Dear all,
the following is been sent on behalf of Prof. Tzartos and all inquiries
should be send to him.
Postdoc protein crystallographer in Greece
A postdoctoral position for a protein crystallographer is immediately
available at the Laboratory of Molecular Neurobiology and Immunology,
There is also a CCP4 prog that compares phase sets,
phistats. Don't know if this does what Phil suggests.
Adam
On Wed, 29 Aug 2007, Phil Evans wrote:
Kevin
Does this give the correlation between two (weighted) complex Fs,
which is arguably (ref Bricogne) the best measure, as it
I'm going to agree with Raji's observations, and fan the flames of his point
a little.
I count myself as lucky that I have had access to certain people during my
crystallographic training who had a good understanding of the theory behind
crystallography (hopefully I have exploited this luck
You could simply hand-edit the PDB file to remove the offending ligand.
Regards,
Tony.
Hi, all
I want to write a specific chain structures(protein). I tried PDBSET and
biopython but they couldn't deal with some exceptional case.
For example, some pdb files contain both protein
If your PDB file conforms to standard
http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
you could do
% egrep ^CRYST|^SCALE|^ATOM your.pdb standard_residues_only.pdb
You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)
Clemens
On Thu, Aug 30, 2007 at 11:22:29PM +0900,
flame
As an aside, does anyone understand why MSE is not an amino-acid?
Phil
/flame
On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote:
If your PDB file conforms to standard
http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
you could do
% egrep ^CRYST|^SCALE|^ATOM your.pdb
On Thu, Aug 30, 2007 at 05:43:35PM +0900, Hyunchul Kim wrote:
Hi, all
I want to write a specific chain structures(protein). I tried PDBSET and
biopython but they couldn't deal with some exceptional case.
For example, some pdb files contain both protein structure and ligand
structure in a
Sure -- PyMOL can be used as a command-line tool to do stuff like this.
pymol -qc input.pdb -d 'remove not polymer;save prot_only.pdb'
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Hyunchul Kim
Sent: Thursday, August 30, 2007 7:25 AM
To:
All you need it this pymol script for one molecule, or adapt it for more pdbs
(I might have missed an aa or you may want to include non-standard ones).
open mol.pdb
select
TRP+HIS+MET+ALA+GLY+PRO+CYS+LYS+TYR+ALA+ILE+VAL+LEU+SER+THR+ASN+ASP+GLN+GLU+PHE+ARG/
save path/mol_out.pdb,(sel01)
Hope
Dear all
I am trying to purify HSP from C.trachomatis,a 57kDa protein for
crystallization.The yield is very good.The problem is autodegradation and
precipitation.I never reached to 1.5mg/ml concentration.There is a His-tag
at C-ter.I appreciate all the suggestins regarding get rid of at least
% egrep '^CRYST|^SCALE|^ATOM|^HETATM.{11}(MSE|PTR|SEP|TPO)' your.pdb
standard_residues_only.pdb
I think the original request was to extract particular chains, so
extending the above further to select (say) chain A
egrep '^CRYST|^SCALE|^ATOM.{17}A |^HETATM.{11}(MSE|PTR|SEP|TPO) A' your.pdb
Dear Shivesh,
Try some buffer screening.
If you have a real-time PCR machine nearby you can easily screen
96 buffer conditions in about an hour.
Check out:
Ericsson et al. Analytical Biochemistry 2006 Aug;357(2):289-98
Best regards,
Martin
On Aug 30, 2007, at 6:06 PM, shivesh kumar wrote:
One more comment on MSE: Does anyone know why MSE was defined without a
'delta' on the selenium? Isn't that obviously wrong? Selenium-delta
should be SED , just like S-delta is SD , so it can't be left off
just because selenium is not a carbon.
Phil Evans wrote:
flame
As an aside, does anyone
Hi,
- I think someone already pointed out that you should try P6522.
- check that it isn't really a twinned P61 or P65 with 2 per asymmetric unit
- buy DNA with BrdU and some more with IdU, and/or grow your protein
in SeMet - at your resolution, the more real phase info the better!
Phil
If MSE were described with ATOM cards then rasmol and other graphics programs
would display it in a sensible manner. This would be contrary to wwPDB policy
which is to make coordinates C++-friendly rather than human-useable.
Pete
Pete Artymiuk
Quoting Phil Evans [EMAIL PROTECTED]:
flame
ALMN will do this ..
It does not have a GUI - Gr
#!/bin/csh -f
#
almn \
hklin /y/people/ccp4/projects/insmon/ins_p1_1,55A-I422cell.mtz \
hklin2 /y/people/jean/Youshang/monomeric/datproc/*mtz eof
CROSS 15
resol 10 3
CRYSTAL FILE 1 ORTH 1
LABIN FILE 1 F=F_P1 SIGF=SIGF_P1
CRYSTAL FILE 2
This is a pre-announcement for the annual CCP4 Study Weekend meeting to be held
the 3rd, 4th and 5th of January 2008 at The University of Leeds, Leeds UK.
Registration will start on the 10th of September via the Study Weekend website
- the website is not yet live but the link will be included
Job Title: Molecular Virologist
Employer: Centers for Disease Control and Prevention (CDC), Molecular Virology
and Vaccines Branch, Influenza Division; Atlanta, GA
Date: 30 August 2007
Job Description:
The Molecular Virology and Vaccines Branch is recruiting outstanding scientists
to join
Kim Henrick wrote:
A standard amino acid is a gene product
with a specific t-RNA.
Isn't it arguable that Met-tRNA is no more specific for S-Met than for
Se-Met, it's just a matter of what the organism has been eating?
Cheers,
Charlie
--
Charlie Bond
Professorial Fellow
University of Western
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