[ccp4bb] TMAO for crystallization
Hi all! Just want to ask whether some of you has experience with TMAO (or similar conformation stabilizers) for setting up crystallization screenings? Which concentration range would you use? Would you add TMAO to the protein tube and afterwards add the mixture to the plates? Just wanted to know your opinion about conformation stabilizers: could they really help to crystallize multi-domain proteins, supposed to be flexible? Thank you very much in advance for your attention, With my best wishes, Ruben
[ccp4bb]
Hi everyone, I am refining a protein structure containing a Beryllium Fluoride (BeF3) ligand. I am using Refmac5 in ccp4i. The distances between the Be and the F atoms are slightly longer than what I would expect (1.7A instead of ~1.5A). Does anyone know how I can fix the distances and restrain the bond lengths for the BeF. Thanks, Yael.
[ccp4bb] Restraints in Refmac5
Hi everyone, I am refining a protein structure containing a Beryllium Fluoride (BeF3) ligand. I am using Refmac5 in ccp4i. The distances between the Be and the F atoms are slightly longer than what I would expect (1.7A instead of ~1.5A). Does anyone know how I can fix the distances and restrain the bond lengths for the BeF. Thanks, Yael.
Re: [ccp4bb] Restraints in Refmac5
One question is, why do you want to fix that and from what literature are you expecting the values? BeF3- is often a ground state analogue for GTP binding proteins for example.. and the depending on the coordination state, the bond angle and length might change a bit I would have thought.. for example, if you have an oxygen from a ligand and a water close enough to the Be, then the bond order of the B-F is lower.. if you have good resolution, this might be interesting in the other way around.. Cheers, Partha On Thu, Jun 26, 2008 at 3:26 PM, [EMAIL PROTECTED] wrote: Hi everyone, I am refining a protein structure containing a Beryllium Fluoride (BeF3) ligand. I am using Refmac5 in ccp4i. The distances between the Be and the F atoms are slightly longer than what I would expect (1.7A instead of ~1.5A). Does anyone know how I can fix the distances and restrain the bond lengths for the BeF. Thanks, Yael. -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] TMAO for crystallization
Hi Ruben, I have never used TMAO myself but this paper might give you a better idea: Jeruzalmi, D. Steitz, T. Use of organic cosmotropic solutes to crystallize flexible proteins: application to T7 RNA polymerase and its complex with the inhibitor T7 lysozyme. J Mol Biol, 1997, 274, 748-56 The authors use 10-20% of cosmotropic solutes. From my experience with several other substances from their list I would use 5-10%. Best regards, christian Ruben Martinez-Buey wrote: Hi all! Just want to ask whether some of you has experience with TMAO (or similar conformation stabilizers) for setting up crystallization screenings? Which concentration range would you use? Would you add TMAO to the protein tube and afterwards add the mixture to the plates? Just wanted to know your opinion about conformation stabilizers: could they really help to crystallize multi-domain proteins, supposed to be flexible? Thank you very much in advance for your attention, With my best wishes, Ruben ___ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA ___
[ccp4bb] Friedel vs Bijvoet
Dear All, I wonder about the conventions using Friedel vs Bijvoet pair. a) there are no differences. As long as h = -h, it's a Friedel or a Bijvoet pair. They are the same. b) A Friedel pair is any reflection h = -h including hR = -h, i.e. including centric reflections. A Bijvoet pair is an acentric Friedel pair, it can carry anomalous amplitude differences, whereas centric Friedel pairs invariably cannot. Actually, Bijvoet pairs (acentric Friedel pairs) invariably do carry anomalous amplitude differences. There is no such thing as no anomalous scattering. We may elect to ignore it, only. c) of course, this all assumes absence of anisotropic AS. def b) seems to be helpful in discussions and make sense given that absolute configuration that needs AS signal is somehow associated with Bijvoet's work. Are any authoritative answers/conventions/opinions available on that ? Thx, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
Re: [ccp4bb] Friedel vs Bijvoet
Friedel pair is strictly F(hkl) and F(-h,-k,-l). Bijvoet pair is F(h) and any mate that is symmetry-related to F(-h), e.g., F(hkl) and F(-h,k,-l) in monoclinic. There are always anomalous differences, though they can be unmeasurably small. Bernie Santarsiero On Thu, June 26, 2008 10:55 am, Bernhard Rupp wrote: Dear All, I wonder about the conventions using Friedel vs Bijvoet pair. a) there are no differences. As long as h = -h, it's a Friedel or a Bijvoet pair. They are the same. b) A Friedel pair is any reflection h = -h including hR = -h, i.e. including centric reflections. A Bijvoet pair is an acentric Friedel pair, it can carry anomalous amplitude differences, whereas centric Friedel pairs invariably cannot. Actually, Bijvoet pairs (acentric Friedel pairs) invariably do carry anomalous amplitude differences. There is no such thing as no anomalous scattering. We may elect to ignore it, only. c) of course, this all assumes absence of anisotropic AS. def b) seems to be helpful in discussions and make sense given that absolute configuration that needs AS signal is somehow associated with Bijvoet's work. Are any authoritative answers/conventions/opinions available on that ? Thx, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
[ccp4bb]
Friedel pairs Bijvoet differences
Re: [ccp4bb] Friedel vs Bijvoet
I've always thought that a Bijvoet pair is any pair for which an anomalous difference could be observed. This includes Friedel pairs (h h-bar), but it also includes pairs of the form h h', where h' is symmetry-related to h-bar. Thus Friedel pairs are a subset of all possible Bijvoet pairs. This is what Ed and I say in our book, at least (shameless plug); and you can buy it from Amazon, so it must be right, yes? Pat On 26 Jun 2008, at 11:55 AM, Bernhard Rupp wrote: Dear All, I wonder about the conventions using Friedel vs Bijvoet pair. a) there are no differences. As long as h = -h, it's a Friedel or a Bijvoet pair. They are the same. b) A Friedel pair is any reflection h = -h including hR = -h, i.e. including centric reflections. A Bijvoet pair is an acentric Friedel pair, it can carry anomalous amplitude differences, whereas centric Friedel pairs invariably cannot. Actually, Bijvoet pairs (acentric Friedel pairs) invariably do carry anomalous amplitude differences. There is no such thing as no anomalous scattering. We may elect to ignore it, only. c) of course, this all assumes absence of anisotropic AS. def b) seems to be helpful in discussions and make sense given that absolute configuration that needs AS signal is somehow associated with Bijvoet's work. Are any authoritative answers/conventions/opinions available on that ? Thx, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch - --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED] http://www.amazon.com/Protein-Crystallography-Eaton-E-Lattman/dp/ 0801888085/ref=sr_1_10?ie=UTF8s=booksqid=1214496225sr=1-10
