*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
Hi Qun Anomalous scattering is a complex subject, I would advise you to read some of the extensive literature on it (I learnt it from Blundell & Johnson, which though in many ways is now very dated, still has a good section on AS - if you have a copy see section 7.4 pp 170-5). Also it's covered extensively in International Tables and several other more recent textbooks. A quick explanation of AS is that the observed handedness of the anomalous pairs (i.e. the observed difference between the intensities of the reflection hkl and its inverted-beam partner -h-k-l) arises through a combination of two factors: namely the handedness of the amino-acids (i.e. an amino-acid and its symmetry inverse are non-superposable), and the presence of one or more anomalously scattering atoms (usually at least as heavy as sulphur). The former results in the reflections hkl and -h-k-l having phases of opposite sign but with equal contributions to the scattered amplitude. The latter always results in the same phase lag of <= 90 deg in the amplitude contribution to hkl and -h-k-l from the constellation of heavy atoms (of the same chemical element), but again with equal contributions to their amplitudes. The summation of the two effects results in a breakdown of Friedel's law, i.e. hkl and -h-k-l having different amplitudes (and intensities); thus the set of intensities is handed (not superposable on its inverse). If there were no anomalous scatterers I(hkl) and I(-h-k-l) would always be equal within experimental error and it would make absolutely no difference whether the matrix inverted the co-ordinate system or not. Otherwise the matrix you use must be a rotation matrix (i.e. determinant = +1), not an inversion matrix (determinant = -1), so that it maintains the correct hand. Looking at your values of averaged intensities I would say that these are weighted averages, i.e. weighted by 1/sigma(I)^2. Averaging in this way is valid provided there is no significant anomalous scattering, otherwise one should use the separate I(+) and I(-) for calculations. BTW I would recommend CC'ing your responses to the BB, that way you'll get a balanced view (I might be spouting complete nonsense for all you know!). HTH! -- Ian > -----Original Message----- > From: Qun Wan [mailto:[EMAIL PROTECTED] > Sent: Tuesday, May 09, 2006 11:06 PM > To: Ian Tickle > Subject: RE: [ccp4bb]: permute unit cell indices > Importance: High > > Hi, Ian: > Thanks for your information! > I do use *-rej-anom.sca file for this comparison of isomorphism. My > crystal has unit cell 73.4 73.5 88.5 with space group P212121. > Therefore, I only need to swap a and b for comparison. I know the > answer that after the swap, to keep the matrix left-handed, I need to > use minus sign. I am not clear about the matrix. I do not think the > handedness is coming from the handedness of the amino acid, it is > from the difference of anomalous pairs. However, I am still confused > why where is handedness in the anomalous difference. Could you > explain that for me? > Also, when I compare the -rej-anom.sca and -rej.sca like the > following, I found some confusion. In anom.sca file, column 4 is the > intensity of hkl, column 5 is the sigma of hkl, colume 6 is the > intensity of > -h-k-l, column 6 is the sigma of -h-k-l. In sca file, I do not know > how the value of column 4 comes from, it is not the average of > intensities in anom.sca file of hkl and -h-k-l columns. Do you know > that? > The -anom.sca file: > 1 > -985 > 72.774 74.053 88.494 90.000 90.000 90.000 > p212121 > 31 5 1 0 -1 166.7 91.7 > 31 5 2 1144.0 134.7 1090.0 103.9 > 31 5 3 46.3 84.2 79.9 118.5 > 31 5 4 369.1 95.8 354.1 158.3 > The sca fiel: > 31 5 1 166.7 91.7 > 31 5 2 1110.2 82.3 > 31 5 3 57.6 68.7 > 31 5 4 365.1 82.0 > > > Your help is greatly appreciated! > > > >Hi Qun > > > >Because the 3 axes in orthorhombic space groups are > non-equivalent but > >in P212121 all are 2-fold screws, there are indeed 6 permutations for > >assigning the axes (unless of course 2 of those are excluded from > >consideration by some other information that you haven't mentioned). > >These are klh and lhk in addition to the ones you mention. For a > >reference see International Tables Vol A, chap. 2, p. 21. > Normally the > >standard permutation is decided by the order of the magnitudes of the > >cell axis lengths, but presumably you are doing this because > all 3 cell > >lengths are very nearly equal (within experimental error including > >possible non-isomorphism), otherwise what you are proposing wouldn't > >make sense. If for example only 2 of the cell lengths were > nearly equal > >this would reduce the number of feasible possibilities to > only 2 (e.g. > >hkl and hlk if a!=b=c). The minus signs in the matrix are > required to > >maintain the same hand after transformation in the case that you have > >measured anomalous differences. Alternatively you could keep the > >indices all positive and change the sign of the delta-anoms > in the cases > >where the permutation is non-cyclic (i.e. hlk, lkh and khl). If you > >have no anomalous data then it makes no difference whether > you have the > >minus signs or not, by Friedel's law the amplitudes of hkl and -h-k-l > >are equal. > > > >HTH! > > > >-- Ian > > > >> -----Original Message----- > >> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > >> Behalf Of Qun Wan > >> Sent: Tuesday, May 02, 2006 10:14 PM > >> To: [email protected] > >> Subject: [ccp4bb]: permute unit cell indices > >> > >> *** For details on how to be removed from this list > visit the *** > >> *** CCP4 home page http://www.ccp4.ac.uk *** > >> > >> > >> Hi, > >> I Have a question about permuting crystal indices. When I > compare two > >> crystal data sets to get crossR value to know how isomorphous they > >> are, I need to permute the indices of one of the crystal. > Both of my > >> crystals have space group P212121. I was told to permute > HKL to LKH, > >> HLK, and KHL. I do not have a clear mind the principle. > For example, > >> by whole arrangement, there will be 6 possibilities for the > >> permutation. Why only four exist here? The second question is more > >> important: if I want to change from HKL to KHL, the new > indices are > >> (0 -1 0 -1 0 0 0 0 -1), not (0 1 0 1 0 0 0 0 1). > Why there > >> is minus sign in the indices? > >> > >> Could anyone recommend me one paper or book to read to solve > >> my puzzle? > >> > >> Your help is greatly appreciated! > > > > >> > > > >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. > > > 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.
