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Re: [ccp4bb] RMSD |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 14 March 2007Subject: Re: RMSD From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM Date: 2007-03-14 inverse variance (of course often they don't tell you which one!). I prefer the latter as it's less skewed by distances with big variances. Of course if the variances are all equal then it won't make any difference. -- Ian > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On > Behalf Of Tim Gruene > Sent: 14 March 2007 09:40 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] RMSD > > Hello, > > I would love to learn how "differently" one can implement the > difference > between two numbers? Or are you referring to 'versions'? > > Cheers, Tim > > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > On Wed, 14 Mar 2007, Dirk Kostrewa wrote: > > > Dear John, > > > > I don't know how different the RMSD values are, and whether > the calculated > > estimates are with or without hydrogen atoms (this can make > a difference). In > > principle, both programs use the Engh & Huber > stereochemistry library, but > > I've observed in the past that different programs used > slightly different > > "implementations" of this library, resulting in different > RMSD values, > > although they should all be the same ... > > > > Good luck, > > > > Dirk. > > > > john kryst wrote: > >> Hi ccp4bb !!! > >> > >> Does the rmsd estimation (for eg. rmsd_bonds ) depends on > the program we > >> use > >> ?? > >> > >> Example : shifting from Refmac to CNS. There appears to be > an increase in > >> rmsd of bonds even without refining the structure in CNS. > Is the estimation > >> methods are different or am i doing something wrong !! > >> > >> Thanks for your valuable inputs. > >> > >> regards > >> john > >> > > > > > > -- > > > > **************************************** > > Dirk Kostrewa > > Paul Scherrer Institut > > Biomolecular Research, OFLC/110 > > CH-5232 Villigen PSI, Switzerland > > Phone: +41-56-310-4722 > > Fax: +41-56-310-5288 > > E-mail: dirk.kostrewa@psi.ch > > http://sb.web.psi.ch > > **************************************** > > > > 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 I.Tickle@astex-therapeutics.com 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. CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 14 March 2007 |
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