Re: [ccp4bb] Cryo-EM
Hi everyone Thanx a lot..Your suggestions are really informative and a valuable source of knowledge.. regards Faisal On 5/20/15, Takanori Nakane takanori.nak...@bs.s.u-tokyo.ac.jp wrote: Hi Faisal, Recordings of MRC-LMB EM-course last year are available at http://www2.mrc-lmb.cam.ac.uk/groups/scheres/impact.html Best regards, Takanori Nakane On 2015/05/20 2:36, Yi-Wei Chang wrote: Hi Faisal, Here is a new series of lecture video called Getting Started in Cryo-EM made by Prof. Grant Jensen at Caltech/HHMI. http://cryo-em-course.caltech.edu/ There are 14.5 hours of lecture total, which starts with the basic anatomy of electron microscopes, an introduction to Fourier transforms, and the principles of image formation. Building upon that foundation, the lecture then covers sample preparation issues, data collection strategies, and basic image processing workflows for tomography, single particle analysis, and 2-D crystallography. It is an excellent introduction that will prepare people for real practical training on the microscope or to engage in serious conversations about cryo-EM: a great way to get started for anyone just joining a cryo-EM lab, or anyone who wants to be sure they have the basic concepts down. Cheers, Yi-Wei -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] Online server for generation of topology cartoons
Dear Mohammad, there is for example pdbsum (www.ebi.ac.uk/pdbsum), where you can upload a pdb and you get various outputs including a topology diagram. Cheers Christian Am 20.05.2015 um 10:50 schrieb Mohammad Khan: Dear all, Is there any good online server for the generation of topology cartoons of proteins, where one can have a clear layout of the various secondary structures? I have tried Pro-Origami, but however I am not veru happy with the output. I have used the default options. Maybe if someone can help me out with various options. I would want to use the output for publication purposes. Thanks Mohammad
[ccp4bb] HIS related crystallography issue
Dear All, Suppose the protein crystal resolution is about 2-3A, then in the map it should be rather difficult to distinguish the C and N in the sidechain of HIS. In this way we may regard the sidechain of HIS is flippable. But suppose in one flipped conformation of the HIS, the free N in the sidechain of HIS can form H-bond with the neighbour H of the OH of the Thr, in the other flipped conformation of the HIS, the free N in the sidechain of HIS cannot form H-bond with the neighbour H of the OH of the Thr (caused by distance issue). Suppose whether the H-bond forms between the free N in the sidechain of HIS and the neighbour H of the OH of the Thr was very important biologically, in this situation how can we distinguish whether the H-bond forms? Smith
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
if it only occurs with the Mac version of Word: a workaround would be to set up a virtual machine on your Mac in which you run Windows and its version of Word. Anybody tried this? Kay
[ccp4bb] Online server for generation of topology cartoons
Dear all, Is there any good online server for the generation of topology cartoons of proteins, where one can have a clear layout of the various secondary structures? I have tried Pro-Origami, but however I am not veru happy with the output. I have used the default options. Maybe if someone can help me out with various options. I would want to use the output for publication purposes. Thanks Mohammad
Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac
Thanks, as always, to everyone for a thoughtful discussion!
Martin Montgomery suggested trying the beta release of the upcoming Office for
Mac suite. I installed this (which required carrying out the update to
Yosemite that I had been putting off), and it turns out that rather than fixing
the bug with Equation Editor (i.e. the one based on the MathType software),
Microsoft removed that option and all that is left is their built-in equation
tool (which it turns out is based on MathML markup)! So it looks like anyone
who likes the Equation Editor will either have to cough up for a licence for
the fully-featured MathType (which creates its own problems collaborating with
people who don't have a licence) or learn to use an alternative.
A few people (Robbie Joosten, Klaus Fütterer and Shing Ho) suggested that I
should bite the bullet and learn how to use the built-in equation tool. I had
tried this and found it unintuitive compared to the Equation Editor, but maybe
that's just because I haven't put in anything like the same amount of time
learning it. This is probably going to be the way I'll go, mostly for
compatibility with collaborators (who are almost all using Word without special
plugins) but partly for journal typesetting considerations mentioned below.
