Re: [ccp4bb] replacement for Scientific Linux
Hi Harry, I started using Debian about 10-15 years ago, and never changed my opinion since. I had tested various others before, like redhat, suse, ubuntu etc. The stable version of Debian is indeed very stable, as there are no version changes, only bug fixes etc. The new release is about every three years, and upgrading does not break the system (with rpm based systems I remember quite frequent re-installs, because the system got messed up). The long-term support is indeed very long. The main repositories of Debian include a great number of scientific / crystallographic packages, e.g. raster3d, pymol, clipper-, ccp4-, mmdb2-libraries and what not. Due to the philosophy of sticking to a version, and only to bug fixes and security releases, Debian is often not affected by security holes, e.g. the SHELX server was save from heart-bleed when it came out, because heart-bleed require more modern versions of whatever library was affected (SSL?). Same is true for the recent foul version of XZ. Debian is POSIX compliant, so it doesn't mess around with standards, and for configuration you can rely on what you find on the web. There is a saying 'even a chicken can install Debian, as you only need to hit Enter', which is not far from true. Cheers, Tim On Fri, 26 Apr 2024 16:46:17 +0100 Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi folks > > For many years I’ve been using Scientific Linux as my OS of choice > (when not using my Mac) - but it’s been discontinued. SL was based on > RHEL, and had useful things like a less-buggy Fortran/C/C++ compiler > than that released by RH. > > What do people here recommend as a replacement? > > Harry > > > 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/ -- 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/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/ pgp4iZKUGAxYg.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography
Hi Fred, You can place the SHELXL binary anywhere, but you need to tell OLEX2, e.g. by modifying the PATH-variable (search for 'ENVIRONMENT' in the WINDOWS search field. The current working directory (CWD) is part of the PATH in Windows by default, hence by copying shelxl.exe to where you installed the olex2-binary is also a solution, but in case you need shelxl.exe for several programs, the PATH variable but circumvent that you need to copy shelxl.exe in all the different directories one by one. The SHELXL download page http://shelx.uni-goettingen.de/download.php tells you exactly that, and, in addition, provides a link how to modify the PATH in Windows. Your claim of the opposite is a bit illiterate. TREF is an instruction for SHELXS and SHELXT to solve a structure, hence not a SHELXL instruction. I am very sure the LST-file would stop right there. When you work more with SHELXL you will notice how useful the concise output to the terminal is, and how useful the separation between logfile and terminal output. Best, Tim On Tue, 12 Mar 2024 16:42:16 +0100 Frederic Vellieux wrote: > Hi, > > In fact the problem was solved with the help of Ivica Dilovic from > Zagreb who suggested some changes to the shelxl .ins file. After > these modifications the cryptic error message was still there, but > the modifications made me try to remove one card. That did it. > > So the part that is concerned with this error in the .ins file is as > follows: > > did not work and gave the cryptic error message: > TITL 240223Ru_complex_0m_5 in P1 > CELL 1.34139 10.36240 11.17780 13.19300 80.8589 73.7519 71.3166 > ZERR2.00 0.00070 0.00080 0.00090 0.0026 0.0023 0.0023 > LATT -1 > SFAC C H N O CL RU > UNIT 62 64 2 10 2 2 > TEMP -163.150 > TREF > L.S. 10 > EXTI 0.001 > WGHT 0.0617 > BOND $H > CONF > HTAB > FMAP 2 > PLAN 20 > FVAR 0.75351 > > worked and gave no error: > TITL 240223Ru_complex_0m_5 in P1 > CELL 1.34139 10.3624 11.1778 13.193 80.8589 73.7519 71.3166 > ZERR 2 0.0007 0.0008 0.0009 0.0026 0.0023 0.0023 > LATT -1 > SFAC C H N O Cl Ru > DISP C 0.0137 0.0067 57.1 > DISP Cl 0.3281 0.5435 4162.2 > DISP H 0 0 0.6 > DISP N 0.0241 0.0134 109.9 > DISP O 0.0389 0.0241 193.4 > DISP Ru -0.076 2.5955 20068.6 > UNIT 62 64 2 10 2 2 > L.S. 10 > PLAN 10 > TEMP -163.15 > CONF > BOND $H > HTAB > MORE -1 > fmap 2 > WGHT 0.1 > FVAR 0.25491 > > I guess it would be much better (from the user's point of view) if > SHELXL would write on the output what the offending line is. > > Also, no indications are given on the SHELX site where the Windows > .exe files are supposed to go. They must be placed in the directory > where the GUI (olex2 or WingX) stores its exe file (olex2.exe or > wingx.exe). I just tried to place them there because I was desperate > and it worked. > > Cheers, and thanks to everyone for their suggestions. > > Fred. > > On 2024-03-12 16:12, Kay Diederichs wrote: > [...] > > > > 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/ -- -- 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/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] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography
Dear Fred, there is a Bruker mailing list (bruker-...@g-groups.wisc.edu), that acts as a ccp4bb for small molecule crystallography. As far as I know, there is no automatic inscription, and you should write to Ilia Guzei It is good you are on linux, that's one thing less to worry about. If you want to use SHELXL with Olex2, you need to add SHELXL to your PATH environment, either in a terminal from which you start Olex2, or into the 'start' script for Olex2. In SHELXLE, you can add the SHELXL command from the last menu item in the menu 'SHELX' SHELXL typically writes these types of error into the lst-file, underneath the line in question. If you copy the line, you most likely will get a quick answer. It probably refers to a line that starts with 4 characters which are neither a recognised SHELXL command (http://shelx.uni-goettingen.de/shelxl_html.php) nor a qualified atom line. Best, Tim On Tue, 12 Mar 2024 10:00:36 +0100 Fred Vellieux wrote: > Hi folks, > > I have a simple question: is there an electronic bulletin board for > small-molecule crystallography? I have checked the list of CCP > projects and there is no CCP-project for small molecule > crystallography in the list. > > I am trying to run SHELXL, and it fails with the cryptic message "** > BAD ATOM OR UNKNOWN INSTRUCTION **". > > The alternative for me would be of course to use software meant for > macromolecular cystallography (that I know) on small molecule > diffraction data. And using the small molecule coordinate files > transformed to a suitable format. I don't know if this is feasible or > even advised. Probably not. > > Thanks, > > Fred. > -- -- 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/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/ pgpU0y8cxa2z8.pgp Description: OpenPGP digital signature
Re: [ccp4bb] mixture
Dear Marius, it looks like you didn't receive an answer, yet. It would be easy in SHELXL. You may convert the PDB file to the starting instruction filewith PDB2INS. Fixing any parameter is done by adding 10 to it, i.e. you can simply run awk on the ins-file to fix x,y,z and Uiso for structure 1, and leave structure 2 to be refined. Actually you would want to add 20 to Uiso and -20 to Uiso for structure 2 in order to refine the fraction of 1:2. Best, Tim On Wed, 28 Feb 2024 16:43:14 + Marius Schmidt wrote: > Dear All, > can someone quickly update me with a > way to refine a mixture of structures in > refmac or phenix. > For example, the mixture consists of > 80 % structure 1 and 20 % structure 2. > It is important that structure 1 is kept > fixed (is not refined) and only structure > 2 is varied. > > Best > Marius > > > Marius Schmidt, Dr. rer. Nat. (habil.) > Professor > University of Wisconsin-Milwaukee > Kenwood Interdisciplinary Research Complex > Physics Department, Room 3087 > 3135 North Maryland Avenue > Milwaukee, Wi 53211 > phone (office): 1-414-229-4338 > phone (lab): 414-229-3946 > email: smar...@uwm.edu > https://uwm.edu/physics/people/schmidt-marius/ > https://sites.uwm.edu/smarius/ > https://www.bioxfel.org/ > Nature News and Views: > https://www.nature.com/articles/d41586-023-00504-4 > > > > > 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/ -- -- 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/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/ pgpR0vQOyi6A6.pgp Description: OpenPGP digital signature
Re: [ccp4bb] what is isomorphous?
Hi Doeke, you can take the coordinates of B and do a rigid body refinement against the data from A. If this map is sufficient to reproduce model A (including model building and more refinement cycles), then B is isomorphous to A. You can do this the other way round, and the result may not be the same - hence, the mathematical definition of isomorphous is not identical to the practical use of 'isomorphous' structures when it comes to phasing. You can repeat this for each side of the triangle (each in two directions) in order to label the semantic triangle. Merry Christmas, more peace on earth and sanity for the elections in 2024! Tim On Wed, 20 Dec 2023 20:15:17 + "Hekstra, Doeke Romke" wrote: > Dear colleagues, > > Something to muse over during the holidays: > > Let's say we have three crystal forms of the same protein, for > example crystallized with different ligands. Crystal forms A and B > have the same crystal packing, except that one unit cell dimension > differs by, for example, 3%. Crystal form C has a different crystal > packing arrangement altogether. What is the right nomenclature to > describe the relationship between these crystal forms? > > If A and B are sufficiently different that their phases are > essentially uncorrelated, what do we call them? Near-isomorphous? > Non-isomorphous? Do we need a different term to distinguish them from > C or do we call all three datasets non-isomorphous? > > Thanks for helping us resolve our semantic tangle. > > Happy holidays! > Doeke > > = > > Doeke Hekstra > Assistant Professor of Molecular & Cellular Biology, and of Applied > Physics (SEAS), Director of Undergraduate Studies, Chemical and > Physical Biology Center for Systems Biology, Harvard University > 52 Oxford Street, NW311 > Cambridge, MA 02138 > Office:617-496-4740 > Admin: 617-495-5651 (Lin Song) > > > > > > 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/ -- -- 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/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/ pgp1Ya3oifqhO.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Photon III vs HPC
Dear Daniel, is this for a Bruker Diffractomete? If you have a choice, I would be surprise, because Bruker refused to offer a new D8 with an EIGER2R500 detector - they'd rather not sell their system, and we got a STOE Stadivari instead. We've had a PhotonIII for about 1/2 year on our D8. It is more sensitive than its predecessors, but it still shows noise. When you are used to HPC detectors, it shows a lot of noise, although others are really happy with their PhotonIII. When we got the upgrade from PhotonII to PhotonIII, this was only a firmware upgrade, the very detector stayed installed on the system. However, the PhotonIII is of course fully integrated with the D8 system. The EIGER2 R500 that we have been using of 1/2a now, is not smoothly integrated, and requires probably a nerd like me to be really pleased with the D8+EIGER2 ;-) page 24 on my lecture note https://homepage.univie.ac.at/tim.gruene/teaching/chemcryst/pdfs/2023/tgruene_chemcryst_2023-v05.pdf is with the PhotonII (maybe PhotonIII, i.e. with firmware upgrade, I need to double-check), while p. 25 is from the EIGER2 R500 (about half the size of the PhotonII). The gain range determined by XDS is 0.97-1.3 for the PhotonII, for the EIGER2, it is 0.96-1.02, i.e. very close to 1.0. This is for CuKa, for MoKa, the gain with the EIGER2 is about 0.7. I could find a data set from the PhotonIII and process them with XDS to get comparable figure for MoKa, in case the info will be of interest for you. Feel free to ask more specific questions, or pass by for a visit in Vienna to take a look at the Eiger2 on D8 and Stadivari. Best wishes, Tim On Mon, 30 Oct 2023 10:19:58 + Daniel Balazs wrote: > Dear colleagues, > > We are in the process of acquiring a new SC-XRD system, and having > difficulties comparing apples with pears without taste buds. I would > be indebted if those of you who have any opinion or experience > regarding the Photon III vs Eiger or Hypix HPC choice shared it with > us (here on the list/privately at daniel(dot)balazs(at)ist.ac.at/via > pigeon post). Best regards, > > Daniel > > - > Dr. Daniel Balazs > Staff Scientist (Crystallography) > Institute of Science and Technology Austria (ISTA) > Am Campus 1, Klosterneuburg, 3400 AT > > > > 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/ -- -- 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/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/ pgp8sebQD_Ihm.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln
On Sun, 15 Oct 2023 19:44:45 + "Hekstra, Doeke Romke" wrote: > Mark is, of course, right that this practice is nearly universal, 'universal' to the universe of the US ;-) in Austria, one typically gets 14 salaries per year, in Germany, the salary year usually has 12 months, following the calendar, including 1 month holidays Cheers, 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/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/ pgp6BebVn_3nW.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Occupancy Refinement limitation
Hi Matt, this can be done with SHELXL, even at 2-3A resolution. Anomalous data do help reduce the correlation between B-factor and occupancy (see e.g. https://doi.org/10.1126/science.1254840 to stick with Pavel's example) SHELXL prints the correlation coefficient between occupancy and b-factor, and also the ESD of the occupancy. The is more reliable with least-square refinement, but for large structures, you may need a lot of RAM. PDB2INS (https://www.nature.com/articles/s41467-018-06957-w) conveniently prepares the INS-file from your PDB for you. Best wishes, Tim On Tue, 5 Sep 2023 19:31:25 +0100 Matt McLeod wrote: > Hi all, > > I am trying to get some insight in the accuracy/precision of > occupancy refinements. I have done some 2-state occupancy > refinements and have observed the refinement achieving ~0.25-0.3 > occupancy for the minor population. This population, when observing > the electron density maps, had essentially no evidence for it being > present. I was wondering: > > What are the errors in the reported occupancies? > > Is there a lower and upper limit to occupancy refinements? As in, if > you occupancy refine two states and one is imaginary will it refine > to approximately 1 and 0? Or does the background noise always given > a positive number to the imaginary set? This would, to me at least, > be the lower and upper limits to the occupancy refinements and could > be used as a normalization factor for other atoms. Maybe my logic is > off... > > Any insight or literature would be appreciated! > Matt > > > > 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/ -- -- 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/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/ pgp3Nciy9jGRf.pgp Description: OpenPGP digital signature
[ccp4bb] 2-years postdoc position on electron crystallography in Vienna
Dear all, the Centre for Chemical structure Analysis at the University of Vienna is offering a 2-years postdoc position. The project is a joint project with the Detector group at the Paul Scherrer Institut. A JUNGFRAU detector will be combined with a JEOL Transmission Electron Microscope for advanced data collection and aims at reaching a new level of data quality in ED. Applicants should apply via the job portal https://jobs.univie.ac.at/job/University-Assistant-postdoctoral/975913901 before end of September 2023. A detailed job description and requirements are available there, too. We aim at starting the project in autumn this year, but are flexible by a few months. We look forward to ambitious applicants for an exciting project. Best regards, Tim Gruene P.S.: yes, this is the same position as posted August 7th, with the updated link to the job portal of the University of Vienna -- -- 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/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/ pgpCVM1UGBWBN.pgp Description: OpenPGP digital signature
[ccp4bb] 2-years postdoc position on electron crystallography in Vienna
Dear all, the Centre for Chemical structure Analysis at the University of Vienna is offering a 2-years postdoc position. The project is a joint project with the Detector group at the Paul Scherrer Institut. A JUNGFRAU detector will be combined with a JEOL Transmission Electron Microscope for advanced data collection and aims at reaching a new level of data quality in ED. The job advertisement will be available at jobs.univie.ac.at with JOB ID 1030 early September this year. Attached is a job description. We aim at starting the project in autumn this year. We look forward to ambitious applicants for an exciting project. Best regards, Tim Gruene sent to the Bruker mailing list and the CCP4BB -- -- 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/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/ Job-Description_ED-Jungfrau.pdf Description: Adobe PDF document pgpSMLypJcP_p.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Patenting ligand binding?
Hi Graeme, in my experience, institutions encourage patents. I suppose it is a simple way to demonstrate that Universities produce something of value (money is easy to count, value of thought is not). Personally, I think research should be as open as possible, in hardware, software, and publications. The best quote is from a patent lawyer during a presentation at Park InnoVaare (PSI - sorry, forgot the person's name) "Industry turns knowledge into money - Research turns money into knowledge." When we take a look at the value of the companies, the money we use for research is well invested (and really just peanuts). Cheers, Tim On Fri, 28 Jul 2023 08:17:35 + "Winter, Graeme (DLSLtd,RAL,LSCI)" wrote: > Discussion topics: > > - does this have any hope of being enforced since - as you point out > - it is a pretty obvious next step from X-rays > - does anyone else who is _already doing this_ care > - should we (individuals, not community) be patenting the obvious / > ideas / “inventions” just in case? > > (well aware that the authors of said patent will wake up to this in a > few hours) > > Personally, I am not comfortable with this, but maybe I am a dinosaur? > > Graeme > > [...] > [...] > [...] > > -- -- 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/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/ pgpOj83pv5Gxv.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Patenting ligand binding?
Hi Graeme, do you want to discuss whether obvious steps can be patented? Cheers, Tim On Fri, 28 Jul 2023 07:45:38 + "Winter, Graeme (DLSLtd,RAL,LSCI)" <6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > Interesting > > https://www.freepatentsonline.com/20230228695.pdf > > Patent for use of electron diffraction to assess ligand binding > > Stumbled across this because the patent application cites my work - > felt that this would be of interest to the community > > … discuss? > > Graeme > > -- -- 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/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/ pgp27QHimu7Qu.pgp Description: OpenPGP digital signature
Re: [ccp4bb] How to calculate experimental residual electron density map
Dear Amkur K Singh, every refinement program (buster, refmac5, phenix.refine, SHELXL) produces coefficients for the electron density map, that you name "2Fmo-dFc", as well es the residual electron density map. That's named 'difference map'. Unless I misunderstand, that is what you are looking for. As you are familiar with MoPro, SHELXL might be easier for you than the other refinement programs listed above. With 'pdb2ins', you can easily generate ins- and hkl-file from a PDB-entry. Best wishes, Tim On Mon, 24 Jul 2023 11:26:07 + Ankur Kumar Singh <a8e375e16ee1-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear Members, > I am trying to generate an experimental residual electron density map > for a protein structure resolved at 1.1 Angstrom. One way to do this > is by refining the structure using an aspherical model of charge > distribution (Multipole density proposed by Hansen and Coppens) in > MoPro. However, I cannot take that approach due to resolution > limitation. Another way to calculate this map is- > > > * Calculate only the atomic density for each atom in the > structure. > * Calculate the electron density for the entire structure which > is 2Fmo-dFc > * Subtract these density to obtain the residual electron density > map. > > Is this approach correct? Assuming it to be correct, I looked for > CCP4 tools to perform this job but I couldn't find it. Can anyone > please suggest or comment on this? > > Thanks in advance. > > -- > Regards, > Ankur K Singh > Ph.D Student > > > > > 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/ -- -- 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/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/ pgpYmGYTWALgh.pgp Description: OpenPGP digital signature
Re: [ccp4bb] AW: quantifying electron density
Hi Jon, this is an interesting link. The quality of the absolute scales can be benchmarked with small molecule data. As F000 for X-ray diffraction is the sum of electrons, it can be conveniently determined from counting when each atom is actually modelled. Maybe this has been done, I only read the introduction. Best, Tim On Sat, 1 Jul 2023 06:01:11 + "Hughes, Jonathan" wrote: > hallo again, > thatnks for your replies and warnings about quantifying electron > density. it seems that there are fundamental uncertainties that make > quantitative measurement difficult or even impossible. however, the > redoubtable david von stetten (alias T-REXX) mentioned that "absolute > maps" try to fix the problem: > https://bl831.als.lbl.gov/END/RAPID/end.rapid/Documentation/end.rapid.Manual.htm > best jon > > -Ursprüngliche Nachricht- > Von: CCP4 bulletin board Im Auftrag von > Hughes, Jonathan Gesendet: Mittwoch, 28. Juni 2023 18:16 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [ccp4bb] quantifying electron density > > hello everyone, > is there software that can use an electron density map to quantify > the number of electrons in a selected volume somewhere in a protein? > cheers jon > > -- > Professor Jon Hughes, BSc, PhD > Department of Physics > Free University of Berlin > Arnimallee 14 > 14195 Berlin > Germany > mobile: (+49/0)1757929098 > email: lv...@posteo.de > homepage: > http://www.uni-giessen.de/fbz/fb08/Inst/pflphys > Sent without the use of Apple products > > > > 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/ -- -- 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/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/ pgpKB0FVIfhyp.pgp Description: OpenPGP digital signature
[ccp4bb] Win 10 DHCP-Server to assign fixed IP-address
Hello everyone, we connected an Oxford Cryo 800 with the windows PC of our Bruker Diffractometer via network cable (as I didn't have a USB-cable at hand). The Oxford Cryo 800 runs a dhcp-client. Is it possible to set up a local dhcp-server with Win 10 in order to assign a local IP-address to the Oxford Cryo 800? Unfortunately, there is no linux computer nearby. I search up and down, but it seems that it requires a Windows Server installation to enable a dhcp-server? Cheers, Tim P.S.: I posted this on the Bruker mailing list last Friday, but heard no response, hence this cross-post. -- -- 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/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/ pgpxDTutz7OZQ.pgp Description: OpenPGP digital signature
Re: [ccp4bb] how to get mol files from PDB and restraint CIF?