[ccp4bb] PDB Ligands, Drug Discovery Informatics, eCheminfo Autumn Meeting
Our eCheminfo Autumn CoP meeting this year includes an extensive session of 1.5 days on PDB Ligands chaired by Marc Nicklaus (NIH) which should be of particular interest to the CCP community. Meeting announcement including CFP and Bursary Award preogram below. best regards Barry Hardy Latest Advances in Drug Discovery Informatics eCheminfo Autumn Community of Practice Meeting 14-17 October 2008 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Conference Link: Website: http://echeminfo.com/COMTY_conferences Blog: http://barryhardy.blogs.com/cheminfostream/ Program (pdf): http://barryhardy.blogs.com/cheminfostream/files/eChemProgramBrynMawr08-Final-v2.pdf Themes: Cheminformatics, Bioinformatics, Medicinal Chemistry, Drug Discovery Innovation, Structure-based Drug Design, Screening, Docking, Structural Biology, Predictive Toxicology, Predictive ADME, Chemogenomics Program Summary Docking ! p; Scoring, chaired by Chaya Duraiswami (GlaxoSmithKline) Application of MM-PBSA Free Energy Methods in Drug Discovery, chaired by Judith Lalonde (Bryn Mawr College) Accurate Calculation of pKas, chaired by Paul Labute (Chemical Computing Group) In Silico-based Chemogenomics, chaired by Fabrice Moriaud (MEDIT) PDB Ligands: Analysing their Structure Binding Data, chaired by Marc Nicklaus (National Institutes of Health) Predictive ADME, chaired by Anthony E. Klon (Pharmacopeia Drug Discovery) Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia) Pre-Conference Workshop, 13 October Best Practices Virtual Screening Workshop chaired by Barry Hardy (Douglas Connect) Speakers John Irwin (UCSF), Georgia McGaughey (Merck), Johannes H. Voigt (Schering Plough), Lance Westerhoff (Quantum Bio), Zsolt Zsoldos (SimBioSys), Alexey Ornufriev (Virginia Tech), David Case (Rutgers University), Rommie Amaro (USCD), Peter Coveney (Univ. College Lond on), Anna Kohlmann (Ariad Pharmaceuticals), Scott Brown (Abbott), Emil Alexov (Clemson University), Jens Erik Nielsen (University College Dublin, Ireland), Matthew Davies (Jenner Institute, UK), Maja Mihajlovic (City College of New York), Michael Keiser (UCSF), Brian Marsden (University of Oxford, UK), Alex Tropsha (UNC), John Westbrook (Rutgers), Howard J Feldman (CCG), Igor V. Filippov (NCI), Raul Cachau (ATP, SAIC-Frederick), Vincent T. Moy (University of Miami), Paul Hawkins (OpenEye), Yulia Borodina (NCBI), Gerhard Wolber (Inte:Ligand, Austria), Marc Nicklaus (NCI), James P. Snyder (Emory), Anne Chaka (NIST), Esther Kellenberger (Univ. Strasbourg, France), Renxiao Wang (SIOC, Shanghai, PR China), Jim Dunbar (University of Michigan), Janna Wehrle (NIGMS), Anton Hopfinger (University of New Mexico), Heidi Einolf (Novartis), Yojiro Sakiyama (Pfizer), Olga Obrezanova (BioFocus DPI, UK), Anthony E. Klon (Pharmacopeia), ! Artem Cherkasov (University of British Columbia, Canada), Ann Richards (US EPA), Curt Breneman (RPI), Barry Hardy (Douglas Connect), Weida Tong (FDA) CFP We invite contributed talks from members of academic, government research and commercial organizations on areas of new research and innovation involving drug discovery research informatics. The work presented should involve innovative new method development or application to drug discovery problems and involving methods from computational chemistry, computational biology, cheminformatics or bioinformatics. Studies including experimental work in medicinal chemistry, screening, experimental toxicology, pre-clinical evaluation, lead optimisation and translational medicine are welcome. Abstracts (300-500 words) should be submitted to echeminfo -[at]- douglasconnect.com by 31 July 2008, and be accompanied by a short biography of the presenting author (300-500 w! ords). Abstracts approved by the scientific organizing committee w ill be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 15 August 2008. Bursary Award Bursary Awards will be used to support the attendance of a selection of academic young investigators at the meeting and workshops. Applicants can be working in any area of research related to drug discovery at the postdoctoral, graduate student and senior undergraduate levels. To apply for the bursary please send an email with a) your abstract and biography (300-500 words each), b) your CV of 1-2 pages, c) a short description of your interests and career motivations related to drug discovery (300-500 words) to echeminfo -[at]- douglasconnect.com by 31 July 2008. The recipients of the bursary awards will be selected based on an evaluation of the quality and innovation of the describe! d research and the potential positive impact of attendance at the meeting on their research and career progress. Authors will be notified of acceptance by 15 August 2008. Poster Session All InterAction Meeting registrants are eligible to present a Conference Poster. The
Re: [ccp4bb] Friedel vs Bijvoet
On Thursday 26 June 2008 09:36:16 am Serge Cohen wrote: Please some one tells me if I'm wrong ... but I though that indeed one is NOT supposed to measure anomalous difference from reflections h and h' if those are related by one of the symmetry operator of the point group... This statement is logically equivalent to what Patrick writes below. You are agreeing with each other. That is in monoclinic (P 1 2 1, more precisely) , (h, k, l) and (-h, k, -l) should have the same F ... (in a determinist's world) Yes, but that is not an example of h and h'. Though (h, k, l) and (-h, -k, -l) are likely to be different, and hence (h, k, l) and (h, -k, l) would show the same difference. Serge. Le 26 juin 08 à 18:07, Patrick Loll a écrit : I've always thought that a Bijvoet pair is any pair for which an anomalous difference could be observed. This includes Friedel pairs (h h-bar), but it also includes pairs of the form h h', where h' is symmetry-related to h-bar. Thus Friedel pairs are a subset of all possible Bijvoet pairs. This is what Ed and I say in our book, at least (shameless plug); and you can buy it from Amazon, so it must be right, yes? Pat On 26 Jun 2008, at 11:55 AM, Bernhard Rupp wrote: Dear All, I wonder about the conventions using Friedel vs Bijvoet pair. a) there are no differences. As long as h = -h, it's a Friedel or a Bijvoet pair. They are the same. b) A Friedel pair is any reflection h = -h including hR = -h, i.e. including centric reflections. A Bijvoet pair is an acentric Friedel pair, it can carry anomalous amplitude differences, whereas centric Friedel pairs invariably cannot. Actually, Bijvoet pairs (acentric Friedel pairs) invariably do carry anomalous amplitude differences. There is no such thing as no anomalous scattering. We may elect to ignore it, only. c) of course, this all assumes absence of anisotropic AS. def b) seems to be helpful in discussions and make sense given that absolute configuration that needs AS signal is somehow associated with Bijvoet's work. Are any authoritative answers/conventions/opinions available on that ? Thx, BR *** Dr. Serge COHEN GPG Key ID: 0B5CDAEC N.K.I. Department of Molecular Carcinogenesis (B8) Plesmanlaan 121 1066 CX Amsterdam; NL E-Mail: [EMAIL PROTECTED] Tel : +31 20 512 2053 *** -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] Friedel vs Bijvoet