As I said before, collaboration considerations rule out a full-scale adoption
of LaTeX for me, but maybe the suggestions of different LaTeX environments will
be useful for others. Perhaps Lyx (George Reeke's suggestion) might be
sufficiently WYSIWYG to convince collaborators to install it, although Blaine
Mooers and Murpholino Peligro pointed out some potential complications with
this solution, particularly in compatibility with bibliography tools.
However, there also seem to be some interesting tools that allow you to prepare
just the equations in LaTeX and paste at least images of those equations into
Word documents. Your collaborators wouldn't be able to edit the equations
without getting the same tools, which is a downside of this option. Several
people (Jonathan Davies, Nicolas Soler, Blaine Mooers) suggested LaTeXit and
Bill Scott suggested TeX-fog. I'm going to play with LaTeXit to see how I like
that, particularly for PowerPoint where there's less of an issue with
collaboration.
Similarly, Adrian Goldman suggested that the Mac Grapher program could be used
to prepare pictures of equations.
Then there was some lateral thinking. Jens Thomas suggested that I could turn
AutoSave off and implement my own replacement from the Terminal window with the
following script:
——
#!/bin/bash
[[ $# -ne 1 ]] echo Usage: $0 path_to_file exit 1
while true;
do
cp $1 ${1}.bak
sleep 60
done
——
Kay Diederichs suggested installing Word for Windows on a Windows virtual
machine, though I balk at paying Microsoft for two more licences to work around
a bug in their software!
Another issue, which I didn't raise in my original post, is what happens when
your file gets to the publisher. Putting my Acta D hat on (and for all of us
as members of the IUCr), we should try to make it easier for our journals.
Also, proofreading is much easier if some poor person hasn't had to retype all
the equations. So I asked at Acta Cryst what happens when papers are submitted
in different formats. One possibility is to submit a LaTeX document for
everything, in which case the equations should be fine. For documents
submitted in Word format, Simon Westrip described their workflow as follows:
——
1) All documents (Word or OpenOffice) are processed using Word on Windows
machines
2) MathType is used to convert any equation objects in the document to Plain TeX
3) If MathType fails (which it often does with Microsofts 'docx MathML'
equations,
then my own software attempts to convert MathML-based equations objects to
Plain Tex.
4) Any remaining equations have to be typeset manually (e.g. those that are
included as
images)
So ideally, in the absence of MathType or any other plugin that can embed
equation 'objects'
in Word documents, we would prefer that the equations be prepared using Word's
built-in editor.
——
As Simon said in a followup, if other solutions become popular, they'll
accommodate them at the IUCr journals. In the meantime, I guess I'll be
learning the built-in editor.
Randy Read
On 18 May 2015, at 09:10, Randy Read rj...@cam.ac.uk wrote:
Rather off-topic, but maybe someone on the list has found a way to work
around this!
There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the
one that is based on a stripped-down version of MathType, which you get with
Insert-Object-Microsoft Equation). You can insert an equation, re-open it
and edit it several times, and then suddenly (and seemingly randomly) the
equation object will be replaced by a picture showing the equation, which can
no longer be edited. I’m writing a rather equation-heavy paper at the
moment, and this
Re: [ccp4bb] HIS related crystallography issue
You can typically assign the histidine orientation based on analysis of the hydrogen bond network. In ambiguous cases you might have to look a few residues deep. WHAT_CHECK does this for you by a global optimization of the hydrogen bond network. Cheers, Robbie Sent with my Windows Phone Van: Smith Liumailto:smith_liu...@163.com Verzonden: 20-5-2015 14:12 Aan: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] HIS related crystallography issue Dear All, Suppose the protein crystal resolution is about 2-3A, then in the map it should be rather difficult to distinguish the C and N in the sidechain of HIS. In this way we may regard the sidechain of HIS is flippable. But suppose in one flipped conformation of the HIS, the free N in the sidechain of HIS can form H-bond with the neighbour H of the OH of the Thr, in the other flipped conformation of the HIS, the free N in the sidechain of HIS cannot form H-bond with the neighbour H of the OH of the Thr (caused by distance issue). Suppose whether the H-bond forms between the free N in the sidechain of HIS and the neighbour H of the OH of the Thr was very important biologically, in this situation how can we distinguish whether the H-bond forms? Smith
