[ccp4bb] Question about the "MStats" utiliy in UPPSALA-mapman
Hi, I am using the "MStats" utiliy in UPPSALA-mapman to compare the density inside and outside of the mask of the model (basically my target is to somehow quantify the level of noise outside the model mask). According to the instructions, I need to do: (1) MAPMAN > re m1 in.map ccp4 ... (2) MAPMAN > re m2 msk.mask mask ... (3) MAPMAN > mstats m1 m2 0.5 But the second syntax "re m2 msk.mask mask" never works. So, I replaced it by "re m2 msk.mask ccp4". Not sure this will be ok or not, although the 3rd line "mstats m1 m2 0.5" went through. However, the output indicate the average density inside and outside the mask are just almost the same. This seems not to be true, since as seen in coot, the higher density always contours around the molecule, and the noise sigma level outside of the mask is really low. So, I am wondering: (1) Will "re m2 msk.mask ccp4" instead of "re m2 msk.mask mask" affect the results? (2) Will comparing the average density inside and outside the mask provide a meaningful quantification of the noise level? Sorry for the long description and thanks for any suggestions. Best Regards, Hailiang
Re: [ccp4bb] Wilson B and Mean B factors
>
>
> I've never looked at this statistics before, so I'm a bit surprised
>
So am I !
> - I was expecting a larger discrepancy between Wilson B and average B at
> low resolution. Although this is probably because PHENIX uses Peter Zwart's
> likelihood-based Wilson B estimation (Peter - what's the reference?), which
> is supposed to be better.
>
The stability at lower resolutions is indeed due to the likelihood based
method that utilizes a reference curve ('standard wilson plot') as obtained
from the PDB.
The original idea came from Sasha Popov & Gleb Bourenkov, both the reference
curve idea as well as the likelihood target. It is in fact the same target
as used for refinement of anisotropic scale during refinement with the
important note that sigmaA = 0.
This is where the likelihood based wilson scaling comes from:
A.N. Popov and G.P. Bourenkov "Choice of data-collection parameters based on
statistic modeling" Acta Crystallogr. (2003). D59, 1145-1153
These are my notes:
http://www.ccp4.ac.uk/newsletters/newsletter42/articles/CCP4_2005_PHZ_RWGK_PDA.doc
HTH
Peter
>
> Pavel.
>
>
>
> On 7/1/10 12:52 AM, Dirk Kostrewa wrote:
>
> Dear Murugan,
>
> at higher resolution, the Wilson plot captures mainly the contribution of
> atoms with lower B-factors which leads to a systematic underestimation of
> the true B-factor distribution. Accordingly, the average B-factor of refined
> structures tend to be higher then the Wilson B-factor, at least in my
> experience. In your case, it is the other way around. One possible problem
> could be, apart from the fit of the Wilson plot as James Holton suggested,
> that you have reflections at very low resolution with underestimated
> intensities due to cut overloads or measurement in the half-shadow of the
> beamstop. This would result in a too low overall B-factor for the model in
> order to try to fit the usually stronger low resolution reflections at the
> cost of the weaker high resolution data. One quick check of this hypothesis
> is to cut the low resolution at, say, 10 A instead of 50 A and run a
> test-refinement. If this results in more realistic model B-factors, you
> should have a closer look at the low resolution data and exclude the
> ill-measured ones.
>
> Best regards,
>
> Dirk.
>
> Am 30.06.10 19:31, schrieb Vandu Murugan:
>
> Dear all,
> If one could find a difference of more than 15 between Wilson B
> factor of the data ( 55) and Mean B factor of the structure, (30) what could
> be the possible reasons? I am seeing it in my structure. Could someone
> tell me why it could be?? Thanks in advance.
