Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

[Kay Diederichs]

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

[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

Re: [ccp4bb] Online server for generation of topology cartoons

[Christian Roth]

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

[Smith Liu]

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

[Robbie Joosten]

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] HIS related crystallography issue

[Mark J van Raaij]

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] SUMMARY: Equation Editor woes with Office 2011 for Mac

[Randy Read]

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 " && 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  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 is drivin

Re: [ccp4bb] Online server for generation of topology cartoons

[Mark J van Raaij]

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

[Tria Giancarlo (M4I)]

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 
form.

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-Iglesias 
(c.lopezigles...@maastrichtuniversity.nl)
 or Alice Voncken 
(alice.vonc...@maastrichtuniversity.nl).
--
Giancarlo Tria
Multimodal Molecular Imaging institute
Maastricht University
Universiteitssingel 50
6229 ER Maastricht
the Netherlands
www.maastrichtuniversity.nl/m4i

Re: [ccp4bb] HIS related crystallography issue

[Pavel Afonine]

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  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

[Chen Zhao]

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 
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

[Gilles Guichard]

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/) 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-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
 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] Deletion of hydrogens

[Nigel Moriarty]

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 
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] Equation Editor woes with Office 2011 for Mac

[James Stroud]

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  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

[William G. Scott]

> On May 20, 2015, at 5:38 AM, Randy Read  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] Equation Editor woes with Office 2011 for Mac

[Steven Chou]

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  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 
> 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] SUMMARY: Equation Editor woes with Office 2011 for Mac

[Ethan Merritt]

On Wednesday, 20 May 2015 05:32:00 PM William G. Scott wrote:
> > On May 20, 2015, at 5:38 AM, Randy Read  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

[Mooers, Blaine H.M. (HSC)]

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  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_Mathematics&d=AwIF-g&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQ&s=Q3biyCgXkL73q4eLw0MovreIp6p923PLHLrEp3AiuBg&e=

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.html&d=AwIF-g&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=U-vNRZjPhftiaADvIzN7HNUo5rnv5-JKR6RwZjW0UDQ&s=UAkZG7nG6yJ1m41HFCqn3Ah_ifo-u-S4N8VwWbtbi3o&e=

[ccp4bb] HIS related crystallography issue

[Smith Liu]

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"  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

[Mohammad Khan]

Thanks for the suggestions!

On Wed, May 20, 2015 at 6:21 PM, Mark J van Raaij 
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
> >
> >
>
>