Dear all,
I have installed ccp4 with the dmg package, and everything is installed nicely
in the Application folder, and I can get ccp4i working just by launching from
the ccp4 icon.
However, I would also like to have the commands working from a X11 terminal, to
get it working for, say xia2.
How
sometimes， a little bit change of concentration of your precipitate or pH
buffer can affect your crystal.
My suggestion is setup a appropriate gradient of your precipitate and additive.
Hi Klaus,
that's pretty much the point.
With the .dmg install, there are no "setup" files coming.
I know I could use fink and Bill Scott's way to install the package, and have
everything running, but was wondering if it would have been possible with the
.dmg installation, much faster and intuiti
Charles and Guillermo, thanks a zillion.
Shame on me, I could't find the scripts!
Well, it'll be good to have already v. 6.2 ...
ciao,
s
On May 3, 2011, at 11:26 AM, Charles Ballard wrote:
> Hi Sebastiano
>
> you open an X11 windows, then source
> /Applications/ccp4-6.2.0/bin/ccp4.setup-sh
Hello all:
I am trying to generate a cif file for a new ligand using PRODRG server. The
server generates cif file without any problem. The problem comes when I try to
load the cif file in Coot and try to model the ligand into the electron
density.
It gives an error message like this..
-
On 03/05/11 14:08, Nalam, Madhavi wrote:
Hello all:
I am trying to generate a cif file for a new ligand using PRODRG server. The
server generates cif file without any problem. The problem comes when I try to
load the cif file in Coot and try to model the ligand into the electron density.
It giv
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Dear Friends,
I have noticed an issue in a pdb file, the term "insertion code".
Does anyone know anything about it? what is it used for?
Thanks in Advance,
Jahan Alikhajeh, Ph.D,
Technical Supervisor,
MAN Corporation LTD,
Keshavarz Boulevard,
Ghods Avenue No. 41,
5th Floor, Tehran,
I suggest that you go to the PDB web site and look through
the format documentation for the description of ATOM records.
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=
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On Tue, 2011-05-03 at 13:27 +, Jahan Alikhajeh wrote:
> term "insertion code".
> Does anyone know anything about it? what is it used for?
It may be used to follow Wu&Kabat numbering for antibodies. Frankly, it
it is something that can be easily avoided (after all, 32A is simply the
33rd resi
what is the difference simulated annealing map and how can i generate it
haytham wahba
Ph.D student
Biochemistry Dep
UdeM
Hi All,
I was wondering if anyone had troubles with PES
(Polyethersulfone)
ultrafiltration membrane filters (Vivaspin, Amicon,...) using 5
mM DTT
containing buffer. It seems whether or not it is possible for
DTT to react with
sulfone g
Hi,
what is the difference simulated annealing map and how can i generate it
>
- difference map is a Fourier synthesis i*Fo-j*Fc, where i and j are some
weights, and Fo and Fc are observed and calculated amplitudes of structure
factors;
- "difference simulated annealing map" is the above map c
My understanding is that it was introduced for cases where an error in
the sequence was discovered long after a large body of literature had
accumulated for the "wrong" sequence. That is, imagine some enzyme
where an important catalytic active site residue was number "152", and
lots of peopl
Hi James,
The concept of insertion code arose when one species
was sequenced and studied and then it turned out that there
were both insertions and deletions in the sequence of the
analogous molecule for some other species.
In analyzing and discussing structure, e.g. the catalytic
tr
James, interesting that you chose residue number 32 for your example,
because that is the number of one of the two active-site ASPs in the
aspartic proteinase family (the other is ASP 215) that I (with Tom
Blundell & others) worked on for many years. So Ed, it's not just
relevant to the "Wu&Kabat
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Just giving this thread a title.
James
On May 3, 2011, at 10:06 AM, Ian Tickle wrote:
> James, interesting that you chose residue number 32 for your example,
> because that is the number of one of the two active-site ASPs in the
> aspartic proteinase family (the other is ASP 215) that I (with T
On Tue, 2011-05-03 at 18:06 +0100, Ian Tickle wrote:
> So Ed, it's not just
> relevant to the "Wu&Kabat numbering for antibodies".
Obviously, it was meant to be an example of use, not the only example.
> The idea that
> one would _not_ use consistent numbering (and therefore insertion
> codes)
Israel,
Here is a paper that describes a phenomenon like what you have observed:
Structure. 2003 Feb;11(2):139-45.
Dehydration converts DsbG crystal diffraction from low to high resolution.
Heras B, Edeling MA, Byriel KA, Jones A, Raina S, Martin JL.
And another review that touches briefly on t
Dear All
I tried to make a stereo picture using Raster3D installed on a linux box with
the following command:
stereo3d -tiff xxx.tif < xxx.r3d
but got an error message:
stereo3d: normal3d seems to be OK
stereo3d: rendering left eye view
stereo3d: rendering right eye view
stereo3d: joining left a
On Tuesday, May 03, 2011 02:00:26 pm jie liu wrote:
> Dear All
>
> I tried to make a stereo picture using Raster3D installed on a linux box with
> the following command:
> stereo3d -tiff xxx.tif < xxx.r3d
>
> but got an error message:
> stereo3d: normal3d seems to be OK
> stereo3d: rendering lef
Dear all, I know I could use your help to work more effectively so here
comes my questions.
I am building a fairly long polypeptide chain (quite a few hundreds of aa)
in Coot. I got the phases from Phenix, which traced much of the main chains
for me already, with each fragments assigned with numbe
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