Dear Rajesh,
We found that LLP has a single bond between C4' and Nz which is not
correct for internal aldimine form of PLP. Please use IT1 from RCSB.
IT1 also has similarly linked PLP and Lys with the correct double bond.
For some other PLP schiff base complexes there are multiple entries in R
Dear Rajesh,
You do not need to define a link between Lys and PLP: PLP linked to Lys
is LLP. You can find examples in PDB. LLP is recognized by Phenix and
Refmac.
Kind regards,
David
On 07/23/2012 07:30 PM, Rajesh Kumar wrote:
> Dear All,
>
> My friend needs a help.
> What is the best way to conne
On 23/07/12 22:46, meisam nosrati wrote:
Dear CCP4ers
It seems like the text has not showed up, but I have a problem with
making pdbs from coot. As I refine my structure ( with MR solution )
the beta sheets become loops while H-bondings are still there.
I am not sure, if the problem is origi
Thanks for the inputs from Markus, Kim, and a local friend. Per Jacqueline's
request, here is a short list of capable services.
1) James Nathlar, Hopeful, Inc, j...@nathlar.com. Jim is happy to help out,
and he is in DC area.
2) ATG Service, Analytical Technologies Group, Ph: 860-449-0886. Jodi Dw
Dear CCP4ers
It seems like the text has not showed up, but I have a problem with making
pdbs from coot. As I refine my structure ( with MR solution ) the beta
sheets become loops while H-bondings are still there.
I am not sure, if the problem is originating from making PDBs from coot.
I will app
> you'll see that some of them are arranged in regular lines.
I am not sure I understand what the line argument implies?
>indicates a very small unit cell, with dimensions probably < 10 A
Very indicative also the few strong and isolated high resolution reflections
Cheers, BR
Dear Zhao -
This is a salt crystal. You do have spots, even if some of them are
streaky, and if you look carefully, you'll see that some of them are
arranged in regular lines. However, there are very few, and no spots
below about 6 A. This indicates a very small unit cell, with dimensions
Dear Rajesh
tutorial on this website is designed exactly for PLP-LYS links
http://www.ysbl.york.ac.uk/mxstat/JLigand/index.html
regards
Garib
On 23 Jul 2012, at 18:30, Rajesh Kumar wrote:
> Dear All,
>
> My friend needs a help.
> What is the best way to connect Lys to PLP with covalent bond
Hi All,
Thanks for the all the advice on my previous question regarding the likely
photo-reduction of my crystals.
I've now collected a data set on these crystals. The protein is a chimera of
two domains of known structure (Ferredoxin domain and Colicin domain), what's
the best way to use all
Dear CCP4BBers:
Sorry to bring up this highly repeated topic again. After some internet
research, we are about to make the commitment to buy an LG D2342P-PN for
setting up a stereo system. I would like to have a final confirmation from
someone with real life experience that this model does work
Scott,
you are asking for opinions when you should be asking for hard data.
CNS, refmac and phenix all can regularize a structural model. If your
primary consideration is speed, you should simply try all three and
compare cpu time.
Cheers,
Ed.
On 07/23/2012 12:50 PM, Scott Foy wrote:
He
Link statement?
LINK NZ LYS A 72 C4A PLP A 500 1555 1555
1.30
There are many examples in the PDB this one 1hkv
Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh
Kumar
Sent: Monday, July 23, 2012 10:30 AM
To: CCP4BB@J
Dear All,
My friend needs a help.What is the best way to connect Lys to PLP with covalent
bond.I am sure there are many ways do it. My friend would appreciate if you
could simplify and explain this so that he could learn it without difficulties.
Also I could learn
I appreciate your time and hel
On Mon, Jul 23, 2012 at 9:50 AM, Scott Foy wrote:
> We are computationally averaging several homologous protein structures into a
> single structure. This of course will lead to a single protein structure that
> possesses poor biophysical characteristics of bond lengths, bond angles,
> steric h
Hello Everyone,
We are computationally averaging several homologous protein structures into a
single structure. This of course will lead to a single protein structure that
possesses poor biophysical characteristics of bond lengths, bond angles, steric
hindrance, etc. Therefore, we will need a r
Hi Faisal,
It looks like your restraints are simply not tight enough. Try optimizing
the restraint weight. You should also run more cycles of refinement to make
sure it converges.
The initial gap between R and R-free is pretty small. Did you do much
refinement before this run?
Cheers,
Rob
Hi Theresa,
If you load both of the proteins in Coot, you can align/superpose them using
least squares fit over a specific residue range. The rmsd will be listed in the
terminal window if you scroll up a bit. Hope this helps.
- Greg
Dear all
i have two basic queries
1> while refining my structure (of resolution 2.2A) i face problem with the
gap in R & Rfree which is around 8. The mosaicity of my data is 1.8. is
this difference is due to large mosaicity or twinning though for twinning i
got nothing when i checked with Xtriag
Dear Theresa,
You could use Gesamt from CCP4 6.3.0, which will align a given range of
residues in one protein onto a range of residues from another protein. Just run
$CCP4/bin/gesamt for usage instructions and selection syntax, or use Structure
Superposition from CCP4i.
Best,
Eugene
On 23 J
One of many possible ways is to use rms_cur command in pymol.
But fundamentally such number is meaningless, since root mean square
deviation is only useful when the average shift between the two
structures is (close to) zero.
On 07/23/2012 11:06 AM, Theresa Hsu wrote:
Dear all
I have two p
Dear all
I have two proteins in PDB each with two subunits. One of the subunits can
align well in both. How do I calculate rmsd for the aligned subunits and the
other non-align subunits *separately*?
Thank you.
Yes we have just contacted Rex & he's nowhere near Spain.
Cheers
-- Ian
On 23 July 2012 12:14, Mark Williams wrote:
> This is almost certainly a scam…
>
> http://www.guardian.co.uk/money/2011/oct/07/email-fraud-wrecking-charity
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Beh
I think that this is the most important bit of gobbledygook
freeglut (./coot-real): OpenGL GLX extension not supported by display ':0.0'
My guess is that you've updated your OS, updated your kernel or changed
your graphics card. The solution is to install/re-install a driver that
provides O
Dear All (possible candidates!),
A 3 year PhD fellowship is available to a suitable candidate for one of the
following projects involving molecular biology and structural biology
techniques:
Molecular characterization of the bio synthetic pathway of amylovoran, a
pathogenicity factor in Erwin
Thank you very much for the reply.
Actually, no water is observed to coordinate with the zinc ion in the
complex structure of the enzyme and a substrate analog. The complex
structure is determined at 2.3 Å resolution. Besides, in the complex
structure, the zinc ion is already coordinated to six at
This is almost certainly a scam…
http://www.guardian.co.uk/money/2011/oct/07/email-fraud-wrecking-charity
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of REX PALMER
Sent: 23 July 2012 11:39
To: ccp4bb
Subject: [ccp4bb] Urgent HelpREX PALMER
How are you doing ? This has
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello JS,
my guess is you need to (re-)install the libcanberra-gtk-module (how
to do this depends on you distribution - linux, I guess).
Cheers,
Tim
On 07/23/12 11:39, Jai-Shin Liu wrote:
> problem in coot, it can't work any more. the message is bel
problem in coot, it can't work any more.
the message is below:
How to fix it?
any help will be appreciated.
JS
(coot-real:2771): Gtk-WARNING **: Unable to locate theme engine in module_path:
"clearlooks",
tk-Message: Failed to load module "pk-gtk-module": libpk-gtk-module.so: cannot
open share
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