Isn't Molprobity too tight anyway for high resolution structures? I have often (for proteins) found it highlighting "outliers" when in fact that is what the density shows.Isn't it a trade off between molprobity and what the measurements show, especially at high resolutions?-Original Messag
Beryllium chloride is very toxic. More care is needed when preparing it.
在 2011年10月4日 上午7:35，Peter Hsu 写道：
> Sorry for the very off topic and dumb question, but does anyone know if BeCl2
> needs to be prepared fresh for use (making BeF3) or can it be stored as a
> solution stock at room temp
Why not just use PROCHECK program?
在 2012年2月22日 下午6:24，Thomas Holder 写道：
> Hi Dialing,
>
> if you know some python you can use PyMOL.
>
> # get C-alpha b-factors as list
> from pymol import cmd, stored
> stored.bfactors = []
> cmd.iterate('name CA', 'store
Birtley and Curry used a novel optimization method, in their paper
"Crystallization of foot-and-mouth disease virus 3C protease: surface
mutagenesis and a novel crystal-optimization strategy", which might be
inspiring for you.
在 2012年4月28日 上午3:21，David Schuller 写道：
> Anisotropic truncation shou
I am working on a data set of an T=4 icosahedron protein crystal, employing
molecular replacement methods.
I've consulted a professor, he told me that my crystal is in fact
isomorphous to the model so that there is no need for MR.
So I figured such command lines:
phenix.refine output.mtz model.p
Hi Theresa,
Per your question about determination of membrane proteins - solution NMR is
quite capable of delivering structures of proteins in the presence of
detergents, such as the KcsA channel (see
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242490/). You should note, though,
that many memb
Dear CCP4BBers:
I'e got a problem about data processing when running SCALEPACK2mtz. Hope
you can give me some advice on that.
Here's my problem:
I have an .sca file processed by HKL2000 about 4 years ago, I just ran the
Scalepack2mtz program in order to transform it into .mtz file. However, the
Hi all,
I recently updated my ccp4 package to Program suite v8.0.002 and i have now run
into a few issues with other programs. The issues are highlighted below...
- When i click 'Open in Coot' on any output through Phenix (so far only tested
phenix.refine and phenix.phaser), i no longer see any
Hi Nick,
Thanks a lot for that advice, directing Phenix to the new coot.app location
appears to have fixed the amino acids restraints issue!
Though still having issue with Phenix not connecting to Coot, perhaps i will
post this issue on the Phenixbb and see what the community has to say.
Dale.
Hi Paul,
I seemed to have fixed the amino acid dictionary issue by following Nick's
suggestion to direct Phenix to the new coot.app location in my ccp4
applications folder.
Though I am still having the issue that Phenix is not connecting to Coot, is
this a known/common issue? Would you please
Hi everyone,
Can anybody tell how to run shelx C/D/E within CCP4 GUI on windows system?
Moreover, since shelx C/D/E within CCP4 using mtz file (structure factor)
instead of sca file (intensity), would this matters in tough conditions?
Thank you!
Best regards
Chen
--
Cheng Chen, Ph.D
Dear all,
this is sent on behalf of Edmund Kunji:
As Chairs, it is our pleasure to invite you to the *2018 Gordon Research
Conference* on *Ligand Recognition & Molecular Gating*, which will be
held in Ventura Beach Marriott, Ventura, 4-9 March 2018. The principle
goal of this GRC is to share
Dear all,
this is sent on behalf of Edmund Kunji:
As Chairs, it is our pleasure to invite you to the *2018 Gordon Research
Conference* on *Ligand Recognition & Molecular Gating*, which will be
held in Ventura Beach Marriott, Ventura, 4-9 March 2018. The principle
goal of this GRC is to share
Hi all,
I am currently trying to generate a Table 1 in Phenix. I currently have
inputted into phenix.table_one, the outputted from model and reflection file
from phenix.refine as well as my .cif restraints file for the bound small
molecule ligand. Source for Rfactors and resolution/bins are set
Dear CCP4 Community,
Montana State University invites applications for a tenure-track faculty
position in cryogenic electron microscopy. The position is formally a joint
appointment between the Department of Chemistry and Biochemistry, and the
Department of Microbiology and Immunology. The ca
Pity there is not a website
cootcootgo
Frances
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On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:
Th
ances
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On Fri, 9
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On Wed, 12 Oct 2
For those who have strong opinions on what data should be deposited...
