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Hi,
I am using CCP4 on Sci Linux machines and running now into some trouble
with update manager and our firewall.
I connect through a proxy and defined the proxy in the ccp4-setup.sh.
Running update-manager gives me an error message; a new window pops up
telling me Downloaded data is corrupt,
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Hi Rohit,
you might be interested in the following paper:
Buried chloride stereochemistry in the Protein Data Bank
BMC Structural Biology 2014, 14:19
doi:10.1186/s12900-014-0019-8
http://www.biomedcentral.com/1472-6807/14/19
Best,
Oliviero
On Tue, January 20, 2015 10:53, Eleanor Dodson
Having configured my CentOS-7 workstation for Stereo today, I have also updated
the Stereo article in the CCP4 wiki (
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo ). It turns
out that there seem to be 8 active monitors (i.e. built-in emitter) that can be
bought in Germany
Dear All,
I wonder if you could help me with this. I am trying to do some
regularisation/real space refinement of a ligand with Coot. The ligand is a
pseudopeptide with two non-standard aminoacids, followed by several standard
ones. I assume that to do this correctly, I would need a cif file
On 20/01/15 15:32, ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ wrote:
Dear All,
I wonder if you could help me with this. I am trying to do some
regularisation/real space refinement of a ligand with Coot. The ligand is a
pseudopeptide with two non-standard aminoacids, followed by several standard
ones. I assume
Hi Emmanuel,
I've never tried something quite as complex as a pseudopeptide but if you can
build your lingand in the coot ligand builder coot will generate a cif file for
you. Previously I have built my ligand, used real space refinement to get it
into position, merged the protein and ligand
Dear Emmanuel,
Is the modified residues are really new, you can make restraint files with
jligand or acedrug (both in CCP4). Make sure the backbone atoms have the same
names as in standard amino acids. Now open de cif-file(s) in a text editor and
set the residue type to 'peptide' (you can use
Hi Emmanuel,
Additionally you can also use the PRODRG server straight away and just
pipe in the coordinates for your peptide and it will give you one cif file
for it.
Cheers,
Karim
##
Karim Rafie; M.Sc.
PhD research studentDaan van Aalten lab
MRC
Try each one, refine, compare resulting b-factors and bond lengths to
surrounding atoms. It’s a chloride though.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li
Sent: Tuesday, January 20, 2015 2:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride
I would say you cannot measure the diffraction pattern of a single
biological molecule accurately thus far, because biological molecules are
not strong scatters and can be damaged easily. For other molecules,
actually you can!
In high-resolution electron microscopy, the diffraction pattern in the
The question is, as I rephrased it, assuming we are able to measure the
diffraction pattern of a single molecule with acceptable accuracy and
precision (comparable to what we have now for the common crystals), is it
better than we measure the diffraction spots from a crystal, given that the
Dear Steven,
Thank you for your reply! I understand that it is nearly impossible to
measure the diffraction of a single molecule, and I am just bringing this
up as a thought experiment to help understand the basics in
crystallography. But I never thought that some molecules actually allow
such
Dear All,
Real space refinement in COOT is one important strategy to reduce Ramachandran
outlier, right?
Dialing
Hi Jacob,
Thanks a lot for your reply! Yes, by comparable data quality I did mean the
comparable resolution and SNR. I now understand the original question and
kinda confirm what I thought. But I am also learning myself and I don't
quite get why the continuous sampling would get rid of the phase
On Tuesday, 20 January 2015 10:18:35 PM Chen Zhao wrote:
Dear all,
I am sorry about this slightly off-topic question. I am now a graduate TA
for crystallography course and one student asked me a question that I
didn't ask myself before. I don't have enough knowledge to precisely answer
this
Hi Rohit,
If it is of some significance you may consider replacing NaCl with KI or NaI in
your crystallization condition and collect a dataset at 1.5-2 Angstrom. The
Iodide anomalous signal might be of some help for identifying Chloride binding
sites.
Without further evidence for a Cl ion,
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