Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?
Hi Gianluca, Have you checked for diffraction anisotropy problems? It might be worth running it through the STARANISO webserver: https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can make your data look twinned and elliptical truncation can help improve maps. Good luck! Best, Jessica On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Hello, can you give us a screenshot of a diffraction image, with the > caveat that they never look all that good with fine-slicing, still it might > help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those > space groups. > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > Sent from Proton Mail mobile > > > > Original Message > On 21 Mar 2023, 16:43, Gianluca Cioci < > 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote: > > > Dear All, > > I have collected a dataset from a small protein diffracting at 2.7A > resolution, here is the space-group determination from XDS: > > * 44aP 0.0 66.3 66.3 83.9 90.2 90.1 98.7 > * 31aP 1.2 66.3 66.3 83.9 89.8 90.1 81.3 > * 14mC 1.3 86.4 100.6 83.9 90.0 90.2 90.0 > * 34mP 2.9 66.3 83.9 66.3 90.2 98.7 90.1 > * 13oC 3.7 86.4 100.6 83.9 90.0 90.2 90.0 > * 10mC 4.9 100.6 86.4 83.9 89.8 90.0 90.0 > > Clearly, something weird is going on... > > The structure can be solved in C2/P21/C2221 with different number of > molecules in the AU, with Phaser complaining about strong tNCS modulation. > > However the maps look bad and the structure is impossible to refine (Rfact > > 0.5) in all the space-groups that I have tried so far... > > Thanks in advance for any advice on how to rescue these data ! > > Cheers, > > GIA > > > [image: Click to zoom the image] > > > -- > Dr. Gianluca CIOCI > Toulouse Biotechnology Institute > (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html > PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/ > > Tel: +33 (0)5 61 55 97 68 > E-mail: ci...@insa-toulouse.fr > > TBI - INSA Toulouse > 135 avenue de Rangueil > 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Regarding the diffraction image
Hi Kavya, As others have mentioned, the unit cell is too small to contain your protein. With a volume of ~4820 Ang^3, the unit cell can contain at most ~268 atoms, excluding hydrogens (divide the volume by 18 to get this number). If the symmetry is P3, then the asymmetric unit can only contain ~89 atoms (divide the number of atoms in the unit cell by 3), which is not a lot. It is most likely something organic from your buffers (the ligand, TCEP, protein fragment, other buffer components, etc). Searching the CCDC (https://www.ccdc.cam.ac.uk/structures/?) or the COD ( https://nanocrystallography.org/search.html) databases may be helpful. The CCDC also has a unit cell searcher tool (CellCheckCSD) that you can download and use without a license ( https://www.ccdc.cam.ac.uk/support-and-resources/downloads/). Collecting higher resolution data (<1 Ang) and trying to solve this with SHELXT would likely get to the bottom of things if you really want to know. Best of luck! Kind regards, Jessica On Fri, Feb 3, 2023 at 7:37 AM Artem Evdokimov wrote: > With 50 mM Zn++ in solution, whatever it is will probably have a Zn salt > in it. So if you wanted to solve it by direct methods or via SAD - that > should do well. Sadly (hur hur) it's probably quite small, whatever it is. > > Artem > > - Cosmic Cats approve of this message > > > On Fri, Feb 3, 2023 at 6:20 AM Mark J. van Raaij > wrote: > >> like others mentioned, looks like something in between a salt and a >> protein, perhaps TCEP, the ligand, a peptide cleaved from your protein by >> trace protease. >> If possible, I would move the detector closer, collect an atomic >> resolution dataset and try to solve the structure by direct methods. You >> never know, it could be something interesting. >> >> Mark J van Raaij >> Dpto de Estructura de Macromoleculas, lab 20B >> Centro Nacional de Biotecnologia - CSIC >> calle Darwin 3 >> E-28049 Madrid, Spain >> tel. +34 91 585 4616 (internal 432092) >> Section Editor Acta Crystallographica F >> https://journals.iucr.org/f/ >> https://namedrop.io/markvanraaij >> >> On 3 Feb 2023, at 09:22, kavyashreem wrote: >> >> Dear all, >> >> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the >> condition 10%PEG3350, 50mM Zinc acetate. >> >> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH >> 8. >> >> Crystal: Crystal: >> crystal under UV m >> >> <8ef9453e.png> >> >> When we collected the data at an in-house facility, it looked something >> like this: >> >> >> >> The minimum resolution spot is around 9Ang and maximum ~2.2Ang. >> >> I have not come across a protein diffraction like this, nor of a salt. >> When I ran the gel for the incubated protein (protein+ligand), there was no >> degradation. >> >> Although, I was sure there is some problem with this image I tried >> processing, which could not be, But indexing showed a unit cell of 11Ang, >> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not >> the third. >> >> Can anyone please shed some light on this diffraction image? >> >> How can it happen? >> >> >> Thank you >> >> Regards >> >> Kavya >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Question about CCP4 monomer dictionaries
Hi Steve, You could cite this book: Müller, P., Herbst-Irmer, R., Spek, A.L., Schneider, T.R., and Sawaya M.R. (2007) Crystal Structure Refinement: A Crystallographer's Guide to SHELXL. IUCr Texts on Crystallography. J Am Chem Soc. 129, 451–451. It also lists the expected bond length for a single bond between two oxygens as 1.48 Ang in Table 12.5. Kind regards, Jessica On Mon, Nov 28, 2022 at 12:04 PM stephen.c...@rc-harwell.ac.uk < 8f3604def7f0-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear BB, > > Thank you for all the helpful responses. To give a bit more context to my > question, I have a 1.2 A structure with a diatomic ligand bound to a metal > at the active site, which we believe is an oxygen species. The bond length > is 1.22 A and I made a comment in the discussion that this was unlikely to > be a peroxide species as the bond length was shorter than the 1.48 A > typically observed. The referee has questioned the validity of the 1.48 A, > which led to my original question. > > Best wishes, > Steve > > PS I have tried Raman spectroscopy with no definitive result. > > Dr Stephen Carr > Research Complex at Harwell (RCaH) > Rutherford Appleton Laboratory > Harwell Oxford > Didcot > Oxon OX11 0FA > United Kingdom > Email stephen.c...