[ccp4bb] twinned data
Dear all Lately i have found my crystals to be pseudomerohedrally twinned with a twin fraction of 0.22..but on doing twin refinement nothing much is changing in terms of statistics as compared to the previously solved data which did not include twin refinement (in present case the data is solved at 2.5A with R/Rfree of 22 and 25)..i may be wrong but i have heard that the data statistics generally improves after twin refinement..can anybody please explain. -- Regards Faisal School of Life Sciences JNU
[ccp4bb] visualizing ds DNA conformation
BSD Dear All, Is there a readily available facility to produce a plot in the same spirit as a protein Ramachandran plot, but for DNA. In particular showing clear differences between different types of double stranded DNA (A vs. B, for example). Thanks Harry - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.ilmailto:harry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel
[ccp4bb] example script to run SCALA while excluding films (frames)
Dear all, We are trying to use the GUI (ccp4i) to run SCALA a second time while excluding data frames. In our hands this fails. It could be for a simple reason (such as the Batches to be excluded must be separated in the list of the GUI by semicolons, colons, commas, whatever... instead of blank spaces). Would anyone have a running SCALA script that corresponds to the GUI defaults but that specifically excludes data frames ? The route that was followed for data processing was XDS, COMBAT and now SCALA. The first run indicated to us what we think is better excluded from the processing. If SCALA cannot remove data frames one can write a specific jiffy program to exclude specific rotation ranges from the XDS_ASCII.HKL file, but I'd prefer to use an existing program if it allows to do what I want to do. Thanks in advance, Fred. -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
[ccp4bb] slightly off-topic: stereo visualisation on the MAC
Hi, has anyone any joy with stereo visualisation on the mac? There's a 9/2012 note on the PyMOL page indicating that Zalman stereo no longer works on the MAC, which is certainly my experience: I don't seem t get stereo using Lion - not in Coot and not in PyMOL. Is it something with my setup, or do others have the same problem? if so, are there _any_ stereo solutions left? Adrian
Re: [ccp4bb] visualizing ds DNA conformation
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Harry, there is such an analysis with plots for RNA in Wadley, L. M., Keating, K. S., Duarte, C. M. Pyle, A. M. (2007). J. Mol. Biol. 372, 942–957. I could send you a program to extract similar data for RNA and DNA from PDB-files based on C1' instead of C4' (George Sheldrick pointed out to me that C1' might be more informative, at least for our purposes; see graph in suppl. material for doi:10.1107/S0108767310039140; already mentioned in Semiautomated model building for RNA crystallography using a directed rotameric approach Keating and Pyle, PNAS (2010) 107(18), 8177-8182, hence the Pyle-group might as well have such software); the graphs can be made with e.g. R or gnuplot, but I would not call that program 'user friendly'. I am not sure there is a more convenient way, but it may also depend on your specific plans since the plots you mention seem already available (unless you want to define the two angles differently). Cheers, Tim On 03/05/2013 02:03 PM, Harry Mark Greenblatt wrote: BSD Dear All, Is there a readily available facility to produce a plot in the same spirit as a protein Ramachandran plot, but for DNA. In particular showing clear differences between different types of double stranded DNA (A vs. B, for example). Thanks Harry - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.ilmailto:harry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRNfpYUxlJ7aRr7hoRAhQnAJ0eKn7m+fT4Q2Kf29sZUcZoBuaHvQCeM1bd JyIF08FGtAnzacRPU5JcqB0= =bRyV -END PGP SIGNATURE-
[ccp4bb] Questionnaire on shape/volume fitting in structural biology
Dear Colleagues, PDBe and STFC are developing a web service as part of the BioMedBridges project (http://www.biomedbridges.eu/workpackages/wp9) that will enable the EMDB and PDB archives to be searched on the basis on 3D volumetric shape matching rather than solely on the basis of metadata and/or coordinate models. For example, users will be able to upload a 50S ribosome map and retrieve aligned maps of other ribosomes in the archives. We will also use the service to automatically fit and segment existing entries when new entries are deposited that share common components, e.g. a newly deposited ribosomal protein will be fitted into ribosomal maps in the PDB/EMDB and the resulting segmentations will be made publicly available. In due course, the service may be extended to other volumetric data, such as from SAXS or soft X-ray tomography. We are taken our first baby steps in this project and need your help to avoid reinventing the wheel - we want to use existing software wherever possible! We would like to know what tools and in which context you use fitting software, including fitting atomic coordinates in a volume, fitting EM single particle volumes in tomograms, comparing an EM volume with a SAXS envelope, and comparing a EM single particle volume with a sub-tomogram average. Please take a moment to fill in our questionnaire on shape/volume fitting in structural biology following this link http://www.surveymonkey.com/s/BioMedBridgesShapeMatchingSurvey to Survey Monkey. We plan to publish an anonymized summary of the survey on the BioMedBridges web site. Kind Regards, Ingvar Lagerstedt Ardan Patwardhan, PDBe and Martyn Winn, STFC * * Dr. Martyn Winn * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) * E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn * -- Scanned by iCritical.