Let's try this again, with definitions, and pls scream if I am wrong: a) Any reflection pair hR = h forms a symmetry related pair. R is any one of G point group operators of the SG. This is a set of reflections (S). Their amplitudes are invariably the same. They do not even show up as individual pairs in the asymmetric unit of the reciprocal space. NB: their phases are restricted but not the same. b) a set h=-h (set F) exist where reflections may or may not carry anomalous signal. They form the centrosymmetrically related wedge of the asymmetric unit of reciprocal space. c) a centric reflection (set C) is defined as hR=-h and cannot carry anomalous signal. Example zone h0l in PG 2. As Ian Tickle pointed out, the CCP4 wiki is wrong: Centric reflections in space group P2 and P21 are thus those with 0,k,0. Not so; an example listing is attached at the end. d) therefore, some e:F exist that carry AS (F.ne.C) and some that do not carry AS (F.el.C). I hope we can agree on those facts. Now for the name calling: (S) is simply the set of symmetry related reflections, defined as hR=h. (F) is the set of Friedel pairs, defined as h=-h. (C) are centric reflections, defined as hR=-h. Thus, only if (F.ne.C), anomalous signal. I thought those are Bijvoet pairs. They are, but it may not be the definition of a Bijvoet pair. Try 1: Bijvoet pair is F(h) and any mate that is symmetry-related to F(-h), e.g., F(hkl) and F(-h,k,-l) in monoclinic. hkl is not related to -hk-l via h = -h. Only h0l is, and those are (e:C). So, I cannot quote follow that, probably try 1 is not a good definition. Try 2: I've always thought that a Bijvoet pair is any pair for which an anomalous difference could be observed. Good start. I subscribe to that. This includes Friedel pairs (h h-bar) Good. That's the definition of F. but it also includes pairs of the form h h', where h' is symmetry-related to h-bar. Ooops. That is the definition of a centric reflection. Thus Friedel pairs are a subset of all possible Bijvoet pairs. Cannot see that. I still maintain that Bijvoet pairs are a subset of Friedel pairs (which does include Pat's definition). I fail to see anything else but Friedel pairs in my list of reflections - some of them carry AS (F.ne.C) and some don't (F.el.C). B = F.ne.C. Seems to be a necessary and sufficient condition, in agreement with Pat's definition (though not the explanation). But - isn't that exactly what I said from the beginning? A Bijvoet pair is an acentric Friedel pair... Or - where are any other Bijvoet pairs hiding? Where did I miss them? (NB: Absence of anisotropic AS assumed -let's not go there) See reflection list P2 (hkl |F| fom phi 2theta stol2) last 3 items: centric flag, epsilon, m(h) 0 0 1 993.54 1.00 179.9965.61 0.581 1 1 2 0 0 -1 993.54 1.00 179.9965.61 0.581 1 1 2 1 0 0 1412.58 1.00 0.1438.22 0.0001711 1 1 2 -1 0 0 1412.58 1.00 0.1438.22 0.0001711 1 1 2 0 0 2 3279.49 1.00 180.3132.80 0.0002323 1 1 2 0 0 -2 3279.49 1.00 180.3132.80 0.0002323 1 1 2 1 0 1 379.89 1.00 180.2530.36 0.0002712 1 1 2 -1 0 -1 379.89 1.00 180.2530.36 0.0002712 1 1 2 -1 0 2 1355.06 1.00 0.1327.97 0.0003195 1 1 2 1 0 -2 1355.06 1.00 0.1327.97 0.0003195 1 1 2 0 1 0 2432.85 1.0021.0924.35 0.0004216 0 2 1 0 -1 0 2434.14 1.00 339.6524.35 0.0004216 0 2 1 0 1 1 621.36 1.00 101.6722.83 0.0004797 0 1 2 0 -1 -1 623.27 1.00 258.4922.83 0.0004797 0 1 2 1 0 2 319.68 1.00 359.9822.65 0.0004874 1 1 2 -1 0 -2 319.68 1.00 359.9822.65 0.0004874 1 1 2 0 0 3 426.17 1.00 180.9921.87 0.0005227 1 1 2 0 0 -3 426.17 1.00 180.9921.87 0.0005227 1 1 2 -1 0 3 1581.93 1.00 0.4420.98 0.0005680 1 1 2 1 0 -3 1581.93 1.00 0.4420.98 0.0005680 1 1 2 1 1 0 338.67 1.0046.5220.54 0.0005927 0 1 2 -1 -1 0 341.71 1.00 314.7020.54 0.0005927 0 1 2 -1 1 1 1649.38 1.0080.9320.26 0.0006089 0 1 2 1 -1 -1 1652.55 1.00 279.9020.26 0.0006089 0 1 2 0 1 2 343.14 1.0066.8619.55 0.0006540 0 1 2 0 -1 -2 345.84 1.00 293.4219.55 0.0006540 0 1 2 -2 0 1 171.90 1.00 358.5919.48 0.0006586 1 1 2 2 0 -1 171.90 1.00 358.5919.48 0.0006586 1 1 2 2 0 0 1238.53 1.00 180.2019.11 0.0006844 1 1 2 -2 0 0 1238.53 1.00 180.2019.11 0.0006844 1 1 2 1 1 1 201.11 1.00 349.9319.00
Re: [ccp4bb] Friedel vs Bijvoet
Hi, Bernhard, Check out page 8 http://students.washington.edu/zanghell/TAs/BSTR521/notes/anomalous_scattering.pdf I thought that Friedels are reflections related by pure inversion symmetry, while Bijvoets are reflections related by non-inversion symmetry of the reciprocal lattice. Thanks, Hidong Bernhard Rupp [EMAIL PROTECTED] Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 06/26/2008 11:35 AM Please respond to [EMAIL PROTECTED] To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] Friedel vs Bijvoet Let's try this again, with definitions, and pls scream if I am wrong: a) Any reflection pair hR = h forms a symmetry related pair. R is any one of G point group operators of the SG. This is a set of reflections (S). Their amplitudes are invariably the same. They do not even show up as individual pairs in the asymmetric unit of the reciprocal space. NB: their phases are restricted but not the same. b) a set h=-h (set F) exist where reflections may or may not carry anomalous signal. They form the centrosymmetrically related wedge of the asymmetric unit of reciprocal space. c) a centric reflection (set C) is defined as hR=-h and cannot carry anomalous signal. Example zone h0l in PG 2. As Ian Tickle pointed out, the CCP4 wiki is wrong: Centric reflections in space group P2 and P21 are thus those with 0,k,0. Not so; an example listing is attached at the end. d) therefore, some e:F exist that carry AS (F.ne.C) and some that do not carry AS (F.el.C). I hope we can agree on those facts. Now for the name calling: (S) is simply the set of symmetry related reflections, defined as hR=h. (F) is the set of Friedel pairs, defined as h=-h. (C) are centric reflections, defined as hR=-h. Thus, only if (F.ne.C), anomalous signal. I thought those are Bijvoet pairs. They are, but it may not be the definition of a Bijvoet pair. Try 1: Bijvoet pair is F(h) and any mate that is symmetry-related to F(-h), e.g., F(hkl) and F(-h,k,-l) in monoclinic. hkl is not related to -hk-l via h = -h. Only h0l is, and those are (e:C). So, I cannot quote follow that, probably try 1 is not a good definition. Try 2: I've always thought that a Bijvoet pair is any pair for which an anomalous difference could be observed. Good start. I subscribe to that. This includes Friedel pairs (h h-bar) Good. That's the definition of F. but it also includes pairs of the form h h', where h' is symmetry-related to h-bar. Ooops. That is the definition of a centric reflection. Thus Friedel pairs are a subset of all possible Bijvoet pairs. Cannot see that. I still maintain that Bijvoet pairs are a subset of Friedel pairs (which does include Pat's definition). I fail to see anything else but Friedel pairs in my list of reflections - some of them carry AS (F.ne.C) and some don't (F.el.C). B = F.ne.C. Seems to be a necessary and sufficient condition, in agreement with Pat's definition (though not the explanation). But - isn't that exactly what I said from the beginning? A Bijvoet pair is an acentric Friedel pair... Or - where are any other Bijvoet pairs hiding? Where did I miss them? (NB: Absence