Hi Frank, in line with Paul's comment, what is so apparent about openbabel not doing the job? I use it frequently to generate the input from PDB to the Grade-Server. Cheers, Tim On Fri, 19 May 2023 10:28:32 +0100 Frank von Delft wrote: > OpenBabel apparently does not. -- -- 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/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/ pgpV4cstNO2ON.pgp Description: OpenPGP digital signature
Re: [ccp4bb] PDB redo R free
Dear Qixu Cai, it is a misconception that Rfree was not free anymore. The gap does not close when you swap the reflections in Rfree set. The 'free' reflections are freed when you do proper refinement, i.e., when the value of the target function becomes stationary. See https://doi.org/10.1107/S0907444997013875 and https://doi.org/10.1107/S0907444999016868 for the mathematical background, https://doi.org/10.1073/pnas.1502136112 for an experimental treatment, and Ian Tickle's explanations on this topic here on the CCP4bb. Best wishes, Tim On Fri, 28 Apr 2023 16:54:07 +0800 Qixu Cai wrote: > Dear Robbie and Tim， > > Thanks a lot for your reply. I just do not understand that if we can > change the R free set during different rounds of refinement, the gap > between Rwork and Rfree would be small, and Rfree would be > meaningless, as R-free set is not "free". > > Best regards, > > Qixu Cai > Email: caiq...@gmail.com > > > > Robbie Joosten 于2023年4月28日周五 > 15:26写道： > > > Hi Qixu, > > > > PDB-REDO tries to have a minimum number test set reflections to > > reduce the error margin in R-free. As Tim says this is not a > > problem but if you reach out privately we can change your > > calculation to use your current testset. That is not recommended > > though. > > > > Cheers, > > Robbie > > > > On 28 Apr 2023 04:51, Qixu Cai wrote: > > > > Dear all, > > > > I'm using the PDB-REDO server to refine my structure. I found that > > PDB-REDO said that 5% R-free set is too small and it created a new > > R-free set. > > > > Is possible for the PDB-REDO server to keep the original R-free set > > to make final Rfree value comparable? > > > > Best regards, > > > > Qixu Cai > > Email: caiq...@gmail.com > > > > > > -- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > -- -- 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/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/ pgpjj_Lr7i04I.pgp Description: OpenPGP digital signature
Re: [ccp4bb] CIF file problem
Dear Ning, their is some confusion. When a small molecule crystal structure is determined, the coordinates and data are usually submitted to the CCDC or the COD (crystallographic open database). The structure receives a checkcif report which, as Phil has pointed out, is specific to small molecule structures. As you submitted a macromolecular structure to the PDB, the PDB code replaces the CCDC ID during the submission process. Best wishes, Tim On Thu, 20 Apr 2023 16:34:18 -0400 Ning Li wrote: > Hi Phil, > > Thank you for the clarification, I didn't realize the CheckCIF is for > small molecules. We tried to submit the manuscript to a chemical > magazine and found "CheckCIF reports must be submitted to the > Cambridge Crystallographic Data Centre (CCDC) *prior to manuscript > submission". In fact I have had the validation for protein structure > as I submitted the structure to PDB library. I'll ask our > collaborator whether they really need it for protein structure.* > > *Thanks* > > *Ning* > > On Thu, Apr 20, 2023 at 4:19 PM Phil Jeffrey > wrote: > > > Hello Ning > > > > CheckCIF checks small molecule crystallographic cif files - the > > dictionaries and expectations on the contents are not the same as > > for mmcif, although the underlying syntax is the same. > > > > I'm unaware of anything that does the equivalent of CheckCIF for > > macromolecular cif files. > > > > Phil Jeffrey > > Princeton > > > > > > On 4/20/23 4:02 PM, Ning Li wrote: > > > Hi all, > > > > > > Does anybody know why I got this error message: > > > > > > /Checking for embedded fcf data in CIF .../ > > > /No extractable fcf data in found in CIF/ > > > > > > as I uploaded the CIF file to https://checkcif.iucr.org/ > > > < > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckcif.iucr.org%2F=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=AGJyz7EJ7Isif6JDsBSfsrr8lg%2BgFsp4gjjA2pOTld0%3D=0> > > for structure validation? The CIF file was directly from > > phenix.refine during structure refinement. > > > > > > Appreciate your help > > > > > > Ning > > > > > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > < > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=lPCCK274is8BSjU5Hl5qTY6wODAdprb5VepQ%2F%2FLJTUA%3D=0 > > > > > > > > > > > > > > ######## > > 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/ -- -- 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/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/ pgpDyo_Z12HSd.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Downloading trouble of SITCOM software
Dear Fu Xingke, the new URL http://webapps.embl-hamburg.de/sitcom/ should work. Best regards, Tim On Wed, 1 Mar 2023 20:13:48 +0800 fuxingke wrote: > Dear Colleagues, > I found SITCOM is useful, but I find the websites can't be > opened. The old from paper is > http://schneider.group.ifom-ieo-campus.it/sitcom. So I can't download > the package to install for using. > > > So, I wuould be really appreciate it if you can provide the > SITCOM installation packages for linux or MacOS. > > > I'm looking forward to your reply. > > > Regards > > > > > > > > Best wishes, > > Fu Xingke > > Institute of Physics CAS > > > > > > 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/ -- -- 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/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/ pgpl8kjutd1CK.pgp Description: OpenPGP digital signature
Re: [ccp4bb] small scale -15C chiller
Hi Artem, the detector has four cables connected: a telephone line, a serial line, a printer-type line, and a USB-cable. I suspect it is easier to use the simulator, which I ordered straight away ;-) Best, Tim On Fri, 3 Feb 2023 10:22:39 -0500 Artem Evdokimov wrote: > Hi Tim > > One last option that's possibly even better, but requires rudimentary > electronics: if you find the logic gate that flips from 0 to 1 (or > backwards) upon thermocouple triggering below threshold temperature, > you can simply supply +5V to the appropriate spot on the PCB, and > Bob's your uncle. > > To find the spot one has to trace the connection a bit, and have a > handy voltmeter with a circuit probe, so when you put the TC into > cold, it will register the signal. This assumes a fairly simple > operation of the circuit - it may be that something much more > sophisticated is taking place, like a signal on a CAN bus or god > knows what else. > > All the best, > > Artem > - Cosmic Cats approve of this message > > > On Fri, Feb 3, 2023 at 2:16 AM Tim Gruene > wrote: > > > Hi Artem, > > > > the simulator is exactly what I was looking for - many thanks! > > We did build a small circuit to generate the voltage (-0.586mV for > > -15C), but this didn't work - probably, our circuit was too simple. > > 12V input looks energetically better to me than using a peltier > > chiller (I meant peliter, not piezo originally...) > > > > Second to that I like Mark's idea of a long cable for the couple and > > stick it in the next -20C cooler. > > > > And yes - I already confirmed with cooling by liquid nitrogen, that > > the concept works: when the thermocouple indicates cold enough, I > > can operate the diffractometer, and hence install our new alien > > detector. I was indeed looking for a long-term solution to make > > overnight measurements. > > > > Thanks to everyone. I feel overwhelmed with the large number of > > quick responses. > > > > Best, > > Tim > > > > On Thu, 2 Feb 2023 20:19:32 -0500 > > Artem Evdokimov wrote: > > > > > A basic Peltier element will likely work (may need a stack of two > > > to reach -20) however the simpler option indeed would be to 'fake > > > out' thermocouple input using a voltage, as described by Ivan. > > > > > > https://us.flukecal.com/Thermocouple-Temperature-Calculator > > > > > > And for $38 one can apparently purchase a thermocouple simulator > > > > > > > > https://www.brightwinelectronics.com/product/temperature-calibrator-k-n-thermocouple-generator-simulator > > > > > > > > Artem > > > > > > On Thu, Feb 2, 2023, 3:42 PM Rajkovic, Ivan < > > > 95c2dc0d4fa4-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > > > > Hi Tim, > > > > > > > > Not sure if this would work, but can you get a voltage supply > > > > and connect it instead of the thermocouple? You would need > > > > something to provide a few mV: > > > > https://www.thermocoupleinfo.com/type-k-thermocouple.htm > > > > > > > > > > > > Ivan > > > > > > > > > > > > > -Original Message- > > > > > From: CCP4 bulletin board On Behalf > > > > > Of Tim Gruene > > > > > Sent: Thursday, February 02, 2023 11:57 AM > > > > > To: CCP4BB@JISCMAIL.AC.UK > > > > > Subject: [ccp4bb] small scale -15C chiller > > > > > > > > > > Good day, > > > > > > > > > > I would like to cool a K-type thermocouple down to -15C. The > > > > > temperature > > > > does > > > > > not need to be very accurate, nor exactly -15C, just below > > > > > that level. > > > > > > > > > > I was thinking of using a piezo-chiller, but they don't seem > > > > > to be very > > > > energy > > > > > efficient. > > > > > > > > > > Could anyone make a recommendation for a simple device to cool > > > > > the tiny thermocouple to -15C to -20C? > > > > > > > > > > For the details: we have an inhouse diffractometer with a dead > > > > > detector. > > > > The > > > > > system is blocked, because the temperature of the detector > > > > > needs to be > > > > below - > > > > > 15C. It is measured with a K-type thermocouple. I
Re: [ccp4bb] small scale -15C chiller
Hi Artem, the simulator is exactly what I was looking for - many thanks! We did build a small circuit to generate the voltage (-0.586mV for -15C), but this didn't work - probably, our circuit was too simple. 12V input looks energetically better to me than using a peltier chiller (I meant peliter, not piezo originally...) Second to that I like Mark's idea of a long cable for the couple and stick it in the next -20C cooler. And yes - I already confirmed with cooling by liquid nitrogen, that the concept works: when the thermocouple indicates cold enough, I can operate the diffractometer, and hence install our new alien detector. I was indeed looking for a long-term solution to make overnight measurements. Thanks to everyone. I feel overwhelmed with the large number of quick responses. Best, Tim On Thu, 2 Feb 2023 20:19:32 -0500 Artem Evdokimov wrote: > A basic Peltier element will likely work (may need a stack of two to > reach -20) however the simpler option indeed would be to 'fake out' > thermocouple input using a voltage, as described by Ivan. > > https://us.flukecal.com/Thermocouple-Temperature-Calculator > > And for $38 one can apparently purchase a thermocouple simulator > > https://www.brightwinelectronics.com/product/temperature-calibrator-k-n-thermocouple-generator-simulator > > Artem > > On Thu, Feb 2, 2023, 3:42 PM Rajkovic, Ivan < > 95c2dc0d4fa4-dmarc-requ...@jiscmail.ac.uk> wrote: > > > Hi Tim, > > > > Not sure if this would work, but can you get a voltage supply and > > connect it instead of the thermocouple? You would need something to > > provide a few mV: > > https://www.thermocoupleinfo.com/type-k-thermocouple.htm > > > > > > Ivan > > > > > > > -Original Message- > > > From: CCP4 bulletin board On Behalf Of Tim > > > Gruene > > > Sent: Thursday, February 02, 2023 11:57 AM > > > To: CCP4BB@JISCMAIL.AC.UK > > > Subject: [ccp4bb] small scale -15C chiller > > > > > > Good day, > > > > > > I would like to cool a K-type thermocouple down to -15C. The > > > temperature > > does > > > not need to be very accurate, nor exactly -15C, just below that > > > level. > > > > > > I was thinking of using a piezo-chiller, but they don't seem to > > > be very > > energy > > > efficient. > > > > > > Could anyone make a recommendation for a simple device to cool > > > the tiny thermocouple to -15C to -20C? > > > > > > For the details: we have an inhouse diffractometer with a dead > > > detector. > > The > > > system is blocked, because the temperature of the detector needs > > > to be > > below - > > > 15C. It is measured with a K-type thermocouple. I tested with > > > liquid > > nitrogen. > > > The system show -64C (probably the limit of the thermocoupe) and > > > I can > > operate > > > the system (and mount our new (brand-alien) detector). > > > > > > Thanks a lot! > > > > > > Best, > > > 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/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/ > > > > > > > > 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/ > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CC
[ccp4bb] small scale -15C chiller
Good day, I would like to cool a K-type thermocouple down to -15C. The temperature does not need to be very accurate, nor exactly -15C, just below that level. I was thinking of using a piezo-chiller, but they don't seem to be very energy efficient. Could anyone make a recommendation for a simple device to cool the tiny thermocouple to -15C to -20C? For the details: we have an inhouse diffractometer with a dead detector. The system is blocked, because the temperature of the detector needs to be below -15C. It is measured with a K-type thermocouple. I tested with liquid nitrogen. The system show -64C (probably the limit of the thermocoupe) and I can operate the system (and mount our new (brand-alien) detector). Thanks a lot! Best, 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/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/ pgpKVPqtSevvD.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Is this Spam? This looks like Spam.
Hi Adrian,
this would be a good reason to upgrade your institutions IT department.
When my electronic signature flags my emails as spam (sic!!!), it is
for sure an Outlook client. It is technically rubbish hiding behind
convenience and lazyness ("we have always been going to lunch at
11:30!").
Cheers,
Tim
On Thu, 12 Jan 2023 06:11:28 +
"Goldman, Adrian" wrote:
> I suspect your institutions are also using office365 outlook (also
> known as crapmail) as mail server
--
--
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
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Re: [ccp4bb] Replacement for Paratone-N?
Hi Yufeng, You can use NVH Oil from jenabiosciences.com as alternative, it is a high viscosity oil. You can also use STP oil tratement. It has been suggested by Vic Young on the Bruker mailing list and approved by several users there. Joe Reibenspiess put it on his web site for utilities https://xray.chem.tamu.edu/documents/tools/tool.php It costs about 10Euro for 1/4l. It is a bit less viscous than Parabar, but this should not be a problem for protein crystals (minerals sink faster, which makes them harder to fish, but not impossible). Best, Tim On Wed, 7 Dec 2022 18:22:38 + Atom Crystal <90477d856f05-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi there, > I just noticed that Hampton Research discontinued Paratone-N and now > recommends Santovac cryo oil. Has anyone tried Santovac and can > comment on how it compares to Paratone? We had some previous success > of using paratone for crystal annealing and felt it was a good > cryoprotectant despite its viscosity. Paratone was a bit tricky to > work with but it is the first cryoprotectant I will try if I want a > quick test of a crystal without having to prepare/optimize glycerol > or EG-based cryoprotectant. Yufeng > > > > > > > > > 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/ -- -- 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/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/ pgpK6G7RJJz3s.pgp Description: OpenPGP digital signature
[ccp4bb] Announcement EMAT workshop on electron crystallography
Dear everyone, On behalf of the organizers, I would like to draw your attention to the forthcoming workshop on Electron Crystallography organized at EMAT (Antwerp) on the 30-31st of May 2023. More information is available at the webpage: https://ecaelectronsig.wordpress.com/schools/upcoming/antwerp-2023/ We are looking forward to seeing you in Belgium. Please circulate this information among your colleagues. 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/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/ pgpM9LM98cxiV.pgp Description: OpenPGP digital signature
Re: [ccp4bb] A challenging MR problem
Dear Medhanjali DasGupta, unless the resolution is really poor, the quickest try would be shelxe, starting from what you already have. It might work at, say, 2.8A resolution or better... Best, Tim On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali DasGupta wrote: > Hello! > My protein structure has a missing domain and I am trying to figure > out the best way to model this missing domain using the solved > (modeled) fixed core domain? My data is also imperfectly twinned, > with 4 twin fractions according to refmac5. > > Any help/ idea is appreciated! > > > -- -- 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/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/ pgpYL0tqPBypu.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Low resolution and high anisotropy
Dear Shenyuan Xu, it is a good sign that the model and density to not match - at 3.07A, one often only has model bias with a poor MR solution. You don't want to start with refinement, better to start with model building: make the model fit the density better, before you run refinement, and check again for R/Rfree. Best regards, Tim On Mon, 24 Oct 2022 09:43:19 +0800 "Xu, Shenyuan" wrote: > Inspecting the electron > density map shows that the model does not fit the electron density > well. -- -- 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/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/ pgph0PwzhE5yN.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Jenkins?