Re: [ccp4bb] H -3
Thanks for the advice. What ultimately worked was going back to CCP4 6.1.3. I was able to use the Scalepack to MTZ in that version and it handled the R -3 (SG 148) just fine. I was able to use the MTZ from 6.1.3 in the current release 6.3 and phaser and refmac ran fine. So the issue was in the way the new scalepack to MTZ handles SG 148. Thanks Brian On 3/1/13, Roger Rowlett rrowl...@colgate.edu wrote: I have found that rumning sort/index and reassigning the space group as h3 sorts this issue. On Mar 1, 2013 8:15 PM, brian walker brianwalkerwash...@gmail.com wrote: I am trying to use H -3 in CCP4i. Scalepack seems to finsh and recognize space group 148. Phaser crashes with input error -1 is not zero or positive. Refmac crashes with child killed: segment violation. Interestingly this is not the first H3 bar space group I have had and when I use a MTZ made with an older version of CCP4i it works. Have the sym libraries changed or anything in new newer versions? I suspect a scalepacktoMTZ issue but I am not sure?
Re: [ccp4bb] How to compare B-factors between structures?
James, Thank you for your help. I appreciate the very thorough explanation. I have never heard of noise although I have produced a 'kicked' map in phenix and refined the structure using those maps..though I guess this is different. I will try it. Thanks. -Yarrow Formally, the best way to compare B factors in two structures with different average B is to add a constant to all the B factors in the low-B structure until the average B factor is the same in both structures. Then you can compare apples to apples as it were. The extra B being added is equivalent to blurring the more well-ordered map to make it match the less-ordered one. Subtracting a B factor from the less-ordered structure is sharpening, and the reason why you shouldn't do that here is because you'd be assuming that a sharpened map has just as much structural information as the better diffracting crystal, and that's obviously no true (not as many spots). In reality, your comparison will always be limited by the worst-resolution data you have. Another reason to add rather than subtract a B factor is because B factors are not really linear with anything sensible. Yes, B=50 is more disordered than B=25, but is it twice as disordered? That depends on what you mean by disorder, but no matter how you look at it, the answer is generally no. One way to define the degree of disorder is the volume swept out by the atom's nucleus as it vibrates (or otherwise varies from cell to cell). This is NOT proportional to the B-factor, but rather the 3/2 power of the B factor. Yes, 3/2 power. The value of B, is proportional to the SQUARE of the width of the probability distribution of the nucleus, so to get the volume of space swept out by it you have to take the square root to get something proportional the the width and then you take the 3rd power to get something proportional to the volume. An then, of course, if you want to talk about the electron cloud (which is what x-rays see) and not the nuclear position (which you can only see if you are a neutron person), then you have to add a B factor of about 8 to every atom to account for the intrinsic width of the electron cloud. Formally, the B factor is convoluted with the intrinsic atomic form factor, but a native B factor of 8 is pretty close for most atoms. For those of you who are interested in something more exact than proportional the equation for the nuclear probability distribution generated by a given B factor is: kernel_B(r) = (4*pi/B)^1.5*exp(-4*pi^2/B*r^2) where r is the distance from the average position (aka the x-y-z coordinates in the PDB file). Note that the width of this distribution of atomic positions is not really an error bar, it is a range. There's a difference between an atom actually being located in a variety of places vs not knowing the centroid of all these locations. Remember, you're averaging over trillions of unit cells. If you collect a different dataset from a similar crystal and re-refine the structure the final x-y-z coordinate assigned to the atom will not change all that much. The full-width at half-maximum (FWHM) of this kernel_B distribution is: fwhm = 0.1325*sqrt(B) and the probability of finding the nucleus within this radius is actually only about 29%. The radius that contains the nucleus half the time is about 1.3 times wider, or: r_half = 0.1731*sqrt(B) That is, for B=25, the atomic nucleus is within 0.87 A of its average position 50% of the time (a volume of 2.7 A^3). Whereas for B=50, it is within 1.22 A 50% of the time (7.7 A^3). Note that although B=50 is twice as big as B=25, the half-occupancy radius 0.87 A is not half as big as 1.22 A, nor are the volumes 2.7 and 7.7 A^3 related by a factor of two. Why is this important for comparing two structures? Since the B factor is non-linear with disorder, it is important to have a common reference point when comparing them. If the low-B structure has two atoms with B=10 and B=15 with average overall B=12, that might seem to be significant (almost a factor of two in the half-occupancy volume) but if the other structure has an average B factor of 80, then suddenly 78 vs 83 doesn't seem all that different (only a 10% change). Basically, a difference that would be significant in a high-resolution structure is washed out by the overall crystallographic B factor of the low-resolution structure in this case. Whether or not a 10% difference is significant depends on how accurate you think your B factors are. If you kick your coordinates (aka using noise in PDBSET) and re-refine, how much do the final B factors change? -James Holton MAD Scientist On 2/25/2013 12:08 PM, Yarrow Madrona wrote: Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type structure. For example, structure2 has a higher B-factor for residue X but how can I show that this
[ccp4bb] Way off topic: Donate V. Cholera Genomic DNA?
