Re: [ccp4bb] Finding NCS operator from one heavy atom site?
Hi, On Thu, May 22, 2008 at 11:22:19AM -0700, Juergen Bosch wrote: You can also scratch your head and look at the selfrotation function of your dataset. Some of that scratching can be done using GETAX for you - it's in CCP4 (for years), but hasn't got a CCP4i interface (yet: next release will have one). If you need help with that, please let me know ... We used GETAX once in about 1997 with a TaBr-cluster derivative (single site, phase information to about 7A) SIRAS, having 20 molecules/asu (2.5 D4 octamers) ... You do need to have a Cn/Dn local NCS though ... You might also try out using only the peak dataset (peak inflection) and see if the other wavelength actually harm your electrondensity, furthermore you could use Sharp to optimize your phases first. Yes, you want to start with the best density map possible :-) Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Finding NCS operator from one heavy atom site?
Hi Partha, ncs6d did really great things to me a while ago. Similar case as yours, only one Met site in each of the 4 monomers, pretty horrible maps. I was amazed how ncs6d could sort its way through the maps and find the ncs operators. As a simple approach I just took a spherical map around the methionine site. In fact it seemed to be easier to find the ncs between two dimers first, improve the operators with imp and then search for the missing operators within the dimer. Sorry, don't have any clever scripts for that, did it all by hand. The maps improve a lot after averaging. However, almost needles to say that cloning, expressing, purifying, crystallizing and solving the same construct of an 85% seq. identical ortholog took less effort than messing around with the bad maps... Good luck Jan 2008/5/22 Partha Chakrabarti [EMAIL PROTECTED]: Hi, Apologies for a non CCP4 question in strict sense. I am trying to work out the NCS operators for a three wavelength Se-MAD data which has only one site. The map is hardly interpretable. I came across the USF Rave package and what I am aiming is creak a mask around the heavy atom site (found by SHELX or Solve) using mama or so, (ideally from resolve.mtz but not necessarily), translate it to the other heavy atom site(s), give a 6d search with NCS6d and perhaps refine the best CC a bit with imp. If it works, I could try use the NCS operator in DM or Resolve etc. I was wondering if someone has a C-shell scripts for dealing with such situation already. Of course if there are other programs for such a task within CCP4, could give it a try. Best Regards, Partha
Re: [ccp4bb] Finding NCS operator from one heavy atom site? (long)
This almost does what you want, but not quite. To quote from the NCS6D manual: NCS6D uses a set of BONES or PDB atoms as input and tries to find a set of rotations and translations which maximise the correlation coefficient between the density at the (BONES) atoms and those at the same atoms after application of the operator. So you cannot use a mask in NCS6D - you can in IMP. In the case where I did something like this, I could see a single helix near the SeMet sites, so I built this helix, then used the following script to find the first NCS relationship: #!/bin/csh -f # /usr/local/Uppsala/rave_osx/osx_ncs6d EOF eden_400.ext P ncs6d_probe.pdb 1 p21212.sym 30.5 6.5 23.0 Y 0 359 10 0 179 10 0 359 10 -10 10 2 -10 10 2 -10 10 2 L rt_best.o EOF Then I wrote a little C program that broke out each of the 100-or-so NCS operators that are in rt_best.o into files called rt_test_NN.o (NN=integer) and ran each and every one of them through Imp: #!/bin/csh -f # # foreach file (rt_test_*.o) \rm LOG /usr/local/Uppsala/rave_osx/osx_imp MAPSIZE 3500 EOF ! LOG eden_400.ext model.mask p21212.sym $file Automatic 1. .02 2.0 .1 .01 .0001 2 Proper Complete Quit rt_test_new.o EOF set cc = `grep Correlation Coefficient LOG` echo $file echo $cc end # I guess you could create a fur ball of Calpha positions for the initial model to force NCS6D to sort of a volume average - or peak-pick the map around the Se sites - I have not tried this. I found that without the IMP step there were too many similar and unimpressive solutions for the NCS operator and the top one was not in general the correct one. This approach has the potential to consume quite a lot of CPU but the initial map was relatively ugly and ultimately it worked rather well. Others might have more elegant ideas. Phil Jeffrey Princeton Partha Chakrabarti wrote: Hi, Apologies for a non CCP4 question in strict sense. I am trying to work out the NCS operators for a three wavelength Se-MAD data which has only one site. The map is hardly interpretable. I came across the USF Rave package and what I am aiming is creak a mask around the heavy atom site (found by SHELX or Solve) using mama or so, (ideally from resolve.mtz but not necessarily), translate it to the other heavy atom site(s), give a 6d search with NCS6d and perhaps refine the best CC a bit with imp. If it works, I could try use the NCS operator in DM or Resolve etc. I was wondering if someone has a C-shell scripts for dealing with such situation already. Of course if there are other programs for such a task within CCP4, could give it a try. Best Regards, Partha
