Re: [ccp4bb] Anomalous signal for chlorides
Dear Yuri, The new program ANODE (J.Appl.Cryst. (2011) 44, 1285-7, Open Access) is designed for this and is very simple to use. It may be downloaded from the SHELX beta-test server (please email me if you require downloading intructions). George On 11/26/2011 06:05 AM, Yuri Pompeu wrote: Hi Boaz, Yes indeed, the phosphate group of the molecule looks quite beautiful at 1.17A and it has a really big peak 18sigma! Is there a utility for calculating anomalous maps, or is it simply an option in the refinement program?
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Does anyone have an up-to-date account of protein structure anlysis from powders? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] Anomalous signal for chlorides
Dear Yuri, In addition to the other good options that have been presented, you can use the log-likelihood gradient maps in Phaser to find anomalous scatterers. We find this to be very sensitive, and it has the advantage of being iterative (i.e. when you find some anomalous scatterers, this improves your model and thus the sensitivity for finding additional sites). When you're starting from a refined model, we think it is best to look for purely imaginary scatterers to add to the real scattering in your model. In the ccp4i GUI, choose the "SAD with molecular replacement partial structure" mode, provide the data (with F+ and F-), the wavelength, and the current model, then turn on LLG-map completion and select the "Complete with purely anomalous scatterer" option. If you want to see the initial LLG map, set the number of completion cycles to 0 and turn on the option to output log-likelihood-gradient map coefficients. Open these in coot as a difference map, choosing the columns FLLG_AX and PHLLG_AX. If you let Phaser complete the sites, then the final LLG map should be nearly flat and you have to look at the PDB file containing the sites that it found. Best wishes, Randy Read On Nov 26 2011, Yuri Pompeu wrote: Hi Boaz, Yes indeed, the phosphate group of the molecule looks quite beautiful at 1.17A and it has a really big peak 18sigma! Is there a utility for calculating anomalous maps, or is it simply an option in the refinement program? -- Randy J. Read
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Since it was powder diffraction that made me fall in love with crystallography as an undergrad (before switching to protein crystallography as a grad student), I was obviously very excited when I first heard about protein powder diffraction in a meeting some years ago, in a lecture by Andy Fitch from the ESRF. I've exchanged some mails with him and also Irene Margiolaki, who were very kind and sent me lots of unpublished stuff and experimental hints (sample preparation is probably the most difficult part in protein powder diffraction). A good idea would be to contact them (it may be easy to find their info in the ESRF website). The GSAS groups was also working on this, and the major difference, from what I remember, is that they were doing all the process (until refinement) in the same way that was done with regular powder samples (with a modified version of the GSAS program), while the group in ESRF converted the powder data to MTZs and then used PX software. By that time it seemed that they were the only groups doing it, but a quick search in pubmed using "protein powder diffraction" shows some recent articles from other groups, so it seems it's pretty much alive. The following articles are from 2011: X-ray diffraction from membrane protein nanocrystals. http://www.ncbi.nlm.nih.gov/pubmed/21190672 Exploiting powder X-ray diffraction for direct structure determination in structural biology: the P2X4 receptor trafficking motif YEQGL. http://www.ncbi.nlm.nih.gov/pubmed/21382498 Lucas Bleicher 2011/11/26 REX PALMER : > Does anyone have an up-to-date account of protein structure anlysis from > powders? > > > Rex Palmer > http://www.bbk.ac.uk/biology/our-staff/emeritus-staff > http://rexpalmer2010.homestead.com
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Re: [ccp4bb] Anomalous signal for chlorides
Not that Phaser needs my approval, but I recently did exactly what Randy recommended and it really found basically all of the S and Cl sites, with data at resolution 2.2 Ang and wavelength 0.979 Ang, too. I also played a bit with the sigma cutoff for adding new sites so that the stronger sites (Se in my case) are found but the weaker ones not. Also, don't forget to click the "output LLG map coefficients" option to get the right columns in your mtz. Jacob On Sat, Nov 26, 2011 at 6:13 AM, Randy J. Read wrote: > Dear Yuri, > > In addition to the other good options that have been presented, you can use > the log-likelihood gradient maps in Phaser to find anomalous scatterers. We > find this to be very sensitive, and it has the advantage of being iterative > (i.e. when you find some anomalous scatterers, this improves your model and > thus the sensitivity for finding additional sites). > > When you're starting from a refined model, we think it is best to look for > purely imaginary scatterers to add to the real scattering in your model. In > the ccp4i GUI, choose the "SAD with molecular replacement partial structure" > mode, provide the data (with F+ and F-), the wavelength, and the current > model, then turn on LLG-map completion and select the "Complete with purely > anomalous scatterer" option. > > If you want to see the initial LLG map, set the number of completion cycles > to 0 and turn on the option to output log-likelihood-gradient map > coefficients. Open these in coot as a difference map, choosing the columns > FLLG_AX and PHLLG_AX. If you let Phaser complete the sites, then the final > LLG map should be nearly flat and you have to look at the PDB file > containing the sites that it found. > > Best wishes, > > Randy Read > On Nov 26 2011, Yuri Pompeu wrote: > >> Hi Boaz, Yes indeed, the phosphate group of the molecule looks quite >> beautiful at 1.17A and it has a really big peak 18sigma! Is there a utility >> for calculating anomalous maps, or is it simply an option in the refinement >> program? >> > > -- > Randy J. Read > -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