The IUCR is just starting a serious discussion of this subject. Two
committees, the "Data Deposition Working Group", led by John Helliwell,
and the Commission on Biological Macromolecules (chaired by Xiao-Dong Su)
are working o
feasible in these areas, and to express
>> their
>> own for everyone to read and discuss.
>>
>> Perhaps John Helliwell can elaborate on this and on the newly created
>> forum.
>>
>>
>> With best wishes,
>>
>> Gerard.
>&
I think that we are using the test set for many things:
1. Determining and communicating to others whether our overall procedure
is overfitting the data.
2. Identifying the optimal overall procedure in cases where very different
options are being considered (e.g., should I use TLS).
3. Calculati
Adding to Tim's comment. In Coot use:
Extensions->Modelling->"Arrange Waters Around Protein..."
B
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Jacob,
to semi-answer your question: coot runs under windows, as far as I know,
but it may not be in the gui.
Tim
On 10/19/2011 08:41 PM, Jacob
John Helliwell points out to me that it might be useful to know what MX
crystallographic data researchers in different countries are already
expected to deposit or save. He notes that research funding agencies in
the UK expect researchers to preserve their raw experimental data for at
least 5 years
Why should we store images?
There are many reasons why storing images can be useful, but one is the
ability to re-analyze the data for a structure, or for all structures, in
a systematic and improved way.
I imagine that in a few years the PDB-REDO approach to rebuilding
structures will be extende
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2011, pp. 38-44.
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For those who may not have made it through all the CCP4bb postings in
October-December 2011 on archiving raw images, I have posted a summary at the
IUCR Diffraction Data Deposition Working Group forum page
http://forums.iucr.org/viewforum.php?f=21 in which I have attempted to list
the unique
You can try the scripts
user-define-restraints.scm/user_defined_restraints.py which allow you to
specify restraints. These are not available in the distribution (yet)
but from google code:
http://code.google.com/p/coot/source/browse/trunk/scheme/user-define-restraints.scm
http://code.google.co
coot new version. I tried as
suggested in coot FAQ page-
1. renamed probe.exe and reduce.exe were put in C:\WinCoot\bin- didnt
show validate/probe clashes as active n coot
2. made changes to group settings.py in wincoot/share/coot/python
folder to
probe_command = "C:\WinCoot\bin\prob
Dear Ros,
I believe I have fixed this in the newer versions. So please update to
the latest pre-release
(http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot_newest_download.php)
and it should work fine. If the problem persists please let me know.
B
Dear All:
I am having trouble with Coot.
The
but not hanging drops,
etc). J
Dr. Brian C. Richardson
Weill Institute for Cell and Molecular Biology
Cornell University
(609)933-4548
From: Matthew Lalonde [mailto:mattc
> d if you do so, be sure to tell us which versions of refmac and coot
you are using
I use Win Coot-0.7-pre-1 (version 4039), and Refmac5 from CCP4i.
It seems you are using an 'old' CCP4 (you dont specify the version,
6.1.3?) with an old(er) dictionary. WinCoot currently uses its own (up
t
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On Fri, 15 Oct 2010, Jacob Keller wrote:
Maybe this will
I have arachidonic acid soaked into my crystal structure and want to model it.
The phenix.refine is allowing my cis double bonds to distort to a gauche or
trans form. Is it the cif file or the refinement restraints in the program that
I need to correct.