Re: [ccp4bb] HIS related crystallography issue
yes, at lowish resolution considering potential H-bonds is often the only way to orient the His, but also Asn and Gln side-chains correctly. Molprobity (http://molprobity.biochem.duke.edu/) and other programs also check this for you, suggesting side-chain flips where necessary or advised. And Coot has a special side-chain 180º flip function for you to flip them easily. At higher resolution you can look at the refined B-factors, if the more electron-rich atoms (N in His, O in Asn/Gln) have a much higher B than the less electron-rich ones (C in His, N in Asn/Gln), this can also mean the side-chain needs flipping. At even higher solution you may see difference density in wrongly oriented His/Asn/Gln side-chains. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 20 May 2015, at 14:10, Smith Liu wrote: Dear All, Suppose the protein crystal resolution is about 2-3A, then in the map it should be rather difficult to distinguish the C and N in the sidechain of HIS. In this way we may regard the sidechain of HIS is flippable. But suppose in one flipped conformation of the HIS, the free N in the sidechain of HIS can form H-bond with the neighbour H of the OH of the Thr, in the other flipped conformation of the HIS, the free N in the sidechain of HIS cannot form H-bond with the neighbour H of the OH of the Thr (caused by distance issue). Suppose whether the H-bond forms between the free N in the sidechain of HIS and the neighbour H of the OH of the Thr was very important biologically, in this situation how can we distinguish whether the H-bond forms? Smith
Re: [ccp4bb] Online server for generation of topology cartoons
There are different servers and programs which I use as guides (TOPDRAW comes to mind), but for publication purposes I always end up drawing topology diagrams myself - for what I consider maximum clarity. It takes time, but I prefer to show things the way I think is best showing them, using the output from one or more of these programs as guide. It is than also easier to change them upon suggestions of collaborators or referees. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 20 May 2015, at 11:50, Mohammad Khan wrote: Dear all, Is there any good online server for the generation of topology cartoons of proteins, where one can have a clear layout of the various secondary structures? I have tried Pro-Origami, but however I am not veru happy with the output. I have used the default options. Maybe if someone can help me out with various options. I would want to use the output for publication purposes. Thanks Mohammad
[ccp4bb] Workshop on 3D solutions in Cryo-Electron Microscopy 2015
Workshop on 3D solutions in Cryo-Electron Microscopy 2015 Event URL: http://www.maastrichtuniversity.nl/web/show/id=7562295/langid=42 Objective The aim of this workshop is to show, through lectures and practical courses, the solutions for 3D reconstruction in Cryo-Electron Microscopy. Methodology The lectures will cover single particle analysis, cryo-tomography of isolated specimens and cryo-tomography of structures inside a vitreous cryo-section or lamella and cryo-CLEM. The practical courses will show to the participants how to do sample preparation (high pressure freezing, plunge freezing, vitreous sectioning and cryo-fibbing), image acquisition in cryo-EM single-particle and cryo-tomography and 3D-reconstruction. When Monday 6 - Friday 10 July Speakers Sjors Scheres MRC Laboratory of Molecular Biology Gabriel Lander The Scripps Research Institute Israel S. Fernández MRC Laboratory of Molecular Biology Friedrich Förster Max-Planck-Institut für Biochemie Ohad Medalia University of Zurich Julia Mahamid Max-Planck-Institut für Biochemie Jürgen Plitzko University of Utrecht Peter Peters Maastricht University Yanhong Xue Maastricht University Vladan Lucic Max-Planck-Institut für Biochemie Rainer Kaufmann Oxford University Marin van Heel Leiden University Raimond Ravelli Maastricht University Group size 5 groups, 5 participants per group Fee Regular Fee: €900,- Lectures Only Fee: €100,- Registration Deadline for registration: 6 June 2015 Selection will be made according the motivation and CV. Click here to go to the registration formhttp://www.maastrichtuniversity.nl/web/Institutes/MaastrichtMultiModalMolecularImagingInstitute/WorkshopOn3DSolutionsInCryoElectronMicroscopy2015/RegistrationFormCryoEMWorkshop.htm. Venue Lectures: Brains Unlimited Building Jo Ritzen Lecture Hall (S0.007) Oxfordlaan 55 6229 EV Maastricht Practical courses: Nanoscopy Lab, room 0.202 Universiteitsingel 50 6229 ER Maastricht Contact If you have any questions please send an email to Carmen Lopez-Iglesiasmailto:c.lopezigles...@maastrichtuniversity.nl (c.lopezigles...@maastrichtuniversity.nlmailto:c.lopezigles...@maastrichtuniversity.nl) or Alice Vonckenmailto:alice.vonc...@maastrichtuniversity.nl (alice.vonc...@maastrichtuniversity.nlmailto:alice.vonc...@maastrichtuniversity.nl). -- Giancarlo Tria Multimodal Molecular Imaging institute Maastricht University Universiteitssingel 50 6229 ER Maastricht the Netherlands www.maastrichtuniversity.nl/m4ihttp://www.maastrichtuniversity.nl/m4i
