Search results for "look through"

Re: [phenixbb] ncs restraints

by Timothy Springer

Thanks, I believe this is an important tip. Tim On Dec 8, 2010, at 12:25 AM, Ralf W. Grosse-Kunstleve wrote: > Hi Tim, > > If you start from nearly identical copies (due to previous refinement), in the absence of a strong signal from the data, it is expected that the copies remain fairly similar even if you increase the sigma / lower the weight. We just added a new feature to phenix.refine that could be useful to introduce differences between the NCS copies, guided by the model density through a new real-space refinement protocol: strategy=individual_sites_real_space plus real_space_refinement.mode=lockit. At your resolution it is turned on by default. I.e. to try it out all you need to do is get dev-602 or higher and run phenix.refine again. Only trouble, those installers aren't generally visible since there were some minor problems, but watch out for a new one soon. > > Ralf > > > > From: Timothy Springer <springer(a)idi.harvard.edu> > To: phenixbb(a)phenix-online.org > Sent: Tue, December 7, 2010 7:31:44 PM > Subject: [phenixbb] ncs restraints > > Hi, I am using NCS restraints for 4 copies of a molecule at 3.05 Å. We are using the standard weights: > coordinate_sigma = 0.05 > b_factor_weight = 10 > and the 4 molecules look identical. What are suggested values for looser restraints? One of my colleagues said that varying them did not make a difference- ncs was still very strict. Is there a way to make them less strict? > Thanks, > Timothy A. Springer, Ph.D. > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

15 years, 2 months

Re: [phenixbb] Dummy atoms

by Pavel Afonine

Hi Frank, thanks a lot for your feedback - as always very useful and critical which is great! > the 2nd-last one of the validation pack, where you recommend against > the use of UNK atoms, but don't say why: > > <snip> > Some programs and people tend to interpret unknown density using "dummy > atoms". In PDB files it typically looks like this: > ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X > ATOM 11 O UNK 2 6.994 -12.600 10.740 1.00 7.16 X > ATOM 12 O UNK 2 6.028 -13.737 10.607 1.00 6.58 X > ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28 > ATOM 14 DUM UNK 2 5.099 -13.727 11.792 1.00 7.15 > - *Do not deposit this in PDB*, especially if chemical element type is > undefined > (rightmost column) > </snip> Sorry for not saying "why". If it ever happens for me to show these slides again in whatever School I promise to improve the slides to be as clear as possible. The problems with records like: ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28 ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28 X are: - the chemical element type (column 77-78 ?) (that one that use in Fcalc calculation and also may provide the charge) is undefined (simply blank or "X"), so there is no way to include these dummy atoms into structure factor calculations; - even if you have "O" like in the first example this often contradicts with "X" in rightmost column, so you have to use guesswork, which is not good for interpreting well defined formatted data files. Plus, of course, not way to tell the charge; - even if you have "O" like in the second example the element type in rightmost column is missing. Therefore it is a weak information to take: we cannot reliably extract scattering type from atom label - classical example CA (Calcium) and CA (C-alpha); - of course, we can make the program simply ignore these atoms (hm... sounds like a bad practice: don't read it if you can't read it - this way we may end up being ignorant -:) ). But are we sure that the original program that put these dummies was also not using them in Fcalc calculation? Or may be it was using some default scattering factor for them? Which one: H or O or N (N better approximates than O)? - furthermore, since we are lacking such a fundamental property of these dummy atoms as scattering type, it it laughable to assign some B-factors to these atoms! Look through PDB: you will find a some smart looking B-factors, such as 8.06 A**2 for an non-existing element X -:) In summary: - do not put there anything hoping that future generation smarter software will find out what it is; - if you want to put something there (which has valid reasons actually - this will improve the overall map quality which is good - then please properly define it). All the best! Pavel.