I appreciate the input Paul and Nigel. The cif dictionary file you sent me
doesn't have matching restraint definitions for 53 atoms in the ACD file. I
opened the cif file you sent and extracted the SMILES code for ACD. Then I ran
it in phenix.elbow to have it generate a pdb of the ACD. Then i wo
Postdoctoral Position: Membrane Protein Structural Genomics
A postdoctoral position is available immediately (!) in the laboratory of
Michael Wiener, University of Virginia. His lab is one of three that comprise
the Membrane Protein Structural Biology Consortium (MPSBC, http://mpsbc.org,
one of
Postdoctoral Position: Structural Biology of Bacterial Active Transport
A postdoctoral position is available immediately (!) in the laboratory of
Michael Wiener, University of Virginia. The laboratory has a long-running
program in structural and functional studies of TonB-dependent outer membran
Dear Colleagues,
We hope that you are planning to attend the International Conference on
Structural Genomics 2011, which will be held in Toronto, Canada on May
10-14, 2011. The meeting is designed to serve as a forum to discuss the
most recent developments in structural genomics, structural/chemic
Hi Seema,
for python scripting in Coot (and syntax) you may want to refer to the
WIKI:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Python_Scripts
or the manual:
http://www.biop.ox.ac.uk/coot/doc/user-manual.html#Scripting
I meant to complete a more comprehensive man
ICSG 2011 Abstract and Early Registration Deadline Feb 28, 2011
Dear Colleagues,
We hope that you are planning to attend the International Conference on
Structural Genomics 2011, which will be held in Toronto, Canada on May
10-14, 2011. The meeting is designed to serve as a forum to discuss the
m
>> Dear all,
>>
>> I found the step refine speed of wincoot is much slower than that of linux
>> coot (with the same pc). Is it normal or I need to configure something with
>> the wincoot?
>>
> There are a number of things that might explain this, for example
>
> 1) You "linux" system is intrinsi
Section 4.4 Atom Colouring
http://lmb.bioch.ox.ac.uk/coot/doc/coot/Atom-Colouring.html
i.e.
add to your ~/.coot file
|
(set-colour-map-rotation-on-read-pdb-c-only-flag 1)|
Or use the preferences (only in newer pre-release versions):
Edit->Preferences->Bonds->Bond Colours
tic
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On Sun, 27 Mar 2011, harry powell wrote:
Yes, this is based on a Neville Shute story, stars
Thank you for the comment. You are correct that there are being backups
made in the newer interruptable fit function (they were't previously in
the uninterruptable fitting). I wasnt thinking about that (*). This may
(especially on windows) slow down things a great deal as we write and
gzip these fi
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On Sat, 2 Apr 2011, Jacob Keller wrote:
I guess I missed it in the flurry of replies to this thread over the
Dear Colleagues,
We hope that you are planning to join us in Toronto, Canada for the
International Conference on Structural Genomics 2011 which will be held on
May 10-14, 2011. We have an excellent scientific program prepared which
includes both oral and poster presentations (please see:
http://w
Here is more information on my problem:
I installed ccp4i in /usr/local as root using the automated install.sh script.
I then sourced the ccp4.setup and ccp4-others.setup for the proper shell,
making sure the environment variables were pointing in the right direction.
Now, if I run ccp4i as a
It was a permissions problem with the tmp directory. I thought I changed it,
but alas it was set to root.
Thanks for your help!
Jason
-Bruno Matias wrote: -
To: Jason C Porta
From: Bruno Matias
Date: 04/30/2011 07:21AM
Subject: Re: [ccp4bb] Error in LABIN
Jason, I think you shoud
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On Tue, 3 May 2011, Jahan Alikhajeh wrote
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Hi Haytham,
I'll respond on the phenix bulletin board (you can sign up at
www.phenix-online.org)!
All the best,
Tom T
>> when i refine using phenix.refine i get this error
>>
>> number of groups of duplicate atom labels:1
>> total number of affected atoms: 2
>> group "HETATM 3466 BR PDB F 1 .*. BR
amount to
theft.
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I found this paper to be very helpful for a similar experiment.
"Elucidation of the mechanism and end products of glutaraldehyde cross-linking
reaction by x-ray structure analysis".
Wine et al. Biotechnology & Engineering, Vol. 98, No. 3, October 15, 2007.
-CCP4 bulletin board wrote: ---
Eric,
That IS the way to do it. Please make sure you have the dictionaries in
the path and check your coot startup script in case it sets
COOT_REFMAC_LIB_DIR back to nothing (and hence falls back to the ccp4
one). Do you get any message in your start up console? BTW which
version of Coot are
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Coot:
Extension -> Modelling -> Residues with Missing Atoms...