@rc-harwell.ac.uk > tel 01235 567717 > -- > *From:* Paul Emsley > *Sent:* 28 November 2022 19:20 > *To:* Carr, Stephen (MRC,RAL,RCAH) > *Subject:* Re: [ccp4bb] Question about CCP4 monomer dictionaries > > > > On 28/11/2022 17:29, stephen.c...@rc-harwell.ac.uk wrote: > > Dear CCPBB, > > I have a question regarding the origin of the monomer libraries in CCP4. > I ask because I have quoted the bond length listed in the monomer library > describing peroxide in a manuscript and a referee has asked for a reference > since they seem to disagree with the quoted value of ~1.48 A. My > understanding is that parameters describing bond length, angles etc are > derived from structures in the CSD is this the case? Is there an > appropriate reference out there somewhere? > > > When you say "peroxide," I presume that you mean H2O2. The entry for > that in the monomer library is PEO. The bond length between the oxygen > atoms in PEO is 1.461A. Perhaps your referee is thinking of the > > peroxide ion, which indeed would have a different bond length (1.15). > > Both PEO and PER would, to my mind, be susceptible to radiation damage, > > so one wonders what is actually in the crystal. To address question, one > > would make an "Fearly-Flate" map. > > > One can (in principle) dig into the Acedrg table of bond lengths to > examine how many > > examples, of this sort of chemistry exist (I did it a few years ago), but > I don't recall > > now how to do it for this example. > > > Regards, > > Paul. > > > > This email and any attachments may contain confidential, copyrightand or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorized 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 > this email. > > > > Any views or opinions presented are solely those of the author and do not > necessarily represent those of the Research Complex at Harwell. > > > > There is no guarantee that this email 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. > > > > We use an electronic filing system. Please send electronic versions of > documents, unless paper is specifically requested. > > > > This email may have a protective marking, for an explanation, please see: > > > http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm > . > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Quantifying electron density inside of a given volume
Hi all, There are lots of great suggestions in this thread. I will just add a little trick from small molecule crystallography: when trying to estimate how many atoms can fit in a given volume, you can use the Rule of 18. Take the volume of interest in Angstroms^3 and divide it by 18 Angstroms^3. This will give you an estimate of the number of atoms that can fit in this volume (ignoring hydrogens of course). This calculation assumes tight packing, like we would see in a small molecule structure, so it should be a good approximation of the maximum number of atoms that can fit in this void and a good place to start for occupancy refinement. Best of luck! Cheers, Jessica On Mon, Aug 15, 2022 at 5:17 PM Pavel Afonine wrote: > Hi James, > > I like your approach with dummy atoms and occupancy refinement. Dealing > with actual maps sounds like hell to me indeed (especially given that we > deal with weighted Fourier maps!). Reading this as someone who immediately > translates this into a computer code (in my mind), a few things that aren't > clear to me: > - Where exactly inside the blob of density do you place these dummy atoms? > - How many do you place? > - Is there a risk of placing them too close to the boundary of the blob > (in which case the question remains: what is the boundary?)? > - I guess O or C as an atom type should do it, but what about B factor > (would you refine B as well?)? > - if you refine B, how do you deconvolute occupancy from refined B values > (and eventually from effects of positional errors of your DAs)? > - > - How all these choices are going to affect the result? > > All the best! > Pavel > > > On Mon, Aug 15, 2022 at 4:38 PM James Holton wrote: > >> There are several programs for integrating electron density, but please >> let me assure you that it is almost always the wrong thing to do. >> >> A much better strategy is occupancy refinement. Throw in dummy atoms, >> turn off non-bonded interactions to them, and refine their occupancy until >> it a) stops changing (may be more than one round), and b) there are no >> Fo-Fc differences left in the region of interest. Then all you do is add >> up the occupancies, multiply by the relevant atomic number (usually 8), and >> voila! you get the best-fit number of electrons in your blob. You may want >> to try re-running with random starting points to get an idea of the error >> bars. >> >> What is wrong with integrating density? Well, for one, it is hard to >> know where to set the boundaries. Integrated density can be VERY sensitive >> to the choice of radius, making your arbitrary decision of which radius to >> use a source of error. Too small and you miss stuff. Too big and you add >> unnecessary noise. Also, neighboring atoms have tails, and if you don't >> subtract them properly, that is another source of error. Also, because of >> the missing F000 term, there is an offset, which adds a term proportional >> to the integration volume. For example, an integral resulting in zero >> "electrons" does NOT mean you have vacuum. It just means that the area you >> integrated has the same average density as the entire map. This may not be >> the number you want. >> >> The beauty of occupancy refinement is that it automatically handles all >> these problems. The "vacuum level" and F000 are known quantities in the >> calculated map. The B factors given to the dummy atoms als o allow the >> borders of your integration region to be "soft": down-weighting the >> contribution of map noise far from your region of interest. And, finally, >> by including atoms in the green density, neighboring atoms won't be sucked >> into it. >> >> Think of it as fitting a smooth curve to noisy data and the number of >> electrons