>
> Yours faithfully,
> Murugan
>
>
>
--
-
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
SASTBX: http://sastbx.als.lbl.gov
-
Re: [ccp4bb] Wilson B and Mean B factors
Hi Dirk, this seems to be the case indeed (*): Resolution_range Wilson_B Average_B Number_of_structures 0.00 - 1.00 9.77 13.11 94 1.00 - 1.25 10.58 16.44 401 1.25 - 1.50 13.50 19.14 1050 1.50 - 1.75 17.20 21.76 3600 1.75 - 2.00 22.27 26.82 5510 2.25 - 2.50 35.70 39.42 3385 2.50 - 2.75 43.71 44.73 2844 2.75 - 3.00 53.86 51.94 1628 3.00 - 3.25 65.11 60.76 780 3.25 - 3.50 81.69 78.70 165 3.50 - 3.75 92.67 88.84 100 3.75 - 4.00 111.83 102.29 30 (*) Wilson_B is computed using phenix.model_vs_data Average_B is computed using phenix.model_vs_data from PDB file (TLS is accounted for) Structures selected such that the recomputed R-factor matches the one in PDB file header within 1%. I've never looked at this statistics before, so I'm a bit surprised - I was expecting a larger discrepancy between Wilson B and average B at low resolution. Although this is probably because PHENIX uses Peter Zwart's likelihood-based Wilson B estimation (Peter - what's the reference?), which is supposed to be better. Pavel. On 7/1/10 12:52 AM, Dirk Kostrewa wrote: Dear Murugan, at higher resolution, the Wilson plot captures mainly the contribution of atoms with lower B-factors which leads to a systematic underestimation of the true B-factor distribution. Accordingly, the average B-factor of refined structures tend to be higher then the Wilson B-factor, at least in my experience. In your case, it is the other way around. One possible problem could be, apart from the fit of the Wilson plot as James Holton suggested, that you have reflections at very low resolution with underestimated intensities due to cut overloads or measurement in the half-shadow of the beamstop. This would result in a too low overall B-factor for the model in order to try to fit the usually stronger low resolution reflections at the cost of the weaker high resolution data. One quick check of this hypothesis is to cut the low resolution at, say, 10 A instead of 50 A and run a test-refinement. If this results in more realistic model B-factors, you should have a closer look at the low resolution data and exclude the ill-measured ones. Best regards, Dirk. Am 30.06.10 19:31, schrieb Vandu Murugan: Dear all, If one could find a difference of more than 15 between Wilson B factor of the data ( 55) and Mean B factor of the structure, (30) what could be the possible reasons? I am seeing it in my structure. Could someone tell me why it could be?? Thanks in advance. Yours faithfully, Murugan
[ccp4bb] Re : Re: [ccp4bb] How to make fft-map more physically meaningful?
Dear Hailiang,As James said, the hermitian symmetry of Fourier coefficients, F(h)=F*(-h), that is known in diffraction theory as the Friedel's law, is an equivalent of the condition that the corresponding function (electron density) is a real function.I think if you need further information you can make a look into some basic textbook or write me (or to somebody on your choice :-) a direct personal mail; I am not sure if we need to bother the whole community by further details of this discussion. You can write and send to CCP4bb the resume afterall if you want.Best regards,SachaDe: James Holton > Uhh. No. You will only get "imaginary" electron > density if your structure factors violate Friedel's law. I am not aware of > map calculation codes that do this (on purpose).> > Yes, I think Fourier synthesis at a finite resolution range > will generate some negative, or more generally imaginary values in real > space (hope I am right again:).
[ccp4bb] Free mounting system ,Resolution improvement
Hi, I am trying to find best methods for controlled crystal dehydration with an aim of improving diffraction resolution (currently at 9A).I have found few references and success stories about Free mounting system. I would be very grateful if you can share your personal experiences with Free mounting system and any other methods that worked best in your hands to improve diffraction limit . Thanks Manoj
Re: [ccp4bb] How to make fft-map more physically meaningful?
