Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
On May 18, 2015, at 4:31 AM, Nicolas Soler nso...@mrc-lmb.cam.ac.uk wrote: You just have to learn the (easy) equation syntax or just use this: http://www.macupdate.com/app/mac/18172/tex-fog William G. Scott http://scottlab.ucsc.edu/~wgscott
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Hi Randy,
It's not ideal, but until the bug gets fixed or there's a more elegant
solution, could you just set up your own autosave?
It'd mean opening a terminal and running a command before starting, but if you
had a little script like the below running while you were working you'd at
least ensure you wouldn't lose too much work if something crashed:
#!/bin/bash
[[ $# -ne 1 ]] echo Usage: $0 path_to_file exit 1
while true;
do
cp $1 ${1}.bak
sleep 60
done
Best wishes,
Jens
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read
[rj...@cam.ac.uk]
Sent: 18 May 2015 09:10
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] Gadolinium complexes- phosphate buffer
Dear Isa, Do you have any cysteines? I assume so given you mention class B metals... If so, and you have a ready supply of relatively isomorphous crystals, I would consider giving native SAD a go, collecting datasets from 5-10 (or however many you need) datasets at a reasonably low energy (say 7keV) and merging. If you have any ordered phosphates they would help here too, of course. You could also try a brief soak in a solution where the PO4 is partially or completely replaced by WO4, which should give a whopping anomalous (and potentially isomorphous) signal. Otherwise yes, Hg or Pt reagents would probably be your best bet. Anionic Gd complexes with chelating ligands will probably not bind so well in the presence of a high concentration of phosphate. We have also had a bit of luck with iodination - I like to dissolve a few crystals of iodine in paraffin oil (gives a beautiful purple oil), and use that to introduce iodine by vapor diffusion into the drop containing the crystals (be careful with this - preferably manipulate in a fume hood, as iodine vapor I imagine is not very good for the lungs). Good luck! Best, Oliver.
[ccp4bb] Several postdoc opportunities, Shanghai University
Posted on behalf of Prof. Ren Wei and Jeffrey Reimers. *Post-Doctoral Fellowships in Quantum Refinement of Protein X-ray Crystallographic Structures and related work in Biophysics, Biochemistry, Biomaterials, Chemistry, and Soft Condensed Matter* Shanghai University (http://www.shu.edu.cn) is seeking multiple outstanding postdoctoral researchers to be part of the newly created International Centre for Quantum and Molecular Structure (ICQMS). Parallel Adjoint Appointments at The University of Technology, Sydney (UTS) ( http://www.uts.edu.au/about/faculty-science/physics-and-advanced-materials), Department of Mathematical and Physical Sciences, will also be available. Most available positions relate to the core project of ICQMS: the development of codes for automatic quantum refinement of protein crystallographic structures. For these positions, previous experience at the PhD or post-doctoral level in the simulation of protein structure is essential. This could involve mastering of quantum-chemical software, molecular dynamics methods, statistical mechanics theories, or protein structure refinement. Positions are available for both software users and methods developers. ICQMS also has a wider view, considering the determination of protein function and spectroscopy, especially for photosynthetic proteins, understanding the effects of solvation and environment on molecular properties, quantum dynamics and coherence in proteins, understanding order/disorder transitions, the fundamental role played by entropy in controlling protein structure, the properties of biomaterials such as cement, general self-assembly processes such as organic self-assembled monolayer formation and properties, and the properties of bulk materials. A position is also available concerning the development and application for GPUs of Hartree-Fock theory or Density-Functional Theory or molecular dynamics. All positions require a PhD in Chemical Physics, Quantum Chemistry, Computational Biochemistry, Crystallography, or related disciplines. Excellent verbal and written communication skills in English are essential. Proven independence is also essential. Candidates that have contributed to scientific-community activities and/or teaching innovation will be considered favourably, as will those that have contributed independently to multidisciplinary team projects. Shanghai University is a well funded, internationally connected, rapidly raising University with a strong profile in Material Science, and indeed under the direction of University President Prof. H. J. Luo is a central player in the extensive Chinese Materials Genome Initiative (MGI) Project. ICQMS extends this vision into mainstream chemical and biochemical research. Adjunct Appointments at the University of Technology Sydney will allow each Postdoctoral Fellow to spend 6 months doing joint research in Sydney with UTS staff. Shanghai University and The University of Technology Sydney have a 20-year history of close collaboration, including the joint Smart Cities Institute and the Sydney Institute of Language and Commerce. This collaboration also includes the dual PhD degree program between the two universities. The negotiable anticipated start date is 2015 between August and December. The positions are available for two years and renewable subject to a performance review. Shanghai University is an Equal Opportunity Employer and all persons are encouraged to apply. Applicants should send their curriculum vitae including lists of publications, summaries of their research interests, lists of prizes and awards, summaries of any teaching, community service or administrative experience, and have three reference letters sent directly to yarulove2...@shu.edu.cn. Further information can be obtained from: ICQMS Director: Jeffrey Reimers reim...@shu.edu.cn jeffrey.reim...@shu.edu.cn or ICQMS Deputy Director: Wei REN ren...@shu.edu.cn Closing Date: 2015 December 31st, or until all positions are filled.
