Re: [ccp4bb] quote source
Hi Bernhard, Google books is your friend... It returns 2 hits for Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy Both are essays / chapters by Max Perutz I Wish I'd Made You Angry Earlier: Essays on Science, Scientists, and Humanity - Page 166 has the quote attributed to Pauling but without reference. http://books.google.com/books?id=GkODMkCWndQCpg=PA166dq=%22Although+the+hydrogen+bond+is+not+strong+it+has+great+significance+in+determining+the+properties+of+substances.+Because+of+its+small+bond+energy%22sig=ACfU3U0HC6n1toHJgD9Z-bedRSs7eVvz8Q And Pioneering Ideas for the Physical and Chemical Sciences: Josef Loschmidt's ... - Page 1 by W. Fleischhacker, Thomas Schönfeld has a chapter titled The significance of the hydrogen bond for physiology by Max Perutz where the quote is attributed to being from Pauling's newly published Nature of the Chemical Bond which Perutz obtained with a Christmas 1939 book token so I presume it was the 1940 version. http://books.google.com/books?id=cMc9BHNyIWsCpg=PA1lpg=PA1dq=%22Although+the+hydrogen+bond+is+not+strong+it+has+great+significance+in+determining+the+properties+of+substances.+Because+of+its+small+bond+energy%22source=webots=sU9k_3dU9wsig=3ZCCE8u8ZpLBa-ycU2v0eT1s4oghl=ensa=Xoi=book_resultresnum=2ct=result The 1960 version of Pauling's book is on Google books and it has a similar but not identical statement. see pp. 449-450. http://books.google.com/books?id=L-1K9HmKmUUCprintsec=titlepagedq=Nature+of+the+Chemical+Bond+Paulingsource=gbs_toc_scad=1#PPA449,M1 Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Wednesday, July 23, 2008 10:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] quote source Dear All, does someone know the proper reference of this L. Pauling statement? Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy and the small activation energy involved in its formation and rupture, the hydrogen bond is especially suited to play a part in reactions occurring at normal temperatures. It has been recognised that hydrogen bonds restrain protein molecules to their native configurations, and I believe that as the methods of structural chemistry are further applied to physiological problems it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature. It is quoted by Perutz but no ref 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] quote source
http://books.google.com/books?id=cMc9BHNyIWsCpg=PA1lpg=PA1dq=%22Although+the+hydrogen+bond+is+not+strong+it+has+great+significance+in%0Adetermining+the+properties+of+substances.+Because+of+its+small+bond+energy%0Aand+the+small+activation+energy+involved+in+its+formation+and+rupture,+the%0Ahydrogen+bond+is+especially+suited+to+play+a+part+in+reactions+occurring+at%0Anormal+temperatures.+It+has+been+recognised+that+hydrogen+bonds+restrain%0Aprotein+molecules+to+their+native+configurations,+and+I+believe+that+as+the%0Amethods+of+structural+chemistry+are+further+applied+to+physiological%0Aproblems+it+will+be+found+that+the+significance+of+the+hydrogen+bond+for%0Aphysiology+is+greater+than+that+of+any+other+single+structural+feature%22.source=webots=sU9k_3eR9Dsig=870tcfA9OiSTbGFiUk9cpExFslshl=ensa=Xoi=book_resultresnum=2ct=result or http://tinyurl.com/linusp On Jul 23, 2008, at 10:26 PM, Bernhard Rupp wrote: Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy and the small activation energy involved in its formation and rupture, the hydrogen bond is especially suited to play a part in reactions occurring at normal temperatures. It has been recognised that hydrogen bonds restrain protein molecules to their native configurations, and I believe that as the methods of structural chemistry are further applied to physiological problems it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature.
Re: [ccp4bb] Acorn question
Sounds like a bug. Curing the symptoms won't help You should send full details to [EMAIL PROTECTED] Since CCP4 6.0.x there has been a substantially new version of Acorn. Source code at http://www.ccp4.ac.uk/download/prerelease_page.php#acorn or try our test 6.1 release ... Martyn On Wed, 2008-07-23 at 13:15 -0400, [EMAIL PROTECTED] wrote: All, In the past couple of days I have been trying to use Acorn (in the CCP4 suite of programs). Consistently it starts up fine and after some small amount of time (5-10 minutes) it has taken up all the physical memory and then it starts to slowly gobble up all the swap space until the only option is to switch the computer off, since all processes (including X and such) are being pushed out of memory and they somehow are not swapped back in. Is there a way to restrict the amount of memory that Acorn is allowed to use? Any other suggestions? Parameters to restrict memory I do not see and the Acorn web page does also not mention that they exist, neither does it have any suggestions what to do. We are using CentOS operating system on 64-bit hardware (I think CentOS is vanilla Linux but 64-bit may not be vanilla). We are using CCP4 version 6.0. Any suggestions are appreciated. Thanks, Mark Mark van der Woerd, PhD Research Scientist II Dept. of Biochemistry and Molecular Biology Colorado State University Fort Collins, CO 80523 Phone (970) 491-0469 __ The Famous, the Infamous, the Lame - in your browser. Get the TMZ Toolbar Now! -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] microfluidics in protein crystallography