Uhh. No. You will only get "imaginary" electron density if your structure factors violate Friedel's law. I am not aware of map calculation codes that do this (on purpose). BTW, "imaginary electrons" are really just "slow" electrons that don't respond to the x-rays as fast as the "average" electron in the unit cell. They can also be "faster" than average. Because of this, if you have a unit cell full of nothing but selenium atoms, you will get all Bijvoet differences equal to zero. Even at the selenium edge! -James Holton MAD Scientist Hailiang Zhang wrote: Dear Sacha: Yes, I think Fourier synthesis at a finite resolution range will generate some negative, or more generally imaginary values in real space (hope I am right again:). For the imaginary values, I think the map should take the amplitude of it (maybe I am wrong). Do they normally make the density negative when the real-space density "phase angle" is between 90-270 degree, and positive other wise, or something else? Thanks a lot! Best Regards, Hailiang Dear Hailiang, This apparently is not the real physics, since the electron density has to be positive everywhere (hope I am right). Yes, you are right when you are talking about the electron density. You are wrong when you are talking about a Fourier synthesis calculated always at a finite resolution (it is what you have, is it?), even when the term F000 is used as suggested. Such a synthesis MUST have NEGATIVE values due to Fourier series truncation. Allowing such negative values was an important point at the beginning of density modification procedures (beginning of 80th) and it was one of the key moments when developping electron density histograms (see for example Lunin, 1988, Acta Cryst A). Moreover, these points even contain some information and can be used for example to identify the macromolecular region (since the deepest minima are usually close to the highest maxima). With best regards, Sacha
Re: [ccp4bb] How to make fft-map more physically meaningful?
Dear Sacha: Yes, I think Fourier synthesis at a finite resolution range will generate some negative, or more generally imaginary values in real space (hope I am right again:). For the imaginary values, I think the map should take the amplitude of it (maybe I am wrong). Do they normally make the density negative when the real-space density "phase angle" is between 90-270 degree, and positive other wise, or something else? Thanks a lot! Best Regards, Hailiang > Dear Hailiang, > >>This apparently is not the real physics, since the >>electron density has to be positive everywhere (hope I am right). > > Yes, you are right when you are talking about the electron density. > > You are wrong when you are talking about a Fourier synthesis calculated > always at a finite resolution (it is what you have, is it?), even when the > term F000 is used as suggested. > > Such a synthesis MUST have NEGATIVE values due to Fourier series > truncation. Allowing such negative values was an important point at the > beginning of density modification procedures (beginning of 80th) and it > was > one of the key moments when developping electron density histograms (see > for example Lunin, 1988, Acta Cryst A). Moreover, these points even > contain > some information and can be used for example to identify the > macromolecular > region (since the deepest minima are usually close to the highest maxima). > > With best regards, > > Sacha > > > >
[ccp4bb] oasis4 _ window or redhat x64 bit
Hi all I am trying to run oasis for my SAD data using dual space iteration. I am using ccp4-6.1.13 and seems it has the older gui and older oasis version 6.0. I downloaded the new oasis4 and ran the program with dual space iteraction option and end up in normal termination with out any output files. I have attached the log file below. I contacted the author did not get any immediate response. Is it any one success in using OASIS4 with dual space iteraction and density modification using ccp4i GUI for redhat X64 bit or in windows? Also I try to get OASIS4 binary for window, but it is not available. (only for Linux and mac) Is it possible to get either new binary OASSIS4 with new graphical interface in CCP4 either linux or windows? Any suggestions will be appreciated. Thanks venk log#CCP4I PID 31264 ### ### ### ### CCP4 6.1: CROSSEC version 6.1 : 06/09/05## ### User: unknown Run date: 7/ 7/2010 Run time: 13:17:47 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. $TEXT:Reference1: $$ comment $$ "Calculation of Anomalous Scattering Factors at Arbitrary Wavelengths", Don T. Cromer. J. Applied Cryst., Vol. 16 (1983) 437-8 $$ $SUMMARY :Reference1: $$ Crossec: $$ :TEXT:Reference1: $$ COMPULSORY KEYWORDS: ATOM- atomic symbol either NWAV - list of wavelengths or CWAV - wavelengths centred on and separated by END or - end input and run OPTIONAL KEYWORDS: NORD- interpolation method (default 2) VERB - verbose output (default only final table) FORMATTED OLD file opened on unit 1 Logical name: CROSSECDATA, Filename: /home/ccp4-6.1.13/lib/data/crossec.lib Data line--- ATOM SE Data line---NWAV 1 0.979 Data line---END Atom symbol and number SE 34 NORD value:2 Number of wave lengths to analysis1 $TABLE:Wave length v F' and F"- SE : $GRAPHS:Lambda v F' and F" SE :A:2,3,4: $$ Atom_type Lambda F' F" $$ Lambda F' F" $$ SE 0.9790-7.3911 3.8404 $$ CROSSEC: Normal termination Times: User: 0.0s System:0.0s Elapsed: 0:00
