Re: [ccp4bb] ideal bond length and bong angel
Please do NOT use the BB for abuse. Eleanor Gerard DVD Kleywegt wrote: Be care, you insolence might get someone sent disappear. is the chinese secret service editing my incoming mail already, or are you merely using a microsoft grammar checker? --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] ideal bond length and bong angel
Please do NOT use the BB for abuse. thank you for your support. although i think some abuse of the english language is unavoidable in an international forum like this --gerard (more important issue: http://www.irrepressible.info/) ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] ideal bond length and bong angel
On 9 Jan 2008, at 10:34, Eleanor Dodson wrote: Bong angels are probably ideal already! There is really no such animal as an ideal bondlength or angle - they depend to some extent on the atomic environment. Not to a complete extent? Stuart
Re: [ccp4bb] ideal bond length and bong angel
Bong angels are probably ideal already! There is really no such animal as an ideal bondlength or angle - they depend to some extent on the atomic environment. There are papers by Engh and Huber who looked at small molecule highly refined structures to get AVERAGE bond lengths and standard deviations - and their targets are the basis for most MX refibnement targets. And there are many other publications trying to extract predictions from quantum chemistry. Eleanor yang li wrote: Dear All, I've wonder for a simple problem for a long time, that is: What is the ideal bond length and angel? Every lecture or book says this is a criteria from small organic molecules, but I still donnot know exactly. Like is bond length point to the peptide bond length? Or many other bonds? Does anyone has a simple and graphic explanation for them? Thanks in advance!
Re: [ccp4bb] ideal bond length and bong angel
Can you explain the define of the bond length and bond angel--especially bond angel--here? i leave the definition of angels (be they ideal or not) to clerics, but if you want to find out about bonds and angles, AND YOUR SUPERVISOR IS REALLY UNABLE OR TOO BUSY TO EXPLAIN THESE BASIC CONCEPTS TO YOU, why not use google (www.google.com), wikipedia (www.wikipedia.org), etc. (and perhaps consider getting a better supervisor)? e.g. http://en.wikipedia.org/wiki/Molecular_geometry and http://en.wikipedia.org/wiki/Dihedral_angle for more links to basic info, see http://xray.bmc.uu.se/gerard/embo2001/modval/03.html under Refresher reading books or reviews (e.g. http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=56) and using those to retrieve original references (such as engh huber) also helps (rhetorical question of the day: just like teaching a person how to fish is better than to give them a fish, isn't providing the url to google or wikipedia better than providing an answer to a basic question?) --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] ideal bond length and bong angel
By the way, I think my bad english embarrassed my meaning. What I want to say is which bond length is used as the standard? the C=N or Ca-N or even the side chains? Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or others. At first I suppose the bond length only calculate the C=N bond, and donnot know which one is used as the aggel. It should be a quite stupid question for whom knows it. Just forget it.
Re: [ccp4bb] ideal bond length and bong angel
Dear Prof Gerard: In fact I have read your Model Validation on-line, and I have to say it is youe lecture that made me to think about this problem, though I have used it as a common stand for the quality of the model without understand it for a long time. And the http://en.wikipedia.org/wiki/Molecular_geometry and http://en.wikipedia.org/wiki/Dihedral_angle, I think both from your lecture, I have checked them today before I post my mail, but unable to access them. For some reason, wiki is forbiddon here. I really coouldnot find the best answer and have discussed with others before, so I just want to make it clear, though maybe nothing to do with practicals. Thanks for your reply again. Best Regards!