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Hi Randy, I too suggest LaTeXiT. To add to what has already been suggested, LaTeXiT allows the assembly of a custom library of equations. You can send your collaborators this library as a file, and they could make minor edits to the equations in LaTexit gui editor without having to learn the full syntax of LaTeX. Minor edits would be self-explanatory to implement. Then they could export the edited equations for insertion into the current draft in MS Word. If they can't install LaTeXiT, you can send them the equations in the LaTeX format in a plain text file, and they could edit the equations in the LaTeXiT syntax, which can be deduced by comparing the syntax to the final equation. They could then return the edited plain text file to you for you to copy and paste into LaTeXiT. If that is too hard for them, they could always write out the edited equation on paper with a pen or pencil, scan it into a pdf, and e-mail it back to you for typesetting in LaTeXiT. An alternative would be to move the document into RMarkdown via RStudio (a gui interface to R) which is much easier to master than LaTeX while still having access to the LaTeX equation syntax. This document can be quickly converted (by knitting) to doc, pdf and html within the RStudio gui. The exported document might require additional editing if the conversion does not go well. If you are using ENDNOTE and not BibTeX for managing citations, the workflow may become more complicated. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Director of the Laboratory of Biomolecular Structure and Function Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-moo...@ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d- Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0 X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read [rj...@cam.ac.uk] Sent: Monday, May 18, 2015 3:10 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.
Re: [ccp4bb] CYS mod
The site swift.cmbi.ru.nl/gv/numbers/ is not official, unpublished, and still poorly maintained. But just for the fun of it, I added a list of modified cysteines. Be aware that the files are big, so better download them and read them in the editor than opening them in the browser. Gert On 05/12/2015 09:30 PM, David Schuller wrote: What are the most likely modifications of a CYS residue? I am attaching images of a couple of residues in my current structure. Blue is 2Fo-Fc, Green is Fo-Fc positive difference, purple is model-phased anomalous differences at 3 sigma, data from 1.70 A source. I am guessing about 3 non-H atoms, probably one of them with anomalous scattering. Not all CYS in the structure are thus modified, only these two, but they show up consistently in 4 noncrystallographic copies. TIA, Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
[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] MOLREP self-rotation matrix
Hi Eleanor, Yeah, the relationship of the XYZ with the unit cell axes is tricky too. Although I can get some clues by looking at the position of the crystallographic symmetry axes on the XY plane, it is better if I could find a definite answer... Thank you, Chen On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Hmm - there are programs which give you the matrix associated with Eulerian or Polar angles. I think one is pdbset.. Or there is documentation in polarrfn or rotmat which describes how to do it.. But remember there are conventions about which axes correspond to the orthogonal X Y Z axes used to define the angles Eleanor On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edu wrote: Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
Re: [ccp4bb] MOLREP self-rotation matrix
Hmm - there are programs which give you the matrix associated with Eulerian or Polar angles. I think one is pdbset.. Or there is documentation in polarrfn or rotmat which describes how to do it.. But remember there are conventions about which axes correspond to the orthogonal X Y Z axes used to define the angles Eleanor On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edu wrote: Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
Re: [ccp4bb] Gadolinium complexes- phosphate buffer
Hi Isa, don't discard SeMet too rapidly if there are few Mets, modern beamlines, high-redundancy data collection techniques, and processing and phasing programs can extract and use small anomalous signal to get structures even if there are less SeMets than generally accepted by the rule of thumb. Especially if you can rotate around more than one axis or merge data from different crystals. And even if the signal is not good enough and you then need additional phasing, the SeMet anomalous maps may be useful in tracing. If you have Cys, try Hg compounds, my favourite is methylmercury chloride. As it binds covalently, even if it precipitates in your drop, you may just get just enough soluble to react. We usually add a few grains of the mercury compound to the reservoir, mix, cover and let equilibrate with the drop for a few hours or overnight, then add a ul of the reservoir to the drop and fish crystals after different incubation times. Greetings, Mark 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 18 May 2015, at 11:42, isabelle Lucet wrote: Hi All, We recently obtained a native data set to 2.8A. With no molecular replacement available we are now moving to heavy atom (not enough methionine coverage for seleno-met). Unfortunately crystals grow is in 1.4 Na/K H phosphate pH 8 and we do not have much room for improvement. Any literature you could point to or experience with for example gadolinium complexes, co-crystallization, soaking in phosphate buffer? Are we better off just focusing on class B metals? Thanks for your advise. Kind Regards, Isa __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