[ccp4bb] One PhD position and one Postdoc position available in structural virology
(1) PhD position One PhD position is available in Dr. Fang Li's lab at the Department of Pharmacology, University of Minnesota Twin Cities. Research involves biochemical and structural studies on proteins that guide invasion and replication of important viral pathogens. Candidates should be highly motivated about scientific research, and have a major in biochemistry or related fields. For more information about Dr. Li's lab, visit http://www.msi.umn.edu/~lifang/. Individuals interested in working with Dr. Li should email him at lif...@umn.edu(2) Postdoc positionApplications are invited for a postdoctoral position in Dr. Fang Li's lab at the Department of Pharmacology, University of Minnesota Twin Cities. Research involves biochemical and structural studies on proteins that guide invasion and replication of important viral pathogens. Strong background in X-ray crystallography and protein biochemistry is required. Candidates must have completed PhD at the time of the appointment. Salary commensurates with experience. Interested applicants should send (1) a resume, (2) a one-page summary of previous research experience, and (3) arrange three letters of recommendation to be sent to Dr. Fang Li via emai: lif...@umn.edu
Re: [ccp4bb] Mysterious density
Cyclized DTT can look similar to this blob. Of course the sulfur atoms would make one end of the blob more dense than the other. Dale Tronrud On 07/09/10 05:12, Nick Quade wrote: > Dear CCP4 community, > > I have solved the structure of a protein in complex with DNA. But, > inside the protein there seems to be a ligand binding pocket with some > strong density > (*http://picasaweb.google.de/113264696790316881054/Desktop#). *The > protein was in Tris buffer, with some NaCl, MgCl2 and DTT and > crystallized in Li2SO4 with MES. What could this density be? I can > exclude MES as crystals grown with citrate buffer have the same density. > So I guess it might be something I co-purified or perhaps some > degradation product of the DNA? The electron density in the pictures is > at 1.5sigma. > > Thanks in advance. > > Nick
Re: [ccp4bb] Mysterious density
Another thing to consider is alternate ligand conformation. The water density (elongated) and the pocket composition (aromatic) could result in two alternative binding orientations (of the buffer? I need 3D). I would play around with models to see if it fits the density. Paula Lario #778-828-3701 On Jul 9, 2010, at 5:12 AM, Nick Quade wrote: > Dear CCP4 community, > > I have solved the structure of a protein in complex with DNA. But, inside the > protein there seems to be a ligand binding pocket with some strong density > (*http://picasaweb.google.de/113264696790316881054/Desktop#). *The protein > was in Tris buffer, with some NaCl, MgCl2 and DTT and crystallized in Li2SO4 > with MES. What could this density be? I can exclude MES as crystals grown > with citrate buffer have the same density. So I guess it might be something I > co-purified or perhaps some degradation product of the DNA? The electron > density in the pictures is at 1.5sigma. > > Thanks in advance. > > Nick
Re: [ccp4bb] Mysterious density
Blobology (a branch of macromolecular crystallography). You could maybe place benzoate in there (the 6 membered ring on "top" in the pictures), refine, compute a new map and see if you can make something out of it. Why benzoate: because the ring would find its place nicely in the "hydrophobic" environment, especially the TYR and TRP side chains. If it does not make sense (difficult to say from pictures, I tried rotating by to no avail...) then place a few waters, refine and see if the new density makes sense after refinement. Fred. Nick Quade wrote: Dear CCP4 community, I have solved the structure of a protein in complex with DNA. But, inside the protein there seems to be a ligand binding pocket with some strong density (*http://picasaweb.google.de/113264696790316881054/Desktop#). *The protein was in Tris buffer, with some NaCl, MgCl2 and DTT and crystallized in Li2SO4 with MES. What could this density be? I can exclude MES as crystals grown with citrate buffer have the same density. So I guess it might be something I co-purified or perhaps some degradation product of the DNA? The electron density in the pictures is at 1.5sigma. Thanks in advance. Nick
