Re: [ccp4bb] Accessing full list of programs in CCP4I2
s. > > Their are two options: > > First via i2: Use the unusual map coefficients Task and choose not to compare > maps, but to generate the map coefficients plus a map (button is in Advanced > tab) the standard grid parameters can be changed, but are actually optimized > already. > > Second just save the map out of Coot (Export map) > > To avoid redundancy, the old fft task was discontinued. i2 works with > coefficients, which generates smaller files and Coot provides all the > functions to generate the map and is its own gui. > > Hope that explains a bit why things are how they are now. > > Cheers > > Christian > > On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin wrote: > > Hi Christian, > > I was in particular looking for the fft program (I couldn't find that using > the method you described) just to convert an mtz into a .map. Before in > version 7.0 I could just browse all programs, now it seems like I cannot do > that (other than using the filter, and some seem to be missing) > > At the end I just used mtz2map in phenix. > > -- > Kelvin Lau > > https://people.epfl.ch/kelvin.lau [1] > > Protein production and structure core facility - PTPSP > EPFL SV PTECH PTPSP > AI 2146 (Bâtiment AI) > Station 19 > CH-1015 Lausanne > Switzerland > Email: kelvin@epfl.ch > Phone: +41 21 69 30267 [2] > > If unreachable: +41 21 69 34494 [2] > > On 06.07.20, 13:34, "Christian Roth" wrote: > > Hi Kelvin, > > not quite sure if I understand you correctly, but if you press the Task > Manager button you get on the right sight a list of topics (import data, > Molecular Replacemnt etc.) each point can be open up like a file tree to see > all programs or pipelines available. You can search with the search field > (Filter) on top for specific program names. > > Does that help? > > Cheers > > Christian > > On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin wrote: > > Hello, > > I am looking for a way to find the list of programs accessible using the new > 7.1 CCP4I2 interface? Is this still possible or do I have to revert back to > version 7.0? > > Best regards, > > Kelvin > > -- > Kelvin Lau > > https://people.epfl.ch/kelvin.lau [1] > > Protein production and structure core facility - PTPSP > EPFL SV PTECH PTPSP > AI 2146 (Bâtiment AI) > Station 19 > CH-1015 Lausanne > Switzerland > Email: kelvin@epfl.ch > Phone: +41 21 69 30267 [2] > > If unreachable: +41 21 69 34494 [2] > > - > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax) Links: -- [1] https://people.epfl.ch/kelvin.lau [2] tel:+41%2021%2069%C2%A030267 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] disinfecting keyboards
http://www.viziflex.com/disposables/universal-disposable-50-pack/ D. On 2020-04-29 01:53 PM, Tim Gruene wrote: Dear all, can you make suggestions for how to disinfect computer keyboards, and instrument panels? Our facility is going to reboot next week, with shifts so that people don't meet. The main interface will be the computer keyboards, as well as the door of our X-ray diffractometer and the mounting of the crystals. The keyboard labels may not like alcohols (and the efficiency of injecting disinfecting through the USB cable is also under discussion, so I heard). One way would be to use individual keyboards, and wearing gloves for replugging, and to use gloves for mounting crystals. But maybe there are other ways that won't require gloves? Best regards, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] HKL2000 - Error model
You should not adjust the error model manually, instead please select the button "use auto corrections" and rely on the automatically adjusted error model. This way you do not have to analyze the changes in the resolution shells. D. On 2019-07-01 01:44 PM, Weston Lane wrote: When you fix the error model in HKL2000 you only have a set of numbered boxes (1-20) and knowing which box corresponds to which resolution bin and corresponding chi^2 value isn't apparent without looking at the log file. Besides using a script the easiest method IMO is graphically: hover your mouse (with the red crosshairs) over the I/s and chi^2 vs resolution plot @ the chi^2=1.0 hash mark and it's easy to see which bin has the outlier values. See the following screen grab for clarity. https://i.imgur.com/sr6JQy6.png Wes To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Call for abstracts for the session "Radiation damage in X-ray crystallography and cryo-EM"