Re: [ccp4bb] MOLREP self-rotation matrix
I got some answers from the previous thread: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html But I just want to make sure what I am doing... Thanks a lot, Chen On Mon, May 18, 2015 at 1:36 PM, Chen Zhao c.z...@yale.edu wrote: Hi Eleanor, Yeah, the relationship of the XYZ with the unit cell axes is tricky too. Although I can get some clues by looking at the position of the crystallographic symmetry axes on the XY plane, it is better if I could find a definite answer... Thank you, Chen On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Hmm - there are programs which give you the matrix associated with Eulerian or Polar angles. I think one is pdbset.. Or there is documentation in polarrfn or rotmat which describes how to do it.. But remember there are conventions about which axes correspond to the orthogonal X Y Z axes used to define the angles Eleanor On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edu wrote: Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
Re: [ccp4bb] MOLREP self-rotation matrix
Sorry for the spaming... Just want to correct that I plan to say covert the MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix... On Mon, May 18, 2015 at 1:44 PM, Chen Zhao c.z...@yale.edu wrote: I got some answers from the previous thread: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html But I just want to make sure what I am doing... Thanks a lot, Chen On Mon, May 18, 2015 at 1:36 PM, Chen Zhao c.z...@yale.edu wrote: Hi Eleanor, Yeah, the relationship of the XYZ with the unit cell axes is tricky too. Although I can get some clues by looking at the position of the crystallographic symmetry axes on the XY plane, it is better if I could find a definite answer... Thank you, Chen On Mon, May 18, 2015 at 1:24 PM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Hmm - there are programs which give you the matrix associated with Eulerian or Polar angles. I think one is pdbset.. Or there is documentation in polarrfn or rotmat which describes how to do it.. But remember there are conventions about which axes correspond to the orthogonal X Y Z axes used to define the angles Eleanor On 18 May 2015 at 17:04, Chen Zhao c.z...@yale.edu wrote: Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine
That problem has been discussed several times on the coot mailing list.
Currently a workaround is to type:
(set-use-stroke-characters 1)
in scheme console (Calculate Scripting Scheme).
(You can also add it to coot settings).
As a side effect fonts will look worse.
I've just tested a better fix (patch attached) and it seems to work,
It requires compilation from source, so for now use the workaround
above.
Marcin
On Sun, May 17, 2015 at 11:10:41AM -0300, Jorge Iulek wrote:
Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check
graphic driver problems (or update them from the vendor, by the way,
controller model Intel HD 4000). Taking some time with this today, I still
feel I will have to study further before making changes.
This poses me yet other question, though maybe it escapes the discussion
list scope, that I must search further: how (and where) different are the
resources used by the virtual machine compared to the host machine, such
that this graphical behavior is different.
Yours,
Jorge
On 05/16/2015 08:39 PM, Jorge Iulek wrote:
Dear all,
My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are
virutal) and 8 GB memory.
For a number of coot versions in it (including the newest one), coot
answers slowly to rotating, but specially the space bar translate is even
more slow (from residue x to x+1 etc.).
Curiously, in either CentOS or even openSuSE in oracle virtualboxes
(under this openSuSE host), to which I liberate only 1 cpu and only 1 GB
memory, it goes much faster, at a very reasonable speed. How could be
that? In principle I thought that the multicore configuration of the host
machine might be the culprit.
So, for coot tasks, I have been using the virtual machine, but that is
impractical.
The closest to this problem I found was
https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I
could not devise any trial to solve the problem. Even trying the
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration
configuration did not solve the problem satisfactorily.
I tried to search wider, but could not find other suggestions. Should
you have one, I would be glad to try.