[ccp4bb] Mysterious density
Dear CCP4 community, I have solved the structure of a protein in complex with DNA. But, inside the protein there seems to be a ligand binding pocket with some strong density (*http://picasaweb.google.de/113264696790316881054/Desktop#). *The protein was in Tris buffer, with some NaCl, MgCl2 and DTT and crystallized in Li2SO4 with MES. What could this density be? I can exclude MES as crystals grown with citrate buffer have the same density. So I guess it might be something I co-purified or perhaps some degradation product of the DNA? The electron density in the pictures is at 1.5sigma. Thanks in advance. Nick
[ccp4bb] Fwd: postdocs
Prof. Gebhard Schertler Head of Biology and Chemistry Biomolecular Research Laboratory Paul Scherrer Institute Anfang der weitergeleiteten E-Mail: Von: Daniel Oprian Datum: 8. Juli 2010 17:16:43 MESZ An: gebhard schertler Betreff: postdocs Dear Gebhard, I am writing to find out if you know of any qualified students looking for postdoctoral positions. We have two positions to fill immediately and another opening within the next year. Current research in the lab is focused on determining the structure and mechanism of activation of complexes comprised of rhodopsin/ transducin, rhodopsin/rhodopsin kinase, and rhodopsin kinase/ recoverin. The work exploits many of the rhodopsin mutants that we have worked with over the years and has the goal of obtaining detailed mechanistic insight into formation and breakdown of the complexes, as well as atomic resolution structures. We are especially interested in candidates with strong biochemistry backgrounds and/or training in x-ray crystallography or NMR spectroscopy. Please ask interested candidates to contact me by email (opr...@brandeis.edu). Thanks, and best wishes, Dan
Re: [ccp4bb] Question about R/Rfree value difference
Hi Tom, very nice tool! It would be good to get numerical values of the plotted distributions as well, like mean, median, standard deviation and so on. Best regards, Dirk. Am 08.07.10 15:20, schrieb Tom Oldfield: Sampath With regard to your question on what sort of statistics you should get within structure determination you might find this service at the PDBe useful : http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp You can view and manipulate distributions of R, Rfree and R-Rfree along within many other data distributions from Xray (also NMR/EM) during structure determination. There are also links (clicking the graph) that list all the depositions that have a particular value within the distribution. I agree with Pavel that from your quoted statistics that it would be un-wise to deposit the structure in the current state of refinement as there is clearly an issue. Regards Tom Oldfield Hi Sampath, this is how the distribution of Rwork, Rfree and Rfree-Rwork look like for 'all' PDB structures refined at around 2A resolution. The "<<<" indicates where your structure stands with respect to this distribution. Histogram of Rwork for models in PDB at resolution 1.90-2.10 A: 0.093 - 0.118 : 2 0.118 - 0.143 : 35 0.143 - 0.168 : 390 0.168 - 0.193 : 1439 0.193 - 0.218 : 1802 <<< your structure 0.218 - 0.242 : 785 0.242 - 0.267 : 159 0.267 - 0.292 : 14 0.292 - 0.317 : 1 0.317 - 0.342 : 1 Histogram of Rfree for models in PDB at resolution 1.90-2.10 A: 0.149 - 0.170 : 10 0.170 - 0.191 : 116 0.191 - 0.213 : 534 0.213 - 0.234 : 1166 0.234 - 0.255 : 1417 0.255 - 0.276 : 942 0.276 - 0.297 : 343 0.297 - 0.319 : 78 0.319 - 0.340 : 17 <<< your structure 0.340 - 0.361 : 5 Histogram of Rfree-Rwork for all model in PDB at resolution 1.90-2.10 A: 0.001 - 0.011 : 41 0.011 - 0.021 : 230 0.021 - 0.031 : 724 0.031 - 0.041 : 1210 0.041 - 0.050 : 1206 0.050 - 0.060 : 654 0.060 - 0.070 : 318 0.070 - 0.080 : 160 0.080 - 0.090 : 56 0.090 - 0.100 : 29 So, it seems your case is the example of typical overfitting, which means the model parameterization or/and the refinement strategy is not good for your data and model. If you send me the data and model files then I will be able (hopefully) to suggest a better refinement strategy or explaine why it's not feasible with available tools. All files will be kept confidentially. The histograms above are obtained using this command from PHENIX family: phenix.r_factor_statistics 2.0 Good luck! Pavel. On 7/7/10 10:17 PM, Sampath Natarajan wrote: Dear all, I have a question about the R free value. I refined a structure with 2A resolution. After model building and restraint refinement using Refmac program, the average B factor was around 50 for all atoms. The R/Rfree were around 22/34. Then used the TLS refinement choosing entire molecule. Then R/Rfree reduced as 20/32. But the average B factor was reduced as 30. The R/Rfree difference is about 12% in final refinement. I feel it is significantly higher. Could any one suggest me to reduce the Rfree value more? or is it good to submit the data in the PDB database with this 12% difference? Thanks for the suggestions. Sincerely, Sampath N -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Beginning crystallography text
