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Dear Alexei, thank your for your clarification. But there is one point that is still not clear to me. If you are giving the keyword LOCK you also have to include self-rotation information that you got by running a self-rotation function with MOLREP before. Does MOLREP try to make sense of all self-rot. peaks you are giving in the self-rot. file - so you would not edit the file to remove some noise or double peaks of the same symmetry element ? Or would you recommend to edit the self-rot. list just to include the peaks you think are important ? In case you have a 72-arrangement: would you give all 7-fold peaks and the 2-folds or is the major 7-fold already enough ? Thanks for your help, /Claus On Fri, 2006-09-15 at 13:24 +0100, Alexei Vagin wrote: > Dear Claus, > > I want to clarify the usage of lock-RF related and NCS related > keywords. > > In the first case, we know relative orientations of molecules but know > nothing of their relative positions. Thus, the keyword LOCK is > relevant only to the RF. It pushes correct orientations toward the top > of the list and/or improves their contrast. The impact of LOCK on the > TF is only that (and when) the list of orientations is changed. This > is your case. See example of using LOCK in the MOLREP tutorial at > > http://www.ysbl.york.ac.uk/~alexei/molrep.html > > (To download the tutorial use the link “tutorial MR” in section > “INSTALLATION”) > > The NCS and relevant keywords assume that the position of the NCS axis > is known. This is unlikely your case. These keywords are used in > fitting into EM maps because the point group and the position of axis > are assumed before the EM maps (so called EM reconstructions) are > generated. > > (MOLREP documentation and “tutorial EM” at the above location contain > more details) > > Regards > > Alexei > > > On 7 Sep 2006, at 15:25, Claus Kuhn wrote: > > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > > > > > Dear all, > > > > > > I am trying to use NCS information that I gained from self-rotation > > function analysis for running MOLREP. > > My molecule obeys 72 point group symmetry with the 7-fold axis > > running > > along c, and the 2-folds perpendicular to the 7-fold along b, one of > > them being the crystallographic 2-fold (unit cell monoclinic C2, > > beta > > 97°, 7copies per AU. > > After running a self rotation function with MOLREP or any other > > program > > I can detect the 7fold axis (chi 52, 105, 157) and the 7 2-folds. > > I can detect the 7 rotations of my model when computing a rotation > > function with MOLREP as well. > > I am trying to input the self rotation peaks, define the NCS > > parameters > > (keywords NCS_ID, ANGLES, CENTRE) and run a locked cross rotation > > function (keywords LOCK, FILE_TSR and NSRF). Additionally I edit the > > rotation list to include just 'my 7 rotations' of the model before > > running a translation search > > What is the best way to use this information in running MOLREP ?? > > Is much of that redundant and may it be useless to use NCS_ID when > > not > > knowing the exact centre of the point group ? > > Thanks for any suggestions, > > > > > > /Claus > > > > > > AG Cramer > > Gene Center > > University of Munich > > Germany > > > > > > > > > >