Sincerely yours,
Jorge
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--- src/graphics-info.cc2014-12-02 16:00:08.0 +
+++ src/graphics-info.cc2015-05-18 18:29:45.420807088 +0100
@@ -1920,7 +1920,8 @@
} else {
glRasterPos3f(x,y,z);
- glPushAttrib (GL_LIST_BIT);
+ glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+ glDisable(GL_FOG);
for (unsigned int i = 0; i s.length(); i++)
glutBitmapCharacter (graphics_info_t::atom_label_font, s[i]);
glPopAttrib();
@@ -4649,7 +4650,8 @@
// GLfloat pink[3] = { 1.0, 0.8, 0.8 };
GLfloat pink[3] = { font_colour.red, font_colour.green,
font_colour.blue };
glColor3fv(pink);
- glPushAttrib (GL_LIST_BIT);
+ glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+ glDisable(GL_FOG);
void *font = graphics_info_t::atom_label_font;
font = GLUT_BITMAP_TIMES_ROMAN_24;
for (unsigned int i=0; igeneric_texts_p-size(); i++) {
--- src/graphics-ligand-view.cc 2014-09-08 20:54:39.0 +0100
+++ src/graphics-ligand-view.cc 2015-05-18 18:27:23.714796284 +0100
@@ -307,7 +307,8 @@
void
graphics_ligand_atom::bitmap_text(const std::string s) const {
- glPushAttrib (GL_LIST_BIT);
+ glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+ glDisable(GL_FOG);
for (unsigned int i = 0; i s.length(); i++)
glutBitmapCharacter (GLUT_BITMAP_HELVETICA_10, s[i]);
glPopAttrib();
[ccp4bb] MOLREP self-rotation matrix
Hi all, I am now trying to convert the NCS axis expressed by theta, phi, chi (or alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed into SOLVE. Would anybody suggest me a correct way to do it? Thank you so much in advance! Best, Chen
Re: [ccp4bb] 1.how to use pymol to choose all the residues that have polar contacts in the complex 2.how to draw a residues-DNA interaction picture
Hi Weifei - The first image looks like it was drawn using a vector drawing program like Adobe Illustrator or Inkscape. If you're looking for something automatically generated, two of the first hits from a Google search for protein interaction diagram are LigPlot+ (http://pubs.acs.org/doi/abs/10.1021/ci200227u) and LeView (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765711/). For your second question, to show the residues on chain A within a cutoff distance (e.g. 3.5Å) of chain E, you could use two PyMOL commands like this: show sticks, br. (chain A and donors) within 3.5 of (chain E and acceptors) show sticks, br. (chain A and acceptors) within 3.5 of (chain E and donors) Check out http://www.pymolwiki.org/index.php/Selection_algebra and http://www.pymolwiki.org/index.php/Single-word_Selectors for more info. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 17, 2015, at 7:08 AM, weifei weife...@outlook.commailto:weife...@outlook.com wrote: Dear all, I am sorry to disturb you. I have two question to ask. The first one is how to draw a residue-DNA interaction picture looks like this one? Mail Attachment.png The second question is how to use pymol to select all the residues of a complex that interact with other protein or DNA by polar contacts? 1.I select chain E (DNA) and choose polar contacts --to other atoms in object. Mail Attachment.png 2.I can see polar contacts between ChainA(protein) and ChainE(DNA) but I want to show all the connected residue in ChainA. How to choose all the residues that have polar contacts in the Protein. Mail Attachment.png Mail Attachment.png Thank you so much for your answear. Best, Weifei
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
sharelatex makes them learn latex, because they can see the output and
the input...
also they can play with lots of examples
2015-05-18 9:57 GMT-05:00 Thomas, Jens jens.tho...@liverpool.ac.uk:
Hi Randy,
It's not ideal, but until the bug gets fixed or there's a more elegant
solution, could you just set up your own autosave?
It'd mean opening a terminal and running a command before starting, but if
you had a little script like the below running while you were working you'd
at least ensure you wouldn't lose too much work if something crashed:
#!/bin/bash
[[ $# -ne 1 ]] echo Usage: $0 path_to_file exit 1
while true;
do
cp $1 ${1}.bak
sleep 60
done
Best wishes,
Jens
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read
[rj...@cam.ac.uk]
Sent: 18 May 2015 09:10
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
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Of course, if you are working with a .docx instead of a .doc file in Word2011
for a Mac, you can always simply insert and “Equation” directly, rather than
the MathType version of Microsoft Equation under the “Insert/Objects” menu.