is just a parameter in that fit, rather than trying to integrate >> the noisy data itself. This is not an analogy. Refinement programs are >> really just very sophisticated curve-fitting programs. And if you have a >> forest of overlapping peaks and you are trying to de-convolute the >> area/volume of one peak, it is best to include that peak in the fit, rather >> than leave it out. Shoulder peaks especially tend to get "eaten" by large >> neighboring peaks. >> >> How do you turn off non-bonds? Well, there is documentation for refmac: >> http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html >> and phenix: >> https://phenix-online.org/documentation/reference/refinement.html >> >> All that said, to answer the original question: >> One very easy thing to do within the CCP4 suite is to use "mapmask" to >> make a mask corresponding to your "sphere", or other region of interest. >> Perhaps place a water at the center of your peak, and either use the >> "border" feature of mapmask, or use "sfall" to compute a calculated map and >> convert that to a mask using "threshold" in mapmask. This mask should have >> values of 0 or 1 at every voxel. (or, if you feel like being clever, >> something between 0 and 1 to reflect how much you
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Comparing two datasets
Hi Mirek, I have absolutely loved this discussion of other options for comparing datasets! But to your original problem: To tell CCP4 where r is installed, you need to add this to your $PATH. You will want to figure out where r is installed on your computer and then add it to your .bashrc file or .zshrc file if you are using a newer Mac. These instructions might be helpful: https://gist.github.com/nex3/c395b2f8fd4b02068be37c961301caa7 . You can follow the instructions for Mac Os or for Linux. You can tell that you have done this correctly by opening a new terminal window and typing "which r" (no quotes) into the command prompt. It should return a path to where you have r installed. You can then launch ccp4 by typing "ccp4i2" into the command prompt. Clicking on the icon might also work, but I generally launch CCP4 from a terminal window. Also, if you have problems launching ccp4 from terminal, add this to your .bashrc/.zshrc, making sure that the path you are listing is correct for your installation of ccp4 and that you re-start your terminal after doing this: #ccp4 source /Applications/ccp4-7.1/bin/ccp4.setup-sh Good luck! Kind regards, Jessica On Tue, Jul 26, 2022 at 8:10 AM Clemens Vonrhein wrote: > Dear all, > > [just to add some caveats in case future students see this thread and > start cut-n-pasting commands to successfully create some kind of MTZ > file of dubious content] > > Unless we're talking about some really old datasets (of historical > interest) or a disastrous situation (all backups lost), by far the > best approach would be to go back to the original data in the form of > the (unscaled) unmerged intensities - in order to do the > scaling+merging of the two datasets then, right? > > One can do all kind of things with amplitudes (F) in MTZ files using > various fabulous CCP4 programs (SFTOOLS, SCALEIT, RSTATS, CAD, > POINTLESS, COMBAT), but be careful that it is not just some > simple/brainless arithmetic on numerical values that happen to be > called F/SIGF. Been there, done that, got the T-shirt ... > > The important thing is to understand what the OP is trying to achive > here. As others mentioned: > > ... calculate R-merge for Fs from two datasets processed from two > different crystals ... > > sounds to like a confusion between > > (1) comparing two sets of amplitudes via an R-factor (not R-merge!) > > * can be done with e.g. SCALEIT or RSTATS > > * with or without scaling? > > * what scale parametrisation (k, k/B, anisotropic)? > > * overall or in bins? What binning? > > (2) getting a "R-merge" value for some kind of "Table-1" (paper or > deposition): > > * can't be done "correctly" from amplitudes > > * go back to original data and (re)processing > > And > > ... would take two mtz files and merge the Fs ... > > might just ask for a method to "average" two sets of amplitudes: > > * inverse-variance weighted? > > * unweighted? > > * for what purpose - and why not go back to the original data to do > proper scaling/merging there? > > The subject line "Comparing two datasets" seems to ask for something > different again: a way of comparing (R-factor? CC?) datasets, not > necessarily combining/merging them? > > Cheers > > Clemens > > > On Tue, Jul 26, 2022 at 02:11:17PM +0100, Phil Evans wrote: > > If you want to merge them then you can use Pointless/Aimless/ctruncate, > with the warning that the conversion from F to I is not ideal, and > ctruncate should be set to regenerate F from I just as sqrt ie not apply > the truncate procedure again. > > Pointless supersedes combat for this conversion > > Again, just for comparison use scaleit > > > > Phil > > > > Sent from my iPhone > > > > > On 26 Jul 2022, at 13:33, Jon Cooper < > 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > > > Hello again, as far as I can tell, the question is about two already > merged/unique datasets which Mirek wishes to merge into one. As far as I > can tell/remember, Scaleit is for scaling datasets side-by-side to get > isomorphous differences, etc, and I don't know of a way that you could get > it to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit > R-factors are different from R-merge, although the latter might be a bit > dubious in the circumstances. Anyway, I think the Combat route is a viable > way of achieving what the questioner wants to achieve ;-0 > > > > > > > > > Sent from ProtonMail mobile > > > > > > > > > > > > Original Message > > > On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com> > wrote: > > > > > > Dear Colleagues, > > > Scaleit is a terrific program. > > > Amongst its strengths already listed I would also mention its > breakdown table with F so that in the strongest F reflections bin any > systematic errors between the two data sets can show up if the Rfactor is > greater than about 1%. > > > Greetings, > > > John > > > Emeritus Professor John R Helliwell DSc > > > >
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] SHELXD - Limit Number of CPUs?
