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
wrote:
> i should rtfm b
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 examples
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 wa
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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
On 17 May 2012 21:27, Eleanor Dodson 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
> model bias will disappe
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
descriptio
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
m
It works!
Thank you very much
Uma
On Thu, May 17, 2012 at 3:16 PM, 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 copy the cell info
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
Maybe it's including "covert structure factors?" See recent ccp4bb post
subject...
JPK
On Tue, May 15, 2012 at 4:28 PM, case 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 everything you cou
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 info
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 non-
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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
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
(
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 file or directory
l
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
(it's listed as peptide in monomer librar
Hi Faisal,
Please read this thread:
http://www.mail-archive.com/coot@jiscmail.ac.uk/msg00645.html
BTW, I had a look at my CCP4(6.2.0) and COOT lib files, it seems the CYS-BME
link is not in the mon_lib_list.cif file yet. Instead, I have two MPR-CYS links:
MPR-CYS MPR ..CYS
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 f
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 f
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 s
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 t
> Your implied question seems to be "How do I know whether my MSA is
> good?" Errors in MSAs arise from two factors. ...
The correct multiple alignment would be the actual reconstruction of the
evolutionary relationship of the sequences concerned. This may not be the
optimal alignment of the p
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
di
i should rtfm but don't you just need a mask per domain?
On 16 May 2012 22:54, Yu Feng 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 Wed, May 16, 2
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