15 years, 6 months

Re: [phenixbb] Sharing a Phenix project via Dropbox

by Derek Logan

Hi Sebastian, Instinctively this sounded like the easiest solution of all those suggested. However when I try to do this for Dropbox through the Preferences it says "Can't create a Dropbox folder in the requested location", so it looks like it's hard-wired to use locations in my home directory. Has anyone else succeeded in moving a Dropbox folder to / ? It doesn't work for Google Drive either - it says the location is not writeable. I have administrator privileges on my Mac. Do I have to change permissions on / manually? Best wishes Derek On 16 May 2014, at 15:56, Sebastiano Pasqualato <sebastiano.pasqualato(a)GMAIL.COM<mailto:[email protected]>> wrote: Hi Derek, the way I work with Google Drive is installing its folder (you can choose where to put it) directly into / (that is /Google Drive - unfortunately you cannot change its name and have to live with the space). If you and your collaborators all do that in your Macs, Phenix will find always the same path and work with no hassles. HTH, ciao, Sebastiano On 16 May 2014, at 15:49, Derek Logan <derek.logan(a)biochemistry.lu.se<mailto:[email protected]>> wrote: Hi Nat, Thanks for your reply. However could it be that it works for you because you have the same user name on each Mac, so that your home directory is always /Users/nat (or whatever)?. Thus the hard-wiring of full paths into the Phenix files would not be a problem for you? In our case there are at least 3 users with different names (in different countries!) who might want to access the same project. Otherwise I would think that Google Drive should behave just like Dropbox? I'm sure Jürgen's idea would work but it would be nice if possible to avoid creating a separate common user. I don't remember having done this since we had a "data processing account" on our microVAXes for integrating film data at Oxford in the early 1990s :-) Any other ideas? /Derek On 16 May 2014, at 14:47, nathanielclar5 . <nathanielclar5(a)GMAIL.COM<mailto:[email protected]>> wrote: Do you have the dropbox app on every computer, so that the files can be accessed through finder? I use Google Drive to sync phenix project directories between my 3 Macs, and usually it works perfectly. If I run a job on one computer, I can open a phenix gui on another, and it will show the intact job history, including jobs run on a different computer. Sometimes I get a error that 'this is not a valid phenix project directory' when I attempt to import a job folder created on a different computer. When that happens, I just make a new sub-folder within it, make that the new project folder, and move on...so maybe I'm running into the same problem as you and ignoring it. Usually it's problem free however. Nat On Fri, May 16, 2014 at 5:03 AM, Derek Logan <derek.logan(a)biochemistry.lu.se<mailto:[email protected]>> wrote: Hi, Has anyone ever successfully shared a Phenix project through Dropbox? I tried Googling for info on this without success. I have tried sharing but it doesn't work because Phenix uses the full path to the project, e.g. /Users/derek/Dropbox/project rather than ~/Dropbox/project, which would work for all users sharing the project. I tried manually editing project.phil in the .phenix directory, but at the end of a run of phenix.refine it was overwritten again. Is there somewhere (job_history.phil?) I can replace /Users/derek with ~ so that it the change will be permanent? I think that this would be a very effective way for me to set up a project being run by one of my PhD students involving people from at least 3 labs that could have opinions on the refinement! /Derek P.S. We are all using Macs. _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit

11 years, 8 months

[phenixbb] Macromolecular Crystallography workshop in South America

by Felipe

Dear colleagues, We are pleased to announce our sixth edition of the Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). This Workshop will cover all aspects of the macromolecular structure determination process using X ray crystallography: starting from data processing, through phasing and refinement to structure completion and analysis. Integrative methods are also being included. In particular, this year an introduction to cryo-electron microscopy has been added to the program. http://pasteur.uy/mx2017 <http://pasteur.uy/mx2017> Dates: November 13 - 23, 2017 Confirmed speakers and tutors: Alejandro Buschiazzo, Montevideo, Uruguay Grzegorz Chojnowski, Hamburg, Germany Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil James Holton, San Francisco/Berkeley/Palo Alto, USA Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Colin Palmer, Oxford, UK James Parkhurst, Oxford, UK Randy Read, Cambridge, UK Clemens Vonrhein, Cambridge, UK Please find the program of the Workshop, the application form and further contact information, at http://pasteur.uy/mx2017 <http://pasteur.uy/mx2017> This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil Applicants: 24 students will be selected, aiming at 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 September 17, 2017. Please address further inquiries to: mx2017(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! Felipe Trajtenberg, PhD Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 143 Fax: +598 25224185 http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular… <http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular…>

8 years, 4 months

[phenixbb] Macromolecular Crystallography workshop in South America 2020

by Alejandro Buschiazzo

Dear colleagues, We are pleased to announce the 8th South American Macromolecular Crystallography School: Macromolecular Crystallography School 2020 "Structural Biology to enhance high impact research in health and disease” To be held at the Institut Pasteur de Montevideo (Uruguay) - September 9-19, 2020 http://pasteur.uy/novedades/mx2020/ The application deadline is July 9, 2020. For further inquiries : mx2020(a)pasteur.edu.uy <mailto:[email protected]> Main Topics: · data processing; · phasing and structure determination; · model refinement and validation; · introduction to crystallography + cryo-electron microscopy integration Confirmed speakers and tutors (so far... a few more will join the crew): Alejandro Buschiazzo (Institut Pasteur de Montevideo, Uruguay) Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK) Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil) Ronan Keegan (STFC Rutherford Appleton Lab - CCP4, Didcot, UK) Eugene Krissinel (STFC Rutherford Appleton Lab - CCP4, Didcot, UK) Joāo Muniz (Instituto de Fisica de São Carlos, Brazil) Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK) Colin Palmer (STFC Rutherford Appleton Lab - CCP-EM, Didcot, UK) James Parkhurst (Diamond Light Source, Didcot, UK) Randy Read (University of Cambridge, UK) Kyle Stevenson (STFC Rutherford Appleton Lab - CCP4, Didcot, UK) Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK) Please find the application form and further contact information at http://pasteur.uy/novedades/mx2020/ (this www site will be updated regularly, so stay tuned!) This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); and the Programa 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: mx2020(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to hosting you in Montevideo!

