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.
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 p
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 boar
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 hi
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 rea
> 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 eyebal
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
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.go
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
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
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 t
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.
Methodolog
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
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
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
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
__
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 s
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 ca
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 he
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
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