i should rtfm but don't you just need a mask per domain?
On 16 May 2012 22:54, Yu Feng yufengc...@gmail.com wrote:
Hi Eleanor,
If you have a large protein and want to apply different ncs operations to
different domains, then you might need to give multiple masks and matrices.
Yu
On
Dear All
I have one query, i have solved one structure where in which near cys
residues i can see density for beta mercaptoethanol (which i have used in
my crystallization cocktail ). i have one query when i am taking BME from
coot library, i can fit it in density but i do not know how to make
Hi,
I think you'll find the Jligand tutorial on the York site very helpful in that regard. It's well worth trying.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone:
Dear all,
in Fedora 15 I am having troubles to get the .plt outputs drawn.
The complaint is
Using CCP4 programs from /protein/ccp4-6.2/ccp4-6.2.0/bin
xplot84driver: error while loading shared libraries: libXaw.so.7:
cannot open shared object file: No such file or directory
libXaw.so.7 is in the
On 17/05/12 11:44, Jan Dohnalek wrote:
Dear all,
in Fedora 15 I am having troubles to get the .plt outputs drawn.
The complaint is
Using CCP4 programs from /protein/ccp4-6.2/ccp4-6.2.0/bin
xplot84driver: error while loading shared libraries: libXaw.so.7:
cannot open shared object file: No such
On 17/05/12 11:44, Jan Dohnalek wrote:
Dear all,
in Fedora 15 I am having troubles to get the .plt outputs drawn.
The complaint is
Using CCP4 programs from /protein/ccp4-6.2/ccp4-6.2.0/bin
xplot84driver: error while loading shared libraries: libXaw.so.7:
cannot open shared object file: No such
On 17/05/12 14:48, Ed Pozharski wrote:
On Thu, 2012-05-17 at 14:13 +0530, Faisal Tarique wrote:
to make disulphide bond ie to connect cysteine with bme
While I believe that CYS+BME is a correct choice ideologically (you had
cysteine and bme reacted with it), note that you can use CME monomer
On Thu, 2012-05-17 at 15:12 +0100, Paul Emsley wrote:
In Coot 0.7, to draw a bond between monomers that don't have an
implicit
connection due their serial number, you need a LINK record. You can
add
a LINK using Extensions - Modelling.
Thanks - is there some way to remove the link
Dear All;
Thank you very much for your comments and advices.
My protein is homo-tetramer. Based on difference density, only one cysteine
(among the four catalytic cysteins) has observed two positive density along
SG-group. This one could be modeled into OCS, while the rest will be
modeled as
Dear All:
I try to convert the .cif files (the structure factor files from PDB) to
mtz file.
From ccp4i, I chose convert to/modify/extend mtz for this purpose.
But program keep complanining:
no cell information in keywords or files
I open the .cif file in text, and could not find any
Maybe it's including covert structure factors? See recent ccp4bb post
subject...
JPK
On Tue, May 15, 2012 at 4:28 PM, case c...@biomaps.rutgers.edu wrote:
On Tue, May 15, 2012, Toth, Eric wrote:
In sports, maximal effort is considered to be 110%, so you're actually
9.9% short of getting
Reflection cif files from the PDB do not always have cell and symmetry
information in them, particularly the older ones, and it sounds like this is
your case.
In that case, you need to manually copy the cell information from the PDB web
page into the ccp4i interface before running.
HTH
Martyn
It works!
Thank you very much
Uma
On Thu, May 17, 2012 at 3:16 PM, martyn.w...@stfc.ac.uk wrote:
Reflection cif files from the PDB do not always have cell and symmetry
information in them, particularly the older ones, and it sounds like this
is your case.
In that case, you need to manually
It would be desirable to actually HAVE the cell information in the cif file,
if simply for assuring/checking consistency between model and data.
Maybe something for the PDB to contemplate
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
I am not familiar with CNS restraints, but whatever the program restraints
are - if you do a omit map, or just set the occupancies of the metal and
its surroundings to 0.00 and do a few cycles of refinement, I believe any
model bias will disappear and what you see will be pretty accurate
On 17 May 2012 21:27, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
I am not familiar with CNS restraints, but whatever the program restraints
are - if you do a omit map, or just set the occupancies of the metal and
its surroundings to 0.00 and do a few cycles of refinement, I believe any
Hi,
there are two points in Herman's post that I'd like to comment upon:
1) in case of XDS, there are two modes of reporting the completeness: one is
triggered with FRIEDEL'S_LAW=TRUE, and the other with FRIEDEL'S_LAW=FALSE.
Obviously the reported completeness will differ between these two
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Department of Biochemistry,
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On 17/05/12 15:29, Ed Pozharski wrote:
On Thu, 2012-05-17 at 15:12 +0100, Paul Emsley wrote:
In Coot 0.7, to draw a bond between monomers that don't have an
implicit connection due their serial number, you need a LINK record. You can
add a LINK using Extensions - Modelling.
is there some
On 17/05/12 20:16, martyn.w...@stfc.ac.uk wrote:
Reflection cif files from the PDB do not always have cell and symmetry
information in them, particularly the older ones, and it sounds like this is
your case.
My understanding is that these days they should have - and if you find
such
Hi Eleanor,
You are right, I just need a mask per domain.
In my case, the protein has more than 10 domains, and I want to input their
masks at the same time. It seems that I have to re-compile DM to run large
proteins.
Yu
On Thu, May 17, 2012 at 4:38 AM, Eleanor Dodson
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