Hi all, Thank you for the excellent advice. I think I have found what I am looking for. To James, I am currently not using a queuing system and I am just launching jobs directly on a shared GPU machine. Soon I will move to a PBS cluster, which should help with all of this. Thanks again! Cheers, Jessica On Wed, Mar 16, 2022 at 10:26 PM Tim Gruene wrote: > 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 > -- Jessica Bruhn, Ph.D Scientific Group Leader, MicroED NanoImaging Services, Inc. 4940 Carroll Canyon Road, Suite 115 San Diego, CA 92121 Phone #: (888) 675-8261 www.nanoimagingservices.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
[ccp4bb] SHELXD - Limit Number of CPUs?
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 -- Jessica Bruhn, Ph.D Scientific Group Leader, MicroED NanoImaging Services, Inc. 4940 Carroll Canyon Road, Suite 115 San Diego, CA 92121 Phone #: (888) 675-8261 www.nanoimagingservices.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
[ccp4bb] Job Openings - Small Molecule Crystallographer (MicroED) and Scientific Programmer
Hi everyone, My group is looking to hire two new people to further expand our small molecule MicroED capabilities here at NanoImaging Services in San Diego, CA. This is an exciting opportunity to help grow and shape our newest service division; and bring impactful crystal structures to chemists working in the pharmaceutical space. Plus, we received an SBIR grant from the NIH to further develop our MicroED pipeline, so these positions will have a significant R&D component. Come be part of an innovative team that is taking cutting edge technology and making it accessible to groups all across industry. *Scientist I/II – Small Molecule MicroED Crystallographer (Full time – San Diego - CA) * https://www.nanoimagingservices.com/about-us/careers#Scientist_I-II_Small_Molecule_MicroED *Scientific Programmer I (Full time – San Diego - CA)* https://www.nanoimagingservices.com/about-us/careers#Scientific_Programmer_I Inquiries can be sent to recruit...@nimgs.com or me directly. Kind regards, 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Contagious, Self-Distributing "Vaccines?"
Hello, There have been some really excellent points raised by others (informed consent, feasibility, etc), but I would like to share a story about another time humans tried to release a virus on a wild population in order to further an arguably noble goal: In the 1850s European rabbits were introduced in Australia for sport hunting. They quickly did what bunnies do and started to become a real problem. In the 1950s, scientists decided to introduce myxoma virus to Australia, which is 90-99% fatal for European rabbits, but less lethal for the native rabbits. They intentionally released this virus and in the first year the mortality rate was 99.8% for the European rabbits. Yay, right??? Unfortunately, in the subsequent year the mortality rate fell to 25% and steadily continued to fall until it was lower than the reproductive rate of the European rabbits. The host-virus interaction played itself out: less-virulent viruses arose and resistant rabbits were selected for. To me it seems unwise to assume a replication competent virus (engineered or not) would refrain from mutating and adapting upon release, especially over the time course that would be required to infect all 7 billion+ humans on this planet. To me, I feel our options are (1) reach herd immunity through natural infection and accept the preventable deaths of many millions of people or (2) continue with non-pharmaceutical interventions (mask wearing, distancing, etc) until we can vaccinate enough people to reach herd immunity and hopefully by that time we have robust testing and treatment options available for those who continue to fall ill after we reach herd immunity. We as humans did something amazing by producing multiple safe and effective vaccines in less than one year, and I would like us to continue trying to save as many lives as possible by employing these vaccines as widely as possible. Anyways, take care. I know the pandemic is hard on all of us. Best regards, Jessica On Thu, Feb 18, 2021 at 6:15 AM Patrick Shaw Stewart wrote: > I agree with those who say that A and B are usually incompatible. > > If we're like chickens-in-a-barn-that-have-been-infected-with-bird-flu, > the virus very rapidly becomes more virulent (hospital and care-home > infections?). It's hard for a virus to infect your nose and throat > quickly, and then stop. > > In the medium term the herd will build up some immunity and then we'll > become more like wandering albatrosses: the virus has to keep us on the > move if it's going to get itself near another susceptible host. > > IMO the way a *respiratory *virus tries to "have its cake and eat it" - > that is, get as much of both A and B as possible - is to develop thermal > sensitivity. I.e. infect nose and throat but keep out of lungs and brain : > > https://www.preprints.org/manuscript/202101.0389/v1 > > > > Thanks, Patrick > > > On Wed, Feb 17, 2021 at 9:46 PM Edwin Pozharski > wrote: > >> I guess for such vehicle to be "extremely contagious" (or contagious at >> all for that matter) it should be capable of rapidly multiplying inside the >> host, so that it outruns immune system mediated destruction for at least >> some time in order to be present in high enough concentration to >> effectively spread via aerosols. Given the range of immunodeficiencies >> present in any population, you are essentially guaranteed to kill at least >> some people whose immune system will not be able to cope with rapidly >> multiplying virus. You can theoretically fine tune the lethality of such >> virus to make sure that number of people you thus murder will be less than >> those that die either in no vaccine or traditional vaccination scenario, >> but that would be ethical equivalent of that modern crypto fascist >> suggestion that we 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