Hello David, maybe a binary in $CBIN with the same name as a system command? (try, e.g. 'apropos truncate' truncate (1) - shrink or extend the size of a file to the specified size ) there used to be a switch to place $CBIN at the end of the $PATH - maybe this helps? Cheers, Tim On Sun, 25 Sep 2022 14:37:38 + "David J. Schuller" wrote: > CCP4 8.0.004 > Scientific Linux 7, kernel 3.10.0-1160.76.1.el7.x86_64 > mate-desktop-1.16.2-1.el7.x86_64 > > This morning I updated my Nvidia graphics driver, then rebooted. When > I logged in again, my desktop (Mate) was all messed up, no > applications menus, etc. I perused the log files and found many lines > similar to these in /var/log/messages: > > Sep 25 09:45:32 titan mate-session[1718]: WARNING: Could not connect > to Systemd: Failed to connect to socket > /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket: > No such file or directorySep 25 09:45:34 titan journal: Error > connecting to system bus: Failed to connect to socket > /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket: > No such file or directory Sep 25 10:12:35 titan pulseaudio[22894]: > [alsa-sink-ALC887-VD Analog] core-util.c: Failed to connect to system > bus: Failed to connect to socket > /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket: > No such file or directory Sep 25 10:12:40 titan pulseaudio[23162]: > [pulseaudio] core-util.c: Failed to connect to system bus: Failed to > connect to socket > /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket: > No such file or directory Sep 25 10:12:40 titan pulseaudio[23162]: > [pulseaudio] core-util.c: Failed to connect to system bus: Failed to > connect to socket > /home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket: > No such file or directory > > I do not have, and have never had, a user "jenkins" on my system. > Note that the CCP4 workspace is implicated. > > I took the CCP4 startup stuff out of my .cshrc login script and > restarted, and everything appeared to be normal. # source > /usr/local/xtal/ccp4/bin/ccp4.setup-csh >& /dev/null > > Why is jenkins mucking about with my desktop settings, and how do I > keep him from doing so? > > > === > All Things Serve the Beam > === > David J. Schuller > modern man in a post-modern world > MacCHESS, Cornell University > schul...@cornell.edu > > > > 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/ -- -- 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/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/ pgpnSwKKTY6eZ.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Quantifying electron density inside of a given volume
Dear Neno, when I asked the same question a few months ago, I ended up writing my own program. We used it for our study of coking in the zeolite ZSM5 (https://doi.org/10.1002/anie.202205413). It is not at all user friendly, and it reads in FCF files, rather than MTZ files. I can send you the source code nevertheless in case you are interested, or a linux binary. It is easy to create an FCF file from your MTZ file with e.g. pdb2ins and a quick run of SHELXL with 'CGLS 0'. Best, Tim On Wed, 10 Aug 2022 09:59:55 -0400 Neno Vuksanovic wrote: > Dear All, > > I would like to quantify electron density inside of positive Fo-Fc > blobs in active sites of multiple protomers in the map and compare > them. I am aware that I can interpolate maps and obtain density > values at coordinate points using either MapMan, Chimera or Coot, but > I would like to know if there is a tool that would let me designate a > sphere of a certain volume and calculate total electron density > inside it? > > Best Regards, > Neno > > > > 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/ -- -- 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/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/ pgp7oYTz8Cc4z.pgp Description: OpenPGP digital signature
Re: [ccp4bb] open review?
ubt that even NSF, DoD, DOE, NIH/HHS or any other government > >>> funding agency will support such initiatives. Transparency and > >>> openness in publishing research is a different ball game, even > >>> though there too there are lopsided effects at the end in many > >>> cases, but overall good for world progress, hopefully. > >>> > >>> Best, > >>> Debanu > >>> > >>> On Wed, Jun 22, 2022 at 6:09 PM James Holton > >>> wrote: > >>>> Greetings all, > >>>> > >>>> I'd like to ask a question that I expect might generate some > >>>> spirited discussion. > >>>> > >>>> We have seen recently a groundswell of support for openness and > >>>> transparency in peer review. Not only are pre-prints popular, > >>>> but we are > >>>> also seeing reviewer comments getting published along with the > >>>> papers themselves. Sometimes even signed by the reviewers, who > >>>> would have traditionally remained anonymous. > >>>> > >>>> My question is: why don't we also do this for grant proposals? > >>>> > >>>> I know this is not the norm. However, after thinking about it, > >>>> why wouldn't we want the process of how funding is awarded in > >>>> science to be at least as transparent as the process of > >>>> publishing the results? Not that the current process isn't > >>>> transparent, but it could be more so. What if applications, and > >>>> their reviewer comments, were made public? Perhaps after an > >>>> embargo period? There could be great benefits here. New > >>>> investigators especially, would have a much clearer picture of > >>>> format, audience, context and convention. I expect unsuccessful > >>>> applications might be even more valuable than successful ones. > >>>> And yet, in reality, those old proposals and especially the > >>>> comments almost never see the light of day. Monumental amounts > >>>> of work goes into them, on both > >>>> sides, but then get tucked away into the darkest corners of our > >>>> hard drives. > >>>> > >>>> So, 2nd question is: would you do it? Would you upload your > >>>> application into the public domain for all to see? What about > >>>> the reviewer comments? > >>>> If not, why not? Afraid people will steal your ideas? Well, once > >>>> something is public, its pretty clear who got the idea first. > >>>> > >>>> 3rd question: what if the service were semi-private? and you got > >>>> to get comments on your proposal before submitting it to your > >>>> funding agency? Would that be helpful? What if in exchange for > >>>> that service you had to review 2-3 other applications? Would > >>>> that be worth it? > >>>> > >>>> Or, perhaps, I'm being far too naiive about all this. For all I > >>>> know there are some rules against doing this I'm not aware of. > >>>> Either way, I'm interested in what this community thinks. Please > >>>> share your views! On- or off-list is fine. > >>>> > >>>> -James Holton > >>>> MAD Scientist > >>>> > >>>> > >>>> > >>>> 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/ > >>>> > >>> > >>> -- > >>> > >>> 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 > > 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/ -- -- 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/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/ pgptsyhvwPsBQ.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Regarding intf error 73
Dear you, your script is expected the files a.asa and b.asa, probably in the current directory. In the opinion of the script or program, these files do not exist. This is irritating for the program to such an extend, that it refuses to work. Therefore it stops. Best regards, Tim On Fri, 10 Jun 2022 05:28:10 +0530 Abhilasha Thakur wrote: > Hello!! > Greetings of the day!! > > I do face this kind of error. I have searched through but didn't get a > positive solution. Please help me in this case. I have attached an > image, PFA. > > > Thankyou > > > > 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/ -- -- 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/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/ pgpGKa6JGB_iM.pgp Description: OpenPGP digital signature
Re: [ccp4bb] SHELXD - Limit Number of CPUs?
Hi Jessica, like most shelx programs, there is a little help message when started without command line options. The option '-tN' sets the number of CPUs to N. If I remember correctly, SHELXD also respects the environment variable OMP_NUM_THREADS. Best, Tim On Wed, 16 Mar 2022 17:21:38 -0700 Jessica Bruhn <450e5de75376-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi all, > > I am wondering if there is a way to limit the number of CPUs that can > be used by SHELXD. It seems that this program uses all that are > available until it hits the NTRY you specified or it finds a .fin > file. Is there a way to limit its CPU and MEM usage? I am running > this on a large cluster along with other jobs and don't want to get > myself into trouble. > > Thanks so much! > > Best, > Jessica > -- -- 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/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/ pgpDOEVyL2SGP.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Affordable open access publishing is finally here!
Hi Bernhard, this is for papers, not for manuscript. 25 bucks is quite dear to print an already published manuscript, as much as I understand that Yeti wants to read your output. Cheers, Tim On Tue, 22 Feb 2022 12:00:54 -0800 Bernhard Rupp wrote: > Glad to bring this opportunity to your attention…. > > > > From: Dr. Adil Laskar > Sent: Monday, February 21, 2022 01:14 > Subject: Need To Response > > > > Respected Researcher, > > > > With our fastest growing Himalayan Journals platform, we have > constructed a management team of highly Interested Scientists & > Research officials who are deeply concerned about your creativity and > exploration. > > Also, we would like to inform you that the creative Articles might > get a special response from the research management team. > > So we would like to invite you to publish your precious creativity > and research articles on our Himalayan Journals. > > > > Our Journals are as follows- > > Himalayan Journal of Agriculture > > Website - https://himjournals.com/journal/hja > <https://signal4domain.com/click?redirect=https%3A%2F%2Fhimjournals.com%2Fjournal%2Fhja=1645434858177=https://himjournals.com/journal/hja> > > > Paper Submission- > > * Online submission - > https://himjournals.com/submit-manuscript > <https://signal4domain.com/click?redirect=https%3A%2F%2Fhimjournals.com%2Fsubmit-manuscript=1645434858177=https://himjournals.com/submit-manuscript> > > > * Email submission - <mailto:himjourn...@gmail.com> > himjourn...@gmail.com > > *WhatsApp submission - +91 9678978384 > > Publication Fee- USD 25 (Foreign)/ Rs.1500 (India) <--<--<--<--<-- > > Indexing and Abstracting > > Google Scholar, Index Copernicus, Research Bible, World Cat, Eurasian > Scientific Journal Index (ESJI) Citefactor, SHERPA/RoMEO, Scientific > Indexing Services (SIS), Road- Directory of Open Access Scholarly > Resources, Directory of Research Journals Indexing (DRJI) and others > in Progress. > > > > > > > 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/ -- -- 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/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/ pgpnxkFA1qqub.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Add hydrogens
Dear Sam, refmac5 has the option of 'geometry optimisation', which doesn't require data. I would assume that you can ask refmac5 to write out the hydrogen atoms for the resulting PDB file. Best regards, Tim On Wed, 29 Sep 2021 19:03:47 +0800 Sam Tang wrote: > Dear community > > This may appear to be a silly question -- I am trying to add > hydrogens to the structure in PDB 1CDW. My initial thought is to run > a single run of refinement with a refinement program. It happens that > I cannot locate the map coefficients under the entry (am I missing > something?) So... is there an easy way to do what I want in this case? > > Warm regards > > Sam > > > > 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/ -- -- 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/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/ pgpKgCsmgnogX.pgp Description: OpenPGP digital signature
Re: [ccp4bb] criteria to set resolution limit
Dear Farhan, did you possibly move the detector too far from the crystal, and the high resolution spots landed on the detector corners? This would explain the good I/sigma at low completeness. In that case, there is no reason to discard the data. You detector was simply not large enough to capture the rest. Best regards, Tim On Sat, 11 Sep 2021 21:25:23 +0530 Syed Farhan Ali wrote: > Dear All, > > I have query regarding one of my dataset. I am running aimless by > keeping highest resolution 1.62 A and getting I/SigI = 2 but data > completeness is around 22 in outermost shell. And if I am increasing > the resolution cutoff up to 1.8 A then I/SigI is 6.2 and completeness > is 82.4. I have attached the screenshot of the result. > What should be the criteria to set the resolution limit? Should I > stick to I/SigI or I have to consider about the completeness of > data. And if completeness is also a guiding factor than how much > minimum completeness I can keep in the higher resolution shell. > > > > > > Regards, > Farhan > > > > 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/ -- -- 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/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/ pgpMVhKk3LGEm.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Dear Robbie, I don't use ccp4 regularly (since our structures are mainly small molecule structures), but when I do, I often use pdbset. I use it to remove het-atoms, or side chains, or water molecules, or reset the B-value. I also use sftools. I have a script for calculating Rcomplete with refmac. This script makes use of sftools in the preparation of the mtz-file. I use these tools, because they are command line tools - much faster than GUI based versions. Best wishes, Tim On Thu, 26 Aug 2021 10:29:22 + Robbie Joosten wrote: > Dear CCP4 users, > > We (as in, the CCP4 developers) are investigating some (potentially) > missing functionality in CCP4i2 and/or Cloud with respect to the > programs pdbset, pdbcur, coordconv, and sftools. Some of these tools > are quite old and may need to be replaced by other tools with similar > functionality. Could you answer a few questions: > > - Do you use any of these tools? > - If so, how often? (Few times a week, month, year, or less than once > a year). > - Which functionality of program X do you use? > - Would you like a graphical interface to that functionality or are > you happy to use the command line? > > Personal example: > I use pdbset a few times a month, but only the "noise" function. I > don't need a graphical interface for it (because it is used in the > context of pdb-redo). I also use sftools, "reduce -> merge average" a > few times a year. Again, only from the command line. > > > Feel free to send your answers directly to me or to the bulletin > board if you want to start a discussion. Tips on alternative CCP4 > tools to achieve similar effects are probably also interesting for > other BB users. > > Cheers, > Robbie > > > > > > > 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/ -- -- 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/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/ pgpenZJvWEENL.pgp Description: OpenPGP digital signature
Re: [ccp4bb] AI papers in experimental macromolecular structure determination
nt from diffraction image (small molecules): > Aguiar, J. A., Gong, M. L., Unocic, R. R., Tasdizen, T. & Miller, B. > D. (2019). Science Advances. 5, eaaw1949. > > Data quality assessment in MX: > - Vollmar, M., Parkhurst, J. M., Jaques, D., Baslé, A., Murshudov, G. > N., Waterman, D. G. & Evans, G. (2020). IUCrJ. 7, 342–354. > > Ligand recognition: > Kowiel, M., Brzezinski, D., Porebski, P. J., Shabalin, I. G., > Jaskolski, M. & Minor, W. (2019). Bioinformatics. 35, 452–461. > > Prediction of missing atoms in small molecular structures: > Thomas, N., Smidt, T., Kearnes, S., Yang, L., Li, L., Kohlhoff, K. & > Riley, P. (2018). > > ADP estimation (small molecules): > Gagner, V. A., Jensen, M. & Katona, G. (2021). Mach. Learn.: Sci. > Technol. 2, 035033. > > > -- > Dr. Andrea Thorn | group leader > andrea.th...@uni-hamburg.de > > Institute for Nanostructure and Solid State Physics, Universität > Hamburg Luruper Chaussee 149 / Bldg. 610 (HARBOR) | 22761 Hamburg | > Germany Tel. +49 (0)40 42838 3651 > www.thorn-lab.de<http://www.thorn-lab.de> | www.insidecorona.net > > > > > 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/ -- -- 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/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/ pgps70GcBjDSY.pgp Description: OpenPGP digital signature
Re: [ccp4bb] using chooch
Dear Eleanor, not sure how to make Chooch happy, but maybe Ethan Merrit can make you happy: there is his excellent server for the anomalous signal for X-ray scattering at http://skuld.bmsc.washington.edu/scatter/ When you choose Br instead of Grr, you find http://skuld.bmsc.washington.edu/scatter/data/Br.dat, or you read your values from the interactive plot http://skuld.bmsc.washington.edu/scatter/AS_form.html Best, Tim On Tue, 20 Jul 2021 12:28:16 +0100 Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Grr - stuck at home - what is f' and f' for Br??? > > All nicely tabulated on my desktop but not here.. > > So use chooch.. > but it grumbles about file name null > > How can I make it happy? > Any help gratefully received > > Eleanor > > > eleanor@wombat cysbfull % chooch -e Br -e 0.92 > == > chooch-5.0.9 > by Gwyndaf Evans Copyright (C) 1994--2013 > gwyn...@gwyndafevans.co.uk > > G. Evans & R. F. Pettifer (2001) >J. Appl. Cryst. 34, 82-86. > == > > License information > --- > Chooch comes with ABSOLUTELY NO WARRANTY; for details > type `chooch -w'. This is free software, and you are > welcome to redistribute it under certain conditions; > type `chooch -c' for details. > > You should have received a copy of the GNU General Public License > along with this program; if not, write to the Free Software > Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA > 02111-1307, USA. > > -e: Atomic element = Br > -e: Atomic element = 0.92 > Fluorescence scan filename: (null) > Chooch output > > > > 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/ -- -- 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/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/ pgpzvxAubn1Ap.pgp Description: OpenPGP digital signature
Re: [ccp4bb] pictures in emails
Hi Ed, dear ccp4bbs
I fully support your email!
Most email clients have a tick box to include a plain text version in
addition of the html-version in their preferences.
Reading plain text emails instead of the html-version (which is also an
available option for most email clients) is a very effective barrier
against spam. People should take this into account, considering the
global rise of ransomware attacks, with serious consequences to some
large institutions and companies.
It has always been good netiquette to at least include a text-version
of your email.
Cheers,
Tim
On Sun, 18 Jul 2021 11:17:26 -0400 Edward Berry
wrote:
> Two suggestions for people sending pictures of electron density to
> the BB:
>
> 1. Reduce the size of the pictures-
> The two pictures in yesterday's email appear nice and small in my
> email client, but still illustrate what is being described. However
> they are actually 4032x3024 and 2040x1458 pixels, making for rather
> large emails. All that extra resolution is wasted unless the user
> opens the image directly ("view image"), and in any case is
> completely unnecessary for the point being made. I think about
> 600x600 pixels is plenty for almost anything you want to show in
> electron density. This does not require manipulation in photoshop or
> such- just reduce the size of the graphics window and take a
> screenshot of that window.
>
> 2. send the picture as an attachment rather than inline. That way it
> won't be included in all the replies. Or if the people replying could
> find some way to exclude pictures or formt the reply as plain-text,
> that would help.
>
> (No, I'm not receiving these emails via 1200 baud modem- but I like
> to save the messages for future reference. If the trend continues
> toward high-resolution inline screenshots, that will take a
> significant amount of disk space. And yes, I know there is an
> archive.) eab
>
>
>
> 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/
--
--
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
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Re: [ccp4bb] Strange indexing problem
Dear Rob, at 1.5A resolution, you can comfortably run shelxe. If there is some useful phase information in your solution, this should complete your model, remove model bias and the resulting composition might tell you the proper space group. Rename your PDB-file into 'mymodel.pda' (pda, not pdb), convert the mtz to 'mymodel.hkl' and run shelxe mymodel.pda -a10 -s0.4 (where 0.4 corresponds to 40% solvent model. You don't need to be very accurate). Good luck, Tim On Mon, 5 Jul 2021 13:54:07 + Robert S Phillips wrote: > I collected data last week on crystals of tyrosine phenol-lyase > obtained under new conditions. The data have higher resolution than > previous crystals, to 1.5 A. However, I can't get them to index in > any space group but P1. Usually, the space group is P21212. The > self-rotation function is attached. The P1 data will give a > molecular replacement solution, but it does not refine below 0.46. > The P1 asymmetric unit fits a dimer, but the assembly is a tetramer. > In the map, I can see the difference peaks from the other dimer of > the tetramer. What could be causing this problem? > > Rob > > Robert S. Phillips > Professor of Chemistry and of Biochemistry and Molecular Biology > University of Georgia > Athens, GA 30602 > Phone: (706) 542-1996 > Fax: (706) 542-9454 > E-mail: rsphill...@chem.uga.edu > Web: > http://tryptophan.net<https://pod51004.outlook.com/owa/redir.aspx?C=ccbf42ffea5f48b1bf8e9bb950454bab=http%3a%2f%2ftryptophan.net> > > > > 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/ -- -- 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/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/ pgpz09vrTitnF.pgp Description: OpenPGP digital signature
Re: [ccp4bb] How to process two datasets 45 degrees apart?
Dear Murpholino, in addition to Graeme's explanation w.r.t. XDS, you probably want to also set the 'STARTING_ANGLE= 90', when you copy UNIT_CELL_A-AXIS= UNIT_CELL_B-AXIS= UNIT_CELL_C-AXIS= from XDS_ASCII.HKL of the first data set into XDS.INP of the second one. Depending on the spacegroup and cell axes, just REFERENCE_DATA_SET= together with SPACE_GROUP_NUMBER= and UNIT_CELL_CONSTANTS= might be sufficient. As a thrid option, you can treat it as one data set and make use of EXCLUDE_DATA_RANGE= 46 89 and integrate the data as a single data set. The latter is probably the most fool proof approach, as long as the file names for B are numbered 90 to 135. Best wishes, Tim for the second data set On Wed, 30 Jun 2021 18:57:03 -0500 Murpholino Peligro wrote: > Hi... > I have a couple of datasets: > A: From 0 to 45 > B: From 90 to 135 > > Can I process them as a unique data set? (with XDS or maybe Mosflm) or > should I process them apart and then merge them? > > > Thanks > > > > 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/ -- -- 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/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/ pgpChgp68KG90.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Co crystalization with less soluble ligand.