Stout and Jensen, "X-ray structure determination", 1989 Solid mid-level theory with practical examples. Most of the hardware discussed is very dates, but otherwise an excellent intermediate text. Nic out Bernhard Rupp wrote: The question of what textbook to use is very much context sensitive, that is, it depends on what the reader wants and needs to know. Unfortunately, this question us easy to answer with hindsight, but not so obvious to the person looking for answers. Having said that, I declare a conflict of interest as one of the mentioned textbook authors. The conflict, however, is modest because I am not aware of anyone making a fortune on crystallography textbooks. I think it is reasonable to delineate the textbook market by what the reader ultimately wants to accomplish. What a structural biologist should know, versus what is expert knowledge, has been a contentious issue for quite some years. A lot of people have thought hard about this, and the education committees of the American Crystallographic Association (ACA) and USNC/Cr organized a crystallography education summit, whose outcome is the consensus policy statement on crystallography education and training available from here: http://www.ruppweb.org/garland/study_group.htm I privately think that as a first contact for the user of structure models, the Rhodes book is a great start. If you are a tad more interested in how it works, Jenny Glusker's old text in its revised form is still one of my favorites, and the Blow book as well Alex's compilation are quite useful. Drenth helps once you are already engaged in the business, and have some idea what it is about. The IUCr compilation is an extremely useful hard core resource if you are interested in the nuz and bolz of crystallography in general. Not to forget the excellent multi-author volumes of Methods of Enzymology as an in-depth resource. Having said that, the reason why I decided to add another tome (BMC) to the already prolific writings in protein crystallography is that I felt that none of the above provided a consistent and modern picture of crystallography in the probabilistic framework it actually operates in. This is - in a crystallographic time frame - ancient history; a first resource being the 1952 work of Crick and Blow, and it continues via French and Wilson to Bricogne and on. So, as a concluding statement, I think there is more to biomolecular crystallography that just nuz and bolz, and it touches many very fundamental challenges and uncertainties, ultimately forcing my emphasis on probabilistic approaches and the resulting digressions in the subversive sidebars. Consequentially, if you like the Schaum series and Kaplan SAT rest prep books, don't waste your money on my book. Instead, get one of the (nearly as expensive by weight and volume) monographs mentioned above, they are in fact good and will lead you in the right direction. If you like Neal Stevenson, Rev. Bayes, and a touch of randomness, and you understand that the probability of receiving the Nobel Price approaches practically zero once you have been infected by the spirit of BMC, go for it ;-) BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert Sweet Sent: Thursday, July 08, 2010 1:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Beginning crystallography text I like David Blow's book for beginners -- one can get the gist of things without having much math: http://www.abebooks.com/servlet/SearchResults?an=blow&sts=t&tn=crystallograp hy&x=35&y=6 Bernhard Rupp's book, mentioned earlier, is the current gold standard, in my view. Bob On Thu, 8 Jul 2010, Prince, D Bryan wrote: Having recently completed the CSHL Macromolecular crystallography course, I can recommend Introduction to Macromolecular Crystallography by Alexander McPherson (ISBN 987-0-470-18590-2). I am posting the link below: http://www.amazon.com/Introduction-Macromolecular-Crystallography-Alexander- McPherson/dp/0470185902/ref=sr_1_1?ie=UTF8&s=books&qid=1278619717&sr=1-1 Kind regards and good luck! Bryan -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Hsu Sent: Thursday, July 08, 2010 3:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Beginning crystallography text Hi all, I haven't gotten past the phase of growing the crystal, but
Re: [ccp4bb] How to make fft-map more physically meaningful?