Re: [ccp4bb] HIS related crystallography issue
This is what we call N/Q/H flips done as part of phenix.refine refinement based on Molprobity evaluation. Pavel On Wed, May 20, 2015 at 2:10 PM, Smith Liu smith_liu...@163.com wrote: Dear All, Suppose the protein crystal resolution is about 2-3A, then in the map it should be rather difficult to distinguish the C and N in the sidechain of HIS. In this way we may regard the sidechain of HIS is flippable. But suppose in one flipped conformation of the HIS, the free N in the sidechain of HIS can form H-bond with the neighbour H of the OH of the Thr, in the other flipped conformation of the HIS, the free N in the sidechain of HIS cannot form H-bond with the neighbour H of the OH of the Thr (caused by distance issue). Suppose whether the H-bond forms between the free N in the sidechain of HIS and the neighbour H of the OH of the Thr was very important biologically, in this situation how can we distinguish whether the H-bond forms? Smith
Re: [ccp4bb] MOLREP self-rotation matrix
Hi Sacha, Thanks you for your advice! I tried it and it does work. And thank you for your effort on this tool. It is really helpful! Have a nice day, Chen On Wed, May 20, 2015 at 3:11 AM, Alexandre OURJOUMTSEV sa...@igbmc.fr wrote: Dear Chen, Thank you for your confirmation (it is a pleasure, not everybody does it!). I am glad that it works for you. Now, if you wish/can spend 5 minutes more, you may (see http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/convrot/Convrot.html): - Do the same (I mean – compile) three other fortran programs of that package - Correct THE FIRST LINE of convrot5.tcl so that it indicates the correct PATH to the command 'wish' of the Tcl/tk libraries (directory where you have this program at your computer) Then normally the GUI version should work; it is more convenient than the on-line fortran version alone. We understand that this is an obsolete way working with programs and by this reason we are finishing its more modern python version (practically done…). As for everybody, the problem is absence of time to do this ! Have a nice day, and good luck ! Sacha *De :* Chen Zhao [mailto:c.z...@yale.edu] *Envoyé :* mardi 19 mai 2015 18:00 *À :* Alexandre OURJOUMTSEV *Objet :* Re: [ccp4bb] MOLREP self-rotation matrix Dear Sacha, I am able to run the program now. Thank you so much! Have a nice day, Chen
[ccp4bb] Postdoc position - IECB, Bordeaux, France
Postdoctoral Fellow European Institute of Chemistry and Biology, France A postdoctoral position in macromolecular crystallography applied to bio-inspired folded architectures (Foldamers) is available, ideally starting between June and September 2015 at the European Institute of Chemistry and Biology (IECB) in Bordeaux. The project is aimed at exploring the structural properties of foldamers designed to mimic alpha-helices and at characterizing complexes formed between such foldamers and proteins. The candidate must hold a PhD in structural biology, with strong expertise in X-ray macromolecular crystallography, biochemistry and molecular biology. We are seeking highly motivated candidates with a curiosity for biopolymer mimicry and an interest in applying standard macromolecular crystallographic methods to novel and atypical structural challenges. The European Institute of Chemistry and Biology ( http://www.iecb.u-bordeaux.fr/ http://www.iecb.u-bordeaux.fr/) is a dynamic research institute, located on the Bordeaux University Campus in south-west France, and equipped with state-of-the-art structural biology equipment. For more information on the position, see : http://www.iecb.u-bordeaux.fr/images/stories/Equipes/Guichard/post-doctoral positionguichardgroup.pdf http://www.iecb.u-bordeaux.fr/images/stories/Equipes/Guichard/post-doctoralp ositionguichardgroup.pdf Candidates interested in applying should send a letter of motivation and a CV including research experience and a list of publications. They should also arrange for two letters of recommendation to be sent to mailto:g.guich...@iecb.u-bordeaux.fr g.guich...@iecb.u-bordeaux.fr Gilles Guichard Univ Bordeaux, CNRS, UMR 5248, CBMN Institut Européen de Chimie et Biologie (IECB) 2, rue Robert Escarpit 33607 Pessac, France
