nation of some of us, can be solved by simply
improving the peer-reviewing procedures.
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel:
Hmm,
My XDS-Viewer.app installation is not in a standard place, more likely
you need:
cd /usr/local/bin
ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin .
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille
Hi Sebastiano,
Yes, you have to put the xds-viewer executable in your PATH. In the Mac
and assuming /usr/local/bin is in your PATH:
cd /usr/local/bin
ln -s
/Applications/Sci/Struct/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin .
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des
ome of the components of the binding
energies, like electrostatic and apolar binding and polar/apolar
solvation terms, you could use something like APBS
(http://www.poissonboltzmann.org/apbs/)
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix
Le 30/10/12 20:28, Jason Busby a écrit :
> Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will
> cycle through all the windows of the current program.
>
> Jason.
>
> --
> Jason Busby
> PhD Student
> Laboratory of Structural Biology
> School of Biological Sciences
> Univ
Le 28/08/12 09:57, cuisheng2007 a écrit :
> Dear all:
>
> Is there software or web-server that can measure DNA geometry (PDB
> coordinates) precisely, such as groove width, helix diameter, helix
> axis, base tilt angle, helix rise per base pair…
>
> It is surely doable to measure and estimate the
Le 15/02/12 11:36, Tim Gruene a écrit :
> Hello Lisa,
>
> which version of coot do you use? Maybe it is outdated and that function
> not yet properly implemented. I can confirm Bill's comment, and we work
> with coot 0.6.2.
>
> Cheers,
> Tim
>
> On 02/15/2012 09:01 AM, LISA wrote:
>> Hi all,
>
Hi Yuri,
To add something nobody else has mentioned yet.
If you are interested in statistics and analysis you may find
interesting the R package. There is an excelent module, called Bio3D for
the analysis of protein structure and sequence data. Have a look here:
http://bio3d.pbworks.com/w/page/78
Le 24/01/12 21:18, Dale Tronrud a écrit :
> On 01/24/12 11:52, Miguel Ortiz Lombardia wrote:
>> El 24/01/12 18:56, Greg Costakes escribió:
>>> Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
>>> redundancies.
>>>
>>
>> But then suppose that one merges data from a crystal that is
Le 19/01/12 14:03, anita p a écrit :
> Hi All,
> Has anyone run a native gel for proteins at pI>8 .
> I want to pour my own native gel. Do I run a discontinuous page or a
> continuous one?? Please help with regards to the buffer system to be
> used, and the dye to be used.
> With regards
> Rashmi
Le 11/01/12 12:23, Federica Basilico a écrit :
> Hi everyone,
>
> I have crystals of a protein of 176 residues, with 5 Cys, 8 His, 3 Met.
> Native crystals grow in 10% MPD, 100mM Bicine pH 9.0. They show a nice
> diffraction, but appear to be perfectly twinned.
> I have crystallised a SeMet deriva
Le 08/11/11 10:15, Kay Diederichs a écrit :
> Hi James,
>
> I see no real need for lossy compression datasets. They may be useful
> for demonstration purposes, and to follow synchrotron data collection
> remotely. But for processing I need the real data. It is my experience
> that structure soluti
Hi community,
I have been waiting for someone more knowledgeable to write about the
passing away of Dennis Ritchie (8 October) especially after the recent
obituaries posted in the list. I confess I know little about him, except:
1/ He created the C language ( and together with Brian Kernighan wro
Message on behalf of Christian Cambillau. Please send your
enquiries/applications directly to his address:
cambil...@afmb.univ-mrs.fr
-
Dear Colleagues,
Within the framework of a French « Agence Nationale de la Recherche »
(ANR) contract, we are studying at A
On 09/09/11 17:29, Ed Pozharski wrote:
> On Thu, 2011-09-08 at 16:58 +0200, Miguel Ortiz Lombardía wrote:
>> Perhaps the Nd/DN issue was solved between revisions 3470 and 3628 ?
>
> Indeed. I just built the rev 3633 and it works fine. Autobuild scripts
> used to have some prob
On 08/09/11 15:35, Ed Pozharski wrote:
> After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I
> have found a problem working with DNA that I have not seen with
> 6.1.13/5.5.0109. Namely,
>
> - if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to
> output DNA as A
On 06/09/11 16:48, Huw Jenkins wrote:
> On 25 Aug 2011, at 14:12, Gregory Bowman wrote:
>
>> When I try to run ARP/wARP classic for loop building, I get the following
>> message in the logfile:
>>
>> QUITTING ... ARP/wARP module stopped with an error message:
>> REFMAC
>
> I get the same error r
On 11/08/11 09:13, Nian Huang wrote:
> To make my idea a little bit clearer, the reviewers first make the
> acceptance decision just based on the paper itself, on the condition the
> coordinate matches the description of the paper. Then the editor
> promises the publication date and the pdb can be
Dear all,
I have successfully compiled ccp4 6.2.0 on an OSX (10.6.8) machine but
I'm failing to do the same in a different one, though with the same
system setup. In the machine giving me trouble I want to install ccp4 in
a nfs disk mounted. When I run configure using exactly the same input as
in
Dear all,
I get this unexpected (by me) message from MrBUMP:
Reindex Warning: spacegroup P43212 does not have an enantiomorph
I thought P41212 and P43212 were enantiomorphs...