This seems to work fairly seamlessly, unless you convert the .docx document
back to .doc
P. Shing Ho, Ph.D.
Professor Chair
Biochemistry Molecular Biology
1870 Campus Delivery
Colorado State University
Fort Collins, CO 80523-1870
970-491-0569 (phone)
From: Murpholino Peligro murpholi...@gmail.commailto:murpholi...@gmail.com
Reply-To: Murpholino Peligro
murpholi...@gmail.commailto:murpholi...@gmail.com
Date: Monday, May 18, 2015 at 12:12 PM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
sharelatex makes them learn latex, because they can see the output and the
input...
also they can play with lots of examples
2015-05-18 9:57 GMT-05:00 Thomas, Jens
jens.tho...@liverpool.ac.ukmailto:jens.tho...@liverpool.ac.uk:
Hi Randy,
It's not ideal, but until the bug gets fixed or there's a more elegant
solution, could you just set up your own autosave?
It'd mean opening a terminal and running a command before starting, but if you
had a little script like the below running while you were working you'd at
least ensure you wouldn't lose too much work if something crashed:
#!/bin/bash
[[ $# -ne 1 ]] echo Usage: $0 path_to_file exit 1
while true;
do
cp $1 ${1}.bak
sleep 60
done
Best wishes,
Jens
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK]
on behalf of Randy Read [rj...@cam.ac.ukmailto:rj...@cam.ac.uk]
Sent: 18 May 2015 09:10
To: CCP4BB@JISCMAIL.AC.UKmailto: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.ukmailto:rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.ukhttp://www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine
Thanks Marcin, I thought I'd patched this already some time ago (shortly after you mentioned it to me), but now that I try to find it in the logs, it seems to have been missed/lost. Paul. On 18/05/15 19:00, Marcin Wojdyr wrote: That problem has been discussed several times on the coot mailing list. Currently a workaround is to type: (set-use-stroke-characters 1) in scheme console (Calculate Scripting Scheme). (You can also add it to coot settings). As a side effect fonts will look worse. I've just tested a better fix (patch attached) and it seems to work, It requires compilation from source, so for now use the workaround above. Marcin On Sun, May 17, 2015 at 11:10:41AM -0300, Jorge Iulek wrote: Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check graphic driver problems (or update them from the vendor, by the way, controller model Intel HD 4000). Taking some time with this today, I still feel I will have to study further before making changes. This poses me yet other question, though maybe it escapes the discussion list scope, that I must search further: how (and where) different are the resources used by the virtual machine compared to the host machine, such that this graphical behavior is different. Yours, Jorge On 05/16/2015 08:39 PM, Jorge Iulek wrote: Dear all, My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are virutal) and 8 GB memory. For a number of coot versions in it (including the newest one), coot answers slowly to rotating, but specially the space bar translate is even more slow (from residue x to x+1 etc.). Curiously, in either CentOS or even openSuSE in oracle virtualboxes (under this openSuSE host), to which I liberate only 1 cpu and only 1 GB memory, it goes much faster, at a very reasonable speed. How could be that? In principle I thought that the multicore configuration of the host machine might be the culprit. So, for coot tasks, I have been using the virtual machine, but that is impractical. The closest to this problem I found was https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I could not devise any trial to solve the problem. Even trying the http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration configuration did not solve the problem satisfactorily. I tried to search wider, but could not find other suggestions. Should you have one, I would be glad to try. Sincerely yours, Jorge
Re: [ccp4bb] Two kinds of solvent-accessible-surface ?
Hi Edward, I just need to comment on this. To define contact atoms, you must use solvated united atoms that is atoms with implicit hydrogens where needed (united radius), this radius being further increased by that of a molecule of water. Why is that? In vacuum, it was shown that at a distance twice the sum of their vdw radii, atoms still attract each other. To take into account the screening effect of water, it has been convened that if a water molecule could fit/pass between two atoms, then the vdw interaction between them would fall off to zero. Therefore, by increasing united radii with the radius of a water molecule, it is easy to calculate the distance, Dij, between atoms i and j, and figure out that when Dij = Ri + Rj + 2 R(H2O), then there is no vdw interaction, that is no contact. Otherwise, contact exists if Dij Ri + Rj + 2 R(H2O). Note that in this case, the solvated united atoms intersect and the surface of the intersection disc would be proportional to the strength of interaction between these atoms. In which case the vdw contact refers to the vdw interaction rather then the vdw radii. Cracks between atoms correspond to reentrant surfaces as defined by Fred Richards. Best regards, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-964 University of Lorraine, Nancy School of Science and Technology and School of Medicine 9, Avenue de la Foret de Haye 54500 Vandoeuvre-les-Nancy, France Tel. (direct) : +33 (0)3.83.68.32.73 Tel. (secretary) : +33 (0)3.83.68.32.92 Cell. : +33 (0)6 11 35 69 09 Fax. : +33 (0)3.83.68.32.79 Email : Nadir.Mrabet at univ-lorraine.fr - Le 15 Mai 15, à 21:07, Edward A. Berry ber...