Hi Frank, heme becomes near completely insoluble when it dimerizes. Fatty acids are also very insoluble. It is quite hard to get them into HSA, as far as I remember. Cheers, Tim On Wed, 23 Jun 2021 10:33:42 +0100 Frank von Delft wrote: > And then of course, you need to decide whether you at all care to > know anything about a compound that is so insoluble that it needs > that kind of treatment :) > > On 23/06/2021 09:52, hoh wrote: > > Hi > > > > As total insolubility does not exist, I regularly use another > > method, which is to deposit a grain of the ligand directly into the > > drop. > > > > In this case, we no longer control the concentration. The goal is > > to regularly freeze crystals (1 hour, 2 days, 1 week ..). Depending > > on the results, it is possible to adjust the time. If after one > > hour, the crystal no longer diffracts, redo the experience by > > freezing at 10s, 30s, 2mn ..). If a blob appears, frozen after 1 > > week. This technique needs 2 things > > , time and several exploitable crystals in the drop. > > > > > > FH > > > > > > 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/ -- -- 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/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/ pgpiKZin1MEqF.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Should Rmerge be reported?
t; > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > -- > Dr. Manfred S. Weiss > Macromolecular Crystallography > Helmholtz-Zentrum Berlin > Albert-Einstein-Str. 15 > D-12489 Berlin > Germany > > > > Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher > Forschungszentren e.V. > > Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. > Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Bernd Rech > (Sprecher), Prof. Dr. Jan Lüning, Thomas Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > 14109 Berlin > Deutschland > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- -- 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/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/ pgppjJ0Q3oRRh.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Meaning of a pdb entry
27 May 2021 at 18:34, Hughes, Jonathan > > mailto:jon.hug...@bot3.bio.uni-giessen.de>> > > wrote: > > > > "B = 8π2 where u is the r.m.s. displacement of a scattering > > center, and <...> denotes time averaging" > > > > Neither of those statements is necessarily correct: u is the > > _instantaneous_ displacement which of course is constantly changing > > (on a timescale of the order of femtoseconds) and cannot be > > measured. So u2 is the squared instantaneous displacement, > > is the mean-squared displacement, and so the root-mean-squared > > displacement (which of course is amenable to measurement) is > > sqrt(), not the same thing at all as u. > > > > Incidentally, the 8π2 constant factor comes from > > Fourier-transforming the Debye-Waller factor expression I mentioned > > earlier. > > > > Also for crystals at least, the averaging is not only over time, > > it's over all unit cells, i.e. the displacements are not only > > thermal in origin but also due to spatial static disorder > > (instantaneous differences between unit cells). > > > > > > it would seem to me that we would be able to interpret things MUCH > > more easily with u rather than anything derived from u². So then I > > think what you mean is sqrt() rather than , which seems not > > unreasonable. > > > > Cheers > > > > -- Ian > > > > > > > > > > > > > > > > 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 > > > > 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/ > > > > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > > > 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/ > > > > 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/ -- -- 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/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/ pgpUzjiG7nbn2.pgp Description: OpenPGP digital signature
Re: [ccp4bb] (R)MS
Hello Jon, Wikipedia has plenty of information on the Debye-Waller factor: https://en.wikipedia.org/wiki/Debye%E2%80%93Waller_factor Best, Tim On Thu, 27 May 2021 12:25:06 + "Hughes, Jonathan" wrote: > o yes! but maybe the crystal people could explain to me why the B > factor is the variance (with units of Ų) rather than the standard > deviation (i.e. RMS, with units of Å) when, to my simple mind, the > latter would seem be the more appropriate description of variability > in space? cheers jon > > Von: CCP4 bulletin board Im Auftrag von > Pearce, N.M. (Nick) Gesendet: Donnerstag, 27. Mai 2021 12:38 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] Analysis of NMR ensembles > > If you want something comparable to B-factors don’t forget to put the > MSF in the B-factor column, not the RMSF. Will change the scaling of > the tube radius considerably! > > Nick > > > On 27 May 2021, at 11:16, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>> > wrote: > > Cool… > > Purely for visualisation this does look like the approved CCP4 way - > > > > Harry > > > On 27 May 2021, at 10:01, Stuart McNicholas > <19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk<mailto:19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>> > wrote: > > Drawing style (right menu in display table) -> Worm scaled by -> Worm > scaled by NMR variability > > in ccp4mg? > > This changes the size of the worm but not the colour. > > On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>> > wrote: > > > Anyway, thanks to all those who answered my original question - > especially > >Tristan: Chimerax (+ his attached script) >Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/) >Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ ) >Rasmus CYRANGE (http://www.bpc.uni-frankfurt.de/cyrange.html) > and https://www.ccpn.ac.uk/ (of course…) Andrew (uwmn - not sure if > this is buildable on a modern box) Smita: PyMol (not sure if I’m > allowed to say that on ccp4bb…) > > or I could script it and use Gesamt or Superpose for the > superposition if I wanted to stay in the ccp4 universe and had the > time to spare ;-) > > Harry > > > > 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<http://www.jiscmail.ac.uk/CCP4BB>, a > mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, > terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > > > > 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<http://www.jiscmail.ac.uk/CCP4BB>, a > mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, > terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > > > > 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 > > 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/ -- -- 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/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/ pgpDnh2b0PHz1.pgp Description: OpenPGP digital signature
Re: [ccp4bb] weight matrix selection
Dear Luca, did you click at the empty line below where it says 'automatic'? Maybe the word 'manual' is just not visible for inappropriate colour settings. Best wishes, Tim On Thu, 8 Apr 2021 18:14:35 +0200 Luca Mazzei wrote: > Dear CCP4 people, > > I am trying to change manually the geometry weight in Refmac, but > something funny is occurring. As you can see in the snapshot I can > not switch from auto to manual. Suggestions? > > Thanks in advance, > > Luca > > > Luca Mazzei - PhD > Laboratory of Bioinorganic Chemistry > Department of Pharmacy and Biotechnology (FaBiT) > Alma Mater Studiorum - University of Bologna > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy > Tel: +39 0512096235 > > > > > > > > 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/ -- -- 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/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/ pgpmlpu0HKlvM.pgp Description: OpenPGP digital signature
Re: [ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand
Dear Fred,
the error message looks like ligplot was started through a script, that
uses an environment variable, which is not set, soemthing like
${MYLIGPLOTDIR}/components.cif
In case MYLIGPLOTDIR is not set, you would get this sort of error
messages.
Best,
Tim
On Tue, 6 Apr 2021 15:47:21 +0200 Fred Vellieux
wrote:
> Hi folks,
>
> I'm trying to run Ligplot on a PDB file that contains a residue with
> type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2
> years now (which means that I had to reinstall, with an expired
> license, and get familiar with it again). I get the following error
> message (rather cryptic):
>
> Calling HBADD ...
> Running HBADD
> Het Group Dictionary: /components.cif
> Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb
> Command: /LigPlus/lib/exe_linux/hbadd
> /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir
> /tmp/lig7141158588178475829/
> java.io.IOException: Cannot run program
> "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory
> Other event: state
>
> Would anyone know what to make out of this message ? Otherwise is
> there another piece of software (called "app" nowadays) that could
> provide me with similar drawings ?
>
> At some stage I ran PRODRG, introduced the cif file in the file
> components.cif used by LigPlot (LigPlus). I also replaced the
> coordinate files by those returned by the PRODRG run. Always with the
> same cryptic error message provided by the software (oops, app).
>
> Thanks,
>
> Fred.
>
--
--
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
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Re: [ccp4bb] Maniatis: Molecular Cloning
Dear Aviv, dear Jeroen, thank you very much for the links to the latest edition! We always called it 'the Maniatis'... I was also pointed at "Current Protocols in Molecular Biology", edited by F. M. Ausubel et al. https://www.wiley.com/en-us/Current+Protocols+in+Molecular+Biology+-p-9780471503385?purchasedProduct=%2Fen-us%2FCurrent%2BProtocols%2Bin%2BMolecular%2BBiology%2B-p-9780471503385# as an alternative Best regards, Tim On Fri, 26 Mar 2021 13:11:08 + Aviv Paz wrote: > Dear Tim, > > Here is a link to the new version (with some author changes): > https://www.cshlpress.com/default.tpl?cart=1616763922770582099=T=full=oop_title&--eqSKUdatarq=934 > > All the best, > > Aviv Paz, Ph.D. > Associate Research Scientist | Hauptman-Woodward Medical Research > Institute Adjunct Associate Professor of Oncology | Roswell Park > Comprehensive Cancer Center p: +1 716 898 8619 | f: +1 716 898 8660 > e: a...@hwi.buffalo.edu > Hauptman-Woodward Medical Research Institute > 700 Ellicott Street | Buffalo, NY 14203-1102 > hwi.buffalo.edu > > > > 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/ -- -- 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/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/ pgpMtyeYf8MWB.pgp Description: OpenPGP digital signature
[ccp4bb] Maniatis: Molecular Cloning
Hello erveryone, does anyone know whether Maniatis/Fritsch/Sambrock "Molecular Cloning" are still being printed and sold? I could not find it by ISBN (0‐87969‐309‐6) at my favourite book store. Or is there anything comparable? 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/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/ pgpQZ7HsLVPcc.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?
Hi Matthias, I have been using Debian for more than a decade. Every stable release is supported for at least 5 years. Many crystallographic libraries and some programs are part of the standard repository, like raster3d, pymol, shelxle, libccp4, libclipper, ... Debian is particularly stable, and requires little maintenance. Cheers, Tim On Fri, 19 Feb 2021 21:35:46 +0100 Matthias Zeug wrote: > Hi all, > > > > I just came across the (already quite old) news that Red-Hat switches > their support-policy for CentOS to a rolling preview model (replacing > CentOS Linux by CentOS Stream): > > https://www.zdnet.com/article/why-red-hat-dumped-centos-for-centos-stream/ > > https://www.enterpriseai.news/2021/01/22/red-hats-disruption-of-centos-unlea > shes-storm-of-dissent/ > > > > I wondered if that has any implications for the community, as > scientific programs - maybe except the big ones like coot, Phenix, > and ccp4 - are often not *that* well maintained for an extended > period. I had the impression CentOS was liked especially for its > "unbreakability," and it seems to be the main developing platform > for some widely used smaller programs (e.g., adxv). > > > > Do you think it would be advisable to switch to a Ubuntu-distro when > setting up new workstations in the future, or is it safe to stick to > CentOS? > > > > Please let me know what you think :-) > > > > Best, > > > > Matthias > > > > > > Matthias Zeug > > Buchmann Institute of Molecular Life Sciences > > Goethe University Frankfurt > > > > > > > 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/ -- -- 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/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/ pgp4oxT5d4_VY.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"
Dear Jacob, you cannot kill a virus. It is not alive, but a complex chemical compound that interferes with the chemistry of the host. So why don't you work on the part of your conept over the week-end and present the concept? Cheers, Tim On Fri, 19 Feb 2021 12:55:32 -0500 Jacob Keller wrote: > I don't think seeing the big picture resolves, or even addresses, the > question of possibly using a live vaccine. Some big-picture > considerations favor each side. > > The concern of mutation is a grave one, and an unknown. I would point > out, however, that the same considerations apply to the wild virus > currently scourging the planet (well, and every other virus currently > slinking around the biome). The distinction would be, I guess, that > we would be actively contributing in some way. On the other hand, > maybe being passive is like not throwing a rope to a drowning man? > > Maybe having a "v-day" would address this: introduce the > virus-vaccine at well-chosen locations, aka super-spreader events, > which, like well-placed demolition dynamite, would cause a "flash > pan-infection." Funnily, this would require all of the pandemic rules > to be turned on their heads! Presumably this generates herd immunity > within a couple of weeks, as well as its fair share of adverse > reactions and deaths. As a safety measure, have two orthogonal > chemical kill switches based on plentiful inexpensive well-tolerated > compounds, say a vitamin or pesticide (yes, pesticide, that stuff > that's always sprayed all over your food). Use those to quench the > vaccine before mutation, say 6-8 wks. Then, back to normal life, and > start honing similar tools for coming pandemics, a "holohomoimmune > system." > > Here's a question to the informed-consent hawks: would exposing > everybody to the virus while providing two compounds to block > completely the effects be considered a valid opt-in/out? Or what if > the default was switched, such that both compounds were required for > infection, and therefore one had to actively opt in? > > I don't know--it seems that many of the objections to the idea are > based on the bioethical concept "first do no harm," but that > principle is not necessarily adopted in all cases. > > One of the best things I learned in med school: > > Medicine is, fundamentally, "uncertainty management:" > > there are almost never any certainties in medicine, and one has to > use a Bayesian framework and a few bioethical principles to figure > out what to do next. > > Anyway, rest assured, I have not yet ordered the primers for creating > such a virus-vaccine... > > All the best, and have a good weekend everyone, > > Jacob > > > > On Fri, Feb 19, 2021 at 5:54 AM Robbie Joosten > wrote: > > > Hi Tim, > > > > Very good points. The big picture is hard to grasp and we end up > > taking political choices rather than anything else. I'm very glad > > that we can outsource these choices to others every four year here. > > > > Lockdowns may save lives in the here and now, but the global > > economic damage makes life for others much harder to a point that > > it may actually kill them. Economic decline in the First World may > > be something with which that we can deal but, like viruses, it > > blows over to other parts of the world where economic growth is the > > real life saver. Does the prolonging of a reasonably measurable > > number well-lived lives in the West outweigh the extinguishing of a > > hard-to-assess number of much younger lives in the rest of the > > world? I'm glad I don't have to make that call. > > > > Cheers, > > Robbie > > > > > -Original Message- > > > From: CCP4 bulletin board On Behalf Of Tim > > > Gruene > > > Sent: Friday, February 19, 2021 09:33 > > > To: CCP4BB@JISCMAIL.AC.UK > > > Subject: Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?" > > > > > > Hi Jessica, > > > > > > one comment: death cannot be prevented. It is a certainty as soon > > > as you are born (well, 9 months before). > > > > > > While this seems an obvious subtlety, many of the current > > > measures seems to be influenced by the (probably unconscious) > > > belief one can defeat > > death. > > > We can only reduce the risk to die at a certain moment and of a > > > certain cause. > > > > > > The example of rabbits in Australia also illustrates how simple > > > minded humans generally are: we focus on one thing, but usually > > > fail to take a > > l
Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"
just have to take it easy > >> until herd immunity is established, even though few million > >> grandparents will die in the process while the rest of us enjoy > >> indoor dining. > >> > >> > >> > >> On Wed, Feb 17, 2021 at 12:33 PM Jacob Keller > >> wrote: > >> > >>> It would seem to me that it should be possible to generate > >>> versions of the Covid virus that would: > >>> > >>> A. be extremely contagious and yet > >>> B. be clinically benign, and > >>> C. confer immunity to the original covid virus. > >>> > >>> If, then, this virus could be released, with appropriate "kill > >>> switch" safeguards built in, would this not solve the world's > >>> pandemic problems? Is there any reason, practically, why this > >>> approach would not be feasible? > >>> > >>> Maybe we don't really know enough to manipulate A, B, C yet? > >>> > >>> Or maybe it's too scary for primetime...nightmare bio-warfare > >>> apocalypse? > >>> > >>> Has this sort of thing been done, or does it have a name? > >>> > >>> Jacob > >>> -- > >>> > >>> + > >>> > >>> Jacob Pearson Keller > >>> > >>> Assistant Professor > >>> > >>> Department of Pharmacology and Molecular Therapeutics > >>> > >>> Uniformed Services University > >>> > >>> 4301 Jones Bridge Road > >>> > >>> Bethesda MD 20814 > >>> > >>> jacob.kel...@usuhs.edu; jacobpkel...@gmail.com > >>> > >>> Cell: (301)592-7004 > >>> > >>> + > >>> > >>> -- > >>> > >>> 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 > >> > > > > > > -- > > patr...@douglas.co.ukDouglas Instruments Ltd. > > Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK > > Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek > > > > http://www.douglas.co.uk > > Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 > > Regd. England 2177994, VAT Reg. GB 480 7371 36 > > > > -- > > > > 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 > > 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/ -- -- 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/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/ pgp6dD8E9yoA7.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"
Hi Jacob, how do you think this should be possible? In order to infect others, the virus particle needs to proliferate (that's the only thing it does). It profilerates by hijacking the machinery of one cell of your body and turn it into a virus factory. Your body does not like this abuse and kills the cell, and also tries to kill the virus particles. The virus does not make you sick, it only captures one cell. The reaction of your body to kick out the virus, and the cell that does not do it's job anymore, make you sick. A and B are mutually exclusive. B + C is named vaccine. Best, Tim On Wed, 17 Feb 2021 12:33:09 -0500 Jacob Keller wrote: > It would seem to me that it should be possible to generate versions > of the Covid virus that would: > > A. be extremely contagious and yet > B. be clinically benign, and > C. confer immunity to the original covid virus. > > If, then, this virus could be released, with appropriate "kill switch" > safeguards built in, would this not solve the world's pandemic > problems? Is there any reason, practically, why this approach would > not be feasible? > > Maybe we don't really know enough to manipulate A, B, C yet? > > Or maybe it's too scary for primetime...nightmare bio-warfare > apocalypse? > > Has this sort of thing been done, or does it have a name? > > Jacob -- -- 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/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/ pgpfkzIv8hSuk.pgp Description: OpenPGP digital signature
Re: [ccp4bb] RCrane in Coot 0.8.9.2 for Mac
Hi Almudena, in my Coot 0.9.2, the Calculate menu has the entry 'RCrane launch' as second last subentry. Best, Tim On Tue, 9 Feb 2021 13:43:25 + Paul Emsley wrote: > On 09/02/2021 13:33, Almudena Ponce Salvatierra wrote: > > > > I have Coot 0.8.9.2 installed on macOS Catalina. I would like to > > launch RCrane, but I can't find it under "Extensions". > > > > Does anybody know whether there is a way I can make it work on the > > version of Coot, or should I rather uninstall it and look for > > another one? > > Hi Almudena, > > I consulted the release notes, and it says that RCrane was restored > in 0.8.9.2, so the fact that you can't find it is perplexing. Maybe > it moved (I don't recall now, it's been a while). > > Maybe you can find it in a more recent version? (although you might > find that other things have moved). > > Paul. > > > > 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/ -- -- 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/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/ pgphbiJPOVHp3.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI
Dear Andreas, the eiger2cbf code also contains a plugin. I have been using it for at least 2 years with the LIB= keywords in XDS. The compilation is not automatically switched on with the Makefile, but it takes very litte adjustment to create the binary plugin-worker and the plugin plugin.so It works greatly. Best, Tim On Mon, 4 Jan 2021 11:10:34 +0100 Andreas Förster wrote: > Dear Graeme, all, > > to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to > process EIGER and EIGER2 data collected at the synchrotron, Herbert > Bernstein created a Windows installer for Takanori Nakane's eiger2cbf > converter. You can find it here: > https://github.com/nsls-ii-mx/eiger2cbf. Documentation is at the > very bottom. It works for CAP. I haven't tried to see how useful it > is in other contexts. It's a converter, not a plugin, but it lets > you work with HDF5 data under Windows. > > All best. > > Andreas > > > > On Mon, Jan 4, 2021 at 10:22 AM Winter, Graeme (DLSLtd,RAL,LSCI) < > graeme.win...@diamond.ac.uk> wrote: > > > Hi All, > > > > Sorry for the slow response - holiday season & all (I am sure many > > of us needed a break at the end of 2020) > > > > Windows is currently not super well supported for xia2 / DIALS work > > and won’t work at all for xia2 / XDS for the simple reason that XDS > > is not available for the platform (hence absence of durin plugin > > for Windows mentioned elsewhere in this thread) > > > > Your data are from 2019 I would guess from the log text > > > > In this case I would honestly suggest that the best method to > > process this data is to either - > > - work on a UNIX based system > > or > > - restage the data to Diamond and process there > > > > I’m happy to help (off list) with the details of this if it would > > help > > > > We probably should invest some effort in properly supporting > > Windows for xia2 / DIALS - however there are a bunch of rather > > nasty jobs to do in making this possible and it’s never “the most > > important thing” sorry :-( > > > > Happy new year & best wishes Graeme > > > > On 22 Dec 2020, at 16:53, Irwin Selvam < > > irwin.sel...@postgrad.manchester.ac.uk> wrote: > > > > Hi, > > > > I'd like to reprocess some data that were collected on an Eiger2 > > detector at Diamond with Xia2Dials using CCP4i2's GUI. I'm running > > CCP4i2 on a 64-bit Windows 10 machine. The data were processed > > successfully at Diamond with no obvious pathologies, the high > > resolution limit was just a little generous. The folder in question > > contains a Diamond specific file (.nsx extension), two image files > > (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've > > tried pointing Xia2 to the folder itself (which works when > > processing data collected on PILATUS detectors) and each of the > > files contained therein (except the Diamond specific file). Each > > time this results in the error " -ERROR- None:56 Error in wrapper > > xia2_dials 0.0:: External process exited with exit code != 0 > > Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in > > wrapper xia2_dials 0.0:: Error in checking external process after > > completion exit status and code: 0 1". I've attached the error, > > debug etc files for a representative 'run' to this email. Which > > files do I need to point xia2 towards to get it to run? Any help > > would be appreciated. > > > > All the best, > > > > Irwin > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > > > > > > > -- > > > > This e-mail and any attachments may contain confidential, copyright > > and or privileged material, and are for the use of the intended > > addressee only. If you are not the intended addressee or an > > authorised recipient of the addressee please notify us of receipt > > by returning the e-mail and do not use, copy, retain, distribute or > > disclose the information in or attached to the e-mail. > > Any opinions expressed within this e-mail are those of the > > individual and not necessarily of Diamond Light Source Ltd. > > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > > attachments are free from viruses and we cannot accept liability > > for any damage which you may sustain as a result of software > > viruses which may be transmitted in or with the message. > > Di
Re: [ccp4bb] version for old AMD processors
Dear Gottfried, you can compile from source, http://www.ccp4.ac.uk/download/#os=src and/or spend 150-200Euro for a new computer. Best, Tim On Thu, 10 Dec 2020 12:07:17 +0100 "Palm, Gottfried" wrote: > Dear all, > > I am running into a "known issue" upon installing ccp4-7.1 on a > pre2010 AMD machine. The download page says > > > > CCP4 7.1: Known issues > ... > Old AMD processors > ... > We are in the process of preparing an alternative release package for > those processors. > > > > Is there a solution in the meanwhile? > Greetings > Gottfried > > > > 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/ -- -- 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/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/ pgptqsB3JlD_L.pgp Description: OpenPGP digital signature
Re: [ccp4bb] wsl2 Ubuntu 20.04
Dear Johannes, w.r.t. shelx-binaries: you can check with #> cat /proc/cmdline whether the linux-kernel option include 'vsyscall=emulate'. Quite some time ago, the linux kernel made vsyscall obsolete. The SHELX-binaries are probably compiled with an old compiler on an old linux system, and require this kernel option to run. Otherwise they trigger a segmentation fault. vsyscall's are considered a small security hole, but unless you run a safety-critical machine, you can probably risk to open this hole in your kernel at the benefit of running the SHELX programs. This link might be related: https://github.com/microsoft/WSL/issues/4694 Cheers, Tim On Mon, 7 Dec 2020 13:50:23 +0100 Johannes Cramer wrote: > Dear board, > > has anyone gotten ccp4 (specifically shelx and arpwarp) installed and > working under wsl2 (windows subsystem for linux)? > arp warp refuses to install with the following error: > > Segmentation fault > *** ERROR *** > This machine cannot run ARP/wARP executables that > are statically linked to glibc. > > shelx does not complain during installation, but when I type shelxc > (or shelxd, shelxe, shelxl, shelxt) I get immediately to the promt. > No error message or anything. > I am using Ubuntu 20.04 LTS. > > Any help would be appreciated. > > Cheers, > Johannes > > > > 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/ -- -- 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/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/ pgp7VNIn7__eg.pgp Description: OpenPGP digital signature
[ccp4bb] Workshop on electron crystallography Dec 17th 2020
Dear all, on behalf of the organisers, I would like to draw your attention to a workshop on electron crystallography, taking place December 17th 2020. Its purpose is to update of developers and users in the field with the current state of their research. You find more information and a link to the registration at the workshop URL https://www.uni-ulm.de/en/einrichtungen/hrem/christmas-elec-crystall/christmas-elec-crystall/ The workshop program will soon be available. Best regards, TG on behalf of Tatiana Gorelik, Mauro Gemmi, Lukas Palatinus, and Stephanie Kodjikian -- -- 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/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/ pgpQb_1GwtDKw.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Stabilizing Mitegen reusable bases/mounts
Dear Patrick,
you can use ordinary glue ("Uhu Sekundenkleber") or nail varnish to glue
the pin into the base. To remove the pin, just keep it in a beaker with
acetone. Both glue and varnish resolve within short time (an hourish?)
This has been practice in the labs where I worked for the past 20
years. I am surprise Mitegen found a market for their 'resuable' bases.
Best,
Tim
On Sun, 15 Nov 2020 15:45:01 -0500
Patrick Loll wrote:
> Hi everyone,
>
> I’ve become very fond of the Mitegen reusable bases for mounting
> crystals, since the reusable aspect savse me from having to discard
> the base every time I break a microloop. However, once the crystals
> arrive at the synchroteon, I observe motions of the loops (some
> gradual, some sporadic). The the amplitudes of these motions are
> becoming significant as I take data from smaller and smaller
> crystals. I don’t think I’m imagining this, since the good folks at
> NSLS-2/AMX have warned me about this very issue.
>
> I’m writing to ask if anyone has any clever ideas about stabilizing
> these assemblies. Obviously, I can epoxy the pins in place, but then
> I’ll probably need to discard the entire assembly when I break a
> loop, and I’d prefer not to waste more money than necessary. I’ve
> considered putting a bead of wax at the point where the pin enters
> the base (although I haven’t yet checked to see if that will survive
> immersion in liquid nitrogen). Does anyone have any other (better)
> ideas?
>
> Much obliged in advance,
>
> Pat
> __
>
> Patrick J. Loll, PhD
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St.
> Philadelphia, PA 19102-1192 USA
>
> (215) 762-7706
> pj...@drexel.edu
>
>
> 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/
--
--
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
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Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data
as > > rigorous as possible: > > > > - is there a 'best practices' order of refinement operations? > > e.g. refine the lattice parameters first, then peak profiles, etc. > > - there is a single peak that is not matching (likely due to a > > slight deviation in atomic positions from the expected simple > > cubic structure) - is refinement capable of moving individual > > atoms or clusters of atoms to better match a small, unaccounted > > for reflection? > > > > For what it's worth, I have been using Reflex in Materials > > Studio; if there is a more appropriate software for this > > application, I would be happy to hear! > > > > If any additional clarification is need, I'll fill it in! > > > > Best, > > Kamil > > > > > > > > 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 > > <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by > > www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & > > conditions are available at > > https://www.jiscmail.ac.uk/policyandsecurity/ > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > -- -- 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/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/ pgpydqmlEDoWo.pgp Description: OpenPGP digital signature
Re: [ccp4bb] R free rising
Dear Nika, XDS probably did what you asked it to do ;-) This is, however, not a problem. You only need to refine for a couple of rounds longer to gain independence of your Rfree set. No need to reassign them. Depending on the refinement program, it may take many rounds. With Refmac (or shelxl), it does not take very long. Wenn you plot the LLgain, listed at the end of the refmac log-file, and its curve flattens out, your Rfree reflections should be independent and not model-biased anymore. Best regards, Tim On Wed, 4 Nov 2020 13:18:06 + Nika Žibrat wrote: > Hello, > > Two days ago I was asking about R free rising. The problem was xds > adds R free flags already and then re-introduced them in Phenix, > causing R free to rise. I would like to thank you for your answers, > they were most helpful. > > Best, > Nika > > > From: Nika Žibrat > Sent: ponedeljek, 02. november 2020 11:26 > To: ccp4bb@jiscmail.ac.uk > Subject: R free rising > > > Hello, > > > > I am trying to solve an X-ray structure of a protein of which the > structure is already known. My aim is to only seek for ligands > (soaking) and interpret any conformational changes. Since I am using > a model with 100% sequence identity from PDB I am not doing Autobuild > after Molecular phasing and continue directly with phenix.refine > according to reccomendations (10 rounds). In accordance with X-triage > I am also using NCS default settings in the refinement. > > > > This refinement produces solid R free and R work values around 0.29 > and 0.22. The problem becomes when I want to manually edit the > structure, correct the loops which are changed upon binding of the > ligand, and correct any outliers. This results in R free slightly > lower than R work. Upon refining, R work drops normally while R free > rises significantly (for 0.2 -0.3). I have been trying to crack this > for a few days with no success. > > > > I read that slightly lower R free can be normal in such cases but > nevertheless both R values should drop, and haven't found anything > about the big rise of this value after refinement. It feels like I am > missing something, since this is my first time solving a structure. > Any advice? > > > > Thank you, > > Nika > > > > > > 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/ -- -- 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/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/ pgpQENZ1hSHVf.pgp Description: OpenPGP digital signature
Re: [ccp4bb] [xds] how to specify measuring angle
Dear Doo Nam Kim, the indexing procedure is independent of the starting angle of the first frame. Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree per frame during data collection? Best regards, Tim On Thu, 8 Oct 2020 09:28:07 +0100 Doo Nam Kim <4e720d49e642-dmarc-requ...@jiscmail.ac.uk> wrote: > I think that my microED data was measured with -60 to 60 rotation > angle. > > However, > STARTING_ANGLE= -60. > in my XDS.INP > > resulted in > ... > # COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES > > 1 0.0020349 0.0108237 0.0096964 1.00 -0.00 -0.00 > 2 -0.0056895-0.0002762 0.0015024 0.001.00 -0.00 > 3 0.0011313-0.0034716 0.0036457 0.00 -0.001.00 > > > * REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 > * !!! ERROR IN REFINE !!! RETURN CODE IS IER= 0 > > I assume that rotation angle should be specified in XDS.INP. > > Anyone knows how to specify measuring angle in XDS.INP? > > If there's no such option in XDS.INP, please let me know as well. > Then, my other part of XDS.INP should be corrected. > > Thank you > > > > 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/ -- -- 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/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/ pgpz9OxPGhw8u.pgp Description: OpenPGP digital signature
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8
Hi Eike, one of the points is that, only because you got used to a certain operation (over many years after someone showed it to you), does not mean it is intuitive. This could be judged by e.g. showing an ignorant user both methods and let the person judge which one is easier to use... Cheers, Tim On Wed, 9 Sep 2020 20:27:55 + "Schulz, Eike-Christian" wrote: > Hi Tim, > > I don't think that metaphor is quite correct. To me it seems that no > matter what button you pushed you got coffee. In my opinion intuitive > software is a blessing and should not easily be disregarded. > > But as I said before, I am happy to read into new stuff. > > Also there seem to be mixed experiences here. Might this be > map-resolution related ? > > Best, > > Eike > > > > -Original Message- > From: CCP4 bulletin board on behalf of Georg > Zocher Reply to: Georg Zocher > Date: Wednesday, 9. September 2020 at 22:17 > To: "CCP4BB@JISCMAIL.AC.UK" > Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot > 0.8 > > Dear Herman, > > Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE: > > The old real-space refinement was intuitive and easy to use and > > did exactly what the user expected, without having to consult > > the manual! The result might not have been perfect, but was > > good enough for subsequent Refmac, Buster, Phenix refinement. > > That fits perfectly to my user experience with RSR in coot 0.8.x. > and also explains why at least a number of people having some issues > with the new RSR. > > All the best, > > Georg > > > > 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/ > > > > > 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/ -- -- 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/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/ pgp75IU5ikbNx.pgp Description: OpenPGP digital signature
Re: [ccp4bb] AW: Going back to Coot 0.8
Dear Georg and others, if I followed the thread correctly, the coffee story should really go like this: for years you have been pushing the button of a machine showing a cup with a black liquid inside. After ten years, the manufacturer of the machine tells you: "Sorry guy, it is not coffee what you have been drinking. If you want to drink coffee, you should push the button down here, which is labelled 'coffee'." Because you drank the other liquid for years, you are very disappointed by the taste of real coffee and keep on pushing the old button that you got used to. That's how I interpret Paul's statement "[...] many people learnt (I discovered, rather late in the day) [...]" Has anyone of the disappointed users asked how to do it properly? Maybe it is just as easy. Cheers, Tim On Wed, 9 Sep 2020 17:22:27 +0200 Georg Zocher wrote: > Dear Paul, > > people are complaining that they have issues fitting their model in > real space using coot 0.9.x. Personally, I very briefly used coot > other the last months but also have problems using RSR properly > because I'm used to do it the way it was over the last 10 years. This > might be due to my ignorance that I did not have a more closer look > into the new features of RSR in 0.9 release and how to use them. But > from the user site it's different to handle now. > > I do not understand your Ferrari comparison (sorry) as I would not > buy one even if I would have more money than one can spend. But I > would take a cup of coffee as an example. If you always go to the > same dealer to get your coffee in the morning as you know you get a > very descent and excellent tasting cup of coffee that you fully enjoy > every morning than you really get used to it. It might be than a hard > time for you if your coffee dealer tells you: Sorry guys, I do have > now an optimized coffee that is much better, taste a lot better, is > fair produced,... It's just not the coffee you drunk over the last 10 > years and I will not offer that one anymore. You might give the new > one a chance, you might find it as excellent as the dealer but you > might not. From my point of view it's the lack of choice that > personally I do not like so much, especially if there is no other > coffee dealer around... > > Nevertheless, I'm aware and fully respect all the effort you put in > the development of coot and I'm really grateful that coot is > available. > > All the best, > Georg > > > > Am 08.09.20 um 17:44 schrieb Paul Emsley: > > On 08/09/2020 16:25, Georg Zocher wrote: > >> > >> > >> we have the same experience in our lab. > > > > > > What experience is that? I am still in the dark about you think is > > now worse. > > > > > >> Personally, I did would not like to judge here, as so far, I did > >> not have had enough time to get into the new RSR of coot 0.9.x by > >> myself. But many colleagues did not like the new refinement module > >> maybe just as they are used to the method in all coot versions > >> before. > > > > > > You have a Ferrari parked beside your house but you want to to take > > the bus to work because that's what you've always done. Or maybe > > the Ferrari is parked around the back and you don't know it's there? > > > > > >> > >> I just thought if it wouldn't be an option to let the user decide > >> what kind of RSR implementation she/he would like to use and give > >> them the choice via an option in coot preferences? > > > > > > That would be possible but not easy. Unlike much of the CCP4 suite, > > Coot is Free Software. But, again... why would you want to take the > > bus? Explain. > > > > > > regards, > > > > > > Paul. > > > > > > > > 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/ > > > > 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/ -- -- Tim Grue
Re: [ccp4bb] Omega angles with molprobity
Hi Joana, unless you are constrained to a molprobity tool, you could use the CCP4 program ANGLES to list the omega angle for each residue. See $CEXAM/unix/runnable/angles.exam for an example. Best, Tim On Fri, 4 Sep 2020 11:28:47 +0200 Joana Pereira wrote: > Dear all, > > Does anyone know which molprobity tool in ccp4/bin lists the omega > angles for each residue? I see Phenix provides a comprehensive > validation based on Molprobity and, from what I understand, lists the > omega angles for each residue. However, I am having troubles to find > which molprobity tool provides that info. Any idea? > > Many thanks! > > Best wishes > > Joana Pereira > -- -- 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/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/ pgpK1J8w6YIc8.pgp Description: OpenPGP digital signature
Re: [ccp4bb] diffdump in CCP4 7.1
Dear David, Kay Diederich's generate_XDS.INP https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP creates the full XDS.INP for you for a large number of frame formats. It is not CCP4, but I think there are no restrictions for using it. Best regards, Tim On Fri, 21 Aug 2020 14:29:26 -0700 Jan Abendroth wrote: > Hi all, > > It looks as if the utility ‘diffdump’ is no longer part of the > standard linux CCP4 7.1 distribution. > > It has been a very handy tool for preparing XDS input files. > > Does anyone know if there is an equivalent script in CCP4 7.1? > > > > Thanks, > > Jan > -- -- 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/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/ pgpaJPbuoodtc.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Problems with refinement of nucleic acid structure
0.0848 |--| 0.5017 | 0.4906 | > | 9 | C 2 2 21 | 0.0871 |--| 0.5059 | 0.4928 | > | 10 | P 43 21 2 | 0.0919 |--| 0.5180 | 0.5109 | > - > | << 10 | P 43 21 2 | 0.0919 |--| 0.5180 | 0.5109 | > - > > R-factor in the original subgroup is (almost) the best. > The original spacegroup assignment seems to be correct. > > According the non-crystallography translation vector, there is an > output from xtriage: > >- >| XYZ | height | p-value(height) | >- >| 0.000, 0.000, 0.334 | 53.049 | 4.456e-05 | >| 0.000, 0.000, 0.167 | 28.966 | 1.681e-03 | >| 0.000, 0.000, 0.500 | 27.692 | 2.102e-03 | >- > > > Jon Cooper wrote: > > Hello, have you tried anisotropic B-factor refinement? It is > > usually very good at cleaning-up the difference map. At that sort > > of resolution, you may still have some way to go in the refinement > > since the R and R-free usually go to about half of what you have, > > at least with proteins. > > Dear Jon. Yes, I used anisotropic refinement as usually for this sort > of resolution (1.4 A or better). But it looks too high for this small > object and very high resolution, in my opinion. > > Best regards, > > Rafal > > > > 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/ -- -- 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/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/ pgpmCFvK2WBBX.pgp Description: OpenPGP digital signature
Re: [ccp4bb] [EXTERNAL] chirality with electron diffraction