Re: [ccp4bb] Challenging Molecular Replacement
Hi Muhammad, It sounds like you are on the right track, but maybe you are in the wrong space group. You could check out Zanuda (part of CCP4). It will refine your solution in other potential space groups and compare the refinement statistics. Best of luck! Cheers, Jessica On Tue, Feb 16, 2021 at 10:39 AM Sharan Karade wrote: > Hi, > > Looks like, you have the solution. Have you tried the Phenix AutoBuild > module? sometimes it works well. > > Best luck > > > On Tue, Feb 16, 2021 at 1:21 PM Muhammad Bashir Khan > wrote: > >> Dear All; >> >> I have data set of about 3.0A. It's a multidomain protein. I tried >> several options with MR but it's was not working. I trimmed one of the >> search models, it does not give any solution using CCP4 molrep. >> >> I used Phenix phaser it gives a solution after several hours with the >> following output. >> >> ** SINGLE solution >> >> ** Solution written to PDB file: MgtA_phaser.1.pdb >> ** Solution written to MTZ file: MgtA_phaser.1.mtz >>Solution annotation (history): >>SOLU SET RFZ=2.7 TFZ=6.3 PAK=6 LLG=62 TFZ==6.5 RFZ=2.2 TFZ=28.0 PAK=9 >> LLG=1207 TFZ==42.0 LLG=1370 TFZ==41.8 PAK=9 >> LLG=1370 TFZ==41.8 >>SOLU SPAC P 21 2 21 >>SOLU 6DIM ENSE ense_1 EULER 269.0 80.4 177.3 FRAC 0.24 -0.22 >> -0.07 BFAC -1.51 #TFZ==6.5 >>SOLU 6DIM ENSE ense_1 EULER 89.0 80.4 177.3 FRAC 0.26 -1.01 >> -0.07 BFAC 2.26 #TFZ==41.8 >>SOLU ENSEMBLE ense_1 VRMS DELTA -0.7291 #RMSD 1.50 #VRMS 1.23 >> >> Running Phenix refine on the solution gives a breakup map and the R >> factors are not decreasing below 47.61 and 50.94. >> >> Thank you for any suggestions in advance >> >> Regards; >> >> Bashir >> >> >> -- >> -- >> Muhammad Bashir Khan, Ph.D. >> Research Associate >> Department of Biochemistry >> Medical Science Bldg. >> Lab 3-27 >> University of Alberta >> Edmonton AB, T6G 2H7 >> >> Phone: 780-492-4577- >> e-mail: m...@ualberta.ca >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > > -- > Sharan Karade > Postdoc-fellow > IBBR-UMD, 9600 Gudelsky Dr, > Rockville > Maryland 20850 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] [Resolved] Re: [xds] how to specify measuring angle
Hi Jon, The goniometer on a TEM microscope typically cannot rotate the full 360 degrees and therefore we can't ramp it up to speed before initiating collection and slow it down after collection has ended as is typically done for X-ray crystallography. This causes the tilt speed and therefore the oscillation per frame to be less reliable in the early and late frames. We added a small delay between starting the stage tilt and exposing the crystal/collecting the first image to help with this. Best regards, Jessica On Wed, Oct 21, 2020 at 2:30 PM Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Hello, I am interested to know why "it is conventional to delete/omit > first/last image". Forgive my ignorance. > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > > > > > Original Message > On 21 Oct 2020, 19:23, Doo Nam Kim < > 4e720d49e642-dmarc-requ...@jiscmail.ac.uk> wrote: > > > Dear all, > > What I knew is starting angle (-60) and ending angle (+60). > Additionally, I know number of image files generated by mrc2smv is 120 > from my mrc files. > > Since it is conventional to delete/omit first/last image, > > changing into a decently "accurate" approximation as > > STARTING_ANGLE=-60 > DATA_RANGE=2 119 > OSCILLATION_RANGE=1 > > reproduced my predecessor's completeness. > > Thank you all > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=1 > > -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] [xds] how to specify measuring angle
Hi Doo Nam Kim, If you do not know your OSCILLATION_RANGE, a good guess would be to take your collection angle range (-60 to +60 or 120 degrees) and divide that by the number of frames. Best, Jessica On Fri, Oct 9, 2020 at 2:00 AM Dirk Kostrewa < dirk.kostr...@lrz.uni-muenchen.de> wrote: > Dear Doo Nam Kim, > > On 09.10.20 08:43, Doo Nam Kim wrote: > > Since I don't know correct value of OSCILLATION_RANGE, I just changed to > the example value (0.1) from (0.89976, I know it is not a positive > multiple of 0.0001, but worked for ketone data). > > without knowing the correct value for the OSCILLATION_RANGE, data > processing might run through but produces non-sense results, independent > of the data processing program you use. So, it is absolutely important > to know the correct value for the oscillation range per frame. > > Cheers, > > Dirk. > > -- > > *** > Dirk Kostrewa > Gene Center Munich > Department of Biochemistry, AG Hopfner > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > D-81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax:+49-89-2180-76998 > E-mail: dirk.kostr...@lmu.de > WWW:www.genzentrum.lmu.de > strubio.userweb.mwn.de > *** > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ > -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Does MicroED (microcrystal electron diffraction) have phase problem ?