6 years

Re: [phenixbb] measuring the angle between two DNA duplexes

by Edward A. Berry

Hi, Pavel, Yes, my suggestion would be specific for double-stranded nucleic acid. A separate but similar one would be required for protein (I've written and used that one). For protein the bf straight line would not be so good because its a single helix, so at the end atoms are on only one side. Say you have 1.5 turns of helix. the best fit line would be skewed to go through the ends of the backbone (as Tim Gruene noted). For a double helix it would be less of a problem since you have one chain on each side of the axis to balance. But in the extreme, say when the length is less than the thickness (i.e. a disk), the best-fit line could be closer to the diameter than the axis. I wouldn't pretend to advise you on programming linear algerba, but for my own edification I will study your matrix and try to understand, with help from the page Tim linked. At first glance it looks like S.V. decomposition on n vectors in 3 space, or 3 vectors in N space, where the singular vectors, values are taken as the eigenvectors, values of the matrix U'V or UV'. Or the normal equations for solving a least-squares problem with a generalized inverse involving [M'M]^-1 but then you would go on to invert the matrix rather than finding its eigenvectors. Pavel Afonine wrote: > Hi Ed, > > interesting idea! Although I was thinking to have a tool that is a > little more general and a little less context dependent. Say you have > two clouds of points that are (thinking in terms of macromolecules) two > alpha helices (for instance), and you want to know the angle between the > axes of the two helices. How would I approach this?.. > > First, for each helix I would compute a symmetric 3x3 matrix like this: > > sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) > sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) > sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2 > > where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over > all atoms, and (xc,yc,zc) is the coordinate of the center of mass. > > Second, for each of the two matrices I would find its eigen-values and > eigen-vectors, and select eigen-vectors corresponding to largest > eigenvalues. > > Finally, the desired angle is the angle between the two eigen-vectors > found above, which is computed trivially. > I think this a little simpler than finding the best fit for a 3D line. > > What you think? > > Pavel > > > On 1/20/14, 2:14 PM, Edward A. Berry wrote: >> >> >> Pavel Afonine wrote: >> . . >> >>> The underlying procedure would do the following: >>> - extract two sets of coordinates of atoms corresponding to two >>> provided atom selections; >>> - draw two optimal lines (LS fit) passing through the above sets >>> of coordinates; >>> - compute and report angle between those two lines? >>> >> >> This could be innacurate for very short helices (admittedly not the >> case one usually would be looking for angles), or determining the axis >> of a short portion of a curved helix. A more accurate way to >> determine the axis- have a long canonical duplex constructed with its >> axis along Z (0,0,1). Superimpose as many residues of that as required >> on the duplex being tested, using only backbone atoms or even only >> phosphates. Operate on (0,0,1) with the resulting operator (i.e. take >> the third column of the rotation matrix) and use that as a vector >> parallel to the axis of the duplex being tested. >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

12 years

Re: [phenixbb] Reduce NQH

by Pavel Afonine

Hello, do you have two-letter chain IDs in PDB file? Pavel On 12/19/13, 4:33 PM, jp d wrote: > hi, > we were going through the logs recently and see something odd during > Reduce N/Q/H analysis > the log file looks like this: > ================================== NQH flips > ================================== > r_work=0.3047 r_free=0.3518 > Analyzing N/Q/H residues for possible flip corrections... > segID AL01 renamed chain A for Reduce N/Q/H analysis > segID AL02 renamed chain B for Reduce N/Q/H analysis > ... > segID AL29 renamed chain Y for Reduce N/Q/H analysis > segID AL30 renamed chain Z for Reduce N/Q/H analysis > segID AL32 renamed chain a for Reduce N/Q/H analysis > segID AL33 renamed chain a for Reduce N/Q/H analysis > segID AL34 renamed chain b for Reduce N/Q/H analysis > segID AL35 renamed chain b for Reduce N/Q/H analysis > ... > segID BL28 renamed chain z for Reduce N/Q/H analysis > segID BL31 renamed chain z for Reduce N/Q/H analysis > segID BL13 renamed chain AA for Reduce N/Q/H analysis > segID BL29 renamed chain AB for Reduce N/Q/H analysis > ... > > we noticed that the lower case chain letters start to duplicate > themselves and are not unique to each segid. > when it starts the two letter chain, everything seems unique again. > forgive me if that is expected, it just seems kind of strange > > this was seen in mutlple log files and we are using version > Version: 1.8.4 > Release tag: 1496 > if you need our files or more details, let me know > > thanks > jpd > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