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
MathType is a Microsoft Word plugin (on both Windows and Mac OSX). It worked very well for me. http://www.dessci.com/EN/products/mathtype/ Best, Steven On Wed, May 20, 2015 at 6:09 PM, James Stroud xtald...@gmail.com wrote: I didn’t see the following solution in any other responses. It’s probably the most reasonable one given the constraints of collaboration and publishing. In the absence of using the best software, I found it practical to write the equations in MathType and save them as MathType PDF equations and then add these equations to the document. It is a portable, cross-platform-ish solution. Others only need to install a MathType player, which is free. The advantage is that if your equation gets hosed in the document, you still have the original, editable equation in the PDF. In such cases, you must re-embed it in your document, but it’s better than fully rewriting it. With that said, if you want to work behind a full-featured word processor and have access to the wonders of TeX typesetting, LibreOffice (OpenOffice) + TexMaths is the best for the author during preparation of a manuscript. At this point it is bug free (to my experience), embeds vector equations (SVG) or raster (PNG), is editable, and looks spectacular both when editing and when publishing/printing. The downside is that you have to collaborate with people you can’t force into using the best software. Worse, journals seem to use proprietary publishing software and they want MathType or equation editor with Microsoft word, hence my first solution. James On May 18, 2015, at 5:10 AM, Keller, Jacob kell...@janelia.hhmi.org wrote: There is the possibility of using one of the open-source versions, like openOffice, but those I guess also have their issues. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read Sent: Monday, May 18, 2015 4:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Equation Editor woes with Office 2011 for Mac Rather off-topic, but maybe someone on the list has found a way to work around this! There's a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert-Object-Microsoft Equation). You can insert an equation, re-open it and edit it several times, and then suddenly (and seemingly randomly) the equation object will be replaced by a picture showing the equation, which can no longer be edited. I'm writing a rather equation-heavy paper at the moment, and this is driving me crazy. This seems to be a known bug, which has existed from the release of Office 2011. Apparently it happens, unpredictably, when an AutoSave copy of the document is saved, so you can avoid it by turning off the AutoSave feature. The last time this drove me crazy, several years ago, I did try turning off AutoSave. For a while, I was very good about manually saving frequently, but I got into bad habits and eventually Word crashed after I had worked for several hours on a grant proposal without manually saving. So I turned AutoSave back on. At the moment, the least-bad solution seems to be to turn off AutoSave while I'm working on a document with lots of equations and then (hopefully) remember to turn it back on after that document is finished. But it would be great if someone has come up with a better cure for this problem. No doubt someone will suggest switching from Word to LaTeX, but I need to be able to collaborate on paper-writing, and even though I might be willing to invest the effort in learning LaTeX, I can't really expect that of my collaborators. Most people in our field do use Microsoft Word, regardless of its failings. I've also tried using the professional version of MathType, but that requires your collaborators to install it as well - and I don't think that cured the equation to picture problem anyway. Thanks! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk -- Steven Chou
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
I didn’t see the following solution in any other responses. It’s probably the most reasonable one given the constraints of collaboration and publishing. In the absence of using the best software, I found it practical to write the equations in MathType and save them as MathType PDF equations and then add these equations to the document. It is a portable, cross-platform-ish solution. Others only need to install a MathType player, which is free. The advantage is that if your equation gets hosed in the document, you still have the original, editable equation in the PDF. In such cases, you must re-embed it in your document, but it’s better than fully rewriting it. With that said, if you want to work behind a full-featured word processor and have access to the wonders of TeX typesetting, LibreOffice (OpenOffice) + TexMaths is the best for the author during preparation of a manuscript. At this point it is bug free (to my experience), embeds vector equations (SVG) or raster (PNG), is editable, and looks spectacular both when editing and when publishing/printing. The downside is that you have to collaborate with people you can’t force into using the best software. Worse, journals seem to use proprietary publishing software and they want MathType or equation editor with Microsoft word, hence my first solution. James On May 18, 2015, at 5:10 AM, Keller, Jacob kell...