Dear All, The deadline for submitting an abstract to the American Crystallographic Association Meeting (https://www.aca2019mtg.com/) that will take place July 20-24 2019 in Cincinnati/Northern KY has been extended to April 12 (Friday this week). Cryo-EM methods are featured at many sessions in the ACA meeting program, including "Radiation Damage in X-ray Crystallography and Cryo-EM" (session 4.1.2), which Gerd Rosenbaum and I are organizing. If you are researching any aspect of radiation damage, please consider submitting an abstract to this session at: https://acaonline.secure-platform.com/a/ I've copied and pasted below a description of what we are looking for, but this isn't a comprehensive list, so don't be shy about sending in your abstract. Best regards, Dominika Borek - Are you wondering why or how your samples keeping dying when you are just innocently trying to solve a structure so that you can complete your Ph.D. or finally publish that important paper? If so, the session “Radiation Damage in X-ray Crystallography and Cryo-EM” is for you! What is radiation dose? What are dose-rate effects and why should you care about them? How should you collect data to minimize radiation damage in X-ray crystallography and cryo-EM? How does radiation damage manifest in a structure? Can radiation damage be useful? These and other questions will be answered during this session. If you plan to participate and have a questions that you wish to be answered during this session, do not hesitate to email these questions to the chairs: Dominika Borek (dominika.bo...@utsouthwestern.edu<mailto:dominika.bo...@utsouthwestern.edu>) and Gerd Rosenbaum (rosenb...@anl.gov<mailto:rosenb...@anl.gov>). ----- -- Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Fix sidechain outliers
You may try Fitmunk for side chains: http://kniahini.med.virginia.edu/fitmunk/server/ D. On 2017-09-04 09:36 AM, rohit kumar wrote: Dear All, Could anyone help me, how I can fix my sidechain outliers or clashscore in coot or in CCP4 tools. Or by using any online severs. Its urgent Thank You in advance -- WITH REGARDS Dr. Rohit Kumar Singh School of Life Sciences, Jawaharlal Nehru University New Delhi -110067 -- Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax)
Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL
Dear C-Daddy, Did you look at the maps? Do you see any astonishing misinterpretations there? Do you think that the completeness in the last resolution shell would affect the maps and the model? If so, why? There are many possible reasons for the discrepancy you pointed out. In I422 a=b, alpha=90.00, so typos in the table are the most probable reason. I did look at the maps after running a quick refinement. Both the structure and the ligand are fine. I would probably add solvent molecules myself, but some conservative crystallographers prefer not to do it, even at 2.5 A. In other words, there is nothing wrong with this deposit. I would even say that the level of sloppiness is below the average for this one. D. On 2017-06-29 11:07 AM, CDaddy wrote: Dear colleagues, I am really astonished by a recently released structure 5XQL. This structure was just published in BBRC with a super fast process (accepted overnight). Significant inconsistences were observed when I compared the Data collection and refinement statistics in the paper and at PDB website. The paper shows the crystal belong to I 4 2 2 with a=135.77, b=136.11, c=95.13 (Å) ; α=90.01. The resolution is 2.5Å with completeness of 99.7 (99.1). However when I checked the released structure I got a= b=135.94, c=95.13 (Å) ; α=90.0. The resolution is 2.5Å with completeness of 81.5 (44.0). The completeness of the highest resolution shell is so low that 2.5Å seems unreasonable. At first I thought that the authors could be rookies in structural biology. But the molecular replacement in this paper could be very difficult due to very low sequence identity between the search model and the final structure. It was unlikely that two new hands could solve it easily. Is there anyone who has this kind of experience and know why? With best wishes, Richard -- Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax)
Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents
You need: a) to have an image of your crystal mounted on the goniometer in orientation, in which the axis of interest (6-fold) is perpendicular to the beam. You should know the system well enough to relate the coordinate system of the crystal on this image to the beam-gravity coordinate system. b) you collect in this orientation diffracion image(s) sufficient for indexing c) index the lattice and chose hexagonal lattice and refine parameters d) then you collect data set from the crystal so you can solve the structure in this coordinate system. Because space group is polar, there are always two non-equivalent choices for the coordinate system and you cannot replace one with another. The critical step is performed after (c) and depends on software -- I describe here HKL2000. On the image oriented according to (a) check where are the positive and negative values of hexagonal index (l index - use zoom window). HKL2000 present the diffraction image of the detector from the perspective of an incident beam. Therefore, you would need to correlate positive and negative values of indices with the optical image coordinate system from (a). Remember that optical axis (of the camera imaging a crystal) may not be along the beam. The structure solution will provide you with the direction of axis c. D. I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine which direction the screw axis is going with respect to top and the base of the pyramidal crystals (right image) so I can gauge how/why the crystals grow this way based on the cell contents. Thanks in advance. --paul Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax)
