Hi Derek The symmetry of the self-RF is explained in detail in the documentation for POLARRFN, in fact I would advise you to use this because you can then plot monoclinic space groups with the unique b axis along the orthogonal Z axis (NCODE = 3) and then the symmetry is *much* easier to interpret. Also POLARRFN allows you to plot all the kappa sections not just 4 selected ones. This can be important if the NCS 2-fold is not exact, i.e. you may see the peaks slightly displaced off the kappa=180 or other point-group sections (60, 90, 120). To do the same with MOLREP requires ~ 70 jobs! Note you may need high resolution data (say 2 Ang or better) for this and also sharpening using ECALC so that the peaks are resolved.
According to polarrfn.doc the symmetry generated by a 2-fold along b parallel to Z is (180-theta, 180-phi, kappa) so the peak in the list (159,180,180) is the same as (21,0,180) which is a NCS 2-fold that you can see just below centre. The peak (111,0,180) is thus the same as (69,180,180) near the top which is another NCS 2-fold perp to the first generated by the crystallographic 2-fold. HTH! -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Derek Logan > Sent: 23 April 2008 13:40 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Help with pseudosymmetry problem > > Hi everyone, > > Can anyone help me with interpretation of a self rotation > function and > native Patterson from a dataset with pseudosymmetry? I've > always been > a bit poor on spherical polars. The space group is P21 with beta = > 92.2°. The kappa=180° section of the SRF, calculated using > Molrep, is at > > http://mole.mbfys.lu.se/~derek/selfRF_180.png > > and contains two big peaks around 7 sigma. I'm having trouble > identifying these in the list of peaks from Molrep: > > theta phi chi alpha beta gamma > Isym_i Isym_j > Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 1 1 > Sol_RF 1 90.00 -90.00 180.00 0.00 180.00 0.00 1 2 > Sol_RF 1 90.00 90.00 180.00 0.00 180.00 0.00 2 1 > Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 2 2 > Sol_RF 2 158.56 180.00 180.00 0.00 42.89 -180.00 1 1 > Sol_RF 2 111.44 0.00 180.00 -180.00 137.11 0.00 1 2 > Sol_RF 2 111.44 0.00 180.00 180.00 137.11 0.00 2 1 > Sol_RF 2 21.44 0.00 180.00 180.00 -42.89 0.00 2 2 > Sol_RF 3 165.65 0.00 180.00 -180.00 28.70 0.00 1 1 > Sol_RF 3 104.35 -180.00 180.00 0.00 151.30 180.00 1 2 > Sol_RF 3 104.35 180.00 180.00 0.00 151.30 -180.00 2 1 > Sol_RF 3 14.35 -180.00 180.00 0.00 -28.70 180.00 2 2 > > It seems to me to be two copies of peak 2. I believe theta starts in > the middle, perpendicular to the page and phi starts on the x axis, > thus the peak just below the centre would be (21.44, 0, 180). I > presume that the second peak is the symmetry-related (158.56, > 180, 0)? > However where is (111.44 0 180)? I would expect to see this near the > bottom of the plot, but it's not there. I'm sure I'm missing > something > fundamental about the symmetry of the SRF projection, but > unfortunately I don't have a supervisor to bug about this (I > *am* the > supervisor...) > > In the native Patterson > > http://mole.mbfys.lu.se/~derek/nativePatterson.png > > there are two peaks of almost equal height. How can this be > reconciled > with having only one strong peak in the SRF? There are most > likely two > dimers in the asymmetric unit, but there may only be one, with very > high resulting solvent content. What's more the molecules are > leucine- > rich repeat proteins and have weak internal symmetry. I believe this > was an issue with the ribonuclease inhibitor, but looking briefly at > the crystallisation article and structure article I wasn't able to > find a rationalisation of this problem. The 2-fold is > perpendicular to > b*. How could this cause the two peaks? > > Thanks > Derek > > 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