Hi Sacha is absolutely right here. This was made plain to me during a plenary session at the recent BCA meeting in Warwick, given by a powder (not protein) crystallographer - who was using histogram matching density modification, with negative densities; an expert in density modification in protein crystallography tells me that "using a map with no truncation (and hence no negative densities) always gives rubbish results in my hands". On 9 Jul 2010, at 06:37, Alexandre Urzhumtsev wrote: > Dear Hailiang, > >> This apparently is not the real physics, since the >> electron density has to be positive everywhere (hope I am right). > > Yes, you are right when you are talking about the electron density. > > You are wrong when you are talking about a Fourier synthesis calculated > always at a finite resolution (it is what you have, is it?), even when the > term F000 is used as suggested. > > Such a synthesis MUST have NEGATIVE values due to Fourier series truncation. > Allowing such negative values was an important point at the beginning of > density modification procedures (beginning of 80th) and it was one of the key > moments when developping electron density histograms (see for example Lunin, > 1988, Acta Cryst A). Moreover, these points even contain some information and > can be used for example to identify the macromolecular region (since the > deepest minima are usually close to the highest maxima). > > With best regards, > > Sacha Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] 8th International NCCR Symposium on New Trends in Structural Biology
Dear colleagues, we have the following announcements to make: 8th International NCCR Symposium on New Trends in Structural Biology 2 + 3 September 2010, ETH Zürich, Lecture Hall HG E7, Zürich, Switzerland For more information about the event format, speaker list, and lecture titles, please see www.structuralbiology.uzh.ch/symposium2010.asp Plenary lecturers: Ad Bax, James U. Bowie, Kathryn M. Ferguson, Rudi Glockshuber, John Kuriyan, Jonathon Howard, Jan Löwe, Krzysztof Palczewski, Bob Stroud, Wilfred F. van Gunsteren Poster presentations by NCCR scientists and guests Online registration to this event is still possible through the symposium homepage or directly at: http://www.structuralbiology.uzh.ch/registration10.asp Please do not hesitate to contact me anytime if you need further information (stic...@bioc.uzh.ch). With best regards, Patrick Sticher The NCCR Structural Biology is a research initiative of the Swiss Science Foundation. Its research encompasses the fields of recombinant protein technologies, macromolecular structure determination and computational biomolecular sciences with a special focus on membrane proteins and supramolecular assemblies/interactions. 13 research groups from Swiss Universities and Research Institutions participate in this network. www.structuralbiology.uzh.ch/ -- _ Visit the NCCR on the Internet www.structuralbiology.uzh.ch Dr. Patrick Sticher Moser NCCR Scientific Officer Institute of Biochemistry University of Zürich Winterthurerstrasse 190 CH - 8057 Zürich Phone +41 / (0)44 / 635 54 84 Fax +41 / (0)44 / 635 59 08 Mailstic...@bioc.uzh.ch
