Hi,
Please try the following web based tool
to get a list of the water networks
in a given PDB file.
http://iris.physics.iisc.ernet.in/psap/
Please click on the option "Display water Bridges".
regards,
Sekar
> Dear all,
>
> I am looking for some software (computer program) that would take a
Dear all,
Here's another non CCP4 question: does anyone know a cheap alternative
to set up a UV source at 280 nm? I'd really like to have one :), but I
really don't have the $20K Dlls needed to buy a UV/white light source
from the crystallographic vendors :(.
Thanks so much in advance for yo
This may be obvious, but I would run a size-exclusion column on the complex
first. This will give you an idea as to how well these two proteins "stick"
together.
On Wed, May 14, 2008 at 4:34 AM, Maarten Dewilde <
[EMAIL PROTECTED]> wrote:
> Dear CCP4bb,
>
>
>
> Can anyone point me to good revie
Hi,
It would be nice if you mention more clearly how you have done
TLS..i.e.,domains or individual residues or molecules !! You should keep in
mind that you have 2.8A data. I would do TLSANL with domains or molecules.
Best regards,
Krishna Ch
PhD Student
Hannover Medical school
Germany
On Wed
Please note that qualified B.S. and M.S. level research associates are
invited to apply.
Structural Chemistry, Structure-Based Drug Design & Discovery
Novartis Institutes for BioMedical Research, Emeryville, California
Use your scientific expertise to aid us in our structure-bas
Dear Users,
The Berkeley Center for Structural Biology (BCSB) is pleased to
announce the launch of a Collaborative Crystallography Pilot
Program (CC) at the Advanced Light Source in Berkeley. Through
this program, scientists will be able to send protein crystals to BCSB
staff researchers for d
On May 14, 2008, at 12:28 PM, Mark Del Campo wrote:
At what refinement resolution or resolution ranges would you call a
structure "high resolution" vs.
"low resolution"? I realize that this may boil down to semantics
(e.g. some may classify structures as
"medium resolution"), but I wanted t
Hi David,
This has already been done with PyMOL. There's a video at:
http://molviz.cs.toronto.edu/molviz/
and the code is downloadable.
The stereo effect isn't so great with both eyes open, but I do think there is
potential for use of head or object tracking as a means of controlling rota
OK, so we weren't on this subject, and all of you are tired of me
asking. However, the following link came to me and I wanted to see some
programmers opinions on this one. The thing I'm wondering is, what
needs to be done on the programming end to make this something that we
could use in a cl
I think this is coupled with the data completeness. Say you have a data
50.0-1.0A resolution, but the completeness in say 3.0-1.0A resolution
range is equal to 10%, and it is 100% complete in 50.0-3.0A.
Pavel.
On 5/14/2008 12:28 PM, Mark Del Campo wrote:
At what refinement resolution or resolu
I don't think you can give a resolution range - you could argue that it
depends on molecular weight, i.e. high resolution for insulin and high
resolution for the ribosome are going to be very different numbers.
Other than that, my answer would be that you know it when you've got it
:)
Cheers,
Ed
At what refinement resolution or resolution ranges would you call a structure
"high resolution" vs.
"low resolution"? I realize that this may boil down to semantics (e.g. some
may classify structures as
"medium resolution"), but I wanted to get an opinion from the pros.
Hello all,
I have a structure that has a Ni coordinated by an Asp residue and
the backbone of two other residues. When I try to include Link
statements for this in my pdb, refmac fails and says that a new ligand
has been found.
I was wondering if anyone knew what proper tag for these intera
parkash wrote:
Hi,
I have one structural refinement problem.
I am working on a protein crystals which diffracted to 2.8 Å. But when
I refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get
high B-factors around 70. But if I do TLS refinement, the R-factors
lower down and B-fa
Vellieux Frederic wrote:
Dear all,
I am looking for some software (computer program) that would take a
full PDB file (including waters) and that would output a list of the
water networks (including the names of the atoms) at the surface of a
protein.
Thank you in advance,
Fred.
watertidy d
Kathleen Frey wrote:
Hello.
