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Re: [ccp4bb] combine Se-SAD phase with Model-phase |
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CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 08 May 2008Subject: Re: combine Se-SAD phase with Model-phase From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM Date: 2008-05-08 > 3. Run SHARP/AutoSHARP with Se Just run autoSHARP in SIRAS mode: you have a native and a derivative (Se). autoSHARP is clever enough to then assign those special Se-S atoms to you derivative, see the explanation at http://www.globalphasing.com/sharp/manual/chapter2.html#MADnative which is for MAD and SHARP, but you'll get the idea also for autoSHARP. This way you get the anomalous and 'isomorphous' differences as signal. > sites upto DM. Then run solvent flattening with model component 1. What do you mean with "model component 1"? Did you include your curent model into the density modification step (good idea)? For how many cycles - and what was the initial CC for the model here? If your anomalous signal of the Se is very weak and borderline you could try and use the model phases as a restraint in SHARP during refinement and LLG map calculation (not for the phasing step!). There are tools in SHARP for that as well. Another trick I use quite often is to estimate the anisotropic B-factor of your data (reference dataset in SHARP jargon): this would take out any anisotropy that you have, leading to more isotropic maps going into density modification - and that could make a lot of difference, since most real-space modificaitons in density modifcation assume some normal shape for electron density (or at least could be thrown off by severe anisotropy). But you have to be careful when dealing with low-resolution data and/or incomplete data (wedges missing etc). Let me know if you need additional info ... 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) *************************************************************** CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 08 May 2008 |
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