Hi Edward, MicroED as defined by Tamir Gonen does not encompass 2D crystals. This is to keep it separate from 2D electron crystallography in which the data is collected in a very different manner. Personally though, I don't see why you couldn't collect microED style data from a 2D crystal. Less copies of the unit cell means you would get less signal and you might have to bump up your dose per frame, which can cause more radiation damage, but these are (probably) not deal breakers. For me, the thing that defines microED is the collection of electron diffraction data using the (continuous) rotation method without precession of the electron beam. It requires microcrystals/nanocrystals because if the crystals are too thick, the electron beam cannot penetrate them. The beauty of collecting data in this manner is that this is the same strategy employed by most X-ray crystallographers and therefore the data can be processed with familiar programs (DIALS, XDS, HKL3000, MOSFLM, APEX3, etc). The reality though, is that data processing is not trivial and there is a lot of room for improvement in handling this data. It is the early days for this field and I am hopeful that things will continue to improve. And in the meantime, we are solving lots of small molecule structures that could not easily be solved by X-ray crystallography or NMR. Cheers, Jessica On Sun, Aug 16, 2020 at 8:32 PM Edward A. Berry wrote: > For my own info, > Does microED encompass work with 2D crystals, or only micro-3D crystals? > > On 08/15/2020 10:40 PM, Jessica Bruhn wrote: > > Hi Alex, > > > > Welcome to the field of microED! From a practical standpoint, microED > also suffers from the phase problem, and somewhat moreso compared to X-ray > crystallography because anomalous signal is very limited. It is true that a > TEM microscope operated in imaging mode produces images that contain both > phase and amplitude information, which you correctly infer means that > single particle cryoEM does not suffer from the phase problem. This is why > a map from cryoEM is generally of higher quality than one determined by > X-ray crystallography at the same resolution, because we don't have to > guess at the phases. > > > > In classic microED data collection, we don't actually take advantage of > the phase information that can be measured using imaging mode. We quickly > find our crystals in imaging mode and then flip the switch to diffraction > mode and collect a dataset devoid of phase information. It has been > suggested that we could use imaging mode to get at the phases of the > diffraction patterns, but I am not aware of anyone actually doing this. > Practically speaking, this would add significant additional time to the > data collection and we likely would only be able to reliably use the phases > for the lower resolution range (though, that might not be a deal breaker). > Thankfully though, molecular replacement and ab initio methods for small > molecules work pretty well on these datasets. Plus, most X-ray structures > are solved this way anyways. > > > > There have been efforts to use radiation damage as a means to phase a > small peptide bound to zinc ( > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313391/ < > https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313391/__;!!GobTDDpD7A!d9GMLVpOCJjYcJ8TK3Sn2QYRR5JPvL8Vb51isRJMME8AssIo499krUEDQ5gHtKOV$>). > And there is some interesting work being done with dynamical scattering as > a way to see differences in Friedel pairs (see Tim Gruene's post here: > https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;b22eae56.2007 < > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;b22eae56.2007__;!!GobTDDpD7A!d9GMLVpOCJjYcJ8TK3Sn2QYRR5JPvL8Vb51isRJMME8AssIo499krUEDQx24VbXZ$>), > but these methods are not "classic microED" and require completely > different data processing software that is unfamiliar to most X-ray > crystallographers. > > > > For now, we just crank up the cycles in SHELXT/SHELXD or hope for a good > molecular replacement model. > > > > Best of luck, > > Jessica > > > > On Sat, Aug 15, 2020 at 6:03 PM Alex Lee <mailto:alexlee198...@gmail.com>> wrote: > > > > Hi, All, > > > > I am new to MicroED (microcrystal electron diffraction). I know that > X-ray crystallography has phase problem, and I think MicroED has phase > problem too (it is diffraction of electron instead of x-ray). However, when > I read the Wikipedia, I could not understand the following description of > MicroED: One of the main difficulties in X-ray crystallography is > determining phases in the diffraction pattern. Because of the complexity of > X-ray lenses, it is diffic
Re: [ccp4bb] Does MicroED (microcrystal electron diffraction) have phase problem ?