Or watch out for the blue bars in the rotamer validation graph in Coot.
B
Dear all,
Does anyone know a program that will check a PDB file for missing
atoms and output a list of the corresponding residues?
Many thanks in advanc
Basically my reasoning for doing this is a low data-to-parameter ratio, which makes B-factor refinement unfeasible. So far I have had nice results with breaking the complex into rigid subdomains. So i was basically just thinking of a way I could refine the structure best, without using too many par
I am wondering , do we need uninstall the previous version of coot to
install this?
No. Many group use more than one version of Coot.
Ah, but perhaps you mean WinCoot? My (limited) experience is that you
can install right over the top of the old one.
WinCoot can be installed on top of eac
Hi Francois,
your mtz file doesnt appear to have any phases, so Coot (or whoever)
cannot make a map. What Coot cleverly tries to do in such a case is to
use calculated phases from the given pdb (and mtz) file. So it runs
refmac with the pdb and mtz to retrieve this phase information. There is
Hi
i am refining a protein strucutre with space group P61. Intesity statistics
doesnot suggest any twining but refmac and phenix xtriage suggest a twin
operator with fraction 0.48. when refined with this twin operator R factors
come dowm by 3-5% and also map looks much better. but upon closer ins
If you want the complete sequence of the material that was
studied, rather than just a list of residues for which there
are coordinates, then the information that you need is on the
SEQRES records. So you could try
grep "^SEQRES"
followed by
cut -c 20-70
with appropriate file names
Hello Rongjin Guan,
your problem most likely comes from different pdb version formats. The
files which work are probably pre pdb v. 3.0. Although (Win)Coot is
mainly v. 3 compliant here we are not (really (*)). A fix (at least for
the files which are not working) may be to change two lines (1
Hi Raja,I assume you are running OS X?I had this same problem since I was running xcode v3.0. The new compiler (the one its complaining about) should be packaged with the xcode on the snow leopard disc, which I believe is the most recent version. I could be wrong, since I haven't yet fixed my own p
Hi Tim,
I cannot comment on the installation/hardware problems. But I can give
you a hint on how to 'invert polarisation': Switch the stereo sides. In
pythonic Coot use:
switch_stereo_sides()
For convenience a while back I made a 'zalman stereo toggle' toolbutton
together with a 'switch sid
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Wasnt there recently a similar discussion(?):
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg16099.html
Maybe try JLigand (www.ysbl.york.ac.uk/mxstat/)
B
Hi all,
I need to create a cif file for a new ligand that does not exist in
the pdb, so far. Normally refmac created such a cif fil
zowski, Ed.
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That was quick. They are all taken.
Frances
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Consultants
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Lane, Bellport, NY 11713-2803
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On Thu, 15 Jul 2010, Gerard DVD Kleywegt wrote:
http://pdbe.org/p
Have you tried sending e-mail to Randy Read?
Frances
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Dear Colleagues,
We are pleased to let you know about the upcoming International Conference
on Structural Genomics 2011, to be held in Toronto, Canada on May 10-14,
2011.
This meeting is the 6th in this series of biennial meetings of the
International Structural Genomics Organization.
The meet
Postdoctoral Positions: Membrane Proteins @ University of Virginia
Due to some recent changes in both funding and personnel, I have several
positions available immediately in my lab. Postdoctoral level preferred, but
more senior (or more junior) positions are possible. Relevant experience is
ce
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On Thu, 30 Sep 2010, Eleanor Dodson wrote:
Does any one have
I recently got the 24 inch Zalman and when the coot window is
maximized the 3D is reversed. I know I can minimize it slightly and
move it up and down a pixel to fix it. Has anyone found a trick to
leave it maximized and correct the 3D. I have tried adjusting screen
position but have not foun
d
the topology and parameter files from HIcCup and put them in the necessary
sections in generate.inp. I have run this before when refining a similar data
set with not as many issues, but I really would like to know what this means.
thanks all
Ainsley
C. Ainsley Davis, Ph.D.
Post-Doctoral
Dear all,
I am trying to solve the structure of a protein complex, via MR, and when the
phasing is complete there is 1/3 of the unit cell that is missing electron
density. The density present looks very good and shows helices in regions that
were disordered in my NMR model, suggesting that it
--
Sarat Chandra Sahu, Ph.D.