I am trying to refine a structure that has 2 ligand conformations as seen in
the electron density. I tried to put both conformations in Coot and format
the PDB similar to a residue alternate conformation and changing the
occupancies to 0.50 for each conformation. This
Hi Liz,
Yes, that's a smart solution. I will have a try on my own data.
Many thanks.
Anders
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Liz Potterton
Sent: 14. maj 2008 14:10
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Graphics software to show
Hello.
I am trying to refine a structure that has 2 ligand conformations as seen in
the electron density. I tried to put both conformations in Coot and format
the PDB similar to a residue alternate conformation and changing the
occupancies to 0.50 for each conformation. This formatting did not wor
Hi Anders and CCP4bb
Would something like
http://www.ysbl.york.ac.uk/~ccp4mg/index_info_5.html
(done with CCP4mg) be useful? In that image the molecule surface is coloured
by electrostatics (but could be any other property) and the contact area to a
ligand is indicated by dots on the surface.
Dear BBorders,
the lab is giving away a complete and perfectly functional Oxford
Cryosystems Cryostream 700 series.
For more information, please contact me outside the bulletin, please.
Best regards
Adriana Erica Miele
-
Adriana E. Miele, P
A few ideas:
1) go even higher with protein concentration. Some ultra-soluble proteins may
need >100 mg/mL. You may have to set up drops at higher ratios of
protein:precipitant to achieve this. e.g. 3:1 or more. Use a test such as the
Hampton PCT to tell you when you are in the right concentrat
Dear all,
I am looking for some software (computer program) that would take a full
PDB file (including waters) and that would output a list of the water
networks (including the names of the atoms) at the surface of a protein.
Thank you in advance,
Fred.
begin:vcard
fn:Fred. Vellieux (Ph.D)
n
Hi Raja
You can use a command-line script like this one:
#!/bin/tcsh
sed -e "/ATOM/ s/'/*/g" -e "/ATOM/ s/O5T/O3T/" -e "/ATOM/ s/ADE/ DA/g"
-e "/ATOM/ s/CYT/ DC/g" -e "/ATOM/ s/GUA/ DG/g" -e "/ATOM/ s/THY/ DT/g"
<$1>refmacok_$1
cat refmacok_$1|grep ATOM|more>/dev/tty
Save the script in a ne
Hi,
I have one structural refinement problem.
I am working on a protein crystals which diffracted to 2.8 Å. But when I
refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get high
B-factors around 70. But if I do TLS refinement, the R-factors lower
down and B-factors come down
I would suggest to open the wells, add some hefty precipitant
to the reservoir, and close the wells again.
The point is to drive the equilibrium further towards high concentration
by drawing more water into the reservoir.
It therefore does not matter what the supplemental precipitant is.
Concentra
Dear Colleague,
This is a gentle reminder of our call for beam time applications
at EMBL Hamburg that we circulated a few weeks ago.
We kindly ask you to complete your beam time proposal
by the deadline of ---> 16 May 2008 <
If you have already taken action, you can ignore this message.
--
Hi,
I have a structure with a metal beautifully coordinated by 3 water molecules.
However, every time I run automated water picking they get removed (due to
combination of being too close to metal/too deep in the density).
So far I've been manually reentering them into pdb but it becomes a
Dear CCP4bb,
Can anyone point me to good reviews or books which describe how to
crystallize protein-protein complexes (or anyone willing to share his/her
experience)? In particular I'm interested in:
(1) which tests to perform on your complex before you even start thinking
about crystalli
... your protein is the dream of any NMR spectroscopist. Small and
ultra-soluble.
Maybe just do the structure by NMR? It should be totally
straightforward for any NMR lab.
A.
On May 13, 2008, at 18:16, Jennifer Han-Chun Tsai wrote:
Hi,
This topic is not related to CCP4. I am having
Dear colleagues,
I am looking for a graphics software program that can make the
following, easily. Make a surface representation of a macromolecule.
That surface should be coloured according to some property. On, or
close to, that surface the outer rim of a binding epitope from a second
molecul
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