I saw also a great domain (around 150aa) movement on one of the subunits
when crystals of the protein (yeast acetylglutamate kinase) were soaked
with its inhibitor (arginine):
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034734
2012/10/9 Alan Cheung
> Depends on what you m
Dear Bill,
You have not missed anything, we do not have a mechanism for delivering source
code *updates* in automatic fashion as yet. Our statistics shows that source
code distributions make only 2-3% of binary downloads, therefore, I hope that
you would understand that we have to prioritise ou
On Tue, Oct 09, 2012 at 11:18:29AM +0200, vellieux wrote:
> Ta very much Tim,
>
> what I did was to edit the ccp4.setup-csh file in order to change the line:
> setenv CCP4I_TCLTK /usr/local/bin
> into:
> setenv CCP4I_TCLTK /home/prog/ccp4-6.3.0/bin
You may source bin/ccp4.setup-csh instead.
In cc
Depends on what you mean by large, but we saw very obvious domain
movement when we soaked a protein (transcription factor TFIIS) into
crystals of RNA Polymerase II (PMIDs 12914699/21346759/22726432). We
recently animated this conformational change, and you can watch it at:
http://www.youtube.
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On 10/7/12 5:43 PM, Joel Tyndall wrote:
Hi Rex,
In Coot, under the file menu, “Get Fragment” and the type LBT (upper
case).
"Get Monomer...", IIUC.
This (LBT) is the three letter code for alpha-lactose. Unfortunately
it is not that easy to find the codes.
I use "Search monomer Lib
Dear Wenhe,
We too have had similar experiences with a couple of other other kinases - CDK2
(PMID: 21291269) and Aurora A (PMID: 22248356), where both soaking and
co-crystallization has resulted in large conformational rearrangement.
Best wishes,
Mat.
From:
On 09/10/12 15:09, William G. Scott wrote:
Dear Ronan et al:
I apologize if I have missed it, but is there a simple way to obtain the
corresponding changes in the source code for those of us who compile ccp4
ourselves?
I looked on the web site and the ftp site but can't seem to find it.
Ca
Dear Ronan et al:
I apologize if I have missed it, but is there a simple way to obtain the
corresponding changes in the source code for those of us who compile ccp4
ourselves?
I looked on the web site and the ftp site but can't seem to find it.
Many thanks in advance.
Bill
On Oct 8, 2012,
Hi Rex -
You can usually get the three-letter code from the PDB itself. At top
of the PDB home page, you can see that one of the options for the search
bar is "Ligand". If you put in a (mostly) correct name for the ligand,
you will get back the three-letter code that the PDB is using. This
Dear Wenhe,
One example we have is the protein kinase Nek2. We co-crystallised with ADP and
then soaked in the inhibitors. The activation loop was free to move around and
adopt a number of different conformations (e.g. to DFG-out conformation).
References:
Westwood I, Cheary D-M, Baxter JE, Ri
Dear CCP4 members,
Recently, I got a ligand soaking structure to clearly show a large domain
(~100 amino acids) movement compared to the no soaking structure. Although
there are some reported examples of this enzyme to suggest the flexibility
of this large domain which is relevant to substrate bin
Hi all,
The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an
expert structural biologist to join the PDBe curation team at the EBI near
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD
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Ta very much Tim,
what I did was to edit the ccp4.setup-csh file in order to change the line:
setenv CCP4I_TCLTK /usr/local/bin
into:
setenv CCP4I_TCLTK /home/prog/ccp4-6.3.0/bin
Then the ccp4i GUI window popped up fine. Problem solved. I didn't
really want to have to "su" every time I wanted t
This is interesting. In principle m and D should provide an optimum map, and
at high resolution they do a reasonable job.
The answer about occupancy is a good point.
You don't say what resolution your data is at, but maybe it is rather low?
I suspect that below ~ 3A the estimates of both m and
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Hash: SHA1
Dear F.V.,
you should check read permissions of the setup-files (e.g.
$CCP4/include/ccp4-setup.sh). For your user, the variable CCP4 seems
to be set, but CCP4I_TCLTK is not (which should be done in the same
setup-file).
Cheers,
Tim
On 10/09/2012 09:
Hi folks,
on my SL6.3 box, only su (root) can lauch and run ccp4i. For other users
I get this cryptic message,
/home/prog/ccp4-6.3.0/bin/ccp4i: line 4: /wish: No such file or directory
/home/prog/ccp4-6.3.0/bin/ccp4i: line 4: exec: /wish: cannot execute: No
such file or directory
Anyone out
Dear Theresa,
concerning your first sentence which is a bit short to my taste: if you index,
you expect to find the cell parameters. These enable you to process the
dataset. At the end of processing, a decision has to be made about the
spacegroup. Only then structure solution can be tried, usin
Dear Theresa
In response to your first question, one way to do this is to look
closely at the image (eg changing the contrast level) with the
predicted pattern superimposed after indexing, or alternatively just
integrate the image and look at the reported mean I/sigmaI as a
function of re
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