of anisotropic AS assumed -let's not go there) See reflection list P2 (hkl |F| fom phi 2theta stol2) last 3 items: centric flag, epsilon, m(h) 0 0 1 993.54 1.00 179.9965.61 0.581 1 1 2 0 0 -1 993.54 1.00 179.9965.61 0.581 1 1 2 1 0 0 1412.58 1.00 0.1438.22 0.0001711 1 1 2 -1 0 0 1412.58 1.00 0.1438.22 0.0001711 1 1 2 0 0 2 3279.49 1.00 180.3132.80 0.0002323 1 1 2 0 0 -2 3279.49 1.00 180.3132.80 0.0002323 1 1 2 1 0 1 379.89 1.00 180.2530.36 0.0002712 1 1 2 -1 0 -1 379.89 1.00 180.2530.36 0.0002712 1 1 2 -1 0 2 1355.06 1.00 0.1327.97 0.0003195 1 1 2 1 0 -2 1355.06 1.00 0.1327.97 0.0003195 1 1 2 0 1 0 2432.85 1.0021.0924.35 0.0004216 0 2 1 0 -1 0 2434.14 1.00 339.6524.35 0.0004216 0 2 1 0 1 1 621.36 1.00 101.6722.83 0.0004797 0 1 2 0 -1 -1 623.27 1.00 258.4922.83 0.0004797 0 1 2 1 0 2 319.68 1.00 359.9822.65 0.0004874 1 1 2 -1 0 -2 319.68 1.00 359.9822.65 0.0004874 1 1 2 0 0 3 426.17 1.00 180.9921.87 0.0005227 1 1 2 0 0 -3 426.17 1.00 180.9921.87 0.0005227 1 1 2 -1 0 3 1581.93 1.00 0.4420.98 0.0005680 1 1 2 1 0 -3 1581.93 1.00 0.4420.98 0.0005680 1 1 2 1 1 0 338.67 1.0046.5220.54 0.0005927 0 1 2 -1 -1 0 341.71 1.00 314.7020.54 0.0005927 0 1 2 -1 1 1 1649.38 1.0080.9320.26 0.0006089 0 1 2 1 -1 -1
Re: [ccp4bb] Friedel vs Bijvoet
I quote from these pages: Bijvoet pairs are Bragg reflections which are true symmetry equivalents to a Friedel pair. These true symmetry equivalents have *equal amplitudes, even in the presence of anomalous scattering*. Sounds more like centric or perhaps simply symmetry related to me. A few lines below: A Bijvoet difference refers to the difference in measured amplitude for a Bijvoet pair I don't think you can have it both ways ?? BR
Re: [ccp4bb] Friedel vs Bijvoet
There was a mistake in the letter that listed the Bijvoet pairs for a monoclinic space group and that is confusing you. Let me try. The equivalent positions for a B setting monoclinic are h,k,l; -h,k,-l. The Friedel mates for the general position (h,k,l) are (-h,-k,-l). This means that the equivalent positions also have Friedel mates at h,-k,l. The Bijvoet mates of h,k,l are therefore, according to the definitions given in previous letters, -h,-k,-l; and h,-k,l. There are more Bijvoet mates to a reflection then Fridel mates. A centric reflection is a reflection that is BOTH a symmetry equivalent reflection AND a Bijvoet mate to some other reflection. This is a very small subset of all reflections. Every reflection has one Friedel mate and has N Bijvoet mates, where N is the number of equivalent positions. Only a small number of reflections are centric (with the limiting case of only F000). Dale Tronrud Bernhard Rupp wrote: Let's try this again, with definitions, and pls scream if I am wrong: a) Any reflection pair hR = h forms a symmetry related pair. R is any one of G point group operators of the SG. This is a set of reflections (S). Their amplitudes are invariably the same. They do not even show up as individual pairs in the asymmetric unit of the reciprocal space. NB: their phases are restricted but not the same. b) a set h=-h (set F) exist where reflections may or may not carry anomalous signal. They form the centrosymmetrically related wedge of the asymmetric unit of reciprocal space. c) a centric reflection (set C) is defined as hR=-h and cannot carry anomalous signal. Example zone h0l in PG 2. As Ian Tickle pointed out, the CCP4 wiki is wrong: Centric reflections in space group P2 and P21 are thus those with 0,k,0. Not so; an example listing is attached at the end. d) therefore, some e:F exist that carry AS (F.ne.C) and some that do not carry AS (F.el.C). I hope we can agree on those facts. Now for the name calling: (S) is simply the set of symmetry related reflections, defined as hR=h. (F) is the set of Friedel pairs, defined as h=-h. (C) are centric reflections, defined as hR=-h. Thus, only if (F.ne.C), anomalous signal. I thought those are Bijvoet pairs. They are, but it may not be the definition of a Bijvoet pair. Try 1: Bijvoet pair is F(h) and any mate that is symmetry-related to F(-h), e.g., F(hkl) and F(-h,k,-l) in monoclinic. hkl is not related to -hk-l via h = -h. Only h0l is, and those are (e:C). So, I cannot quote follow that, probably try 1 is not a good definition. Try 2: I've always thought that a Bijvoet pair is any pair for which an anomalous difference could be observed. Good start. I subscribe to that. This includes Friedel pairs (h h-bar) Good. That's the definition of F. but it also includes pairs of the form h h', where h' is symmetry-related to h-bar. Ooops. That is the definition of a centric reflection. Thus Friedel pairs are a subset of all possible Bijvoet pairs. Cannot see that. I still maintain that Bijvoet pairs are a subset of Friedel pairs (which does include Pat's definition). I fail to see anything else but Friedel pairs in my list of reflections - some of them carry AS (F.ne.C) and some don't (F.el.C). B = F.ne.C. Seems to be a necessary and sufficient condition, in agreement with Pat's definition (though not the explanation). But - isn't that exactly what I said from the beginning? A Bijvoet pair is an acentric Friedel pair... Or - where are any other Bijvoet pairs hiding? Where did I miss them? (NB: Absence of anisotropic AS assumed -let's not go there) See reflection list P2 (hkl |F| fom phi 2theta stol2) last 3 items: centric flag, epsilon, m(h) 0 0 1 993.54 1.00 179.9965.61 0.581 1 1 2 0 0 -1 993.54 1.00 179.9965.61 0.581 1 1 2 1 0 0 1412.58 1.00 0.1438.22 0.0001711 1 1 2 -1 0 0 1412.58 1.00 0.1438.22 0.0001711 1 1 2 0 0 2 3279.49 1.00 180.3132.80 0.0002323 1 1 2 0 0 -2 3279.49 1.00 180.3132.80 0.0002323 1 1 2 1 0 1 379.89 1.00 180.2530.36 0.0002712 1 1 2 -1 0 -1 379.89 1.00 180.2530.36 0.0002712 1 1 2 -1 0 2 1355.06 1.00 0.1327.97 0.0003195 1 1 2 1 0 -2 1355.06 1.00 0.1327.97 0.0003195 1 1 2 0 1 0 2432.85 1.0021.0924.35 0.0004216 0 2 1 0 -1 0 2434.14 1.00 339.6524.35 0.0004216 0 2 1 0 1 1 621.36 1.00 101.6722.83 0.0004797 0 1 2 0 -1 -1 623.27 1.00 258.4922.83 0.0004797 0 1 2 1 0 2 319.68 1.00 359.9822.65 0.0004874 1 1 2 -1 0 -2 319.68 1.00 359.9822.65 0.0004874 1 1 2 0 0 3 426.17 1.00 180.9921.87 0.0005227 1
Re: [ccp4bb] Friedel vs Bijvoet
Bernhard Rupp wrote: I quote from these pages: Bijvoet pairs are Bragg reflections which are true symmetry equivalents to a Friedel pair. These true symmetry equivalents have *equal amplitudes, even in the presence of anomalous scattering*. This is poorly worded. I would change it to A Bijvoet MATE IS A Bragg reflection which IS A true symmetry equivalent to THE Friedel MATE OF SOME OTHER REFLECTION. These true symmetry equivalents have *equal amplitudes, even in the presence of anomalous scattering*. Note that the Bijvoet mate is symmetry related to the Friedel mate not the original reflection. Dale Tronrud Sounds more like centric or perhaps simply symmetry related to me. A few lines below: A Bijvoet difference refers to the difference in measured amplitude for a Bijvoet pair I don't think you can have it both ways ?? BR
Re: [ccp4bb] Friedel vs Bijvoet