Dear Herman, no, I don't think this is routine, yet! First of all, instrument manufacturers need to catch up. What's on the market is quite behind what is possible - although, I don't have the instrument I'd love to have, but at least the meta data transfer to the image headers only works when you work with a native CCD camera (stone age, I know), not with a hybrid pixel detector. Secondly, Lukas Palatinus' software is, as far as I know, not yet compatible with the rotation method, i.e. when you use XDS or DIALS or mosflm, etc, you cannot use his software for dynamic refinement. I also understand that dynamic refinement is quite time consuming. Lukas is working on this, though. Best wishes, Tim On Mon, 20 Jul 2020 10:36:49 + "Schreuder, Herman /DE" wrote: > Hi Tim, > > thank you for your reply. The 1998 Schenk paper is "new" to me, I had > seen this one: > https://science.sciencemag.org/content/sci/364/6441/667.full.pdf The > background of my question was about the status in practice: Is it > possible to routinely determine the absolute configuration of small > molecules by electron diffraction, or is it something that in theory > can be done, but only difficult in practice? > > Best, > Herman > > > > -Ursprüngliche Nachricht- > Von: Tim Gruene > Gesendet: Montag, 20. Juli 2020 11:03 > An: CCP4 bulletin board ; Schreuder, Herman > /DE Betreff: [EXTERNAL] chirality with > electron diffraction > > EXTERNAL : Real sender is tim.gru...@univie.ac.at > > > > Dear Herman, > > The absolute configuration can be determined, although very > differently from X-ray ccrystallography. > > So far, two different experimental approaches have been published: > Ma, Oleynikov, Terasaki (2017), https://doi.org/10.1038/nmat4890 > > and Brazda et al (2019), 10.1126/science.aaw2560 > > The former is based on imaging, the latter is based on dynamical > refinement: Jansen, Tang, Zandbergen, Schenk (1998), > https://doi.org/10.1107/S0108767397010489 > > There is a very interesting paper by Burmester and Schroeder > Scanning Microscopy Vol. 11, 1997 (Pages 323-334). According to this > paper, the anomalous signal in ED is actually stronger than in X-ray > crystallography. As far as I know, this has not been pursued further. > > Best wishes, > Tim > > P.S.: This is a response to your email to Jessica Bruhns in the > thread 'quote source inquiry'. This thread has reached an overflow, > so I took the liberty to adjust the subject. > > -- > -- > 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 -- -- 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/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/ pgprjT4eCQVZI.pgp Description: OpenPGP digital signature
[ccp4bb] chirality with electron diffraction
Dear Herman, The absolute configuration can be determined, although very differently from X-ray ccrystallography. So far, two different experimental approaches have been published: Ma, Oleynikov, Terasaki (2017), https://doi.org/10.1038/nmat4890 and Brazda et al (2019), 10.1126/science.aaw2560 The former is based on imaging, the latter is based on dynamical refinement: Jansen, Tang, Zandbergen, Schenk (1998), https://doi.org/10.1107/S0108767397010489 There is a very interesting paper by Burmester and Schroeder Scanning Microscopy Vol. 11, 1997 (Pages 323-334). According to this paper, the anomalous signal in ED is actually stronger than in X-ray crystallography. As far as I know, this has not been pursued further. Best wishes, Tim P.S.: This is a response to your email to Jessica Bruhns in the thread 'quote source inquiry'. This thread has reached an overflow, so I took the liberty to adjust the subject. -- -- 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/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/ pgpb5PLDIIARa.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Quote source inquiry
Dear Garib, thank you very much for the details! If everything goes to plan, we are going to use the Dectris QUADRO in September(ish), ideally also with some protein crystals. In ED, distance calibration is more difficult than with X-rays because of instabilities in the lens system (at least with the older instruments), and because I do not work with a parallel beam, but focus the beam onto the detector surface. This is not a very reproducible process. In those cases where I got high resolution data, the cell is often quite stable, and the distance can vary by about 5%... Best regards, Tim On Thu, 16 Jul 2020 23:21:54 +0100 Garib Murshudov wrote: > One correction: Model should after molecular replacement and few > cycles of refinement (perhaps with a little bir relaxed geometry, but > not too much). > > There is an option to use a model after molecular replacement but it > is being migrated to another program that will have proper tests. > > Regards > Garib > > > > On 16 Jul 2020, at 22:34, Garib Murshudov > > wrote: > > > > Hi Tim, > > > > There is an option to do unit cell parameter refinement (for all > > six parameters in general which can only happen in P1). It is > > undocumented. > > > > Celrefine/lattice refine all # if you give scale instead of all > > then only one parameter is refined. > > > > Cellrefine select . # use only atomic B value < Bmedian + > > alpha * Binterquartile_range > > > > > > The last command was added to to reduce effect of wrong atoms. > > > > These command should enable refinement all parameters with due > > account for symmetry. But I am worried about refinement of cell > > parameters using atomic models. The problem is that it affects B > > values and I think if model is not good then cells will be expanded > > to reduce non-bonding interactions. I think it will give biased > > results. For ideal case (when you deliberately change cell > > parameters) it worked perfectly when I tried. However, for real > > cases I could not convince myself to claim that it would give > > unbiased results. My current thought is that either a model after > > molecular replacement should be used or cell parameters should be > > refined outside using data only (then you can only make cell > > parameters consistent with each other). > > > > If you still would want to use refmac to do this calculations then > > you should do it iteratively. Refine cell, then change mtz file > > (different cell parameters) then refine cell again. Please also > > note that if you are refining cell parameters then the resolution > > of the data will also change (if you are refining all six > > parameters then changes will be anisotropic) > > > > > > In general it is a trivial but extremely trivial problem. > > > > Regards > > Garib > > > > > > > >> On 16 Jul 2020, at 18:31, Tim Gruene >> <mailto:tim.gru...@univie.ac.at>> wrote: > >> > >> Hi Jessica, > >> > >> Jens Luebben wrote cellopt for this purpose. It is available from > >> github, https://github.com/JLuebben/CellOpt > >> <https://github.com/JLuebben/CellOpt> > >> > >> It is based on the idea available in whatcheck, i.e. to optimise > >> the unit cell parameters based on geometry restraints DFIX/DANG. > >> Those need to be three-dimensional: I've had cases where the > >> restraints do not span all three dimensions. In this case one of > >> the cell parameters can refine to unrealistic values. > >> > >> We are quite slow on the manuscript for its reference, but for the > >> time being, please quote the nanoArgovia (www.nanoscience.ch > >> <http://www.nanoscience.ch/>) project A12.01 (A3EDPI). > >> > >> cellopt is called liked a shelxl job, i.e. like 'cellopt name' > >> where name.ins and name.hkl are present in the directory. You can > >> add some constraints to the lattice type. > >> > >> Refmac5 can also refine the unit cell parameters (Max Clabbers has > >> made use of this feature), but as far as I understand, refmac5 > >> only scales the unit cell volume isotropically - I am happy to be > >> corrected. > >> > >> When you resolution is quite high, say 0.7A like what we get for > >> zeolites and some organic compounds, you can refine the cell and > >> the distance simultaneously, only the BEAM correlates heavily with > >> the distance. DIALS can produce plots for the correlation between > >> refined
Re: [ccp4bb] Quote source inquiry
. Kleywegt > > > > > > http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se > > > ** > > > The opinions in this message are fictional. Any similarity > > > to actual opinions, living or dead, is purely coincidental. > > > ** > > > Little known gastromathematical curiosity: let "z" be the > > > radius and "a" the thickness of a pizza. Then the volume > > >of that pizza is equal to pi*z*z*a ! > > > ** > > > > > > ## > > > ## > > > > > > 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/ > > > > > > > > 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/ > > > > > > > > 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/ > > > > -- -- 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/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/ pgpp3nA9yY9xU.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Accessing full list of programs in CCP4I2
cribe 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 > > 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/ -- -- 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/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/ pgpIFuqSQdGSS.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Lost extension bar in Coot
Dear Kahkashan, check out the Calculate->Modules... menu. Best, Tim On Thu, 11 Jun 2020 17:56:11 +0530 Firdous Tarique wrote: > Hi > > Just downloaded the new CCP4-7.1. Wondering where the extension bar > in Coot 0.9 has gone. Please help me to find it. I think it is hidden > somewhere. > > Best > > Kahkashan > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?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/ -- -- 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 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/ pgp5ZkJb_Fmag.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Question about small molecule crystallography
Dear Francois, provided you are not restricted to the trademark term 'microED', but open minded to include '3D electron crystallography', there are plenty of published structures of small compounds, both organic and inorganic. Several of them date back to 2005, and include complex structures like MOFs, (Xiaodong Zou, Stockholm), twinned structures (Gemmi/Mugnaioli, Pisa), and really good quality work (Parsons/Zou). Usually, crystals are not "present in powder", they compose the powder, in particular if you use products at 99.9% purity from Sigma-Aldrich 'off the shelf' is it was put, and such powders are not amorphous (if you read bioarxiv) or 'simingly amorphous' (if you read the peer-reviewed version)... Scotch is not the same as adhesive tape, and pampers is not the same as diapers (c.f. also Gerard Bricogne's post on this bb, 29th April 2020). Best, Tim On Tue, 2 Jun 2020 10:52:45 +0200 hoh wrote: > Hi everyone > > > Pr Tamir gonen (UCLA, los Angeles) have solved (not published) few > chemical compounds structures with mircoED. And, the more important > is that crystals were present in the powder (whatever condtions to > get it (preciptation, evaporation ..). I have myself test with 2 > powders coming from Chemists, here in Montpellier, and there were > bunch of nano crystals in both powders, and both diffract at 0.6 A. > And, as the wavelenght in microED in very short , Xds or Dials (with > some specifics parameters) are working well. And ,finally, you need > only around 0.01ug of product to put on the grid (without blotting, > in dry method) with result almost warranty > > So, think about microED for small molecules.. > > FH > > > François Hoh > > Centre de Biochimie Structurale, > UMR 5048 CNRS, UMR 1054 INSERM > 29, rue de navacelles > 34090 Montpellier Cedex, France. > Phone: +33 467 417 706 > Fax: +33 467 417 913 > > > -- -- 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 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/ pgpSrJ2FDqtxh.pgp Description: OpenPGP digital signature
Re: [ccp4bb] Strange Pseudosymmetry Effects
Dear Eddie, dear all According to ftp://ftp.ccp4.ac.uk/ccp4/newsletter/jun_95/, this article appeare in Newsletter June 95. It is mentioned in the table of contents, "Correction on perfection: primary extinction correction in protein crystallography" by Polykarpov and Sawyer. Unfortunately, the article itself is not there Extinction is not the same as the dynamic effects that James mentioned, but this seems the closest match. Would anyone have a copy they can share with me? Thanks a lot! Best, Tim On Thu, 28 May 2020 15:43:00 + Edward Snell wrote: > This jogged my memory of a CCP4 newsletter article many years ago > covering kinematical versus dynamic scattering in protein crystals > and offering a correction that could be used. I think it was Lindsay > Sawyer and Igor Polikarpov in the late 90’s. I apologize if I have > the authors wrong but I thought it was a commentary well ahead of its > time and with modern sources and low noise detectors, I am wondering > if anyone has revisited this? Protein crystals are remarkably high > quality until you cryocool them. Serial methods combined with > instrument capabilities may rate a revisit to the use of the > kinematical approximation versus application of dynamical theories? > Certainly the computational power is available. > > Just my 2 cents for the day. > > Best, > > Eddie > > > Edward Snell Ph.D. > > Director of the NSF BioXFEL Science and Technology Center > President and CEO Hauptman-Woodward Medical Research Institute > BioInnovations Chaired Professorship, University at Buffalo, SUNY > 700 Ellicott Street, Buffalo, NY 14203-1102 > hwi.buffalo.edu<http://hwi.buffalo.edu/> > Phone: (716) 898 8631 Fax: (716) 898 8660 > Skype:eddie.snell Email: > esn...@hwi.buffalo.edu<mailto:esn...@hwi.buffalo.edu> Webpage: > https://hwi.buffalo.edu/scientist-directory/snell/ [hwilogo] > Heisenberg was probably here! > > > > From: CCP4 bulletin board On Behalf Of James > Holton Sent: Thursday, May 28, 2020 11:34 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Strange Pseudosymmetry Effects > > Be careful with electron diffraction and apparent absence violations. > It is possible these weak spots are simply due to multiple > scattering. If so, you would see them relatively stronger with > larger crystals,but much weaker relative to the strong reflections > when the crystal is smaller. Do you? > > -James Holton > MAD Scientist > On 5/27/2020 6:49 PM, Jessica Bruhn wrote: > Hello, > > I am wondering if pseudosymmetry can cause weak reflections that > mimic the doubling of one unit cell axis' length. Has anyone seen > something like this before? > > I am processing data from a small molecule sample collected with > electron diffraction from multiple crystals. For the b axis, it is > not clear if the length should be 10A or 20A. There are spots with > the correct spacing for b=20A, but every other spot seems weaker than > the spots along k if I choose b=10A (this extends beyond (0,k,0)). I > am unable to phase the b=20 data. I have solved this structure in P1 > with b=10 and found four molecules in the ASU and in P212121 with > b=10 resulting in one molecule in the ASU. In P1, three of the four > molecules adopt the same conformation, but the fourth molecule is in > an alternate conformation that causes only ~1/2 of the molecule to be > consistent with the first three. In P212121 I see density for part of > this alternative conformation, but the full molecule in this > alternate conformation cannot pack properly in P212121. Based on > these results and some orthogonal data, I think I should refine the > solution in P1 with b=10. Does it seem reasonable that pseudosymmetry > is causing these weak reflections along k hinting at a doubling of > the b axis? > > Thanks in advance! > > Best, > Jessica > > -- > Jessica Bruhn, Ph.D > Principal Scientist > NanoImaging Services, Inc. > 4940 Carroll Canyon Road, Suite 115 > San Diego, CA 92121 > Phone #: (888) 675-8261 > www.nanoimagingservices.com<http://www.nanoimagingservices.com> > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > Thi
Re: [ccp4bb] What refinement programs are fully Open Source?
> > > > To unsubscribe from the CCP4BB list, click the following link: > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1data=02%7C01%7Cpr159%40leicester.ac.uk%7Cf8cc2fb23bb84707d7a708d7f2a96338%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637244681673138009sdata=nfhtEWy2FS96MYwaHsT4qoQi%2BMbPetQdTwfAf3FDjGg%3Dreserved=0 > > > > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 pgpdxMmHrBirD.pgp Description: OpenPGP digital signature
Re: [ccp4bb] disinfecting keyboards
> >> *To:* CCP4BB@JISCMAIL.AC.UK > >> *Subject:* Re: [ccp4bb] disinfecting keyboards > >> > >> EXTERNAL MAIL > >> > >> You could try doing what my technician does with her keyboard; > >> she wraps it in a clear, thin food wrap that can be taped to the > >> back of the keyboard. This is usually done to keep food and other > >> things (liquids) from damaging the keyboard, but you could simply > >> replace the wrap every time someone else uses it. > >> > >> > >> Personally I like using a Kimwipe soaked with 100% isopropanol, > >> I've never yet encountered a keyboard that suffered from having > >> the writing removed with that or 100% ethanol. Both work and as > >> long as they are 100% (no water), the keyboard and mouse have no > >> issues. > >> > >> > >> Diana > >> > >> > >> ** > >> Diana R. Tomchick > >> Professor > >> Departments of Biophysics and Biochemistry > >> UT Southwestern Medical Center > >> 5323 Harry Hines Blvd. > >> Rm. ND10.214A > >> Dallas, TX 75390-8816 > >> diana.tomch...@utsouthwestern.edu > >> (214) 645-6383 (phone) > >> (214) 645-6353 (fax) > >> > >> *From:* CCP4 bulletin board on behalf of > >> Tim Gruene > >> *Sent:* Wednesday, April 29, 2020 1:53 PM > >> *To:* CCP4BB@JISCMAIL.AC.UK > >> *Subject:* [ccp4bb] disinfecting keyboards > >> 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 > >> > >> > >> > >> UTSouthwestern > >> > >> Medical Center > >> > >> > >> The future of medicine, today. > >> > >> > >> ------------ > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > >> > >> CAUTION: This email originated from outside UTSW. Please be > >> cautious of links or attachments, and validate the sender's email > >> address before replying. > >> > >> > >> > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > >> > > -- > > Dr. Andrea Thorn | group leader > > andrea.th...@uni-wuerzburg.de > > +49 931 31-83677 > > > > Rudolf Virchow Center, University of Wuerzburg > > Josef-Schneider-Str. 2 | 97080 Wuerzburg | Germany > > https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/ > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 pgp5_tFJTrMcq.pgp Description: OpenPGP digital signature
[ccp4bb] disinfecting keyboards
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 pgp1PC7XeJlSP.pgp Description: OpenPGP digital signature
Re: [ccp4bb] superimposition of 3D structures with the DNA part only
Hallo Fred, lsqman (Uppsala software factory) is another option. With lsqman you can give explicit atom names, so that it works e.g. even for small molecule structures that do not follow PDB conventions. @Paul Emsley: a graphical option that let's you e.g. click on 2x3 corresponding atoms in Coot would come very handy ;-) Best, Tim On Fri, 24 Apr 2020 13:08:26 +0200 "Fred. Vellieux" wrote: > Hi folks, > > Some of you may have had to do this already. Either in the lab or > more recently perhaps from home. > > I have two structures that I wish to superpose (two protein:dsDNA > complexes). Not using the protein part, but superposition through the > dsDNA. > > I'm not quite certain what is the "best" way of doing this. > > Your suggestions will be appreciated, thanks. > > Fred. Vellieux > -- -- 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 pgpaEk1qq2mbC.pgp Description: OpenPGP digital signature
Re: [ccp4bb] New phasing approach
Dear Bernhard, your paper is actually not so much of a joke. Are you aware of K. Huemmer's and E. Weckert's three-beam experiments? See e.g. https://link.springer.com/chapter/10.1007/978-1-4615-5879-8_24 Best regards, Tim On Wednesday, April 1, 2020 4:00:19 AM CEST Bernhard Rupp wrote: > Hi Fellows, > > > > just in time for a little reading during quarantine-induced boredom here > preprint pages > > (embargoed until 04.01) from my recent Phys. Rev. paper with a different > take on phasing > > https://tinyurl.com/Phys-Rev-2020 > > > > Enjoy, BR > > -- > > Bernhard Rupp > > <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/ > > <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org > > +1 925 209 7429 > > -- > > Department of Genetic Epidemiology > > Medical University Innsbruck > > Schöpfstr. 41 > > A 6020 Innsbruck > > <mailto:bernhard.r...@i-med.ac.at> bernhard.r...@i-med.ac.at > > +43 676 571 0536 > > -- > > Many plausible ideas vanish > > at the presence of thought > > -- > > > > > ######## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight
Dear Jurgen, https://lmgtfy.com/?q=ccp4+twitter do you need more? Best, Tim On Wednesday, April 1, 2020 5:19:13 PM CEST Jurgen Bosch wrote: > #theBB is too slow :-), Honestly, we probably should have an official CCP4BB > Twitter account monitored by a few administrators to post relevant things > more publicly - just a thought. > > Thanks for the update and good to know it’s moving forward fast. > I had to renew my license for a software I use for shape complementarity > searches, so I have not been able yet to contribute, but I reached out to > my MedChem friends and made them aware of it. Even if they can’t synthesize > stuff right now because we are mostly shut down, they can use their brains > to make suggestions. > > Jürgen > > > On Apr 1, 2020, at 10:15 AM, Frank von Delft > > wrote: > > > > All - last week's call for compound designs to the CoV-2 main protease > > (https://covid.postera.ai/covid <https://covid.postera.ai/covid>) > > elicited an astonishing response... (I confess I was quite taken aback.) > > > > I just realised I should let this BB know the second call for designs is > > now open. Deadline is tomorrow 23:59 PST (April 2nd). (Apologies for > > those that weren't following on twitter.) > > > > Two things: > > we're asking for designs especially focusing on covalent inhibitors (read > > more here > > <https://discuss.postera.ai/t/screening-cascade-fast-track-and-regular-tr > > ack-of-designs/567>) the most convincing designs will be fast-tracked by > > spending more money to cut several weeks off the testing (read more here > > <https://discuss.postera.ai/t/screening-cascade-fast-track-and-regular-tr > > ack-of-designs/567>) Happy designing! > > > > Frank > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> > #### > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)
Dear Gerard, you are wrong. 'he' in this context has as much information as 'someone' and 'person'. It does not refer to the sex of the person spoken about. Best regards, Tim On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote: > >>> Sorry to have taken this matter up in such a visible manner: I > >>> noticed > >>> > >>> this very wrong formula in someone's paper, and that person then told me > >>> where he had found it. Having landed on that page, I didn't know where > >>> to go > For the students: > > "someone" = systematic absence of information = 0 bits > "person" = systematic absence of information = 0 bits > "he" = 1 bit of information! > > --The other Gerard (1 bit of information!) > > ** > Gerard J. Kleywegt > >http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se > ** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. > ** > Little known gastromathematical curiosity: let "z" be the > radius and "a" the thickness of a pizza. Then the volume > of that pizza is equal to pi*z*z*a ! > ** > > ############ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
[ccp4bb] arpnavigator: change contour plane orientation
Dear all,
the arpnavigator can display the contour levels of a map ("map style plane").