Re: [ccp4bb] ideal bond length and bong angel
them today before I post my mail, but unable to access them. For some reason, wiki is forbiddon here. I really coouldnot find the best answer and have discussed i am shocked. i just checked with one of my 25 chinese students here and indeed even universities in china do not have access to a basic site such as wikipedia. the some reason of course being that china is still a totalitarian communist state where the government deems it necessary to control what information its citizens can and cannot access. in this year of the olympics shouldn't the scientific community put some pressure on the chinese government, e.g. through an appeal in nature or science? ccp4 care to take the initiative? i'm supposed to teach in a course in beijing this spring but if my innocent web-based practicals cannot be used to their full extent i'm not so sure anymore --gerard (note to self: don't pack the 'free tibet' t-shirt for the beijing trip!) ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] ideal bond length and bong angel
Hey Gerard, wikipedia might tell you how to angle for fishes, but I fear it falls short of teaching you how to fish for angels. Andreas Imperial College of Aquatic and Fisheries Sciences London Gerard DVD Kleywegt wrote: Can you explain the define of the bond length and bond angel--especially bond angel--here? i leave the definition of angels (be they ideal or not) to clerics, but if you want to find out about bonds and angles, AND YOUR SUPERVISOR IS REALLY UNABLE OR TOO BUSY TO EXPLAIN THESE BASIC CONCEPTS TO YOU, why not use google (www.google.com), wikipedia (www.wikipedia.org), etc. (and perhaps consider getting a better supervisor)? e.g. http://en.wikipedia.org/wiki/Molecular_geometry and http://en.wikipedia.org/wiki/Dihedral_angle for more links to basic info, see http://xray.bmc.uu.se/gerard/embo2001/modval/03.html under Refresher reading books or reviews (e.g. http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=56) and using those to retrieve original references (such as engh huber) also helps (rhetorical question of the day: just like teaching a person how to fish is better than to give them a fish, isn't providing the url to google or wikipedia better than providing an answer to a basic question?) --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] ideal bond length and bong angel
On Wed, 2008-01-09 at 12:47 +0100, Gerard DVD Kleywegt wrote: (rhetorical question of the day: just like teaching a person how to fish is better than to give them a fish, isn't providing the url to google or wikipedia better than providing an answer to a basic question?) You can read a few paragraphs about The spirit of helpfulness here: http://en.wikipedia.org/wiki/Wikipedia:Help_desk/How_to_answer - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] ideal bond length and bong angel
Simply use a bong for a while, and you will hear the angels sing :) It's amazing to see how this thread devolved, within two or three posts, into a discussion about drug abuse and totalitarian political regimes... Good way to start the day :) On Jan 9, 2008, at 8:35 AM, Jim Pflugrath wrote: Bong angels are probably ideal already! Please explain, so that I can teach this to my students. :) Jim Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
Re: [ccp4bb] ideal bond length and bong angel
Bong angels are probably ideal already! Please explain, so that I can teach this to my students. :) Jim
Re: [ccp4bb] ideal bond length and bong angel
Hi Yang Li: Macromolecular crystal refinement programs use ideal bond lengths and angles. The simplest ones just assume any carbon-carbon single bond (C-C) is the same as any other, and use one average value, and any carbon-carbon double bond (C=C) is the same as any other, and use another average value, and so on for all possible linkages. Better ones treat individual cases differently, so that the Calpha-Cbeta bond in amino acids is compared only to other Calpha-Cbeta bond lengths, for example. The best ones will have a specific average value for each Calpha-Cbeta bond length for each amino acid that has this bond. Similarly for angles. The standard value is usually established from very high resolution crystal structures of (for example) individual amino acids, and/or quantum chemistry calculations. Various different methods are employed to penalize deviation from ideality in a refinement. It is common to use a simple quadratic penalty, which can be characterized by a Hook's Law spring constant, and this is justified where the harmonic approximation for bond potentials is valid (and it should be in crystal structures). Each refinement program has its own way of implementing the above, so the best thing to do is to look at the bond parameter dictionaries that your program uses. I hope that comes closer to answering your question. All the best, Bill Scott yang li wrote: By the way, I think my bad english embarrassed my meaning. What I want to say is which bond length is used as the standard? the C=N or Ca-N or even the side chains? Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or others. At first I suppose the bond length only calculate the C=N bond, and donnot know which one is used as the aggel. It should be a quite stupid question for whom knows it. Just forget it.