@upstate.edu a écrit : If I remember correctly, there are two different ways to calculate a surface by rolling a ball over it, and i think that I want a program to calculate the non-conventional one. As I understand, the ASA is defined as the surface traced out by the _center_ of the rolling sphere, i.e. one radius above the vdw surface. The justification being that an atom (i.e. it's center coordinates) can't get any closer to the surface than that. The second type of surface is defined by the closest approach of the _surface_ of the rolling sphere, i.e. it would be the vdw radius of the (protein) but not descending into cracks between atoms where the rolling ball won't fit. For making models of a multisubunit protein, and wanting to be able to assemble the separately-made subunits so that they make intermolecular vdw contacts, the second kind of surface would be desirable, as otherwise atoms won't be able to get their surfaces closer than twice the sphere radius. Is that an option that can be chosen in pymol or such? Thanks, eab
Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine
Dear Marcin, Yes, it worked pretty fine. As for the side effect , I could not, for while, observe any degradation. Thank you very much. Jorge On 05/18/2015 03:00 PM, Marcin Wojdyr wrote: That problem has been discussed several times on the coot mailing list. Currently a workaround is to type: (set-use-stroke-characters 1) in scheme console (Calculate Scripting Scheme). (You can also add it to coot settings). As a side effect fonts will look worse. I've just tested a better fix (patch attached) and it seems to work, It requires compilation from source, so for now use the workaround above. Marcin On Sun, May 17, 2015 at 11:10:41AM -0300, Jorge Iulek wrote: Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check graphic driver problems (or update them from the vendor, by the way, controller model Intel HD 4000). Taking some time with this today, I still feel I will have to study further before making changes. This poses me yet other question, though maybe it escapes the discussion list scope, that I must search further: how (and where) different are the resources used by the virtual machine compared to the host machine, such that this graphical behavior is different. Yours, Jorge On 05/16/2015 08:39 PM, Jorge Iulek wrote: Dear all, My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are virutal) and 8 GB memory. For a number of coot versions in it (including the newest one), coot answers slowly to rotating, but specially the space bar translate is even more slow (from residue x to x+1 etc.). Curiously, in either CentOS or even openSuSE in oracle virtualboxes (under this openSuSE host), to which I liberate only 1 cpu and only 1 GB memory, it goes much faster, at a very reasonable speed. How could be that? In principle I thought that the multicore configuration of the host machine might be the culprit. So, for coot tasks, I have been using the virtual machine, but that is impractical. The closest to this problem I found was https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I could not devise any trial to solve the problem. Even trying the http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration configuration did not solve the problem satisfactorily. I tried to search wider, but could not find other suggestions. Should you have one, I would be glad to try. Sincerely yours, Jorge
Re: [ccp4bb] Gadolinium complexes- phosphate buffer
Also you can treat your SeMET as heavy atom derivative with your native dataset. J?rgen .. J?rgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Streetx-apple-data-detectors://4, W8708 Baltimore, MD 21205x-apple-data-detectors://5/0 Office: +1-410-614-4742tel:%2B1-410-614-4742 Lab: +1-410-614-4894tel:%2B1-410-614-4894 Fax: +1-410-955-2926tel:%2B1-410-955-2926 http://lupo.jhsph.eduhttp://lupo.jhsph.edu/ On May 18, 2015, at 13:37, Mark J van Raaij mjvanra...@cnb.csic.esmailto:mjvanra...@cnb.csic.es wrote: Hi Isa, don't discard SeMet too rapidly if there are few Mets, modern beamlines, high-redundancy data collection techniques, and processing and phasing programs can extract and use small anomalous signal to get structures even if there are less SeMets than generally accepted by the rule of thumb. Especially if you can rotate around more than one axis or merge data from different crystals. And even if the signal is not good enough and you then need additional phasing, the SeMet anomalous maps may be useful in tracing. If you have Cys, try Hg compounds, my favourite is methylmercury chloride. As it binds covalently, even if it precipitates in your drop, you may just get just enough soluble to react. We usually add a few grains of the mercury compound to the reservoir, mix, cover and let equilibrate with the drop for a few hours or overnight, then add a ul of the reservoir to the drop and fish crystals after different incubation times. Greetings, Mark 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 18 May 2015, at 11:42, isabelle Lucet wrote: Hi All, We recently obtained a native data set to 2.8A. With no molecular replacement available we are now moving to heavy atom (not enough methionine coverage for seleno-met). Unfortunately crystals grow is in 1.4 Na/K H phosphate pH 8 and we do not have much room for improvement. Any literature you could point to or experience with for example gadolinium complexes, co-crystallization, soaking in phosphate buffer? Are we better off just focusing on class B metals? Thanks for your advise. Kind Regards, Isa __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