@janelia.hhmi.org wrote: There is the possibility of using one of the open-source versions, like openOffice, but those I guess also have their issues. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read Sent: Monday, May 18, 2015 4:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Equation Editor woes with Office 2011 for Mac Rather off-topic, but maybe someone on the list has found a way to work around this! There's a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert-Object-Microsoft Equation). You can insert an equation, re-open it and edit it several times, and then suddenly (and seemingly randomly) the equation object will be replaced by a picture showing the equation, which can no longer be edited. I'm writing a rather equation-heavy paper at the moment, and this is driving me crazy. This seems to be a known bug, which has existed from the release of Office 2011. Apparently it happens, unpredictably, when an AutoSave copy of the document is saved, so you can avoid it by turning off the AutoSave feature. The last time this drove me crazy, several years ago, I did try turning off AutoSave. For a while, I was very good about manually saving frequently, but I got into bad habits and eventually Word crashed after I had worked for several hours on a grant proposal without manually saving. So I turned AutoSave back on. At the moment, the least-bad solution seems to be to turn off AutoSave while I'm working on a document with lots of equations and then (hopefully) remember to turn it back on after that document is finished. But it would be great if someone has come up with a better cure for this problem. No doubt someone will suggest switching from Word to LaTeX, but I need to be able to collaborate on paper-writing, and even though I might be willing to invest the effort in learning LaTeX, I can't really expect that of my collaborators. Most people in our field do use Microsoft Word, regardless of its failings. I've also tried using the professional version of MathType, but that requires your collaborators to install it as well - and I don't think that cured the equation to picture problem anyway. Thanks! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac
On May 20, 2015, at 5:38 AM, Randy Read rj...@cam.ac.uk wrote: Thanks, as always, to everyone for a thoughtful discussion! Alternatively, as a scientific community, perhaps it is finally time for us to untwist Clippy, bending him backwards and forwards until he snaps at those horrid beady little eyeballs, ditch the Comic Sans, flip Redmond the bird, HTFU and learn to use LaTeX equation markup, and ask that our journals do the same. It really isn’t any harder than learning basic HTML (and predates it as one of the original mark-up languages). Journals and funding agencies should not be demanding that we use crappy broken and restrictive proprietary formats for submitting papers and proposals. Ascii text documents provide the ultimate form of universal interchangeability. The syntax is actually quite straightforward and easy to learn (or look up), eg: http://en.wikibooks.org/wiki/LaTeX/Mathematics LaTeX allows you to focus on content rather than document formatting. Although it is definitely more badass to do this in vim, other ascii text editors often have very useful LaTeX functionality. (My favorite on OS X is TextMate, version 2 of which is now free. If you code on OS X, you should take a look at this.) Once you make the small investment of time learning LaTeX, it makes other tasks easier. For example, you can use jsMath to embed LaTeX-encoded equations (including chemistry symbols) in web pages, eg: http://www.math.union.edu/~dpvc/jsmath/examples/welcome.html
Re: [ccp4bb] Deletion of hydrogens
Reduce also has an option to remove hydrogens at the command line. [phenix.]reduce -Trim model.pdb Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, May 19, 2015 at 8:49 AM, Nikhil Bharambe nikh...@mbu.iisc.ernet.in wrote: Dear Mohammad, You can use 'modify pdb' tool in phenix utilities and select remove hydrogen option. Also, if you are familiar with Vim editor in linux then there is easy command (:g/ H/d). Regards, NIKHIL G BHARAMBE, Ph.D Student, Prof. K. Suguna's Lab Molecular Biophysics Unit (MBU) IISc, Bangalore. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac
On Wednesday, 20 May 2015 05:32:00 PM William G. Scott wrote: On May 20, 2015, at 5:38 AM, Randy Read rj...@cam.ac.uk wrote: Thanks, as always, to everyone for a thoughtful discussion! Alternatively, as a scientific community, perhaps it is finally time for us to untwist Clippy, bending him backwards and forwards until he snaps at those horrid beady little eyeballs, ditch the Comic Sans, flip Redmond the bird, HTFU and learn to use LaTeX equation markup, and ask that our journals do the same. It really isn’t any harder than learning basic HTML (and predates it as one of the original mark-up languages). I don't know that we have much leverage over the whole range of relevant publishers and journals, but certainly the IUCr journals have in my experience always welcomed latex submissions. The IUCr web site provides templates and examples. I highly recommend LyX as an alternative to Word and its ilk. I've been using it for years to write and prepare papers for submission, to Acta and elsewhere. I happen to know that the IUCr website also provides a LyX layout template to improve the WSIWYG experience in LyX (because I donated it :-) Contrary to rumors mentioned up-thread, I have LyX/latex documents going back 10+ years that open just fine in the current version of LyX. Yes, older documents may go through a markup conversion step when opened, but the one-time delay is no big deal. You can save the updated version or not, as you choose. You don't really need to learn any latex to use LyX, although it does help if you want to customize the output (i.e. you aren't using a journal-supplied template). None of this, however, addresses the problem of collaborating with people who want to use MSWord. I have not found anything better than running MSWord in an emulator, and this of course does not address bugs or other problems in MSWord itself. (Well actually it does, kind of. It used to be that fonts, PDF conversion, and some graphics worked better inside a linux+wine emulation than they did in the same MSWord executable running natively on Windows. I don't know if this is still true). Journals and funding agencies should not be demanding that we use crappy broken and restrictive proprietary formats for submitting papers and proposals. Thankfully the NIH now wants PDF. I use LyX for my NIH proposals also. I could package up a template and bibtex style sheet if there is interest. Ethan Ascii text documents provide the ultimate form of universal interchangeability. The syntax is actually quite straightforward and easy to learn (or look up), eg: http://en.wikibooks.org/wiki/LaTeX/Mathematics LaTeX allows you to focus on content rather than document formatting. Although it is definitely more badass to do this in vim, other ascii text editors often have very useful LaTeX functionality. (My favorite on OS X is TextMate, version 2 of which is now free. If you code on OS X, you should take a look at this.) Once you make the small investment of time learning LaTeX, it makes other tasks easier. For example, you can use jsMath to embed LaTeX-encoded equations (including chemistry symbols) in web pages, eg: http://www.math.union.edu/~dpvc/jsmath/examples/welcome.html -- mail: Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac
I have had good experiences with MathJak for html. It too gives beautiful renderings on webpages of equations encoded in LaTeX. It is very easy to use. It grew out of jsMath. http://www.mathjax.org/ Best regards, Blaine Mooers From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of William G. Scott [wgsc...@ucsc.edu] Sent: Wednesday, May 20, 2015 7:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac On May 20, 2015, at 5:38 AM, Randy Read rj...@cam.ac.uk wrote: Thanks, as always, to everyone for a thoughtful discussion! Alternatively, as a scientific community, perhaps it is finally time for us to untwist Clippy, bending him backwards and forwards until he snaps at those horrid beady little eyeballs, ditch the Comic Sans, flip Redmond the bird, HTFU and learn to use LaTeX equation markup, and ask that our journals do the same. It really isn’t any harder than learning basic HTML (and predates it as one of the original mark-up languages). Journals and funding agencies should not be demanding that we use crappy broken and restrictive proprietary formats for submitting papers and proposals. Ascii text documents provide the ultimate form of universal interchangeability. The syntax is actually quite