So, am I wrong ?
(PS: I'm looking for indications on how to use MrBUMP on a cluster with
a SGE queueing system. Any poi
Le 01/04/11 12:39, REX PALMER a écrit :
> Dear Protein Crystallographers
> I would like to share with you something I came across today.
> Unfortunately I was only able to copy the first 4 pages of the article
> by MV King as I need to post the email before 12am and the quality of
> the copy is som
Hi Fred,
I would say that the helix stability will generally be affected by its
context within the protein, unless it is (unlikely?) separated from the core
of the protein and it has intrinsic stability (some peptide sequences do).
Also, in a particular context, you may have mutations that unfold
Hi,
Water is not very nice a medium for a polyanion such as DNA when
concentrated. Better use a basic buffer, even 10 mM Tris pH 8.0-8.5 would
do. Another important thing is, as you have already partly tried, ionic
strength but also the nature of the ions. You need monovalent cations as
well. I wo
Dear list members,
Sorry to bother you with a personal reflection that somehow asked for a way
out of my mind after the umpteenth announcement of this kind. Please, no bad
feelings for that post, no more than for any other of its kind, anyway.
As it often happens, my reflection takes the form of
Don't know for the phaser problem, I had it once, but it was because I had
phenix installed as well and I had set them both up in the same shell. That
was something suggested already, so I guess it's not your problem.
As for refmac: the tar.gz file you download from Garib's webpages is not a
CCP4i
field supported by
pd2pqr.
It produces a "bild" object that can be loaded in the program Chimera from
the UCSF. But it can be easily re-written to produce output for other
graphic programs. Feel free to do it!
Cheers,
Miguel
2008/1/26, Miguel Ortiz-Lombardía <[EMAIL PROTECTED]>
Hi Zheng,
I have python script that does so if you have the program 'pdb2pqr'
installed (http://pdb2pqr.sourceforge.net/)
Let me know if you're interested.
Cheers,
Miguel
2008/1/19, Zheng Zhou <[EMAIL PROTECTED]>:
>
> Hi, All
>
> Sorry about non-CCP4 questions. It is the best board I find so
Unless there is pseudo-symmetry, I would say that the self-rotation
indicates that crystal point group is 422... Did the indexing program
suggested something with this symmetry?
Cheers,
Miguel
2007/8/20, Wim Burmeister <[EMAIL PROTECTED]>:
>
> Yanming Zhang a écrit :
> > Hi,
> >
> > Would some e
Hi Satinder,
Did you checked if your SAD dataset (2.9A) and the dataset you're using in
the refinement (2.3A) are in the same setting? The 'cad' program can do that
for you.
Cheers,
Miguel
2007/7/27, Satinder K. Singh <[EMAIL PROTECTED]>:
>
> Hello,
>
> I have a SAD data set to 2.9A and a na
Hi Mona,
No idea what format may be that file, but if you find it out, most often in
these cases openbabel (http://openbabel.sourceforge.net/wiki/Main_Page) is
your friend.
M.
2007/7/24, Mona N. Rahman <[EMAIL PROTECTED]>:
Hello all,
I have a coordinate file of an energy minimized molecule
Hello Hyunchul Kim,
I found this paper very interesting:
Novotny M, Seibert M, Kleywegt GJ.
On the precision of calculated solvent-accessible surface areas.
Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):270-4. Epub 2007 Jan
16.
PMID: 17242521 [PubMed - indexed for MEDLINE]
http://www.n
Hi Bernhard,
You can get this one and the others from here:
http://epubs.cclrc.ac.uk/index
Search for 'CCP4' and you'll find it among other jewels.
HTH,
Miguel
2007/7/8, Bernhard Rupp <[EMAIL PROTECTED]>:
Wonder where I might find the older study weekend archives on the CCP4
site...
loo
g
FC=g77 F77=g77 ./configure linux
(you should use g77 rather than gfortran. The programs compile but do not
work
properly, especially with mosflm in Harry Powell's experience).
Tim
On Thursday 28 June 2007 20:32, Miguel Ortiz-Lombardía wrote:
> Dear all,
>
> Has anyone succeeded
Dear all,
Has anyone succeeded at compiling the latest release of CCP4 with gcc-4.1.2
This is the compiler version in Ubuntu 7.04 (Feisty Fawn)
At the very beginning (ccif lib compilation), I get this error:
/usr/bin/ld: final link failed: Nonrepresentable section on output
I looked around and
Hi Simon,
What graphics program are you using to inspect the density? Are you reading
in directly the maps produced by CNS or converting them to some other
format? If you convert it, the most likely culprit is the conversion
procedure...
Miguel
2007/6/27, Kolstoe S.E. <[EMAIL PROTECTED]>:
Hi Michal,
Hmmm... Was it kicked out upon crystallisation or was crystallisation
possible because most of your pentamers were not fully occupied by ligand so
allowing the possibility of good contacts? ;-)
What was the excess of ligand? Do you know its affinity?
Miguel
2007/6/24, Michal Harel
36 matches
Mail list logo