[ccp4bb] Postdoc and PhD student positions
Open positions in the laboratory of Lari Lehtiö at the Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu,University of Oulu, Finland. The research group focuses on structure, function and inhibition of ADP-ribosyltransferases (ARTDs/PARPs). We use protein X-ray crystallography, activity assays and complementing biophysical techniques to understand how the signaling enzymes work. We also use screening of compound libraries and structure-based design of specific inhibitors for the enzymes to be used as chemical probes as well as drug leads. More information of our research is available on the web pages (http://www.oulu.fi/biocenter/groups/lehtio). Postdoctoral researchers We have 2 positions for postdoctoral researchers. One position is available immediately until 31.12.2016 with possible extension depending on funding. Second positions is for 1.9.2015 until 31.8.2018 with possible extension depending on funding. We are looking for researchers holding a doctoral degree or soon to receive one and having interest in structural biology and drug discovery. Work includes cloning, expression, purification and characterization of recombinant proteins as well as structural studies using X-ray crystallography and small-angle X-ray scattering. Experience in protein characterization, medicinal chemistry or structural biology is considered beneficial. The salary will be based on the demand level 5 of the salary system in Finnish Universities and includes a component based on personal performance. The application should include 2 pdf files 1) a motivation letter (1 page) describing prior knowledge and interests 2) a complete CV containing contact information of two references. Application should be sent to Lari Lehtiö by email (lari.lehtio(at)oulu.fi) with a subject line “Application for a Postdoctoral position”. First position is filled as soon as a suitable candidate is found. For the second position the applications are accepted until 14.6.2015. PhD student A position is available for a PhD student with funding currently available for three years. Position is available immediately and it will contain a trial period. We are looking for a student holding a MSc degree and with interest in structural biology and drug discovery. Work includes cloning, expression, purification and characterization of recombinant proteins as well as structural studies using X-ray crystallography. The aim of the project is to develop selective inhibitors for human mono ADP-ribosyltransferases. The salary will be based on the demand levels 2-4 of the salary system in Finnish Universities and includes a component based on personal performance. The application should include 2 pdf files 1) a motivation letter (1 page) describing prior knowledge and interests 2) a complete CV containing contact information of two references. Application should be sent to Lari Lehtiö by email (lari.lehtio(at)oulu.fi) with a subject line “Application for a PhD position”. Applications are accepted until 14.6.2015. Best regards, Lari __ Lari Lehtiö, PhD, Docent/Adjunct Professor Biocenter Oulu Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://cc.oulu.fi/~llehtio/ _
Re: [ccp4bb] Crystal morphology
Dear Bishwa,What about Hamptons Izit dye. S.M.Jaimohan, Ph.D On Monday, 18 May 2015 7:50 AM, Engin Özkan eoz...@uchicago.edu wrote: Magnesium phosphate crystals? I've definitely seen salt crystals with that morphology before. Check out the Ksp for Mg3(PO4)2. Engin On 5/17/15 6:45 PM, Bishwa Subedi wrote: Hi All, I know that its hard to say if the crystal is protein crystal just by looking at its morphology, however I was wondering if any of you have ever come across protein crystals as one attached here. It would help build up my confidence :) and work further until I put them on to X-ray beam. I could notice similar crystals with two different proteins one in the initial screen and one after pH screening the similar condition and involves NPS (Nitrate, phosphate and Sulphate) from Morpheus screen. To mention, MgCl2 (0.01M) is also added directly to the protein as a co-factor. Crystal condition : NPS (0.9M)+ Buffer System 2 0.1M (i.e. HEPES and MOPS) as well as with buffer system 3 0.1M (TRIS and BICINE) at pH 7.5 and 8.5 respectively and P550MME_P20K 30.0% Thank you for your opinion. Bishwa
Re: [ccp4bb] Crystal morphology