Does anyone know how to change the orientation of the plane, i.e. the normal
of the cutting plane?
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:
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Re: [ccp4bb] Overrefinement considerations and Refmac5.
Dear TO, at medium to poor resolution, I prefer to set the weighting myself rather than use the automatic weighting. At 3'ish A resolution, I would start with 0.01 or 0.005 with many more than the default 10 cycles, maybe 50 or 100. The numbers you list below go in the other direction (>4). Best, Tim On Friday, March 6, 2020 2:36:01 PM CET M T wrote: > Dear BBers, > > I am trying to refine a structure using COOT and Refmac5 and I have some > concerns about overrefinement and x-ray term weight in Refmac5, based on > the fact that during refinement to let R factor to drift too far from Rfree > is not good... > > So... First question about that : what is too far ? I have some values in > mind like 6% of difference is OK, 10% is not... But is there a relation in > between resolution of the structure and this difference? Should it be > higher at lower resolution, or always around 6-7% independently of the > resolution? > > Second question is, ok, I have a too big difference, lets say 9-10%... What > could be the reason of that and on what to play to reduce this difference? > > One way I choose is to look at the x-ray term weight (even if I am totally > sure that Refmac5 is doing things better than me), because I saw that the > final rms on BondLength were to constraint (I have in mind that this value > should stays in between 0.02 and 0.01). > So I looked into Refmac log to know where was the starting point and I > found 8.75. > Then I tried several tests and here are the results: > * > > R factor > > Rfree > BondLength > > BondAngle > > ChirVolume > > Auto weighting and experimental sigmas boxes checked > > 0.1932 > 0.2886 > > 0.0072 > > 1.6426 > > 0.1184 > > Weighting term at 4 and experimental sigmas box checked > > 0.1780 > 0.3159 > > 0.1047 > > 8.1929 > > 0.5937 > > Weighting term at 4 > > 0.1792 > 0.3143 > > 0.1008 > > 7.8200 > > 0.5667 > > Weighting term at 15 and experimental sigmas box checked > > 0.1783 > 0.3272 > > 0.2020 > > 1.6569 > > 0.9745 > > Weighting term at 15 > > 0.1801 > 0.3279 > > 0.2022 > > 12.5748 > > 0.9792 > > Weighting term at 8.75 > > 0.1790 > 0.3235 > > 0.1545 > > 10.5118 > > 0.7909 > > Auto weighting box checked > > 0.1948 > 0.2880 > > 0.0076 > > 1.6308 > > 0.1176 > > > > *Refinement Parameters* > [image: image.png] > > So like nothing looks satisfying I decided to ask my questions here... > > What do you recommend to fix my problem, which is a too large difference > between R and Rfree? > > Thank you for answers. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] Hydrogens in PDB File
by phenix.ready_set, whereas for the Buster > >> refinements the hydrogenate tool was used. My understanding is that both > >> of these eventually call the reduce tool from MolProbity. > >> Unsurprisingly, > >> the presence of hydrogens on the model led to both better model geometry > >> and lower R-factors, although at these resolutions there is no observable > >> density for the vast majority of the H-atoms in any of the refined maps. > >> > >> Because the presence of the hydrogens improved the model, I have decided > >> to > >> leave the hydrogens at their refined positions for deposition. > >> > >> I do want to point out one thing for readers interested in this topic: > >> based on all the replies I received, there are a number of differing > >> opinions (and therefore different practices) as to whether hydrogens > >> should be included in deposited structures. The expressed opinions > >> ranged from the ethical (if the hydrogens were there for refinement, > >> then it’s only fair that they be present in the deposited structure so > >> that downstream users know what went into generating the reported > >> statistics) to the practical (if the paper’s conclusions don’t rely on > >> any arguments based on hydrogen atom positions, then there’s no > >> compelling reason for them to be there; include them or don’t, it > >> doesn’t matter.) Because opinions seem to vary, perhaps it would be > >> worthwhile for the PDB to issue some guidance on the matter for the > >> future. > >> > >> Have a nice weekend, everyone. > >> > >> Matthew > >> > >> --- > >> Matthew J. Whitley, Ph.D. > >> Research Instructor > >> Department of Pharmacology & Chemical Biology > >> University of Pittsburgh School of Medicine > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] MX data processing with GPUs??
Dear Ana, you may want to check how many single board computers (like the Raspberry Pi or true open source hardware platform) you can buy for a single GPU high end graphics card. It may be cheaper at better performance compared to GPU computing. XDS (and possibly also DIALS) can distribute its job across ssh, hence you only need the appropriate network connections. XDS wouldn't run on Raspberry Pi, although it may not be difficult to port. Best, Tim On Tuesday, February 18, 2020 8:48:17 PM CET Ana Carolina de Mattos Zeri wrote: > Dear all > we have asked this of a few people, but the question remains: > does any of you have experienced/tried using GPU based software to treat MX > data? for reducing or subsequent image analysis? is it a lost battle? > how do you deal with the crescent amount of data we are facing, at > Synchrotrons and XFELs? Here at the Manaca beamline at Sirius we will > continue to support CPU based software, but due to developments in the > imaging beam lines, GPU machines are looking very attractive. many thanks > in advance for your thoughts, > all the best > Ana > > > > Ana Carolina Zeri, PhD > Manaca Beamline Coordinator (Macromolecular Micro and Nano Crystallography) > Brazilian Synchrotron Light Laboratory (LNLS) > Brazilian Center for Research in Energy and Materials (CNPEM) > Zip Code 13083-970, Campinas, Sao Paulo, Brazil. > (19) 3518-2498 > www.lnls.br<http://www.lnls.br> > ana.z...@lnls.br<mailto:ana.z...@lnls.br> > > > > > > > > > Aviso Legal: Esta mensagem e seus anexos podem conter informa??es > confidenciais e/ou de uso restrito. Observe atentamente seu conte?do e > considere eventual consulta ao remetente antes de copi?-la, divulg?-la ou > distribu?-la. Se voc? recebeu esta mensagem por engano, por favor avise o > remetente e apague-a imediatamente. > > Disclaimer: This email and its attachments may contain confidential and/or > privileged information. Observe its content carefully and consider possible > querying to the sender before copying, disclosing or distributing it. If > you have received this email by mistake, please notify the sender and > delete it immediately. > > #### > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] [3dem] [ccpem] Which resolution?
Hi Marin, crystallography has long moved away from the term 'resolution', see e.g. https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2. It is merely a ballpark number, and it is good to know whether crystallographic data were cut at 1, 2, or 3 Angstrom, but not very important. What counts is the interpretation of the model and conclusion that can be drawn on the system under study. It requires a broader understanding of crystallography in order to understand whether the conclusions are justified. Resolution plays only a minor role in this. It is more useful to take a look at the crystallographic map itself in order to understand. EM is totally different from crystallography, and why would one mix concepts between the fields? Best, Tim On Thursday, February 13, 2020 12:07:15 AM CET Marin van Heel wrote: > Hi Tim, > Good to hear from you! No longer at PSI?? > See... You are already touching upon one of the logical breaking points in > the resolutiton story...! X-ray crystallography resolution criteria like > R-factors make absolutely no sense outside the field of crystallography and > of structural biology. It is the result of a hybrid iterative optimisation > process between the phases of a model structure and the measured amplitudes > of a diffraction experiment! The FRC/FSC resolution criteria, in contrast, > are universal quality metrics not at all coupled to Cryo-EM or structural > biology. Using structural biology arguments like how well I see an alpha > helix or how well I see the hole in an aromatic ring as an assessment > criterion of whether a metric is good or not is a waste of time! (Moreover > filtering a map can completley change its appearance without changing its > information contents). Even some my own (ex-)students and (ex-)postdocs > sometimes completely miss this fundamental point. The FRC and FSC criteria > are now used as quality metrics in all walks of image science like X-ray > tomography and super-resolution light microscopy, fields of science where > atomic coordinates of proteins are not an issue. The FRC / FSC functions > are universal and very direct metrics that compare both the amplitudes and > the phases of two independent measurements of images or 3D-densities of the > same object. For more details, see the 2017 bioRxiv paper and references > therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my > #WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal > structures: the final phases - Current opinion in structural biology 10 > (2000) 259-264. > > Cheers, > Marin > > On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene wrote: > > Dear Marin, > > > > I did not read the enire thread, nor the manuscript you point at - > > apologize > > in case this has been discussed before. > > > > What about a practical approach to determine the resolution of a cryoEM > > map: > > one could take a feature with scales of interest, e.g. an alpha-helix, and > > shift and/or rotate it in steps of, say, 0.3A in several directions to > > see, at > > which magnitude (degree / distance) refinement does not take the helix > > back to > > its original position (within error margins). > > > > One could also take a Monte-Carlo approach and do an arbitrary number of > > random re-orientations of such a helix, refine, and calculate the > > variation in > > position and rotation. > > > > This would reflect my understanding of resolution, much more than any > > statistical descriptor. > > > > Best regards, > > Tim > > > > On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote: > > > Hi Laurence, > > > > > > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc > > > are > > > also based on the same SLOPPY STATISTICS as are all fixed-valued FSC > > > thresholds. This controversy has been ragings for a long long time and > > > > the > > > > > errors made were extensively described (again) in our most recent paper > > > (Van Heel & Schatz 2017 BioRxiv: > > > https://www.biorxiv.org/content/10.1101/224402v1) which has been > > > > downloaded > > > > > more than 3000 times. Further papers on the issue are in the pipeline. > > > > The > > > > > math BLUNDER behind this controversy is simple: the inner product > > > > between > > > > > a signal vector and a noise vector is NOT zero (but rather proportional > > > > to > > > > > SQRT(N) where N is the length of the vectors) and cannot be left out of > > > > the > > > > >
Re: [ccp4bb] refinement of 0.73A data in shelxl
Hi Phil, yes, you are right. I mixed up the occupancy number with the part number. I find these things easier in front of the res-file. Thanks a lot for correcting this. Best, Tim On Thursday, February 6, 2020 10:26:51 PM CET Phil Jeffrey wrote: > That doesn't sound right re: PART numbers > > classically: > > PART 1 > majority disordered atoms with FVAR/occupancy of e.g. "21." instead > of usual "11." > PART 2 > minority disordered atoms with FVAR/occupancy of e.g. "-21." > PART 0 > The 21.000/-21.000 pairs makes the sum of occupancies add to 1.0, but > the actual value of each group is defined by the second free variable. > > See: http://shelx.uni-goettingen.de/shelxl_html.php#PART > The "PART 1" atoms would not interact with the "PART 2" atoms. > There's even an example for a disordered SER in the documentation. > > PART -n is used for disorders that overlap on themselves on symmetry > axes. "If n is negative, the generation of special position constraints > is suppressed and bonds to symmetry generated atoms with the same or a > different non-zero PART number are excluded; this is suitable for a > solvent molecule disordered on a special position of higher symmetry > than the molecule can take". > > I use PART 1/PART 2/PART 0 all the time in "small molecule world" but > I've used PART -1 precisely once. > > Phil Jeffrey > Princeton > > On 2/6/20 4:15 PM, Tim Gruene wrote: > > Dear Matthias, > > > > > > some developers introduce new features of their refinement programs with > > the words " ... which has been there in SHELXL since the beginning of > > time". > > > > If you are only looking for two conformations, you are looking for the > > combination of free variable number N with part N and part -N. In case you > > deal with more than two conformations, take a look at SUMP (as Jon > > suggested). > > > > The use of free variables is easier to explain right at the computer, so > > please ask a colleague near you office, who is familiar with SHELXL for > > the > > details. > > > > Best, > > Tim > > > > On Thursday, February 6, 2020 8:10:01 PM CET Barone, Matthias wrote: > >> Sorry if the mail was not clear. I figured that out now yes. As I wrote > >> in > >> the update, I found this stupid error I made and now everything looks > >> good. > >> > >> Now that I got the feeling of how shelxl works, I miss one of it's > >> features > >> in the pdb format, namely the possibility to link occupancies of a double > >> confirmation to another moiety, say a water or a double confirmation of > >> the > >> ligand. It's there a way to use something similar like FVAR in a pdb > >> file? > >> > >> > >> > >> > >> Dr. Matthias Barone > >> > >> AG Kuehne, Rational Drug Design > >> > >> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > >> Robert-Rössle-Strasse 10 > >> 13125 Berlin > >> > >> Germany > >> Phone: +49 (0)30 94793-284 > >> > >> > >> From: bogba...@yahoo.co.uk > >> Sent: Thursday, February 6, 2020 5:01:14 PM > >> To: Barone, Matthias > >> Cc: CCP4BB@JISCMAIL.AC.UK > >> Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl > >> > >> > >> Hello, hope I can help. > >> > >> > >> OK, so here is the disp table... > >> > >> SFAC C H CL N O > >> > >> DISP $C 0.005100.00239 15.73708 > >> > >> DISP $H-0.20.0 0.66954 > >> > >> DISP $CL0.188450.21747 1035.16450 > >> > >> DISP $N 0.009540.00480 28.16118 > >> > >> DISP $O 0.016050.00875 47.79242 > >> > >> > >> If we take these coordinates... > >> > >> N 30.414964 -0.1476350.11689611.00.19533 > >> 0.44341 = > >> > >> H0A 20.427823 -0.1386560.12325611.0 -1.5 > >> > >> C 10.348035 -0.1607760.11097911.00.20723 > >> 0.28451 = > >> > >> O 40.363785 -0.1741540.10290611.00.21226 > >> 0.22954 = > >> > >> SG50.1773030.1012670.04057210.040000.06849 > >> 0.03024 = > >> > >>
Re: [ccp4bb] refinement of 0.73A data in shelxl
035 -0.1607760.11097911.00.20723 >0.28451 = O 40.363785 -0.1741540.10290611.0 > 0.212260.22954 = SG50.1773030.1012670.040572 > 10.040000.068490.03024 = O 40.2413040.071735 > 0.03856710.960000.149820.12755 = > > And here are some atoms of the inhibitor: > > OBM 50.3251700.4417900.18177711.00.42576 > 0.30731 = <- oxygen CE1 1 -0.0364970.2621770.187030 > 11.00.120560.22455 = <- carbon HE1 2 -0.0288980.247344 >0.18766311.0 -1.2 <- proton NAY 40.107745 > 0.3877040.21097211.00.167190.14264 = <- nitrogen CLAA > 3 0.028744999 0.27121 0.199305996 0.5<- Chloride > > Turned out that Jon had a good feeling about the swapping of the lines and I > did not understand Tim's comment "The scattering factor is derived from the > number next to the name." Once I adjusted the numbers in the second column > of my inhibitors to match the DISP list numbering, Rfree dropped to 16.96% > and the map looks notably better (see attached snap shot). > > > Again, thank you very much for such an incredible feedback. > > Best, Matthias > > > > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > > > From: CCP4 bulletin board on behalf of Tim Gruene > Sent: Tuesday, February 4, 2020 9:24:24 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] refinement of 0.73A data in shelxl > > Dear Jon, > > in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you > like. The scattering factor is derived from the number next to the name. > The name is just that, and identifier. > > Best, > Tim > > On Monday, February 3, 2020 9:20:03 PM CET 0c2488af9525-dmarc- > > requ...@jiscmail.ac.uk wrote: > > Remembered earlier that if the "CL" is not shifted one place to the left, > > Shelx and probably most other programs treat it as carbon, i.e. its > > assumed > > to have 6 rather than 17 electrons. Trust occupancies OK, too ;-? > > > > > > Jon Cooper > > > > > > On 3 Feb 2020 18:26, "Barone, Matthias" wrote: > > > > > > Hi Pavel > > > > glad you write me. I was hoping you would read my post. > > > > - Yes, protons are added, both on the protein as well as on the molecule > > > > - I initially only refined protein and ligand anisotropically, now Im > > running a refinement with all atoms anisotrp except Hs. This would then > > also be the same as shelxl is doing. > > > > - Alternate conformations are modeled, also on the ligand. There are > > plenty, sure, but I think I got most of them. > > > > - I already used Water update during refine, there are some NO3s in the > > structure. I got them in. There is a second ligand somewhere as artifact. > > its density is not well defined, so I hope to get that in once the map > > clears up more. > > > > - I let phenix.refine optimize adp and chemisty weights, but as Petri > > suggested, Im manually increasing the scale factors to match the ones from > > shelxl (just to compare them properly). Im aiming for an rsmd of > > 0.02-0.03A > > like Petri suggested and keep an eye on how tight the structure is refined > > in shelxl. > > > > > > > > > > About the Rfact and the gap. Yes, thats what I was expecting. I hope if I > > add more anisotropic B fact, the Rfacts should go down to at least what > > shelxl yielded. > > > > > > > > > > thank you all again for the massive feedback, ideas and help. > > > > > > > > > > > > > > > > > > > > > > Dr. Matthias Barone > > > > AG Kuehne, Rational Drug Design > > > > > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > > Robert-Rössle-Strasse 10 > > 13125 Berlin > > > > Germany > > Phone: +49 (0)30 94793-284 > > > > > > From:Pavel Afonine > > Sent:Monday, February 3, 2020 7:14:25 PM > > To:Barone, Matthias > > Cc:CCP4BB@JISCMAIL.AC.UK > > Subject:Re: [ccp4bb] refinement of 0.73A data in shelxl > > > > Hi Matthias, > > > > > > did you use correct model parameterization and opt
Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020
ma Iberoamericano > de Ciencia y Tecnologia para el Desarrollo (CYTED) through de MICROBES > consortium. > Organizers: > Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay > Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United > Kingdom Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, > Brazil > Applicants: > 25 students will be selected, prioritizing advanced PhD, postdocs and young > researchers. The Course will provide financial support covering > registration fees, and for the case of those students coming from abroad, > all local expenses (lodging, per diem and local transportation). Look in > the www site for details on application procedures. > The application deadline is July 9, 2020. > > Please address further inquiries to: > mx2...@pasteur.edu.uy<mailto:mx2...@pasteur.edu.uy> > Looking forward to hosting you in Montevideo! > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] refinement of 0.73A data in shelxl
hat contains the inhibitor. Hence, I used pdb2ins and the pdb from PRODRG > to produce SFAC for the inhibitor Cloride. I then pasted this line > > > DISP $CL0.188450.21747 1035.16450 > > > > into the .res file and updated the UNIT line. Shelxl runs through, and the > density looks ok on the Chloride now. However Rfree is back up at 24% and > the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg): now, > very distincitvly, backbone carbonyls and NHs show difference density. > > Am I right in my assumption, that the SFAC of Cloride is not properly > calculated at the given wavelenght? And if so, how do I guess it correctly? > > > > > > Thank you very much for your help! > > Best, matthias > > > > > > > > > > > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] Protein concentration for the initial crystallisation trials