Dear List, please pardon the major off-topicity, but I need a trace amount of V cholera genomic DNA to PCR from, and it just kills me to spend ~$300 to order it for this one and only use. Is anyone in the DC/Baltimore area willing and able to donate this? I travel on the capitol beltway daily, so anything nearby would work, esp. NIH. Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: k j-kell...@northwestern.eduell...@janelia.hhmi.org ***
[ccp4bb] CCP4 Update 017
Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes: * Aimless Bug fixing in task interface * ccp4i Fixed long-standing issue on Linux and Mac: system Python was used instead of the one distributed with CCP4 * QtPISA Added output of monomer, interface and assembly details in plain text; eliminated Qt widget flashing If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have the CCP4 Update Manager (ccp4um) integrated. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4 Eugene Krissinel -- Scanned by iCritical.
[ccp4bb] Postdoctoral research opportunity
Greetings everyone. I'd like to call your attention to the following postdoc opportunity: Postdoctoral research opportunity in antibiotic drug resistance Applications are invited for a postdoctoral position to study the structural biology of proteins and enzymes that comprise AmpC beta-lactamase induction pathway. Beta-lactam antibiotics act to disrupt bacterial cell wall metabolism. Numerous bacterial pathogens respond to this disruption by inducing the expression of AmpC beta-lactamase. AmpC is of considerable clinical concern since it confers broad-spectrum resistance against beta-lactams. We focus on understanding the structural biology of bacterial cell wall metabolism and the development small molecule based strategies to block AmpC gene expression during antibiotic therapy. Additional information about our research and recent publications in the area can be found at: http://home.cc.umanitoba.ca/~bmark/Welcome.html We seek an enthusiastic, hard working individual who holds a PhD in biochemistry or related field. Candidates should have a strong background in molecular biology and protein X-ray crystallography. Experience in membrane protein crystallography would be an asset. We are located in the Department of Microbiology, University of Manitoba, Winnipeg, Canada. The laboratory offers state-of-the-art X-ray instrumentation (Rigaku), crystallization robotics (Art Robbins), and on-going user access to the Canadian Light Source Synchrotron via mail-in service, remote robotics, or in-person visits. The University of Manitoba (http://umanitoba.ca/) is the largest University in the province (over 30,000 students, faculty, and staff) and hosts a dynamic biomedical research community. Winnipeg is a vibrant, multicultural city with numerous cultural events and festivals (http://www.destinationwinnipeg.ca/). Salary will be in accordance with the Canadian Institutes of Health Research (CIHR) (http://www.cihr.ca/ ) standards. The position also includes a University benefits package. All qualified candidates are encouraged to apply. Please direct inquiries, including a cover letter, brief description of your career goals and CV (including names of three referees) to Brian Mark at the following email address: brian.m...@ad.umanitoba.camailto:brian.m...@ad.umanitoba.ca = Brian Mark, MSc, PhD Associate Professor Manitoba Research Chair in Structural Biology Department of Microbiology Department of Biochemistry and Medical Genetics Mailing/Courier address: Department of Microbiology Rm 418 Buller Building University of Manitoba 45 Chancellor's Circle Winnipeg, Manitoba CANADA R3T 2N2 Phone (204) 480-1430 Fax (204) 474-7603 Web: http://home.cc.umanitoba.ca/~bmark/Welcome.html
Re: [ccp4bb] Qt PISA text copy?