Also while we're on the subject of novel crystallisation tricks, does anyone out there have any first-hand impressions of this technique: http://jjap.ipap.jp/link?JJAP/44/1365/ Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Isabel Garcia-Saez Sent: 22 July 2008 10:34 To: CCP4BB@JISCMAIL.AC.UK Subject: microfluidics in protein crystallography Dear CCP4ers, I would like to have more info about microfluidics in protein xtallography: has anyone out there used it with success?. Thanks, Isabel Isabel Garcia-Saez PhD Institut de Biologie Structurale Jean-Pierre Ebel Laboratoire des Protéines du Cytosquelette 41, rue Jules Horowitz F-38027 Grenoble CEDEX 1 France tel.: 00-33-438 789615 FAX: 00-33-438 785494 e-mail: [EMAIL PROTECTED] http://www.ibs.fr 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] Renumber atoms with Moleman
Dear all I can not read a pdb file in Moleman due probably to double conformation in some residues in my pdb. Then, I am not able to renumber the atoms to send the structure to Protein Data Bank. Can anyone help me?. Thanks for your attention Marta Dr. Marta Martínez Júlvez Departamento de Bioquímica y Biología Molecular y Celular Facultad de Ciencias Universidad de Zaragoza Pedro Cerbuna 12 50009-Zaragoza Spain Phone: +34 976 762841/1287 Fax: +34 976 762123 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] quote source
Hi Bernard, I googled the phrase 'hydrogen bond for physiology and got lots of results as many people have cited that paragraph. But the following result should give you what you need. http://books.google.com/books?id=OnSG9cMHqnkCpg=PA851lpg=PA851dq=%22hydrogen+bond+for+physiology%22source=webots=bRKyaTlA5ysig=diWzE3c6AQmQbwgE7GWDpwUGEZchl=ensa=Xoi=book_resultresnum=4ct=result Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** [EMAIL PROTECTED] *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2008, Bernhard Rupp wrote: Dear All, does someone know the proper reference of this L. Pauling statement? Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy and the small activation energy involved in its formation and rupture, the hydrogen bond is especially suited to play a part in reactions occurring at normal temperatures. It has been recognised that hydrogen bonds restrain protein molecules to their native configurations, and I believe that as the methods of structural chemistry are further applied to physiological problems it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature. It is quoted by Perutz but no ref 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] os x wiki
Hi Folks, Following on from this, does anyone have a copy of the information on how to get coot working in intel mac 10.5.x? I downloaded the linked disk image and coot tarball, planning to print the instructions the following day. As Homer would say, D'Oh! Just the place you are supposed to unpack the tarball to would be a valuable pointer - it was somewhere specific I remember... Many thanks, Graeme 2008/7/23 William Scott [EMAIL PROTECTED]: Hi Patrick: I'm afraid all the insidious stupidness originates from moi. Anyway, the machine hosting this thing has a roached power supply, thanks to the fact that the University electrical supply resembles that produced by, in terms of its stability and reliability, an underfed gerbil-wheel-powered generator in Guatemala. So we ordered a new one from Apple, and hopefully within the next three or four years I will have it back on line. I backed up the mysql database for the wiki every day, but I can't get it to work on any other computer, doubtless due to my complete inability to follow simple instructions or to remember any of the passwords I had used. Hence the first sentence. Sorry 'bout this. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 23, 2008, at 12:27 PM, Patrick Loll wrote: Does anyone know if the Crystallography on OS X Wiki is down? I haven't been able to access the site for a few days, but I don't know if the site is down, or if some new and insidious stupidness has been perpetrated by the rocket scientists who control IT in our institution...thanks. Pat --- 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]
[ccp4bb] light-zapped crystallization
Doesn't the technique in that paper seem like just a fancy way to elevate the temperature briefly? What else could zapping with a 780 nm laser do? Also, it seems that since N = 1, the technique is way too nascent (and it might be stillborn) to be applied. Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: Ian Tickle [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, July 24, 2008 4:52 AM Subject: Re: [ccp4bb] microfluidics in protein crystallography Also while we're on the subject of novel crystallisation tricks, does anyone out there have any first-hand impressions of this technique: http://jjap.ipap.jp/link?JJAP/44/1365/ Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Isabel Garcia-Saez Sent: 22 July 2008 10:34 To: CCP4BB@JISCMAIL.AC.UK Subject: microfluidics in protein crystallography Dear CCP4ers, I would like to have more info about microfluidics in protein xtallography: has anyone out there used it with success?. Thanks, Isabel Isabel Garcia-Saez PhD Institut de Biologie Structurale Jean-Pierre Ebel Laboratoire des Protéines du Cytosquelette 41, rue Jules Horowitz F-38027 Grenoble CEDEX 1 France tel.: 00-33-438 789615 FAX: 00-33-438 785494 e-mail: [EMAIL PROTECTED] http://www.ibs.fr 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
Re: [ccp4bb] os x wiki
Thanks to the incredibly helpful generosity of Hari Jayaram at Brandeis, we have it now at http://sage.ucsc.edu/xtal/wiki This will soon be aliased to the url http://xanana.ucsc.edu/xtal/wiki On Jul 23, 2008, at 12:27 PM, Patrick Loll wrote: Does anyone know if the Crystallography on OS X Wiki is down? I haven't been able to access the site for a few days, but I don't know if the site is down, or if some new and insidious stupidness has been perpetrated by the rocket scientists who control IT in our institution...thanks. Pat --- 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]
