Hi Boaz,
I get the same thing when I try to run it from the command line. Well as
a workaround I used mosflm instead...
Best
Sabine
On 08/09/2011 11:33 PM, Boaz Shaanan wrote:
Hi Sabine,
What happens if you try to run it from command line? Just curious. It's a
useful program (though not
Dear all,
I'm using MOLREP in CCP4 for MR. The problem is that it doesn't output a pdb
file although the last contrast value written in the log file is 3.13! Are
there certain criteria which have to be fulfilled before it gives a pdb file or
is it a bug?
Thanks for your help!
Eric
Dear All,
I have inside cavity in my protein structure with some conserved
residues. We do not know function or ligand for that domain.
How I could find ligand candidates which fit to this cavity? Maybe
somehow with pdbe?
Thank you,
Heidi
Hi Heidi
You can try hunting for similar structural motifs which are likely
to be involved in ligand binding or function:
http://www.russelllab.org/cgi-bin/tools/pints.pl
You can then try fitting suggested ligands to the cavity.
good luck
Alex
On 10.08.2011 13:46, Heidi Tuominen wrote:
Dear
Dear colleagues,
I am trying to install the ccp4 GUI for aimless (both Ubuntu 10.04 LTS and
SuSE SLES 11.0 on 64bit machines):
- I downloaded aimless-0.0.16.linux from ftp.mrc-lmb.cam.ac.uk/pub/pre/ (I
also tried aimless-0.014.linux64), in addition, I downloaded
aimless_ccp4i_0.8.tar.gz.
-
You also need to install the updated task for pointless, from the same ftp site
ftp.../pub/pre/pointless_ccp4i_1.4.tar.gz
sorry about this, but I had to change that to make the pointless/aimless task
work
Phil
On 10 Aug 2011, at 14:11, Ulrich Gohlke wrote:
Dear colleagues,
I am trying to
Dear all,
how do you extract segments from a pdb file, so that from an input pdb
file you get output like this:
10-103, 120-174, 200-240
or, better yet:
A: 10-103, 120-174, 200-240
B: 10-104, 120-174, 199-241
if the N terminus is missing and there are two gaps in the structure.
I tend to
If you mean what I think you mean, then use the SUMMarise option of
pdbcur. That gives output like:
Chain A has 505 residues
in 7 spans: 1-305 307-500 711-711 716-716 719-719 721-722 730-730
0 residues have alternative conformations
Composition: ALA 23 ARG 23 ASN 36 ASP 24
I see that my questions was highly ambiguous/unclear. Martyn saw
through it anyway. pdbcur does what I want.
Andreas
On 10/08/2011 5:32, Martyn Winn wrote:
If you mean what I think you mean, then use the SUMMarise option of
pdbcur. That gives output like:
Chain A has 505 residues
Dear CCP4 users,
I just wonder if this problem can be solved using Sketcher.
When i use Sketcher (PC or linux) in the CCP4 GUI to generate the
monomer_lib.cif of a ligand (V3OAc.pdb) obtained from CCDC, the geometry of
this
ligand change (see V3Oand the attached files are used. Any comment is
On 10/08/11 18:42, Dr. STEPHEN SIN-YIN, CHUI wrote:
Dear CCP4 users,
I just wonder if this problem can be solved using Sketcher.
When i use Sketcher (PC or linux) in the CCP4 GUI to generate the
monomer_lib.cif of a ligand (V3OAc.pdb) obtained from CCDC, the geometry of
this
ligand change
Hi all,
The Protein Data Bank in Europe (PDBe; http://pdbe.org) continues to improve
its services to the scientific community. As part of our recent website
update, the EM resources at PDBe (http://pdbe.org/emdb) have been improved.
EMDB (http://emdatabank.org) contains over 1000 maps and is
Time to fuel up the gossip engines for the approaching weekend:
http://www.sciencedirect.com/science/article/pii/S096921260800186X
RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus
Bound to the G-Protein Dimer G?_1 ?_2
Structure, Volume 16, Issue 7
On the surface it doesn't seem as bad as others, i.e., it does not
seem to be a real fake--perhaps just a strong form of wishful thinking
and creative density interpretation. I wonder what would be a good
metric in which to establish a cutoff for present/not present in
density. CC, maybe?
Jacob
CC alone wouldn't be totally sufficient. CC is scale independent. For
example, if you compare two very weak densities, say visible at below 0.1
sigma, and If these densities are similar enough then you will still get
good CC.
Therefore it's good to use CC and map values together. This is exactly
For some ideas on this see my presentation to the last CCP4 study weekend
(with some further ideas in Acta D, to be published):
http://www.cse.scitech.ac.uk/events/CCP4_2011/talks/tickle.pdf
Cheers
-- Ian
On Wed, Aug 10, 2011 at 10:35 PM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
Just another example of where it would have been good for the reviewers to
get access to the data during the review process... and where at least one
of the reviewers *should* be a protein crystallographer...
Filip Van Petegem
On Wed, Aug 10, 2011 at 2:01 PM, David Schuller dj...@cornell.edu
I've made a quick look at the model and the paper - and it doesn't
need more than a quick look. The description of the model in
the paper sounds great. The problems in the model are clear. My
favorite is the quote Trp-477 of PTH1R makes several van der Waals
contacts with Trp-339 and Lys-337
Oops! My bond length rmsd was 0.106 not 0.160 A. Still unacceptable
but not quite as bad.
Sorry,
Dale Tronrud
On 08/10/11 15:45, Dale Tronrud wrote:
I've made a quick look at the model and the paper - and it doesn't
need more than a quick look. The description of the model in
the
The paper with this structure was published in the year 2008, following
which, the PI and coPIs who co-authored the paper would have submitted
grants using this information as preliminary data. It is possible some
of these grant applications may even have got funded at the expense of
other
I Agree with the idea of adding crystallographer reviewers. But accessing to
data is not feasible unless there is a good way to protect authors. For
example, the editor should agree to publish the paper swiftly in advance
before the data become accessible to reviewers.
In any case, the flaw of
the editor should agree to publish the paper swiftly in advance before the
data become accessible to reviewers.
This seems to miss the point - how is the reviewer then supposed to judge
the map?
BR
Nian
On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem
filip.vanpete...@gmail.com
On Wednesday, 10 August 2011, Nian Huang wrote:
I Agree with the idea of adding crystallographer reviewers.
But accessing to data is not feasible unless there is a good way
to protect authors.
Disagree.
The data supporting a paper's claims should always be made available
to the reviewers.
The reviewers who wish to get access to raw data should reveal their
identity by signing the report!
-Sankar
On Thu, Aug 11, 2011 at 10:28 AM, Ethan Merritt merr...@u.washington.eduwrote:
On Wednesday, 10 August 2011, Nian Huang wrote:
I Agree with the idea of adding crystallographer
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