Hi Mohan, I have seen these too with the C row of morpheus, unfortunately they are most likely to be salt. Try repeating the same screen but skipping adding extra Mg to the macromolecule. Good luck. Regards Saba Shahzad | PhD candidate, Martin Hallberg group Department of Cell and Molecular Biology Karolinska Institutet From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jai mohan [jaimoha...@yahoo.co.in] Sent: Monday, May 18, 2015 8:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Crystal morphology Dear Bishwa, What about Hamptons Izit dye. S.M.Jaimohan, Ph.D On Monday, 18 May 2015 7:50 AM, Engin Özkan eoz...@uchicago.edu wrote: Magnesium phosphate crystals? I've definitely seen salt crystals with that morphology before. Check out the Ksp for Mg3(PO4)2. Engin On 5/17/15 6:45 PM, Bishwa Subedi wrote: Hi All, I know that its hard to say if the crystal is protein crystal just by looking at its morphology, however I was wondering if any of you have ever come across protein crystals as one attached here. It would help build up my confidence :) and work further until I put them on to X-ray beam. I could notice similar crystals with two different proteins one in the initial screen and one after pH screening the similar condition and involves NPS (Nitrate, phosphate and Sulphate) from Morpheus screen. To mention, MgCl2 (0.01M) is also added directly to the protein as a co-factor. Crystal condition : NPS (0.9M)+ Buffer System 2 0.1M (i.e. HEPES and MOPS) as well as with buffer system 3 0.1M (TRIS and BICINE) at pH 7.5 and 8.5 respectively and P550MME_P20K 30.0% Thank you for your opinion. Bishwa
[ccp4bb] Gadolinium complexes- phosphate buffer
Hi All, We recently obtained a native data set to 2.8A. With no molecular replacement available we are now moving to heavy atom (not enough methionine coverage for seleno-met). Unfortunately crystals grow is in 1.4 Na/K H phosphate pH 8 and we do not have much room for improvement. Any literature you could point to or experience with for example gadolinium complexes, co-crystallization, soaking in phosphate buffer? Are we better off just focusing on class B metals? Thanks for your advise. Kind Regards, Isa __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Hi Randy, You could try the beta version of the forthcoming version of Word and see if the bug is fixed. Obviously, it is a beta version and therefore a bit risky but it installs along side the current version and I’ve been trying it on my laptop without issue so far. One improvement for me is that this version of Word now uses the Mac’s in built special character palette and we use a lot of Greek characters. This works a lot better than symbol browser in the current version of Word where we still see some of the greek characters getting screwed up when saving as PDF or sharing with a Window’s PC. One thing to watch is that the beta version .docx format has changed so you should be careful to save as compatible with Office 2011. https://products.office.com/en-us/mac/mac-preview https://products.office.com/en-us/mac/mac-preview Regards MGM Martin G Montgomery ATP Synthase Group MRC Mitochondrial Biology Unit Wellcome Trust/MRC Building Cambridge Biomedical Campus Hills Road Cambridge Great Britain CB2 0XY www.mrc-mbu.cam.ac.uk 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 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
[ccp4bb] Third CCP4-OIST workshop in Okinawa, second call
Dear Colleagues, we are pleased to announce the third CCP4 structure solution school at the Okinawa Institute of Science and Technology (OIST), Okinawa. All details can be found at http://www.ccp4.ac.uk/schools/OIST-2015 Title: CCP4 school: From data processing to structure refinement and beyond Dates: November 2 to 7, 2015 Site: Okinawa Institute of Science and Technology, Okinawa, Japan The school content: Software workshop: the workshop will be taught by authors and other experts, including Garib Murshudov (refmac), Victor Lamzin (arp/warp), Robbie Joosten (pdb_redo) and Phil Evans (aimless). It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. We will also be covering the use of DIALS for data processing and the new ccp4 interface. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 25 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is 22 August. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/OIST-2015 Fees: There is no fee for the workshop. The students will be responsible for their transportation costs outside Okinawa. Lodging will be provided at the OIST Guest House Seaside House. The workshop will also cover the expenses for all meals and refreshments. Fadel Samatay, Charles Ballard
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
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] Equation Editor woes with Office 2011 for Mac
Do your collaborators need to edit the equations? If not you can use LaTeXiT (sorry I'm that person!) which allows you to write your equation in LaTeX then export directly into word as a pdf. Link below.. http://www.chachatelier.fr/latexit/ Regards, Jonathan Davies PhD Student Department of Biology and Biochemistry University of Bath On 18/05/15 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 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] Equation Editor woes with Office 2011 for Mac
Hi Randy, although learning Latex as a whole can for sure be time-consuming, an alternative solution is to use a Latex equation editor like Latexit. You just have to learn the (easy) equation syntax and then you can drag and drop the formatted result into Word or Page, it's rock solid : http://www.macupdate.com/app/mac/17889/latexit Hope that helps, Nicolas Le 18/05/15 09:10, Randy Read a écrit : 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 -- Nicolas Soler Roger Williams group, PNAC MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom phone : +44(0) 1223 26 76 20 mail : nso...@mrc-lmb.cam.ac.uk