straightforward and easy to learn (or look up), eg: https://urldefense.proofpoint.com/v2/url?u=http-3A__en.wikibooks.org_wiki_LaTeX_Mathematicsd=AwIF-gc=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEkr=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdIIm=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQs=Q3biyCgXkL73q4eLw0MovreIp6p923PLHLrEp3AiuBge= LaTeX allows you to focus on content rather than document formatting. Although it is definitely more badass to do this in vim, other ascii text editors often have very useful LaTeX functionality. (My favorite on OS X is TextMate, version 2 of which is now free. If you code on OS X, you should take a look at this.) Once you make the small investment of time learning LaTeX, it makes other tasks easier. For example, you can use jsMath to embed LaTeX-encoded equations (including chemistry symbols) in web pages, eg: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.math.union.edu_-7Edpvc_jsmath_examples_welcome.htmld=AwIF-gc=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEkr=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdIIm=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQs=UAkZG7nG6yJ1m41HFCqn3Ah_ifo-u-S4N8VwWbtbi3oe=
[ccp4bb] HIS related crystallography issue
Dear All, Suppose my protein has 4 same subunits (not exactly 4 subunits, in order to explain things clear, it contains not less than 2 identical subunitss), each subunit has the potential H-bond involving N of HIS. I have run the optimization by both PDB_REDO and the Phenix refine with the phenix flips checked. I have checkecd the PDB_REDO refine results and the Phenix refine results, the answer is, suppose in PDB_REDO it tells us subunit A has that specific H-bond formed, Phenix refine rells us that subunit B has that specific H-bond formed. In fact, supposing it has 4 subunits, the symmetry determines that the 4 subunits should be identical, and they should all contains the specific H-bonds, or all do not contains the specific H-bonds. Any more suggestions welcome. Smith At 2015-05-20 22:55:13, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Smith, Just to contrast Pavel's phenix plug. PDB_REDO does HQN-flips automatically based on WHAT _CHECK results and refines your model in Refmac. Cheers, Robbie Sent with my Windows Phone Van: Robbie Joosten Verzonden: 20-5-2015 14:30 Aan: Smith Liu; CCP4BB@JISCMAIL.AC.UK Onderwerp: RE: [ccp4bb] HIS related crystallography issue You can typically assign the histidine orientation based on analysis of the hydrogen bond network. In ambiguous cases you might have to look a few residues deep. WHAT_CHECK does this for you by a global optimization of the hydrogen bond network. Cheers, Robbie Sent with my Windows Phone Van: Smith Liu Verzonden: 20-5-2015 14:12 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] HIS related crystallography issue Dear All, Suppose the protein crystal resolution is about 2-3A, then in the map it should be rather difficult to distinguish the C and N in the sidechain of HIS. In this way we may regard the sidechain of HIS is flippable. But suppose in one flipped conformation of the HIS, the free N in the sidechain of HIS can form H-bond with the neighbour H of the OH of the Thr, in the other flipped conformation of the HIS, the free N in the sidechain of HIS cannot form H-bond with the neighbour H of the OH of the Thr (caused by distance issue). Suppose whether the H-bond forms between the free N in the sidechain of HIS and the neighbour H of the OH of the Thr was very important biologically, in this situation how can we distinguish whether the H-bond forms? Smith
Re: [ccp4bb] Online server for generation of topology cartoons
Thanks for the suggestions! On Wed, May 20, 2015 at 6:21 PM, Mark J van Raaij mjvanra...@cnb.csic.es wrote: There are different servers and programs which I use as guides (TOPDRAW comes to mind), but for publication purposes I always end up drawing topology diagrams myself - for what I consider maximum clarity. It takes time, but I prefer to show things the way I think is best showing them, using the output from one or more of these programs as guide. It is than also easier to change them upon suggestions of collaborators or referees. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 20 May 2015, at 11:50, Mohammad Khan wrote: Dear all, Is there any good online server for the generation of topology cartoons of proteins, where one can have a clear layout of the various secondary structures? I have tried Pro-Origami, but however I am not veru happy with the output. I have used the default options. Maybe if someone can help me out with various options. I would want to use the output for publication purposes. Thanks Mohammad
