Hi Riya,
You'll need to install at least one of these programs for it to work.
What kind of operating system have you got? Clustalw/2 is about the
easiest to install and is available from here:
ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.11/
Let me know if you need any further help with i
Dear all,
I run refmac5 on TLS & restrained refinement mode. my pdb input file contain
anisotropic temp for the amino acid and isotropic temp for the cofactors and
water. The refinement parameters is set on mixed isotropic/ anisotropic temp
and in TLS parameters the check box add TLS contributio
Dear all,
thanks to everybody who offered their experience and hints.
The most convenient way of preparing a packing diagramme, at least for
me, was via PyMol as suggested by Michael Klein (see below).
One can do something similar with the CCP4 graphics package, but for
some reason the pro
Dear ccp4bb-people,
I would like to depict my protein with curved cylindrical helices
using PyMOL.
(I know and use bobscript "rod fitted" for this purpose and like it.)
Anyway, I wonder if anybody has a script or knows how to tell PyMOL
to follow the curvature of helices in the cylindrical
Hi Susanne,
On the Pymol menu go to Setting --> Cartoon --> Cylindrical Helices
Kianoush
--- On Thu, 8/27/09, Susanne Ressl wrote:
From: Susanne Ressl
Subject: [ccp4bb] curved cylindrical helices in PyMOL?
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday, August 27, 2009, 7:34 AM
Dear ccp4bb-peop
Actually, PyMOL cannot bend cylindrical helices. The workaround is to break
them manually:
load $PYMOL_PATH/test/dat/1tii.pdb
as cartoon
set cartoon_cylindrical_helices
# Insert a break into the longest helix (only slightly bent)
cartoon skip, C/216/CA
Cheers,
Warren
PS. This is the CCP4
On Thursday 27 August 2009, Elad Binshtien wrote:
> Dear all,
> I run refmac5 on TLS & restrained refinement mode. my pdb input file contain
> anisotropic temp for the amino acid and isotropic temp for the cofactors and
> water. The refinement parameters is set on mixed isotropic/ anisotropic tem
In the latest versions of refmac, it has a default selection of TLS
groups so that you don't need to create a TLSIN file. I believe this
default selection includes waters in the first hydration shell. You
should be able to override this with an explicit selection in TLSIN.
Cheers
Martyn
On Thu, 2
Dear All
Is there any easy to way write topology and parameter file for a cofactor with
specific conformation.
Thanks a lot
Sajid
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Hi,
I'll take the liberty of replying instead of Elad (my student) who probably
won't be back on the net till next week.
The feature/problem he reported seems most likely as a difference between the
linux and Windows version, unless there is also a difference between v 6.1.1
and 6.1.2 on that
I suspect that your question is CNS-related. Easy is relative, but what
you need to do is to uncomment the appropriate DIHEDRAL statements
(assuming that used xplo2d, they will be there but mostly commented
out). Just figure out what values you need for particular angles.
If it is wise to fix li
maybe a little offtopic, but I really need anotehr model buiding software that
can run on windows system ( I already have coot)
I am not a linux guy, I prefer running everything on my PC---I can run ccp4 and
coot on PC without any problem.
I found Alwyn Jones 's website, which has versio
Hello All,
I dug around on the net and found this method to remove lipids from
proteins:
"Wessel & Fluegge (1984), Anal. Biochem. 138:141-143. It´s a methanol/
chloroform precipitation and gives you a pellet that is easily
redissolved. The method was especially devised for removing lipids
Hi,
We have recently installed a new home source diffraction system using
MAR 345 dtb. It works much better than the rigaku because this new
device has automatic motor control system. However, we have a lot of
trouble to mount crystals. The magnet of MAR goniometer is
significantly weak
I dug around on the net and found this method to remove lipids from
proteins:
More precisely, from denatured proteins. That's what methanol/chloroform
phase does for most proteins.
"Wessel & Fluegge (1984), Anal. Biochem. 138:141-143. Itґs a methanol/
chloroform precipitation and gives you a
Dear Aidong,
there are some permanent magnet adapters, which you can get from
MAR or which you can make yourself. These help, especially with
your old pins.
Cheers, Manfred.
Quoting aidong :
Hi,
We have recently installed a new home source diffraction system
using MAR 345 dtb. It works mu
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