Re: [ccp4bb] HKL2000 Display
You are using an incorrect site file. Whatever you provided to the program as description of the detector used during data collection needs to be changed. D. Muhammed bashir Khan wrote: Hi All; Could somebody explain why my Display image in HKL2000 look like that. Image attached. Thanks for help in advance. Bashir Department of Biochemistry University of Alberta Edmonton Canada Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax)
Re: [ccp4bb] scaling HKL2000
1. You should always use the absorption correction (your previous e-mail). 2. The statistics are bad because the crystal was not cryoprotected properly -- data are contaminated with ice. You need to decrease the box size during data integration to 24 x 24 mm. This will result in rejecting ice-affected reflections. Dominika Monica Mittal wrote: Dear all I need an advice at the part of scale.log file that i am attaching herewith this mail that do i have to compromise the resolution as I/sig and Rsymm seem to be bad in resolution shell 2.3 to 2.18. Kindly suggest Thanx Monica Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-6378 (phone) *** 214-645-6353 (fax)
Re: [ccp4bb] Strange diffraction
Small unit cell and strong diffraction -- I agree with Artem. D. Muhammed bashir Khan wrote: Hi All; I have a strange diffraction pattern from a membrane protein in one of the PEG containing conditions. Could somebody suggest/comments about this diffraction pattern. Please find the diffraction image attached. According to my experience these are protein crystals but gives a strange diffraction. Thanks for your help Bashir Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-6378 (phone) *** 214-645-6353 (fax)
Re: [ccp4bb] Scalepack error model?
Described in: Borek, D., Minor, W. Otwinowski, Z. (2003) Measurement errors and their consequences in protein crystallography. Acta Cryst. D59: 2031-2038. http://scripts.iucr.org/cgi-bin/paper?ba5035 (open access) or http://bones.swmed.edu/pdf/7_Borek_et_al_ActaCrystD_2003_D59_2031-2038%5B1%5D.pdf Dominika Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. -- Dominika Borek UT Southwestern Medical Center 5323 Harry Hines Boulevard Room ND10.214 Dallas, Texas 75390-8816 phone: +1 214-645-6378 fax: +1 214-645-6353 domin...@work.swmed.edu
Re: [ccp4bb] The importance of USING our validation tools
and keep for a reasonable amount of time all the primary data for experiments. In the case of crystallography, this would reasonably be interpreted to mean preservation of X-ray diffraction images. It should be required that authors retrieve and provide these data in case of controversy. In any case, the key results are deposited in the PDB. As long as structure factors are deposited it is effectively impossible to do a credible job of fabricating data, as has been discussed. G. Sheldrick:” The deposited structure 2HR0 shows all the signs of having been refined, deliberately or accidentally, against 'calculated' data. The model used to 'calculate' the data had (almost) constant B values in a rather empty cell containing no solvent. For example, it could have been a (partial?) molecular replacement solution obtained using real data. It seems to me that it is perfectly possible that two reflection files (or two columns in an mtz file) were carelessly exchanged by a crystallographically inexperienced researcher.” This scenario is impossible. If this had happened, then subsequent refinement (which we did) of the structure would produce impossibly low R-factors. The calculated structure factors were randomized to prevent this occurrence, indicating strongly that it was done intentionally. There are more indicators of intentional fabrication/falsification of data. The structure factors used in refinement are clearly derived from a model of low quality, which suggest a model derived from a low resolution dataset. But the most convincing indicator is the form of the response to the Brief Communication by Janssen et.al. If it would be any kind of mistake it would have to be of a very obvious nature, and the authors would recognize it and state it in a public response. Their defense does not make any sense in terms of crystallography when combined with inspection of the deposited data. Dominika Borek UT Southwestern Medical Center 5323 Harry Hines Boulevard Dallas, Texas 75390-8816 phone: +1 214-645-6378 fax: +1 214-645-6353 [EMAIL PROTECTED]
