What does ProCheck say?
Xiaopeng Hu wrote:
Dear all,
I just notified that there is a big difference between the Ramachandran plot
analysis results produced by Coot and Morprobity (or Phenix). For the structure
I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%,
Oh god no don't ask Procheck , its Rama plot is a complete disaster zone - for
one thing, it's * ancient*. Doesn't discriminate between amino avoid types.
Grrr. To be avoided at all costs.
Sent from tiny silly touch screen
- Reply message -
From: Edward A. Berry ber...@upstate.edu
Hello everyone,
I am refining a structure to 2.4A with 2-fold NCS and twinned.
Maps look ok and Rfree is 0.27however as I start checking my validations I
notice that after refinemnt
my geomtry gets significantly worse. especially the rama plot. Initially I have
2 outliers and I end up with 32
Hi William,
It is essentially BSD unix. So it should be fine, unless they continue
to lobotomize everything and make it into an iPod on a stick.
:-)) +1
Thankfully, it is possible to gcc-cross-compile for MacOSX (both i686 +
ppc) from a GNU/Linux machine (the procedure for getting it to
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Hello Yuri,
the ramachandran restraints can be imposed on with coot. I am not aware
if refmac5 does that directly, but using a reference model should fix it.
As far as I understand you cannot directly put in the reference model
but have to use a tool
Hi Sam
Except for torsion angles, here is a good tutorial for you (the second one)
http://www.ysbl.york.ac.uk/mxstat/JLigand/
Andrey
On 29 Sep 2011, at 22:12, Sam Arnosti wrote:
Hi every one
I have a problem with docking my ligand into the electron density map and
make the connections (
Dear members,
I use stereo-view to show my structure, and label the residue name on the
figs. But after labeling, the label and the residues are not in the same
place from the stereo angle. Anyone know how to fix this?
Regards,
Yuan
On 09/29/2011 10:12 PM, Sam Arnosti wrote:
Hi every one
I have a problem with docking my ligand into the electron density map and make
the connections ( bonds ) with the protein.
It is a Lysine residue that makes a Schiff Base with a long chain aldehyde.
I do not know how to make the bonds
On 09/30/2011 08:01 AM, Yuri Pompeu wrote:
Hello everyone,
I am refining a structure to 2.4A with 2-fold NCS and twinned.
Maps look ok and Rfree is 0.27however as I start checking my validations I
notice that after refinemnt
my geomtry gets significantly worse. especially the rama plot.
Dear All,
There is a free alternative to MS Office, OpenOffice from Oracle. It
can read and write MS Word files and save as PDF. There are some issues
with names of spreadsheet functions when moving from OO to MS Office.
If you use latex and beamer then there is no need to either ;-). I
Dear Yuan,
it depends which software you are using, usually it is not so convenient to add
labels with good font sizes, colors etc.
So the way I do it is to put the 2 pictures next to each other in powerpoint
(at good resolution, e.g. A3 format),
add labels on the one on the left in text mode,
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The actual free alternative is called libreoffice, the successor of
openoffice after it was taken over by Oracle - a company, in my personal
opinion, is by orders of magnitudes less 'free' than microsoft.
On 09/30/2011 11:42 AM, Adam Ralph wrote:
Hello all,
We have been looking for path to future for our aging CRT-Stereo
solution and I found out that some people have successfully used Samsung
3D TV's for editing 3D Stereo movies on Macs.
So my question is does anyone have experiences with such setup? One
problem I can see is that
Rather than crossover office we now use VirutalBox and have a Windows
XP installation with Office for those of us who can't live without it.
You can backup the virtual machine (which is simply a big file) for
the virtual OS before you do an upgrade of your host OS (Ubuntu in my
case) and copy that
Hi Xiaopeng,
If you are feeding both programs exactly the same file then you are not
doing anything wrong. Notice that, if you calculate the Ramachandran plot on
Molprobity and then you go on coot, do a round of manual refinement, and
only then calculate the Ramachandran, then that can be the
Dear Yuri,
Since the number of reflections depends inversely on the cube of the resolution,
it is easy to show that a perfectly twinned 2.4A structure will have the same
data to parameter ratio as an untwinned 3.0A structure. This determines how
much
you can refine and which restraints are
On 09/29/2011 03:55 PM, Dima Klenchin wrote:
I have a feeling that the lack of Windows software continues to be
mostly due to the irrational animosity toward it rather than the
platform-specific issues. After all, there seemed to be many developers
who were happy to code for MacOS 7-9 but
Yes, Open Office has forked, and LibreOffice is now the choice in Fedora
Linux. I have used OpenOffice and LibreOffice, and they have some
trouble with recent .docx files generated in MS Word, specifically with
embedded image files.
On 09/30/11 06:06, Tim Gruene wrote:
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On 09/28/11 20:26, Jacqueline Vitali wrote:
...
--I am happy with any Linux. However, the system needs updates for
security purposes (the University requires it). Do I have to remake
the NVidia driver every time there is a kernel update or is there a
way around it for this NVidia card?
Postdoc Position in Structural Biology of Microtubule Assembly
The Knossow group at the Laboratoire d’Enzymologie et Biochimie
Structurales in Gif-sur-Yvette (near Paris), France seeks to recruit
a postdoctoral scientist in structural biology. The research focus is
directed towards
Hi there,
I am a full professor at Harbin Institute of Technology, China. Could you
please place my open positions on your website? Below is the details. Thanks
in advance.
