccp4bb] Why the name aimless
Martyn Winn martyn.w...@stfc.ac.uk writes: I think Phil saw something nasty in the woodshed ... HTH Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto Battistutta Sent: 02 May 2013 11:07 To: ccp4bb Subject: [ccp4bb] Why the name aimless Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. We mustn’t forget, we already have a name, due to Zbigniew Dauter, for a future combination of pointless + aimless—“hopeless”. -- Ian ◎
Re: [ccp4bb] Why the name aimless
Occasionally given to losing extremities. is that a good thing? Yes. Outlier removal BR Andreas On 02/05/2013 11:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto.
Re: [ccp4bb] showing electron density on an ipad
Sorry - I went back to look at that. The ipad app for pymol does not have an option to load a map. You can only load structures. I like that you can load your own structures (from a dropbox folder), that's nice. It's very powerful, and I can do a lot with it, but I would like to show electron density and can't find a way. I got good suggestions yesterday. Imolview does work well for loading pdb files. I don't have a way to get the browser that goes with it to run on my linux box. I tried it, but was unsuccessful, so I don't know if it displays density or not. The CueMol does not show density. So, both of these are nice for pdb files (I like Imolview better), but neither will easily show electron density. I just want an app that will display a pdb file and a map file. I can convert maps to whatever format is necessary (as long as it's crystallographic). That I can't seem to find. No worries. Thanks for all the suggestions Dave On 5/2/2013 2:35 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Dave, could you explain what you mean by it doesn't work? I understand that you convert a ccp4 mtz-file to ccp4 map format (which pymol can read) and load it into pymol on your ipad which does not display. Is this correct? If so, do you get any error messages? Could you use coot instead? Best, Tim On 05/01/2013 09:56 PM, David Roberts wrote: Hello all, So, I find an ipad is a wonderful device for teaching (any tablet really - but I'm partial to the ipad). I can project it in a classroom, run pymol and a few other chemistry/biochemistry things, and really get the students interested in these subjects easily. I actually don't have a laptop - and our classrooms are such that there are computers connected to the projectors but they have standard University software packages installed on them. It would be very helpful if I could just display electron density using an ipad. The pymol app will load a map (it is an option) - but when I take a map from my linux machines it doesn't work. Any thoughts here? Has anybody done this Thanks Dave - -- - -- 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/ iD8DBQFRggkUUxlJ7aRr7hoRAilLAJ9G2JTUu9hYnH+Hsf+LViBFHNqC6QCggGaR /r2Il4d2qklnV/IGJWxpZpw= =QOT4 -END PGP SIGNATURE-
Re: [ccp4bb] Why the name aimless
That's right. Useless always refers to us users. :) On 5/2/13 5:45 AM, Ian Clifton ian.clif...@chem.ox.ac.uk wrote: Martyn Winn martyn.w...@stfc.ac.uk writes: I think Phil saw something nasty in the woodshed ... HTH Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto Battistutta Sent: 02 May 2013 11:07 To: ccp4bb Subject: [ccp4bb] Why the name aimless Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. We mustn’t forget, we already have a name, due to Zbigniew Dauter, for a future combination of pointless + aimless―“hopeless”. -- Ian ◎
Re: [ccp4bb] detectors on home sources
I can not really speak for a home-source setup, but here at the SLS MX group we run two Pilatus6M (one of which is the first Pilatus ever made) and one Pilatus2M. In nearly four years since we installed the first one we never had any hardware issue other than users damaging the case. So I'd say the reliability of the DECTRIS detectors is excellent. Cheers, Florian - Paul Scherrer Institut Dr. Florian Dworkowski Beamline Scientist X10SA Swiss Light Source WSLA/219 5232 Villigen PSI Switzerland Phone +41 56 310 3584 Fax +41 56 310 5292 florian.dworkow...@psi.ch http://www.psi.ch/macromolecular-crystallography blocked::http://www.psi.ch/macromolecular-crystallography From: Fareed Aboul-Ela [mailto:faboul...@zewailcity.edu.eg] Sent: Dienstag, 30. April 2013 21:01 Subject: detectors on home sources I'm involved in advising my institute on an X-ray home source for a core facility. The vendors are offering some new configurations. Whatever the claimed advantages/disadvantages, I'm hesitant to make a decision without consulting someone with direct experience with them. In particular, has anyone had any experience with using the photon100 CMOS detector being offered by Bruker, or the pilatus 200K detector being offered by Rigaku? I'd also appreciate hearing from anyone with experience with the latest Bruker microfocus rotating anode generator (called the Turbo or TXS)? Many thanks for sharing your experiences. Fareed Aboul-ela Associate Professor Zewail University Zewail City of Science and Technology Giza, Egypt faboul...@zewailcity.edu.eg
Re: [ccp4bb] Why the name aimless