On Thursday 26 June 2008 11:35:31 am Bernhard Rupp wrote: Let's try this again, with definitions, and pls scream if I am wrong: a) Any reflection pair hR = h forms a symmetry related pair. ??? Maybe you meanh' = hR R is any one of G point group operators of the SG. This is a set of reflections (S). Their amplitudes are invariably the same. They do not even show up as individual pairs in the asymmetric unit of the reciprocal space. That last statement means nothing to me. NB: their phases are restricted but not the same. Correct. b) a set h=-h (set F) exist where reflections may or may not carry anomalous signal. They form the centrosymmetrically related wedge of the asymmetric unit of reciprocal space. Makes no sense. h=-h=hR can only be true for h = [000] or for R = I(identity operator) c) a centric reflection (set C) is defined as hR=-h and cannot carry anomalous signal. Example zone h0l in PG 2. I think this is way off base. As Ron Stenkamp just pointed out to me, centric refers to the intensity distribution of a class of reflections. See for example Lipsonn Cochran (1957) page 36. Yes, the h0l zone in P2 is an example. They _do_ carry an anomalous _signal_, but not an anomalous _difference_. That is, the phases are affected but the pairs have equal intensity. But please stay tuned Ethan (channeling Ron) As Ian Tickle pointed out, the CCP4 wiki is wrong: Centric reflections in space group P2 and P21 are thus those with 0,k,0. Not so; an example listing is attached at the end. d) therefore, some e:F exist that carry AS (F.ne.C) and some that do not carry AS (F.el.C). I hope we can agree on those facts. Now for the name calling: (S) is simply the set of symmetry related reflections, defined as hR=h. (F) is the set of Friedel pairs, defined as h=-h. (C) are centric reflections, defined as hR=-h. Thus, only if (F.ne.C), anomalous signal. I thought those are Bijvoet pairs. They are, but it may not be the definition of a Bijvoet pair. Try 1: Bijvoet pair is F(h) and any mate that is symmetry-related to F(-h), e.g., F(hkl) and F(-h,k,-l) in monoclinic. hkl is not related to -hk-l via h = -h. Only h0l is, and those are (e:C). So, I cannot quote follow that, probably try 1 is not a good definition. Try 2: I've always thought that a Bijvoet pair is any pair for which an anomalous difference could be observed. Good start. I subscribe to that. This includes Friedel pairs (h h-bar) Good. That's the definition of F. but it also includes pairs of the form h h', where h' is symmetry-related to h-bar. Ooops. That is the definition of a centric reflection. Thus Friedel pairs are a subset of all possible Bijvoet pairs. Cannot see that. I still maintain that Bijvoet pairs are a subset of Friedel pairs (which does include Pat's definition). I fail to see anything else but Friedel pairs in my list of reflections - some of them carry AS (F.ne.C) and some don't (F.el.C). B = F.ne.C. Seems to be a necessary and sufficient condition, in agreement with Pat's definition (though not the explanation). But - isn't that exactly what I said from the beginning? A Bijvoet pair is an acentric Friedel pair... Or - where are any other Bijvoet pairs hiding? Where did I miss them? (NB: Absence of anisotropic AS assumed -let's not go there) See reflection list P2 (hkl |F| fom phi 2theta stol2) last 3 items: centric flag, epsilon, m(h) 0 0 1 993.54 1.00 179.9965.61 0.581 1 1 2 0 0 -1 993.54 1.00 179.9965.61 0.581 1 1 2 1 0 0 1412.58 1.00 0.1438.22 0.0001711 1 1 2 -1 0 0 1412.58 1.00 0.1438.22 0.0001711 1 1 2 0 0 2 3279.49 1.00 180.3132.80 0.0002323 1 1 2 0 0 -2 3279.49 1.00 180.3132.80 0.0002323 1 1 2 1 0 1 379.89 1.00 180.2530.36 0.0002712 1 1 2 -1 0 -1 379.89 1.00 180.2530.36 0.0002712 1 1 2 -1 0 2 1355.06 1.00 0.1327.97 0.0003195 1 1 2 1 0 -2 1355.06 1.00 0.1327.97 0.0003195 1 1 2 0 1 0 2432.85 1.0021.0924.35 0.0004216 0 2 1 0 -1 0 2434.14 1.00 339.6524.35 0.0004216 0 2 1 0 1 1 621.36 1.00 101.6722.83 0.0004797 0 1 2 0 -1 -1 623.27 1.00 258.4922.83 0.0004797 0 1 2 1 0 2 319.68 1.00 359.9822.65 0.0004874 1 1 2 -1 0 -2 319.68 1.00 359.9822.65 0.0004874 1 1 2 0 0 3 426.17 1.00 180.9921.87 0.0005227 1 1 2 0 0 -3 426.17 1.00 180.9921.87 0.0005227 1 1 2 -1
Re: [ccp4bb] Friedel vs Bijvoet
Also only centric phases are restricted. Yes. *Related* would have been be the proper term for symmetry related reflections. In detail: The phases of symmetry related reflection still are *related* by phi(hR)=phi(h)-2pihT (no restrictions on phi(h)) For centrics phi(h)=pihT or pi(hT+1) the phases are *restricted* to certain phi(h) values. I failed to state the exact phase relations. Sorry for the confusion. Thx, BR -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: 26 June 2008 19:54 To: 'Hidong Kim' Cc: CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Friedel vs Bijvoet I quote from these pages: Bijvoet pairs are Bragg reflections which are true symmetry equivalents to a Friedel pair. These true symmetry equivalents have *equal amplitudes, even in the presence of anomalous scattering*. Sounds more like centric or perhaps simply symmetry related to me. A few lines below: A Bijvoet difference refers to the difference in measured amplitude for a Bijvoet pair I don't think you can have it both ways ?? BR 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 [EMAIL PROTECTED] 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] summary: headhunters [off-topic]
Hi Citizens: I've taken the liberty of summarizing/anonymizing/interpreting a bit with the varied and colo[u]rful responses. They fell into three general categories. Thanks to all who responded and offered sage advice... 1. The unanimous consensus was that headhunters aren't useful for finding consulting gigs (my main purpose for asking is the desire to supplement my current salary, or lack thereof -- the California dollar makes the US dollar look robust). Rather, several replies underscored the importance of connections. Headhunters might be of use for finding (full-time) industrial positions. Several people suggested where to look for possible consulting arrangements (which I believe will be immensely helpful). Some people suggested there might be good money to be made from people willing to pay me not to offer my opinions. 2. There were several trouble in paradise/are you insane/being sarcastic type inquiries. These best answered by the following Woody Guthrie quote (1937): California is a garden of Eden, a paradise to live in or see, But believe it or not, you won't find it so hot If you ain't got the do re mi. 3. By the way, can you fix my computer/update coot/etc? No, but I did find a good motivational poster like the ones you see advertised in magazines on airplanes: http://despair.com/consulting.html Cheers, Bill
Re: [ccp4bb] helix stability
