Dear All
Applications are invited from scientists in the fields of X-ray crystallography
or Structural Biology. You will have a strong commitment to excellence in
research and teaching, be expected to develop an active, externally funded
research group and contribute to the undergraduate teachi
One would assume that Windows software would read DOS/Windows type text
files...
Open the file in Wordpad. Unlike Notepad, it is able to work with Windows and
Unix type text files. If you edit something and save the file, it will be in
Windows style. If Superpose stops on that, it should really
Dear all,
A two year post-doctoral position associated with the macromolecular
crystallography group at the Australian Synchrotron is currently open for
applications.
To read the position description and application instructions please go to
http://www.synchrotron.org.au/index.php/about-us/working-
Hi Citizens:
We seem to run through high voltage tanks on our Raxis IV like guano goes
through a goose. Has anyone else had this problem, and, more importantly, what
is the best way to protect them. I am assuming it might have something to do
with our electrical supply, which is a bit unrelia
On Sep 22, 2011, at 9:29 AM, Ben Eisenbraun wrote:
> Desmond 3.0 Tutorial
2.2 was quite impressive.
(sorry.)
On 09/27/2011 09:55 AM, David Veesler wrote:
Hi François,
Chainsaw should do the job for you if you input a clustal alignment.
Cheers
David
Thanks! I'm happy I asked. I'll give a try at chainsaw.
Hope to not cut one of my fingers during the process...
Le 26 sept. 2011 à 17:44, Francois Beren
Hi François,
Chainsaw should do the job for you if you input a clustal alignment.
Cheers
David
Le 26 sept. 2011 à 17:44, Francois Berenger a écrit :
> Hello,
>
> I have one bound complexe (a ligand + a protein in holo conformation).
> I also have the apo structure for a very similar protein.
>
Hello,
I have one bound complexe (a ligand + a protein in holo conformation).
I also have the apo structure for a very similar protein.
Is there a tool to create a new PDB, whose coordinates are
taken from the holo structure but residue names and numbers
are taken from the alo structure (by look
Hi Zhiyi,
I am trying to refine a structure with two domains. The electron
> density of one domain is reasonable, but that of the other domain is
> poor. So, I am wondering whether the refinement by Phenix or Refmac
> can be done locally with two parts, the first domain is refined with
> normal r
I think something in your workflow is inserting dos line feeds (\n\r or \r\n, I
can't remember which).
If I have guessed correctly, you want to remove those "\r"s before proceeding
(or never let them get in there in the first place).
You claim to open it with MS something, which would insert do
>>> The outputfile appears to have additional line feeds (see picture) which,
>>> however are not seen in the windows notepad.
What application ARE the extra lines seen in?
Sounds like a problem with different newline conventions-
vs vs -
although I shouldn't have thought extra carriage return
Hi again,
Thanks for your quick replies but I think I made myself not clear. here
is what I'm doing:
1) superpose proteinA.pdb onto proteinB.pdb : works, but gives out
proteinA_lsq1.pdb with extra empty lines (not the anisou lines ;o) )
2) superpose proteinA_lsq1.pdb onto proteinC.pdb : do
-Just to make a note, there has actually been some discussion in the
published literature recently (ok maybe past ten years) about what
terms; simply steric (as originally) or hydrogen bonding etc
might be needed to explain observed backbone angular values.
Tommi
On Sep 26, 2011, at 5:44 PM
I vaguely recall notepad doing something wacky with files in certain
cases...why don't you get the excellent text editor NoteTab Light
[sic] (I use it all the time--free and works great), then take a look
at your files and see whether MS notepad altered the files.
JPK
On Mon, Sep 26, 2011 at 2:42
On Mon, 2011-09-26 at 20:42 +0100, Matthias Zebisch wrote:
> However, it is not
> possible to use it within CCP4, eg. for a subsequent superposition.
What do you mean by that? Do you get an error when you use the
superpose output pdb with some other program?
--
"I'd jump in myself, if I wer
Dear CCP4 users,
I am using the ccp4i version 6.2.0 under windows 7. I've come across a
problem with superpose.
The outputfile appears to have additional line feeds (see picture)
which, however are not seen in the windows notepad.
The structure can also be opened in coot and pymol. However, it
Frank,
I don't have a plan, but as the consultation seeks the views of the
community. I would urge those with views to write to to STFC expressing
them, and mention this to their friends/colleagues/students/PI. Although I
suspect that the views of people from industry will have more weight than
Dear Nat,
yes, I fully agree - all these restraints that improve the geometry
either by restraining to high-resolution structures or by introducing
H-bond restraints for secondary structures are very useful for
low-resolution structures!
I see your argument with the Ramachandran plot. But im
On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa
wrote:
> when I played with H-bond restraints for secondary structures for the
> refinement of a 4.3 A structure (only a few weeks before they were
> introduced in phenix), I've made the following observation: at low
> resolution without H-bond restra
Sorry,
I should have had a look also at the CCP4 site:
updated version of molrep from Aug 8.
http://www.ccp4.ac.uk/updates/linux/ccp4-6.2.0/bin/
Cheers
Guenter
Dear Zhong Chen and CCP4 users,
I get the very same error on a Centos 5 box. Is there a solution yet?
Best regards,
Guenter
Dear all,
Dear Zhong Chen and CCP4 users,
I get the very same error on a Centos 5 box. Is there a solution yet?
Best regards,
Guenter
Dear all,
Recently, I used MOLREP to molecular replacement.
My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 .
When I run a pdb file and mtz by MOLREP w
The position is available in the laboratory of Aitor Hierro to work in the
area of *structural
biology* and *membrane trafficking*.
We study the interactions, in molecular mechanistic detail, that underlie
the selectivity of
cargo transport vesicles for recognizing the correct target membrane. We
Dear Colleagues,
I would like to point your attention to a number of PhD positions in
structural biology that are available through the international PhD
program at the Max Planck Institute for Developmental biology in
Tuebingen, Germany.
For detailed information, please visit:
http://www.p
At this resolution you may/ should be able to find anamalous scatterers
using the anom signal from P and S. the SHELXC/D/(E) package is very
good at this!
Once you have the sites for the heavier atoms I would expect most direct
methods programs couild extend that sub-structure.
Certainly ACOR
Dear Nat and other interested colleagues,
when I played with H-bond restraints for secondary structures for the
refinement of a 4.3 A structure (only a few weeks before they were
introduced in phenix), I've made the following observation: at low
resolution without H-bond restraints for seconda
25 matches
Mail list logo