Dear Armando, in case you have enough material to spare, I would use a concentrator to create a saturated solution, i.e. concentrate until it precipitates. Measure the concentration of the saturated solution, i.e., supernatant without disturbing the solution with the precipitate. You can start crystallisation trials at 70-90% of this concentration. Best, Tim On Wednesday, January 8, 2020 5:16:31 PM CET Armando Albert wrote: > Dear all, > I was wondering how to guess the optimal protein concentration for the > initial crystallisation trials. Is there any trick or assay other than the > classic PCT from Hampton? Armando > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] 8/ 2263 spots indexed XDS
Dear Almudena, SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to increase in your situation. The default is 3. Try e.g. 5, and increase slowly to make sure that the suggested solution makes sense Best regards, Tim On Friday, November 29, 2019 12:48:11 PM CET Almudena Ponce Salvatierra wrote: > Dear all, > > I have some data sets that don't want to be processed :p > > In one of them, when I look at IDXREF.LP I see virtually none of the found > spots were indexed and the reason is that they are "too far from the > expected position". The spots are smeary and elongated, so not the > prettiest. > > I have managed to process so far only one data set with decent statistics > from another crystal harvested from the same drop, where the diffraction > spots look better. > > I am trying to find in the xds wiki the keyword I should fine tune in order > to make those spots indexable. > > Could you help me please? > > Thank you very much in advance. > > Best wishes, > > Almu > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] Shelx and debian 10
hared library: > > [libgfortran.so.3] > > 0x0001 (NEEDED) Shared library: [libm.so.6] > > 0x0001 (NEEDED) Shared library: [libgcc_s.so.1] > > 0x0001 (NEEDED) Shared library: [libc.so.6] > > 0x000f (RPATH) Library rpath: [$ORIGIN/../lib] > > Note the special token "$ORIGIN", which means the directory containing > the executable (this is documented in the 'man' page for ld.so). The > RPATH item is set to the above value with an option like > '-Wl,-rpath,\$ORIGIN/../lib' (where the '$' character needs to be > escaped from the shell, obviously). > > Note that -rpath is not the same as -L: -L is used at link-time to find > the libraries needed to check that all the symbols are resolvable. > -rpath is used to locate shared libraries at run-time: its argument > doesn't even have to exist at link-time. If you go down this route, you > will need to specify both -L and -rpath. > > > What do users think? > > As for which is the best approach, I'll let others make their opinions > known, but I hope that this explanation has helped. > > Regards, > > Peter. > > > Best wishes, George > > > > On 08.10.19 11:04, Peter Keller wrote: > >> HI Tim, > >> > >> On Mon, 7 Oct 2019, Tim Gruene wrote: > >>> Date: Mon, 07 Oct 2019 23:04:28 +0200 > >>> From: Tim Gruene > >>> To: Peter Keller > >>> Cc: CCP4BB@jiscmail.ac.uk > >>> Subject: Re: [ccp4bb] Shelx and debian 10 > >>> > >>> > >>> > >>> @Peter: are you sure that without 'vsyscall=emulate' linux binaries > >>> need to be > >>> dynamically linked? I would be very surprised if the linux kernel would > >>> disable statically linked binaries. I rather think that the vanilla > >>> versions > >>> of shelx c/d/e (from shelx.uni-goettingen.de) are compiled with an > >>> obsolete > >>> compiler / obsolete compiler options. > >> > >> You're right, I wrote my reply to Bernhard too rapidly, and conflated > >> two separate issues. Debian 10 still supports static binaries of > >> course, but in its default configuration (without vsyscall=emulate), > >> those static binaries must be linked with a version of glibc that > >> doesn't require vsyscalls. OTOH, dynamic binaries don't suffer from > >> this problem, because they can use vDSO provided by the running > >> (rather than the build) system. > >> > >> I think that part of the problem is that traditionally when we want > >> to build portable linux binaries, we tend to build on the oldest > >> distribution that we want to support, relying on backwards > >> compatibility to provide the portability that we are after. We often > >> build statically, because it is a robust way of including all the > >> required libraries and is less fiddly and error-prone than providing > >> them as dynamic libraries. There is also no danger of breakage caused > >> by rogue values of LD_LIBRARY_PATH (which users shouldn't be setting > >> of course, but we have no way of stopping them). The drawback of this > >> approach is that when backwards compatibility is broken, there is no > >> application-level fix. > >> > >> These kinds of problems are rare, but when they do happen the onus is > >> on those of us who distribute binary applications to find solutions. > >> Some sysadmins may have good reasons for being reluctant to change > >> kernel parameters to get third-party applications to work. > >> > >> Regards, > >> Peter. > >> > >>> On Monday, October 7, 2019 5:53:44 PM CEST Peter Keller wrote: > >>>> Dear Bernhard, > >>>> > >>>> We had this issue drawn to our attention last year by an early adopter > >>>> of Debian 10 while it was still in testing. I thought that it was a > >>>> bug, > >>>> and submitted a report accordingly here: > >>>> <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=889965>. I was told > >>>> that it is not a bug, but a feature ;-) > >>>> > >>>> If you are able, you could try setting the kernel parameter > >>>> vsyscall=emulate. In the longer term, SHELXC/D/E will have to be > >>>> rebuilt > >>>> to support systems where the vsyscall has been disabled. This means > >>>> they > >>>> ha
Re: [ccp4bb] Shelx and debian 10
Dear Bernhard, as Peter mentioned, you need to reboot the system with the kernel parameter vsyscall=emulate. On Debian, you edit the file /etc/default/grub and modify the value of GRUB_CMDLINE_LINUX_DEFAULT="quiet vsyscall=emulate" (default here is GRUB_CMDLINE_LINUX_DEFAULT="quiet") Once saved,you run the command 'update-grub' and reboot the system. @Peter: are you sure that without 'vsyscall=emulate' linux binaries need to be dynamically linked? I would be very surprised if the linux kernel would disable statically linked binaries. I rather think that the vanilla versions of shelx c/d/e (from shelx.uni-goettingen.de) are compiled with an obsolete compiler / obsolete compiler options. Best regards, Tim On Monday, October 7, 2019 5:53:44 PM CEST Peter Keller wrote: > Dear Bernhard, > > We had this issue drawn to our attention last year by an early adopter > of Debian 10 while it was still in testing. I thought that it was a bug, > and submitted a report accordingly here: > <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=889965>. I was told > that it is not a bug, but a feature ;-) > > If you are able, you could try setting the kernel parameter > vsyscall=emulate. In the longer term, SHELXC/D/E will have to be rebuilt > to support systems where the vsyscall has been disabled. This means they > have to be dynamic executables that include the following in the output > of 'ldd': > > % ldd /bin/bash > linux-vdso.so.1 (0x7fff50952000) > > > All current distros use vDSO, so this shouldn't cause portability > problems by itself, but handling dynamic executables can be trickier > than static ones. > > For a little more background, see <https://lwn.net/Articles/446528/> > > Finally, you have my commiserations: although this change has been a > long time coming, it hasn't attracted a lot of attention. It was bound > to catch users of static executables by surprise. > > Regards, > > Peter. > > On 07/10/2019 16:05, Bernhard Rupp wrote: > > Hi Fellows, > > > > we updated to Debian 10 on the local workshop computers, and reinstalled > > > > Coot and ccp4. All fine. > > > > Problem: Shelxc/d/e/ does not run, and > > > > the call exits immediately sans any message. > > > > This holds for the binaries included in ccp4 as well as for those from > > the SHELX site. > > > > The executables from CCP4 and SHELX site – same file size, probably > > same - run fine under Debian 9. > > > > I suspect a library problem. > > > > Does some kind soul have CDE binaries for Debian 10 to share? > > > > Many thx in advance, BR > > > > -- > > -- > > > > Bernhard Rupp > > > > Department of Genetics and Pharmacology > > > > Institute of Genetic Epidemiology > > > > Medical University Innsbruck > > > > Schöpfstrasse 41 > > > > A 6020 Innsbruck – Austria > > > > +43 (676) 571-0536 > > > > bernhard.r...@i-med.ac.at > > > > -- > > -- > > > > k.k. Hofkristallamt > > > > San Diego, CA 92084 > > > > 001 (925) 209-7429 > > > > b...@ruppweb.org > > > > b...@hofkristallamt.org > > > > http://www.ruppweb.org/ > > > > --- > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] Rfree from another mtz file
Dear Mariana, you can simply create a new set for Rfree, independently of the previous one. It will be as good as the copied one, and there is no reason why you would need to maintain the same flags. As Ian Tickle explained only briefly ago, your new data set will have new, independent errors. Best regards, Tim On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote: > Dear all, > > We tried to use the Rfree set from a lower resolution data with a higher > resolution from the same Crystal. To do so We used aimless at ccp4i with > the option use free flag from another mtz file and extend the data. > > I think it worked, but now we don't know how to be sure we have the same > Rfree set. Does anyone have a way to prove it? > Thank you in advance, > Best, > Mariana > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
Re: [ccp4bb] AW: [bruker-axs] cbf to sfrm
Dear Holger,
thanks a lot for the prompt reaction! This will be very useful, in particular
in case of proper twins.
I look forward to the update,
Tim
On Thursday, August 29, 2019 11:32:00 AM CEST bruker-...@lists.wisc.edu wrote:
> Dear Tim,
>
>
>
> Thanks for having brought the bug to our attention. It got fixed in the
> PROTEUM3/APEX3 2019.1 version which will be available for download next
> week.
>
>
>
> Cheers,
> Holger
>
>
> Dr. Holger Ott
> Global Application Coordinator SC-XRD & Senior Application Scientist
> Chemical Crystallography
>
> Bruker AXS GmbH
> Oestliche Rheinbrueckenstr. 49
> 76187 Karlsruhe, Germany
>
> Phone: +49 721 50997-5628
> Fax: +49 721 50997-45628
>
> Holger.Ott@bruker<mailto:Holger.Ott@bruker>.com
> www.bruker.com<http://www.bruker.com/>
>
>
>
>
>
> Sitz der Gesellschaft/Registered Office: Karlsruhe, HRB 107524 Amtsgericht
> Mannheim, Umsatzsteuer-Ident.Nr. DE812037551, Geschäftsführer/Managing
> Directors: - Dr. Frank Burgäzy, Dr. Klaus Gohlke
>
> Diese E-Mail einschließlich etwaiger Anlagen kann vertrauliche Informationen
> enthalten. Sie ist daher vom Adressaten vertraulich zu behandeln und darf
> nicht veröffentlicht werden. This email, including possible attachments,
> may contain confidential information. It should therefore be treated as
> confidential by the addressee and may not be published.
>
>
>
>
>
> -Ursprüngliche Nachricht-
> Von: bruker-...@lists.wisc.edu [mailto:bruker-...@lists.wisc.edu]
> Gesendet: Sonntag, 28. Juli 2019 18:25
> An: bruker-...@lists.wisc.edu; ccp4bb@jiscmail.ac.uk;
> pheni...@phenix-online.org Betreff: [bruker-axs] cbf to sfrm
>
>
>
> Dear all,
>
>
>
> recently the conversion from CBF to SFRM frame format with APEX was
> discussed on the Bruker mailing list ("Synchrotron data with Bruker
> Software"), including a potential bug that parameters in the frames other
> than the first frame are not set correctly. The workaround to re-convert
> from SFRM to SFRM a second time did not help in my case.
>
>
>
> I therefore updated my program sfrmtools, available at https://
> homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/
>
>
>
> With the option '-u',you can provide the first frame of the run, and via
> '-p'
>
> a parameter file that contains the critical parameters (see documentation at
> above URL) to update the header for all frames in this run. In case you
> have twinned data and want to benefit from SAINT, this should be possible
> with this feature.
>
>
>
> Both 64bit Linux binary and the source code are available. The program has
> no dependencies and should compile under any platform.
>
>
>
> I did not debug this new feature very thoroughly, but it worked for me so
> far.
>
> Any bug reports are welcome to this address
> tim.gru...@univie.ac.at<mailto:tim.gru...@univie.ac.at>
>
>
>
> I hope this is helpful for one or two users.
>
>
>
> I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM
> header format.
>
>
>
> Kind regards,
>
> Tim
>
>
>
> cc Bruker mailing list, CCP4BB, phenixBB
>
> --
>
> --
>
> 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
--
--
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
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Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant
Dear Ernst, depositing raw data would add about 100 Bytes of storage per structure to the RCSB, about the length of a DOI. This is because there are existing repositories for data storage: data.sbgrid.org (only data related to an already published manuscript), zenodo.org, and a few more. They may not have the capacity for serial crystallography data sets, but for the typical data set, they should be sufficient. In neither case to depositors have to pay. Best regards, Tim On Thursday, August 1, 2019 9:48:40 AM CEST Schonbrunn, Ernst wrote: > I totally agree with the deposition of raw data along with the coordinate > set(s). It is the only way to independently validate a model that has been > generated by somewhat subjective procedures of data reduction and scaling, > structure solution and refinement. > More importantly, algorithms and procedures steadily evolve, thanks to you > folks. Raw data of important structures re-processed using future (or > present) algorithms may result in much clearer pictures of > structure-function relationships than those of original interpretations. > What would be the best way to deposit raw data? How much would this add to > the storage and maintenance capabilities of RCSB? Likely requires > additional funding. If grant opportunities exist one could make a strong > case. > Ernst > > > > From: CCP4 bulletin board On Behalf Of Kay > Diederichs Sent: Thursday, August 1, 2019 1:54 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: EXT: Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not > relevant > First of all, you are of course correct, Rmerge (as Rmeas, Rpim, CC1/2, > I/sigma ...) is not detector-dependent. > Second, when looking at the "experiment" section of the PDB deposition, I > note that some Rmerge values are even given there! The statistics there are > dubious, e.g. seemingly the I/sigma in the high resolution shell is 2.2 > meaning that they could have used higher resolution data. > Third, look at the sliders on the entry page: the validity of this PDB entry > is suspicious - quite bad Rfree and geometry. > One more case for the deposition of raw data. In my eyes, the RCSB policy > should be that raw data must be deposited when accepting such a bad entry. > > HTH, > Kay > > On Wed, 31 Jul 2019 17:49:47 +0100, Weston Lane > mailto:wesl...@gmail.com>> wrote: > > >I was looking at the following structure in the PDB: > >http://www.rcsb.org/structure/6HR5<http://www.rcsb.org/structure/6HR5> I > >noticed that the R/Rfree stats were pretty high for 2.9A resolution so I > >followed up by looking for the "Table 1" statistics in the journal > >article. Link to article: > >https://www.nature.com/articles/s41589-019-0311-9<https://www.nature.com/a > >rticles/s41589-019-0311-9> Table is located in the supplemental materials > >"Table 9". > >From the processing statistics it's clear that the diffraction from that > >crystal wasn't great but I don't want to get hung up on the processing or > >the validity of the structure. What struck me what this little explanation > >the authors included to explain the outlier statistics in the table: > >"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge data > >are not relevant." > >We all know that Rmerge isn't a great metric for data quality but I've > >never heard that it's detector-dependent. This doesn't make sense to me. > >If it's actually true can someone explain, please? > >Thanks! > > > >Wes > > > > > > > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<https://www.j > >iscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<https://www.ji > scmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> > Please consider the environment before printing this email. > > This transmission may be confidential or protected from disclosure and is > only for review and use by the intended recipient. Access by anyone else is > unauthorized. Any unauthorized reader is hereby notified that any review, > use, dissemination, disclosure or copying of this information, or any act > or omission taken in reliance on it, is prohibited and may be unlawful. If > you received this transmission in error, please notify the sender > im
[ccp4bb] cbf to sfrm
Dear all,
recently the conversion from CBF to SFRM frame format with APEX was discussed
on the Bruker mailing list ("Synchrotron data with Bruker Software"),
including a potential bug that parameters in the frames other than the first
frame are not set correctly. The workaround to re-convert from SFRM to SFRM a
second time did not help in my case.
I therefore updated my program sfrmtools, available at https://
homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/
With the option '-u',you can provide the first frame of the run, and via '-p'
a parameter file that contains the critical parameters (see documentation at
above URL) to update the header for all frames in this run. In case you have
twinned data and want to benefit from SAINT, this should be possible with this
feature.
Both 64bit Linux binary and the source code are available. The program has no
dependencies and should compile under any platform.
I did not debug this new feature very thoroughly, but it worked for me so far.
Any bug reports are welcome to this address tim.gru...@univie.ac.at
I hope this is helpful for one or two users.
I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM
header format.
Kind regards,
Tim
cc Bruker mailing list, CCP4BB, phenixBB
--
--
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
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Re: [ccp4bb] Resonant Scattering Directionality
Dear Jacob, closely related to Ethan's explanation, but not quite the same, the contribution of f' and f" is still affected by the fall off from the ADPs, i.e. they also fall off exponentially, even for high quality crystals with a very low B-factors. The effect that you describe, however, still has to be accounted for during refinement, which is why you have the DISP command in SHELXL. Best, Tim On Thursday, July 25, 2019 8:23:34 PM CEST Keller, Jacob wrote: > Dear Crystallographers, > > It seems to be a usual assumption that anomalous scattering is essentially > angularly-independent, e.g.: > > http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm > > But why the can't we see anomalous-only spots at e.g. 1 Ang resolution in a > 2 Ang data set? > > This actually has some repercussions for a non-x-ray (but still resonance) > idea, so it would be helpful to know... > > All the best, > > Jacob > > + > Jacob Pearson Keller > Research Scientist / Looger Lab > HHMI Janelia Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > Desk: (571)209-4000 x3159 > Cell: (301)592-7004 > + > > The content of this email is confidential and intended for the recipient > specified in message only. It is strictly forbidden to share any part of > this message with any third party, without a written consent of the sender. > If you received this message by mistake, please reply to this message and > follow with its deletion, so that we can ensure such a mistake does not > occur in the future. > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- -- 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 signature.asc Description: This is a digitally signed message part.