Hi Fred, I would say that the helix stability will generally be affected by its context within the protein, unless it is (unlikely?) separated from the core of the protein and it has intrinsic stability (some peptide sequences do). Also, in a particular context, you may have mutations that unfold or distort the helix, without seriously affecting the stability of the protein as a whole, for this can be compensated by new interactions. Therefore, unless you have good reasons to consider the helix separated from the rest, I would always consider the whole protein. Now, for stability calculations, you can use a range of methods to estimate their free energy change; from simple approaches available on-line such as that of the CUPSAT server (http://cupsat.tu-bs.de/) to more complicated ones involving molecular dynamics and MM-PBSA or MM-GBSA calculations. Concerning the dipole moment (whether of the helix or of the whole protein), if you have the pdb2pqr program available, or if you generate a pqr file online (for example at: http://pdb2pqr-1.wustl.edu/pdb2pqr/) from your coordinates, you can use a simple python script (dipole.py) that you can download from: http://www.ysbl.york.ac.uk/~mol/scripts.htmlhttp://www.ysbl.york.ac.uk/%7Emol/scripts.html The script will tell you the magnitude and orientation of the dipole. It will also produce a bild file that can be read by programs such as Chimera ( http://www.cgl.ucsf.edu/chimera/) to represent the dipole moment vector. Miguel 2008/6/26 Frederico Moraes Ferreira [EMAIL PROTECTED]: Hi everyone, Has anybody know some program to calculate the dipole moment of helices? Which relevant parameters should I have to calculate to compare stability of helices? I would like to compare the stability of different mutations on helices, but don't know if it makes sense when you take the helix out of the protein. Thanks in advance, Fred -- University of Sao Paulo School of Medicine Sao Paulo Brazil -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens
Re: [ccp4bb] Friedel vs Bijvoet
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Le 26 juin 08 à 18:49, Ethan Merritt a écrit : On Thursday 26 June 2008 09:36:16 am Serge Cohen wrote: Please some one tells me if I'm wrong ... but I though that indeed one is NOT supposed to measure anomalous difference from reflections h and h' if those are related by one of the symmetry operator of the point group... This statement is logically equivalent to what Patrick writes below. You are agreeing with each other. Indeed I was thinking of Bernie Santarsiero mail when sending this mail. Bernie's mail was confusing my understanding. To quote the part I was referring to : Friedel pair is strictly F(hkl) and F(-h,-k,-l). Bijvoet pair is F(h) and any mate that is symmetry-related to F(- h), e.g., F(hkl) and F(-h,k,-l) in monoclinic. That is in monoclinic (P 1 2 1, more precisely) , (h, k, l) and (-h, k, -l) should have the same F ... (in a determinist's world) Yes, but that is not an example of h and h'. You mean that in P 1 2 1, h,k,l and -h,k-l are not strictly equivalent? In the context of my message h and h' were defined as : reflections h and h' if those are related by one of the symmetry operator of the point group To come back to the initial mail : b) A Friedel pair is any reflection h = -h including hR = -h, i.e. including centric reflections. I find this notation confusing since (I guess) the '=' does not mean the same thing in both cases : In the first case it means the pair (h, -h) (or more precisely what I understand it means) While the second really means There is a R operator of the PG such that -h = Rh (if the first case had to be understood this way, the only Friedel pair would be (0,0,0) ). So if I try to put this definitions of terms as I understand them: Friedel pair : (h, g) There is a operator R of the P.G. such that -Rh = g Bijvoet pair : (h, g) There is a operator R of the P.G. such that -Rh = g AND : For all operator R of the P.G. : Rh != g Hope I'm getting it right ... and I'm not adding to the overall confusion ;-) Serge. *** Dr. Serge COHEN GPG Key ID: 0B5CDAEC N.K.I. Department of Molecular Carcinogenesis (B8) Plesmanlaan 121 1066 CX Amsterdam; NL E-Mail: [EMAIL PROTECTED] Tel : +31 20 512 2053 *** -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkhj+MEACgkQlz6UVQtc2uw7FACguUgF1+XrN9xdRTcLLdShA/Eu A2UAniYPecEAz5BJ/ljrQYymnGRK7Mor =SItL -END PGP SIGNATURE-
[ccp4bb] Reminder - still no 3D stereo under OS X 10.5
Hi Everyone, I am writing everyone just to remind all those who are thinking of upgrading to 10.5 that currently quad-buffered stereo will not work for coot, pymol etc... since Apple has not done a good job with the video drivers in Leopard. So if you would like to use 3D stereo viewing, do not purchase any new Mac hardware since it will not run OS X 10.4. Eric -- Eric Ortlund, Ph.D. Assistant Professor Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 30322 Tel 404-727-5014 Fax 404-727-2738 [EMAIL PROTECTED]
Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
Is this true for native aqua gui programs, or just the X11 ones? On Thu, June 26, 2008 1:50 pm, eortlund wrote: Hi Everyone, I am writing everyone just to remind all those who are thinking of upgrading to 10.5 that currently quad-buffered stereo will not work for coot, pymol etc... since Apple has not done a good job with the video drivers in Leopard. So if you would like to use 3D stereo viewing, do not purchase any new Mac hardware since it will not run OS X 10.4. Eric -- Eric Ortlund, Ph.D. Assistant Professor Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 30322 Tel 404-727-5014 Fax 404-727-2738 [EMAIL PROTECTED] William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
Just to add on that: I converted to OSX in 2001 when it first appeared. Before I was Irix/Linux and -alas- the relatively happy owner of a SONY VAIO with Windows XP. For 8 years I remained impressed. But, 10.5 has been a massive disappointment after being spoiled for so long, with stable working features. X11 implementation is bad; Spaces breaks down all the time and is useless at least when using two monitors; time machine is sad that it is shipped without a proper scheduler; some developer trouble with older versions and PPC; and my Safari died during upgrade to 10.5.3 and I cant install a new version for a week (I am at 10.5.3 but Safari installer says I am at 10.5.2); and all the Stereo trouble. I still think OSX is from a different planet than Vista and I still prefer it for a personal machine compared to Linux, but I liked being spoiled. A. On 26 Jun 2008, at 22:50, eortlund wrote: Hi Everyone, I am writing everyone just to remind all those who are thinking of upgrading to 10.5 that currently quad-buffered stereo will not work for coot, pymol etc... since Apple has not done a good job with the video drivers in Leopard. So if you would like to use 3D stereo viewing, do not purchase any new Mac hardware since it will not run OS X 10.4. Eric -- Eric Ortlund, Ph.D. Assistant Professor Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 30322 Tel 404-727-5014 Fax 404-727-2738 [EMAIL PROTECTED]
Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
On Thu, Jun 26, 2008 at 02:00:45PM -0700, William Scott wrote: Is this true for native aqua gui programs, or just the X11 ones? According to Warren Delano, the PyMOL developer, it's affects native apps as well: http://tinyurl.com/6ohzfc I emailed him for clarification and he replied: as soon as any other window overlaps the stereo 3D OpenGL context (e.g. a File Open Dialog...), Mac OS starts randomly dropping screen updates, causing PyMOL's UI to become unusable. I have second hand reports that O works with stereo 3d under 10.5, but I haven't seen it personally. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu
Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
