Bernhard Sorry I left out chiral restraints: these do not contribute to the restraint count at all because they do not reduce the effective no of parameters, they merely select between 2 alternative minima. As you say the magnitude of the chiral volume (though obviously not the sign) is completely determined by the bond lengths and angles, and provided you have the right enantiomer will have no significant effect on the refinement (assuming the target chiral volume is consistent with the target bond lengths & angles as it should be). The chiral restraint is effectively an inactive/active-type restraint which only kicks in when you get the chirality wrong, otherwise it's effectively inactive.
I think Refmac must only list active VDW restraints (there are potentially a very large number of inactive ones!). -- Ian > -----Original Message----- > From: Bernhard Rupp [mailto:[EMAIL PROTECTED] > Sent: 14 February 2008 19:09 > To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] counting constraints? > > The point where this restraint discussion regarding > counting of restraints seems to become murky imho, is when > it comes to 'independence' of restraints. > > Ok - say only active and independent restraints (AIRs) count > in the determination of observation/parameter ratio, > where observations includes data and AIRs. > > Then taking the following example, how many independent restraints > do I have here (leaving aside the vdW active vs inactive issue, assume > they are all inactive for simplicity). > > REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT > > REMARK 3 BOND LENGTHS REFINED (A): 1809 ; 0.010 ; 0.022 > > REMARK 3 BOND ANGLES REFINED (DEGREES): 2451 ; 1.324 ; 1.964 > > REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 6.466 ; 5.000 > > REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 59 ;40.002 ;25.932 > > REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 292 ;11.833 ;15.000 > > REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;15.038 ;15.000 > > REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 271 ; 0.086 ; 0.200 > > REMARK 3 GENERAL PLANES REFINED (A): 2049 ; 0.006 ; 0.020 > > REMARK 3 NON-BONDED CONTACTS REFINED (A): 308 ; 0.191 ; 0.200 > > REMARK 3 NON-BONDED TORSION REFINED (A): 866 ; 0.174 ; 0.200 > > REMARK 3 H-BOND (X...Y) REFINED (A): 131 ; 0.139 ; 0.200 > > REMARK 3 SYMMETRY VDW REFINED (A): 41 ; 0.165 ; 0.200 > > REMARK 3 SYMMETRY H-BOND REFINED (A): 25 ; 0.149 ; 0.200 > > REMARK 3 > > REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT > > REMARK 3 MAIN-CHAIN BOND REFINED (A**2): 1192 ; 1.739 ; 5.000 > > REMARK 3 MAIN-CHAIN ANGLE REFINED (A**2): 1903 ; 2.691 ; 7.000 > > REMARK 3 SIDE-CHAIN BOND REFINED (A**2): 646 ; 3.451 ; 9.000 > > REMARK 3 SIDE-CHAIN ANGLE REFINED (A**2): 545 ; 4.886 ;11.000 > > > Bond distances (1-2) and angles (1-3) are certainly > independent and count > fully. > For B-factor restraints, I don't exactly understand what a restraint > across an angle is - is a 1-3 B-factor restraint independent of a > 1-2 B-factor restraint? > > The torsions can assume values independent of bond and angle, > so I would > count them in. To a degree, torsions also influence VdW - a > poor torsion > can 'activate' a vdW repulsion... > > Planarity - even if they are implemented as 1-4 dihedrals > they are not quite independent of 1-2 and 1-3 restraints. So > - no count, > half count? > > Chirals are also not independent - if implemented as a volume, they > depend on 1-2, 1-3 restraints in their chivolume value in addition to > sign if they are wrong. > > What H-BOND (X...Y) exactly is I don't know, suppose it is some > restraint for explicit directional H-bonds; if so, I would count them. > > Soo.....what is the total count of independent restraints here? > > So far I have divergent answers/opinions, and I would like to > find some > agreeable compromise to this question... > > Note: As we cannot know which of the nonbonded restraints > were active, we > have > no clear answer for those - this is something > that REFMAC might be able to tell us - maybe an independent > active restraint count printed might be a useful number. > > Best, BR > > > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Ian > Tickle > Sent: Thursday, February 14, 2008 9:58 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] counting constraints? > > Peter, Bart > > Actually the restraint weight doesn't affect the restraint > count one iota > and as far as counting is concerned each restraint has > exactly one 'vote' in > the count. However there is an important proviso: the > restraints must be > completely independent to contribute fully to the count. > Suppose you have a > torsion restraint say on an methoxyphenyl group (an example > close to my > heart since we have endless debates about it!), and suppose > the weight on > the restraint is absolutely miniscule, but still non-zero > (we'd better say > it's > than the machine precision to avoid rounding > problems). Provided no > other restraint or observation (restraints and observations > are of course > essentially the same thing) affects that torsion angle it > will have its full > effect, in fact the effect won't depend on the weight. Of > course as soon as > you have other restraints which affect that same torsion > angle they will > compete with each other depending on their relative weights, > and you can't > count them as independent any more. > > To answer Peter's original question each *active* restraint > is counted. > The question of inactive restraints becomes relevant when > considering e.g. > VDW restraints which normally only become active when the > distance becomes > less than a threshold. > > -- Ian > > > -----Original Message----- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Bart Hazes > > Sent: 14 February 2008 15:53 > > To: Meyer, Peter > > Cc: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] counting constraints? > > > > Hi Pete, > > > > In your example it would count as 4 restraints, not > constraints, and > > certainly not 4 observations or 4 parameters. It is not clear to me > > how to quantify the information content in restraints, it probably > > depends on the type of restraint and surely on the weight. Maybe > > information theory has some ideas if you are really interested. > > For real constraints, which fix parameters of the model one way or > > another, it may be easier. For instance imposing exact NCS 2-fold > > symmetry reduces the parameters by a factor of 2. > > > > Bart > > > > Meyer, Peter wrote: > > > Hi, > > > > > > The recent discussion on Rwork/Rfree ratio reminded me of > > something I was wondering about (*). When counting constraints as > > observations for determining the observation to parameter ratio, is > > each unique constraint counted, or each time a given constraint is > > used. For example, if there are 4 carbon oxygen bonds > (assuming the > > same parameters, let's say serine beta-carbon to serine > gamma-oxygen), > > would this count as 4 constraints as observations, or 1? > > > > > > Intuitively, it seems to me like it should be counting > > unique constraints (although as near as I can tell these > aren't listed > > in refmac5 logfiles). But I don't have a clear explanation > for why, > > and of course I could be wrong on this. > > > > > > > > > Thanks, > > > > > > > > > Pete > > > > > > * Rough translation - I'm about to ask another stupid > > question. Not like it's the first time. > > > > > > > > > > > > -- > > > > ============================================================== > > ================ > > > > Bart Hazes (Assistant Professor) > > Dept. of Medical Microbiology & Immunology University of Alberta > > 1-15 Medical Sciences Building > > Edmonton, Alberta > > Canada, T6G 2H7 > > phone: 1-780-492-0042 > > fax: 1-780-492-7521 > > > > ============================================================== > > ================ > > > > > > > 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 > > > 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