Hi Alex, Welcome to the field of microED! From a practical standpoint, microED also suffers from the phase problem, and somewhat moreso compared to X-ray crystallography because anomalous signal is very limited. It is true that a TEM microscope operated in imaging mode produces images that contain both phase and amplitude information, which you correctly infer means that single particle cryoEM does not suffer from the phase problem. This is why a map from cryoEM is generally of higher quality than one determined by X-ray crystallography at the same resolution, because we don't have to guess at the phases. In classic microED data collection, we don't actually take advantage of the phase information that can be measured using imaging mode. We quickly find our crystals in imaging mode and then flip the switch to diffraction mode and collect a dataset devoid of phase information. It has been suggested that we could use imaging mode to get at the phases of the diffraction patterns, but I am not aware of anyone actually doing this. Practically speaking, this would add significant additional time to the data collection and we likely would only be able to reliably use the phases for the lower resolution range (though, that might not be a deal breaker). Thankfully though, molecular replacement and ab initio methods for small molecules work pretty well on these datasets. Plus, most X-ray structures are solved this way anyways. There have been efforts to use radiation damage as a means to phase a small peptide bound to zinc (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313391/). And there is some interesting work being done with dynamical scattering as a way to see differences in Friedel pairs (see Tim Gruene's post here: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;b22eae56.2007), but these methods are not "classic microED" and require completely different data processing software that is unfamiliar to most X-ray crystallographers. For now, we just crank up the cycles in SHELXT/SHELXD or hope for a good molecular replacement model. Best of luck, Jessica On Sat, Aug 15, 2020 at 6:03 PM Alex Lee wrote: > Hi, All, > > I am new to MicroED (microcrystal electron diffraction). I know that X-ray > crystallography has phase problem, and I think MicroED has phase problem > too (it is diffraction of electron instead of x-ray). However, when I read > the Wikipedia, I could not understand the following description of MicroED: > One > of the main difficulties in X-ray crystallography is determining phases in > the diffraction pattern. Because of the complexity of X-ray lenses, it is > difficult to form an image of the crystal being diffracted, and hence phase > information is lost. Fortunately, electron microscopes can resolve atomic > structure in real space and the crystallographic structure factor phase > information can be experimentally determined from an image's Fourier > transform. The Fourier transform of an atomic resolution image is similar, > but different, to a diffraction pattern—with reciprocal lattice spots > reflecting the symmetry and spacing of a crystal. > > Does the above description mean that MicroED, or more broadly electron > crystallogaphy does NOT suffer from phase problem? How about single > particle cryo electron microscopy, it should NOT have phase problem, right? > > Thanks for any input in it. > > Best, > Alex > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Structural Importance of Methionine
-983-3516 > email pegea at mednet.ucla.edu > <https://urldefense.proofpoint.com/v2/url?u=http-3A__mednet.ucla.edu&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=zarhu_AFfXHIr7BLs8GQXPvC2gpkmnikRXKYvnCJnk0&m=FpV2vp6oO-Ox53M7Ncww74udjlwJMJXwqJ_i-3DFZv4&s=fFkbpZheDOEaefToqqTQ-h4wEjpuzPAc8QJzA7SJDn8&e=> > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=zarhu_AFfXHIr7BLs8GQXPvC2gpkmnikRXKYvnCJnk0&m=FpV2vp6oO-Ox53M7Ncww74udjlwJMJXwqJ_i-3DFZv4&s=gmuTxUEHrZ6ZtiOB-dDVGLUQs1EgipJhjkBC0O24LHQ&e=> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] AW: [EXTERNAL] chirality with electron diffraction
t; > 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&A=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/ > -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Quote source inquiry
meters) 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 parameters, which is very handy for electron diffraction > data. > > Best wishes, > Tim > > > On Thu, 16 Jul 2020 > 08:20:11 -0700 Jessica Bruhn > <450e5de75376-dmarc-requ...@jiscmail.ac.uk > <mailto:450e5de75376-dmarc-requ...@jiscmail.ac.uk > <450e5de75376-dmarc-requ...@jiscmail.ac.uk>>> wrote: > > As someone working with continuous rotation electron diffraction, > mostly with small molecules, I am often very concerned about the > accuracy of my cell dimensions. I have to heavily restrain my > experimental geometry, including the detector distance, because > they are so unusual compared to X-ray setups. I also suspect that > my goniometer is less able to maintain a constant speed, > resulting in small errors in the oscillation per frame, > especially for early and late images. I have calibrated my > microscope's camera length (analogous to detector distance) with > powder diffraction and even include an elliptical distortion > correction in DIALS, and I validated my setup with some single > crystal data. > > I am wondering if there is a way to refine my unit cell at the > model refinement step? Most of my structures are 0.9-1.1A and are > refined in SHELXL. I would think that refining my cell with the > goal of bringing my bond lengths closer to ideal lengths would be > helpful. Is there a way to do this? > > Best, > Jessica > > On Thu, Jul 16, 2020 at 7:36 AM Edward Snell > mailto:esn...@hwi.buffalo.edu > >> wrote: > > Not completely related to the question but at one particular > European synchrotron there were a group of beamline scientists > that also kept honey bees. The wax from each hive gave very > beautiful powder diffraction patterns with the scattering being > similar but distinctive to each hive. I was fortunate to observe > this before my data collection - this was their calibration of > the beam center. > > In the US, many years before BluIce there was a 'jiffy' software > routine that would take a powder pattern and accurately calculate > the beam center. This saved one of our structures. Wax, silicon > powder, and other test samples were used. If I remember correctly > cryo-vials had a powder signature and a magnet with part of a > vial glued to it became part of the tool kit when one would still > routinely travel to the beamline. > > I've been
Re: [ccp4bb] Quote source inquiry