I think it is only X11 apps. I am able to use 3D stereo using MacPyMOL on my Mac tower runing 10.5.2. Cheers, Scott Is this true for native aqua gui programs, or just the X11 ones? On Thu, June 26, 2008 1:50 pm, eortlund wrote: Hi Everyone, I am writing everyone just to remind all those who are thinking of upgrading to 10.5 that currently quad-buffered stereo will not work for coot, pymol etc... since Apple has not done a good job with the video drivers in Leopard. So if you would like to use 3D stereo viewing, do not purchase any new Mac hardware since it will not run OS X 10.4. Eric -- Eric Ortlund, Ph.D. Assistant Professor Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 30322 Tel 404-727-5014 Fax 404-727-2738 [EMAIL PROTECTED] William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ *** Scott T. R. Walsh, Ph.D. Assistant Professor Department of Molecular and Cellular Biochemistry The Ohio State University College of Medicine 467 Hamilton Hall (Office) 479/483 Hamilton Hall (Lab) 1645 Neil Avenue Columbus, OH 43210 E-Mail: [EMAIL PROTECTED] Office Phone: 614-688-5802 Lab Phone: 614-688-8630 Fax: 614-292-4118 --
Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
A follow up note: I was at Apple's WWDC a couple weeks ago, and during one of the lunch time sessions for scientists, several people brought up the fact that stereo 3d was still broken on Leopard, and asked for it to be fixed. The Apple engineer present hemmed and hawed a bit, and finally said that fixing it would not be easy and that Apple was not sure that this was a technology that they wanted to pursue. As another note, Jordan Hubbard, who the Director of Engineering of UNIX Technologies at Apple has said that they don't have the internal resources to fix this in a timely manner. http://lists.apple.com/archives/x11-users/2008/Apr/msg00130.html Even if/when Apple fixes stereo on Leopard, I don't think I'll be recommending OS X for stereo applications. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu
Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
Has anyone tried XQuartz for this: http://xquartz.macosforge.org/trac/wiki On Jun 26, 2008, at 2:24 PM, Ben Eisenbraun wrote: A follow up note: I was at Apple's WWDC a couple weeks ago, and during one of the lunch time sessions for scientists, several people brought up the fact that stereo 3d was still broken on Leopard, and asked for it to be fixed. The Apple engineer present hemmed and hawed a bit, and finally said that fixing it would not be easy and that Apple was not sure that this was a technology that they wanted to pursue. As another note, Jordan Hubbard, who the Director of Engineering of UNIX Technologies at Apple has said that they don't have the internal resources to fix this in a timely manner. http://lists.apple.com/archives/x11-users/2008/Apr/msg00130.html Even if/when Apple fixes stereo on Leopard, I don't think I'll be recommending OS X for stereo applications. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
Hello All, Since I have long been such a big Mac stereo 3D proponent in the past, it is especially important that I go on the record with an updated perspective. Based on all of the accumulated evidence to date, a verdict can now be rendered: we have lost the case. For stereo 3D visualization, Open-source Linux has beaten out Proprietary Mac OS X. Given that Leopard stereo 3D still isn't entirely functional after three OS updates, and that Apple doesn't permit its customers to run old (yet fully-functional) operating systems on new hardware, if you purchase a Mac Pro today, then you are going to have to run Linux natively (through Boot Camp) in order to get your work done in stereo 3D. Though it is hard not to love Apple hardware, there are less expensive options for people who must run native Linux in order to do your job. So together now, everyone: Linux rules! Long live community-driven open source solutions! In point of fact, however, Linux-based stereo 3D remains dependent on proprietary graphics drivers tied to the underlying hardware. There is no 100% open-source option for stereo 3D visualization. Therefore, the scientific visualization community has no choice but to rely upon a proprietary solution to a significant extent, irrespective of who provides it. Given my own past efforts, I am more sorry than anyone else that things haven't worked out for stereo 3D with the company formerly known as Apple Computer, Inc. Fortunately, however, nVidia has maintained uninterrupted Linux stereo 3D support on higher-end Quadro cards. I am not sure what the situation is with respect to AMD/ATI, but it appears that they are still supporting Linux stereo 3D as well. Though I remain an ardent fan of relying upon the new Apple, Inc. to meet needs which clearly overlap those of mainstream consumer markets (e.g. the need for sleek, fast, Intel-based laptops), given the company's increasing emphasis on consumer devices, music and the like, we simply cannot rely upon them for niche business, scientific, or professional computing solutions unless or until consumers find matched uses for such solutions as well. For example: imagine future adoption of stereo 3D in movies, videoconferencing, or games. That it what I believe it would take in this case. By the way, instead of Linux, you could also just run Windows XP. In contrast to Apple, Microsoft stops short of forcing its customers to run Vista on newly minted PC hardware. Whereas consumers don't typically need to run older operating systems on current hardware, businesses and professionals often do. It all makes perfect sense when you think about it... Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ben Eisenbraun Sent: Thursday, June 26, 2008 2:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5 A follow up note: I was at Apple's WWDC a couple weeks ago, and during one of the lunch time sessions for scientists, several people brought up the fact that stereo 3d was still broken on Leopard, and asked for it to be fixed. The Apple engineer present hemmed and hawed a bit, and finally said that fixing it would not be easy and that Apple was not sure that this was a technology that they wanted to pursue. As another note, Jordan Hubbard, who the Director of Engineering of UNIX Technologies at Apple has said that they don't have the internal resources to fix this in a timely manner. http://lists.apple.com/archives/x11-users/2008/Apr/msg00130.html Even if/when Apple fixes stereo on Leopard, I don't think I'll be recommending OS X for stereo applications. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu
[ccp4bb] Concentrating protein
Dear All, we have GCSF protein produced in inclusion bodies. we solubilise it refold it and then concentrate it using proflux system. still the concentration of the protein we get is less and volume is more for us to load in Ion exchange chromatography. is there any simple technique that can be performed in lab without using any hi-fi instrument to concentrate the protein in small volume of buffer. the protein we obtain is about 0.7 mg/ml and we get 450 ml solution. our column is 110ml lab scale and we have to work in that only. i have heard of NH4SO4 precipitation. but it requires protein conc more than 1 mg/ml. kindly help me to progress in my experiment.