Zhiwei
*Location:* Harbin, China
*Department: *Harbin Institute of Technology BIO-X Center
*Start Date:* Negotiable
2011/9/29 Xiaopeng Hu huxp...@mail.sysu.edu.cn
I just notified that there is a big difference between the Ramachandran
plot analysis results produced by Coot and Morprobity (or Phenix). For the
structure I am working now, Phenix(Morprobity) gives out Ramachandran
outliers 0.2%, favored 95.2%,
...resisted the temptation to express redundant/easily
objectionable/useless opinion on the virtues of different OS
environments for two days... can't hold any longer... the power of one
ring is too strong... the only useful suggestion on automatic update of
proprietary nvidia drivers has already
Has anyone encountered a case in which a construct with the native sequence
expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding
construct with a codon-optimized sequence expressed well? (The gene in question
is from cerevesiae)
Thanks,
Pat
On Fri, 2011-09-30 at 10:49 -0400, Patrick Loll wrote:
Has anyone encountered a case in which a construct with the native
sequence expressed poorly (or not at all?) in Rosetta(DE3), but the
corresponding construct with a codon-optimized sequence expressed
well? (The gene in question is from
Rosetta strains carry a plasmid that supplies several tRNAs that match codons
that are rare in E. coli. This is quite different than being explicitly
optimized to express mammalian proteins. We (the Center for Eukaryotic
Structural Genomics, a PSI-1 and PSI-2 center) used strains with the
We codon optimised a poorly expressed gene from neisseria meningitides based on
a codon usage table derived from the Welch (etal, 2009) paper below. The
optimisation is specifically for overexpression in BL21 (DE3). The optimised
gene increased protein expression by at least a factor of 10, and
INSTITUTE OF HUMAN VIROLOGY
UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE
A postdoctoral positions are available immediately for a highly motivated
candidates in the Institute of Human Virology http://www.ihv.org at the
University Of Maryland School Of Medicine (UMSOM;
opinion on the virtues of different OS environments for two days
It might be of interest to look back on the original poster's question, because
all she asked were a few questions about a specific computer (HP Z210 8 GB
with a low end Quadro Nvidia 400 512 MB) running any Linux, and a
Bill
Thanks for focusing the thread
to the original poster:
If you're going to go OSX I would wary away from the iMac. The all-in-one
desktop solution in small form factor has its downfalls, particularly when the
mechanical disk (undoubtedly) fails.
I have an iMac from 2007 and the
In theory, if the rare codons are all covered by Rosetta's extra
tRNAs, codon optimization should not make any difference.
In practice it does because frequently it's not codon optimization per se
but changing local mRNA structure.
- Dima
To me, the key question would seem to be, if I can't win them all, how many
more do I win if I go to the trouble?
Brent
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Keys
Sent: Friday, September 30, 2011 8:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] is
Is there a general consensus that this is true? I’ve heard exactly the
opposite, i.e., that codon optimization rarely gives you dramatically improved
yields of soluble protein. Are there any published studies on this topic? This
seems like something that might come out of one of the SG centers.
Well, codon optimization is not really trouble, it's money. The money are worth
it usually anyway, since the optimized genes are easy to clone if you make many
constructs out of one gene, as you better do anyway ... Compared with
downstream expenses, optimized genes are these days almost always
We recently published something really old-related about it:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021035
My two cents. Best, Alfredo.
Alfredo Torres-Larios, PhD
Assistant Professor
Instituto de Fisiologia Celular, UNAM
Mexico
Have a look at this paper:
http://www.ncbi.nlm.nih.gov/pubmed?term=18289875
the bottom line appears to be that, in most cases, co-transforming with
plasmids expressing rare tRNAs is just as good as codon optimizing the gene for
your protein of interest. In addition to the financial
I would disagree about the disk issue. That's not the failure mode we have seen
in the iMacs. Fwiw. Anyway, if it were to fail you could just attach an
external disk and continue merrily along - macs will boot from external
FireWire (and I assume thunderbolt?) disks.
We are putting money
Postdoctoral position – University of British Columbia, Canada
We are seeking a self-motivated postdoctoral researcher with experience in
protein crystallography to investigate the structural biology of natural
product biosynthetic enzymes. The successful candidate will optimize expression
and
On Sep 30, 2011, at 12:07 PM, Adrian Goldman wrote:
I would disagree about the disk issue. That's not the failure mode we have
seen in the iMacs. Fwiw. Anyway, if it were to fail you could just attach an
external disk and continue merrily along - macs will boot from external
FireWire (and
The Phenix developers are pleased to announce that version 1.7.2 of Phenix is
now available. Binary installers for Linux, and Mac OSX platforms are available
at the download site:
http://phenix-online.org/download/
Some of the new features in this version are:
Graphical interface:
Hi all,
.
recently,I got a crystal of protein-DNA crystal.i used silver stainto prove
that it is a protein crystal.Does anyone have method to detect if there is
DNA in the crystal.
any suggestion will be appreciated.
Regards,
deng
Try the program DIBER to evaluate the likelihood your crystal contained ordered
nucleic acid in addition to protein. See Acta Cryst. (2010). D66, 643-653
“DIBER: protein, DNA, or both?” by G. Chojnowski M. Bochtler.
Good luck, Pete
From: CCP4 bulletin
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