aphers > > and reviewers one would think > > > > It would be interesting to see what would happen if the wavelength would > be set 5% too high. > > > > --Gerard > > > > > > > > On Thu, 16 Jul 2020, Clemens Vonrhein wrote: > > > >> Hi Robbie, > >> > >> On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote: > >>> At the same time if you have a a more relaxed approach to restraints > >>> than you might find systematic deviations in bond lengths. A test > >>> for that has been in WHAT_CHECK for decades and it actually works > >>> surprisingly well to detect cell dimension problems. > >> > >> Indeed. > >> > >>> That said, the problem is uncommon now. > >> > >> Not so sure about that: we all rely on an accurate value of the > >> energy/wavelength from the instrument/beamline - and if that is off > >> (for whatever reasons) it will result in incorrect cell dimensions > >> and a systematic deviation from the various restraints. > >> > >> This would even affect the best experiment done on the best crystal > >> ... so fairly easy to spot at the refinement stage, especially if > >> such an energy/wavelength offset is constant over a long period of > >> time on a given instrument. To spot this at the data collection stage > >> one would hope that at some point a crystal with very pronounced > >> ice-rings will be looked at properly (and the fact these are not > >> where we expect them to should cause some head-scratching). > >> > >> Cheers > >> > >> Clemens > >> > >> # > >> ### > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ > >> > > > > > > Best wishes, > > > > --Gerard > > > > ** > > 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/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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&A=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/ > -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Question about small molecule crystallography
Hi Jiyuan, I don't have much to add on the small molecule crystallization advice, but I will put in another plug for electron diffraction (microED). You could first check to see if you already have microcrystal by performing some X-ray powder diffraction or XRPD (many CROs offer this service). If your spectra looks good, you can move straight to data collection with electron diffraction. If you don't already have crystals, I would proceed as suggested with crystallization trials. If you get big crystals, great! Go for single crystal X-ray diffraction. If you find that you can only make microcrystals, I would try to do microED. Best of luck! On Mon, Jun 1, 2020 at 3:01 PM Jiyuan Ke wrote: > Hi Everyone, > > I want to crystallize a small organic molecule. I have very limited > experience in small molecule crystallography. I found that the Crystal > Screen HT from the Hampton research is good for both small molecule and > macromolecule crystallization. Plan to set up a sitting drop screen just > like setting up protein crystallization. I don’t know if this is the proper > way to do it. Is the MRC sitting drop 2-well plate (HR3-083) used for > protein crystallization good for small molecule crystallization? Are there > any special plates used for small molecule crystallization? Is room > temperature ok or not? > > For data collection, can I use the beamline for protein crystals to > collect data on small molecule crystals? Larger oscillation angle, shorter > exposure, reduced beam intensity? > > For structure determination, is SHELXL the preferred software for solving > small molecule structures? > > If anyone has experience in small molecule crystallography, please help. > Thanks! > > Best Regards, > > -- > > *Jiyuan Ke, Ph.D.* > > > Research Investigator > > H3 Biomedicine Inc. > > 300 Technology Square, Floor 5 > > Cambridge, MA 02139 > > Phone: 617-252-3923 > > Email: jiyuan...@h3biomedicine.com > > Website: www.h3biomedicine.com > > > > > > > [This e-mail message may contain privileged, confidential and/or > proprietary information of H3 Biomedicine. If you believe that it has been > sent to you in error, please contact the sender immediately and delete the > message including any attachments, without copying, using, or distributing > any of the information contained therein. This e-mail message should not be > interpreted to include a digital or electronic signature that can be used > to authenticate an agreement, contract or other legal document, nor to > reflect an intention to be bound to any legally-binding agreement or > contract.] > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=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/
[ccp4bb] Strange Pseudosymmetry Effects
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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=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] Low Solvent B Factors
Hi Everyone, Thanks so much for all of your responses! It is encouraging that when I look at the b factors of the protein atoms around my waters/ligands, the b factors track well. All of my lower b factor waters seem to be hydrogen bonding with low b factor residues. I modeled in a few more sodiums and a chloride, which seem reasonable. I tried modeling in some potassiums, but the bond distances seemed to be more consistent with sodium. Now the lowest b factor seen for any water or ligand is around 30 and the average is 40. This seems reasonable especially if you look at my distribution of b factors (the atomic properties tab in Phenix Refine). My overall b factors are spread between 13 to 130 with an average of 60, but I seem to have a bimodal distribution. My first peak is around 40 and my second peak is around 85. I think I’m just modeling the waters present in the more ordered part of my structure. To Kay, thank you for bringing that paper to my attention. I don’t think it is reasonable to expect that I could possibly get better R factors given the resolution of my data. I have some data at 2.6A, but because of my anisotropy and ellipsoidal truncation, the majority of my data is at much lower resolution (3.5A and 3.7A in the other two dimensions). This particular combination of space group and twin law was the only one which reduced my R factors (I tried about six different combinations), which is encouraging. But yes, I agree that my poor data quality is contributing to the odd spread of B factors. Thanks again to everyone who took the time to think about my problems. Best, Jessica On Jun 2, 2016, at 7:43 AM, Kay Diederichs wrote: > > Hi Jessica, > > those "relatively decent R-values of 28%/31%" may not really indicate that > your model is good. Take a look at > http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors#what_kinds_of_problems_exist_with_these_indicators.3F > . It cites Phil Evans and Garib Murshudov's paper > http://journals.iucr.org/d/issues/2013/07/00/ba5190/index.html which shows > that refining a perfect model against pure noise for a perfect twin will give > you R-values of 29.1%. So I'd expect a good model to give much lower R-values > against data that are better than noise. > > In light of this, it is maybe not a surprise that the solvent B factors > appear weird. > > best wishes, > > Kay > > On Wed, 1 Jun 2016 20:48:41 +, Jessica Bruhn wrote: > >> I was wondering if anyone had any explanations or tips for fixing things. >> This dataset was highly anisotropic, so I ellipsoidally truncated >> my data (2.6A, 3.5A and 3.7A in each direction). This dataset is also >> twinned with a 49% twin fraction. Despite all of that, I was able to build >> a relatively decent structure (28%/31%) that agrees well with the same >> protein in a different space group. > >