Research Biologist
Department of Biological Sciences
Carnegie Mellon University
4400 Fifth Avenue
Pittsburgh, PA 15213-2683
E-Mail:[EMAIL PROTECTED]
Phone: (412)268-7338/3396 (O)
(412)683-0444 (R)
(412)478-4595 (Cell)
Fax : (412)268-7083
Hi Bill,
Peptide cutter does work for several cleavages.
http://www.expasy.ch/tools/peptidecutter/
regards
Manish
William Scott <[EMAIL PROTECTED]> wrote: Hi Citizens:
What programs/web sites would you recommend for prediction of enzyme
cleavage sites in a protein sequence?
Many thanks.
I agree with you Mark. Even in my case the twinning fractions
varied substantially among the different crystals grown in same
drop. Moreover, I feel the fractions may vary at different part of
the crystal too. Please correct me if i am wrong.
regards
Manish
Mark Mayer <[EMAIL PROTECTED]> wro
Alejandro,
As others have said, the most likely explanation is the attenuation of the air
scatter by the sample holder. There is no sharp edge to the shadow which
indicates the source of scatter is along an extended path. Ed Berry pointed out
that he didn't see spots in the shadow. This might be
You can use Coot to find the centre of mass. In the scripting window just
type:
in scheme:
(centre-of-mass yourmoleculenumber)
or in python:
centre_of_mass(yourmoleculenumber)
Bernhard
BTW the American spelling of centre (center) should work too...
> Dear all,
>
> I was trying to do a NCS
Seems to be a general issue.
Read the editorial in Nature 10 May 2007 Volume 447 Number 7141, pp116.
"Under the microscope - The use of 'black box' techniques carries risks."
Colin
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Flip Hoedemaeker
Sent: 10 May
Hi Junhua & Bill,
I wonder about growing crystals in some kind of gel. Long back, i
received the crystals in gel, and they did diffract. Is it still in
practice ?
regards
Manish
William Scott <[EMAIL PROTECTED]> wrote: Hi Junhua:
These are ccp4 bb questions, so don't apologize (or we all wi
error than if
one just refined into the twinned data? Is truncate and the twinning server
ever wrong in their diagnosis of twinning?
Secondly, this structure still has an area of missing density parallel to the
a-b plane which never resolves (1/6 at top and bottom along c). This is the
case for
Apologies for the late posting (been away). Interesting question from James and
an interesting answer from Ian!
There should be a radiation pressure effect here resulting in a transfer of
energy and momentum to the sample. The effect is very small (the term includes
flux density divided by spee
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===
Dear Craig,
It seems Refmac is not reading the user supplied dictionary. I expected a line
near Makecif parameters like this.
"User supplied dictionary entries: /home/pathak/junk.cif"
regards
Manish
Craig McElroy <[EMAIL PROTECTED]> wrote: Hi all,
I am trying to refine a structure with a
While the topic of "fabrication" is still hot, I thought I too could add
a few thoughts.
Our Mathematician friends always make fun of us (Biologists/ Biochemists/
crystallographers!) that our papers are accepted within 4-8 weeks of
submission.
This is not to talk of Science/ Nature/ Cell, whe
Good summary as expected from James.
"Have you ever heard of photon-photon scattering?"
Well yes! See for example
http://2physics.blogspot.com/2006/03/photon-photon-scattering.html
which says "according to Quantum Electrodynamics (QED), particles can still be
created in this emptiness of vacuum th
Dear Vineet,
It seems, in your input PDB file the atom level for CA and CL in the last
column is C. It should be CA & CL respectively. The atom name in the
input file and Dictionary doesn't match.
all the best
Manish
Vineet Gaur <[EMAIL PROTECTED]> wrote: Hi all
i am
Hi,
I would like to invite you to submit articles for a special issue of
IEEE Software on
"Developing Scientific Software". The call for articles is below, and
also at:
http://www.computer.org/portal/site/software/menuitem.538c87f5131e262449
55a4108bcd45f3/index.jsp?&pName=software_level1&path=sof
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