I am very happy to confirm that the latest update, CCP4 6.3.0 Update 018 (not 017 as in the latest update notice), added this functionality. Thank you. I think we all agree about the awesomeness of the new CCP4 update mechanism! Engin On 3/4/13 3:36 AM, eugene.krissi...@stfc.ac.uk wrote: Apologies, I'd like to retract my post, it is indeed that only general lists of interfaces and assemblies are exported in plain text. We will try to fix this as soon as feasible. Eugene On 4 Mar 2013, at 11:13, eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.uk wrote: Dear Engin, QtPISA outputs the same textual information as the previous command-prompt routine, check File/Export plain text. What is probably confusing is that it does not export everything in one go, but rather precisely the portion that is currently displayed in the right-hand side of the window. E.g., if you'd like to export all tables for 1st stable assembly, navigate to that assembly in the result tree on the left (that means, open Assemblies/Stable and highlight 1st assembly), and then choose File/Export plain text from windows' menu. I hope that this helps, Eugene On 4 Mar 2013, at 07:13, Engin Özkan wrote: Hi everybody, I was just trying out the new QT PISA interface in CCP4 6.3.0 (updated to -017). I realized none of the beautiful tables produced can be easily extracted/copied/captured into a human readable form. There are many output options, including PDB files, a binary-formatted .pisa file, XMLs, and a very short summary text file. I can copy the tables line by line by command-C (on Mac 10.6), but any means of selecting and copying all rows have failed. I had to resort to running pisa command-line, and thankfully got the tables there. This can also be accomplished simply by a copy and paste from a browser when using the webserver. I must clearly be missing something using the new and beautiful Qt interface (otherwise why produce these tables?). Could someone please direct me to how to do this? Cheers, Engin -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 w ph: (650)-498-7111 cell: (650)-862-8563 -- Scanned by iCritical. -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
[ccp4bb] Fwd: FINAL REMINDER: ALS Call for General User Proposals - DEADLINE March 6 2013
Dear Users, I am forwarding the reminder mail from ALS to submit your proposal for the CC time and general user time at ALS. Please submit your proposals before time. Thanks Banu FINAL REMINDER: CALL FOR GENERAL USER PROPOSALS AT THE ALS The User Services Office is accepting General User Proposals from scientists who wish to conduct research at the ALS in the next cycle. PROPOSAL SUBMISSION DEADLINE cycle: 2013-2 August-December Deadline: March 6, 2013 NEW PROPOSALS Please follow the instructions for proposal submission at: http://www-als.lbl.gov/index.php/user-information/user-guide/58.html BEAM TIME REQUEST for an ACTIVE PROPOSAL Proposals remain active for two years (up to four cycles), but beam time is only allocated if a beamtime request is made each cycle. After two years the proposal expires and a new proposal must be submitted. If you have an eligible active proposal you will already have received an email from us which includes your login number and password. PUBLICATION REMINDER The proposal form now includes a section on publications from previous ALS work. Please make sure your publications are entered into our database: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PublicationSearch.shtml/Initialize If you have questions, please feel free to contact me. Cheers, Clyde Lewis Proposal Coordinator ALS
[ccp4bb] ion in refinement
Hi, Everybody, For refinement of ion in my structure, I used phenix.metal_coordination to produce a geometry restraints file elbow.edits. But after including the file in the phenix refinement, the refined pdb has clash between metal and one of the coordinated atoms, as shown in the attachment. I double checked elbow.edits file, the bond restraint between the two clashed atoms is clearly in the file and included in the refinement. Is this a bug in phenix or I did something wrong? Thanks! attachment: tmp.png
Re: [ccp4bb] ion in refinement
Hi Mike, if you send me the inputs (data, model and any parameter files) I will tell you what's wrong. If you choose to send the files, please do so to my email address (not the whole mailing list). FYI: there is Phenix mailing list for questions like this. Pavel On Tue, Mar 5, 2013 at 10:11 PM, Mike John perturb-w...@hotmail.com wrote: Hi, Everybody, For refinement of ion in my structure, I used phenix.metal_coordination to produce a geometry restraints file elbow.edits. But after including the file in the phenix refinement, the refined pdb has clash between metal and one of the coordinated atoms, as shown in the attachment. I double checked elbow.edits file, the bond restraint between the two clashed atoms is clearly in the file and included in the refinement. Is this a bug in phenix or I did something wrong? Thanks!