Oh no, that software is still in works and it is called clueless... Cheers, N. - Original Message - From: Christopher Colbert christopher.colb...@ndsu.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, May 2, 2013 8:48:50 AM Subject: Re: [ccp4bb] Why the name aimless That's right. Useless always refers to us users. :) On 5/2/13 5:45 AM, Ian Clifton ian.clif...@chem.ox.ac.uk wrote: Martyn Winn martyn.w...@stfc.ac.uk writes: I think Phil saw something nasty in the woodshed ... HTH Martyn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto Battistutta Sent: 02 May 2013 11:07 To: ccp4bb Subject: [ccp4bb] Why the name aimless Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. We mustn’t forget, we already have a name, due to Zbigniew Dauter, for a future combination of pointless + aimless—“hopeless”. -- Ian ◎
Re: [ccp4bb] Why the name aimless
i.e. the next program will be Graceless or Feckless? On 2 May 2013, at 12:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it
Re: [ccp4bb] Why the name aimless
I've always thought gormless is a woefully underused word. Eric On Thu, May 2, 2013 at 11:53 AM, Mark van Raaij mjvanra...@cnb.csic.eswrote: i.e. the next program will be Graceless or Feckless? On 2 May 2013, at 12:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it
Re: [ccp4bb] Why the name aimless
Moreorless? Dolores? JPK On Thu, May 2, 2013 at 12:22 PM, Eric Williams ericwilli...@pobox.comwrote: I've always thought gormless is a woefully underused word. Eric On Thu, May 2, 2013 at 11:53 AM, Mark van Raaij mjvanra...@cnb.csic.eswrote: i.e. the next program will be Graceless or Feckless? On 2 May 2013, at 12:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Why the name aimless
Some of my undergraduate students need the CCP4 program feckless. :) ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 5/2/2013 12:22 PM, Eric Williams wrote: I've always thought gormless is a woefully underused word. Eric On Thu, May 2, 2013 at 11:53 AM, Mark van Raaij mjvanra...@cnb.csic.es mailto:mjvanra...@cnb.csic.es wrote: i.e. the next program will be Graceless or Feckless? On 2 May 2013, at 12:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it mailto:roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 tel:%2B39.049.827.5262 fax. +39.049.827.5829 tel:%2B39.049.827.5829 roberto.battistu...@unipd.it mailto:roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ http://www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 tel:%2B39.049.7923.236 fax +39.049.7923.250 tel:%2B39.049.7923.250 www.vimm.it http://www.vimm.it
[ccp4bb] Not to refine B factors, not to refine coordinates
Dear all, hi!! I need help in order to use Refmac in two particular ways. On one hand I would like to ask the program not to refine B factor values (whichever the selected refinement mode was) and in the other I would like to ask it not to refine coordinates (whichever the selected refinement mode was). How can I do this? There must be more than one way...? Pros and cons... Clarifications: It is not about setting initial B values neither to set Bavg to a certain value so that scaling goes well. Thks in advance! Horacio attachment: hbotti.vcf
[ccp4bb] PhD (DPhil) place available: Marie Curie Action
PhD (DPhil) place available: Marie Curie Action DPhil in Biochemistry University of Oxford in association with Molecular Dimensions Ltd. New Approaches to Membrane Protein Structural Biology using Micro-focus X-ray beams X-ray Free Electron Laser based Serial Femtosecond Crystallography. Supervisors Simon Newstead and Elspeth Garman For details see: http://ec.europa.eu/euraxess/index.cfm/jobs/fgDetails/52824 -- European Crystallography Meeting, Warwick University 25-29th August 2013. Registration for ECM28 is open at: http://ecm28.ecanews.org Professor Elspeth F. Garman, Director of Systems Biology Programme, Doctoral Training Centre. Postal address: Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Tel: (44)-1865-613297 South Parks Road, FAX: (44)-1865-613201 OXFORD, OX1 3QU, U.K. E-mail: elspeth.gar...@bioch.ox.ac.ukmailto:elspeth.gar...@bioch.ox.ac.uk www.bioch.ox.ac.uk/garmangrouphttp://www.bioch.ox.ac.uk/garmangroup -- The University of Oxford's Doctoral Training Centre has three available programmes for October 2013 entry: Life Sciences Interface Doctoral Training Centre, Systems Biology Doctoral Training Centre and Systems Approaches to Biomedical Science Industrial Doctorate Centre. To find out more, visit: http://www.dtc.ox.ac.uk/
Re: [ccp4bb] Why the name aimless
Nevertheless? JPK On Thu, May 2, 2013 at 2:18 PM, Roger Rowlett rrowl...@colgate.edu wrote: Some of my undergraduate students need the CCP4 program feckless. :) ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 5/2/2013 12:22 PM, Eric Williams wrote: I've always thought gormless is a woefully underused word. Eric On Thu, May 2, 2013 at 11:53 AM, Mark van Raaij mjvanra...@cnb.csic.eswrote: i.e. the next program will be Graceless or Feckless? On 2 May 2013, at 12:10, Phil Evans wrote: Reference: Gibbons, S. (1932) Cold Comfort Farm, Longmans, London On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi everyone, just a curiosity, why the name aimless for the recent data reduction and analysis program in CCP4? You know, my students are curious ... Thank you, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