12 years, 1 month

Re: [phenixbb] alternatives to RMSD

by Tim Gruene

Hi Patrick, why don't you superimpose only the matching segments and report their RMSD? It is the common procedure for RMSD's from superpositions to report the aligned residues together with the RMSD. The advantage compared to a map CC is similar to that of R_sym over R_meas: readers have a better concept (from experience) of what the numbers mean. Best, Tim On 07/02/2014 05:15 PM, Patrick. C wrote: > Hi Phenix users, > > I am not a crystallographer but I though you guys might be a good place to ask > this question. > > I have 2 super secondary structures, A and B and they consist of Helix-turn-Strand > > Due to the turn the two structures have a poor RMSD because the two flanking > fragments of Helix and Strand are far from each other but when I superimpose the > two fragments individually(helixA with helix B and standA with strandB in Pymol > they align very well). > > Now, is there a way to express this instead of using the RMSD? > When the two structures align well the RMSD is very good but a slight movement > and the RMSD is awful. > But looking at the two structures I can see they follow the same path through space. > > Thank you, > Patrick > > > -------------------------------------------------------------------------------- > 3D Earth Screensaver Preview <http://www.inbox.com/earth> > *Free 3D Earth Screensaver* > Watch the Earth right on your desktop! Check it out at www.inbox.com/earth > <http://www.inbox.com/earth> > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

11 years, 7 months

Re: [phenixbb] Figure of merit from refinement

by Alexandre OURJOUMTSEV

Dear Andre, (I repeat here the same message that I've just sent through the ccp4bb; sorry for answering late) I would strongly advice you to look at the article by Lunin and Skovoroda (Acta Cryst, A, 1995) that addresses exactly your question: https://scripts.iucr.org/cgi-bin/paper?vs0124 The authors remind a very important point that after model refinement ML phase errors are strongly underestimated if using all reflections, as that was done in the original works (see references in the article). While the same ML estimates work perfectly for unrefined models, that's not the case for refined ones, as was observed yet in the beginning of 80ths. These authors show then that using the test-set of reflections (the same as for R-free) is crucial to get the correct phase error estimates and respective FOMs for all cases, as this is implemented now in modern refinement programs, e.g. phenix.refine. See also the article by Pannu & Read (Acta Cryst, A, 1996) https://onlinelibrary.wiley.com/doi/pdf/10.1107/S0108767396004370 A more recent important article on this topic is that by Praznikar and Turk (Acta Cryst, D, 2009) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257616/ who discuss what can be done if a statistically significant test set of reflections is not available. I hope this helps you. I am ready to answer you further eventual questions (probably, in a private correspondence). With best wishes, Sacha Urzhumtsev ________________________________ -------- Forwarded Message -------- Subject: [phenixbb] Figure of merit from refinement Date: Tue, 1 Oct 2019 08:15:14 -0300 From: Andre LB Ambrosio <andre(a)ifsc.usp.br><mailto:[email protected]> To: phenixbb(a)phenix-online.org<mailto:[email protected]> Dear all, How is the FOM calculated for a given reflection specifically in the context of model refinement? How useful is it in assessing the phase quality, when not for initial experimental phases? Many thank in advance, -- Andre LB Ambrosio

6 years, 4 months

[phenixbb] Group ADP refinement restraints

by Taylor Stevens

Hello, I am currently refining a low-ish resolution structure (through the phenix.refine GUI) with phenix version 1.14 and had some questions about the use of restraints in group ADP refinement. In the phenix.refine documentation (https://www.phenix-online.org/documentation/reference/refinement.html#refin… <https://www.phenix-online.org/documentation/reference/refinement.html#refin…>) it is stated that “Group isotropic ADP or TLS refinement do not use any restraints”, however, this does not seem to be the case. If I look in the log file I can see the following lines of text which I believe indicate that the restraints are being applied: |-group b-factor refinement (macro cycle = 0; iterations = 0)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = None | |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 1; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 2; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 3; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| If I manually set the wu parameter to 0 under “Refinement target weights" nothing changes, however, if I navigate to "All parameters > ADP settings > Group B-Factors" in the GUI there is a “Use restraints” box that is checked by default. If I uncheck this box, there are no longer any restraints being applied according to the log file, and in the case of the structure I am refining, there is a substantial drop in the rfree/rwork. Is this an issue with the program or documentation? Or am I misunderstanding how the program is supposed to work? Is it generally a good idea to use group ADP refinement without restraints? Thanks, Taylor

6 years, 2 months

Search results for query "look through"