Re: [ccp4bb] Concentrating protein
Concentration of large volumes is a common bane of many biochemistry/protein production labs. Diaflow can be quite expensive and regular concentrators tend to take forever. Thus, my preferred solution is not to use concentrators at all. 1. AS cuts do not really *require* high protein concentrations. Hit it with high enough AS, and most proteins will precipitate. However, high AS cuts present a different problem - namely the density of the 'floaties' can be close enough to (or even less than) the density of the AS solution so that settling via centrifugation becomes difficult. Therefore: 2. Why concentrate at all when you can instead dilute the protein solution down to the ionic strength where the Q column is binding, then load the whole thing. As a rule of thumb, if you dilute to below 5-8 mS/cm most proteins (with the exception of seriously basic ones) will bind to Q resins. You can load in batch (by stirring the resin for an hour or two with your diluted sample), then spin the resin (gently), resuspend in small volume of buffer and pack a column. This will help you avoid flow issues, if your column cannot take enough pressure to allow fast flow loading. When you elute the protein from the column it will act as a concentrator since the elution profile may be controlled by means of gradient adjustments. If you have e.g. His-tag on the protein, you can use it to concentrate as well, via the same general principle. Do the math: at 20 ml/min (which is not even remotely close to what a properly packed XK 50 column would allow) you will only need 50 minutes to pass 1 liter of solution through your ion exchange column. In comparison, concentrating 1 liter down to e.g. 20 ml can take 30-60 minutes on a diaflow device, and several hours using a conventional concentrator. If you use batch, then the volume becomes nearly irrelevant and the time scheme looks like this: Stir (or nutate) protein solution with resin - 2 hrs. Spin the whole thing - 30 minutes at 5000 rpm. Resuspend, pack a column - 20 minutes. Run column - 30 minutes. This way you can process arbitrary amounts of stuff (up to the limit of your centrifugation volume, typically 6 liters) in about 3 hours. Artem P.S. It's kind of sad that people forget the 'poor student' techniques of protein biochemistry. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Exec Sent: Thursday, June 26, 2008 11:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Concentrating protein Dear All, we have GCSF protein produced in inclusion bodies. we solubilise it refold it and then concentrate it using proflux system. still the concentration of the protein we get is less and volume is more for us to load in Ion exchange chromatography. is there any simple technique that can be performed in lab without using any hi-fi instrument to concentrate the protein in small volume of buffer. the protein we obtain is about 0.7 mg/ml and we get 450 ml solution. our column is 110ml lab scale and we have to work in that only. i have heard of NH4SO4 precipitation. but it requires protein conc more than 1 mg/ml. kindly help me to progress in my experiment.
Re: [ccp4bb] Concentrating protein
I have found that ion exchange is a good way to concentrate protein. If there is no reason that you can't pass the whole 450 mls through the column then you should do that. Another way to do this would be to add ion exchange resin straight into the 450 mls, stir for a bit, let it settle, pour off the supernatant and load the remainder into an empty column for washing and elution. I'm assuming from the wording of your email that your refolding buffer is a suitable binding buffer for the subsequent ion exchange step. Other things you might like to try are to engineer a hexahis tag onto your protein. After resolubilisation you can bind the protein to metal affinity resin in a centrifuge tube in the presence of urea, pellet the resin, remove the urea and resuspend the resin in refolding buffer. Wash a few times and elute the protein in as small a volume as you like. Another way to keep the initial volume low would be to dialyse your urea away instead of refolding by dilution. I realise that the slower pace of dialysis and the higher protein concentration might reduce your refolding efficiency but if you haven't tried it then the advantages of smaller volumes might make it worth while. In short, if there was a way that I could avoid routinely having to use cross-flow to reduce 450 mls of buffer then I'd be pursuing that. I hope that was helpful. Nathan Begin forwarded message: From: Exec [EMAIL PROTECTED] Date: 27 June 2008 1:28:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Concentrating protein Reply-To: Exec [EMAIL PROTECTED] Dear All, we have GCSF protein produced in inclusion bodies. we solubilise it refold it and then concentrate it using proflux system. still the concentration of the protein we get is less and volume is more for us to load in Ion exchange chromatography. is there any simple technique that can be performed in lab without using any hi-fi instrument to concentrate the protein in small volume of buffer. the protein we obtain is about 0.7 mg/ml and we get 450 ml solution. our column is 110ml lab scale and we have to work in that only. i have heard of NH4SO4 precipitation. but it requires protein conc more than 1 mg/ml. kindly help me to progress in my experiment.
Re: [ccp4bb] Concentrating protein
Nathan Cowieson: I have found that ion exchange is a good way to concentrate protein. If there is no reason that you can't pass the whole 450 mls through the column then you should do that. Another way is to load dilute protein onto small hydroxylapatite column. Provided that the buffer does not have phosphates, almost all proteins bind to hydroxylapatite regardless of the salt (at least up to 0.5 M). The obvious advantages is that one does not need to dilute and that for most proteins elution can be done with only 50-100 mM Pi. The disadvantage in comparison to ion exchangers is about 4-fold lower - usually, around 20-30 mg/ml of the sorbent. Dima
