Yuri wrote:
Hello Everyone,
A little off topic but, what is a good way to show (publication
quality) multiple sequence alignment?
I am trying to show conserved regions in related proteins from
different organisms.
Thank you
--
Yuri Pompeu
or clustalw, e.g.
http://npsa-pbil.ibcp.fr/cgi-bin/ali
Hi Suda,
You can do this in Coot by loading the two structures, then using the tool
Calculate-> SSM superpose.
The rmsd value and sequence identity should be reported within your terminal
window.
Hope that helps.
-Joe
Date: Thu, 18 Aug 2011 14:40:32 +0530
From: biobud...@gmail.com
Subje
Use ALINE sequence editor. if you multiple sequence alignment file from
clustalW, you can open in ALINE software and generate publication quality of
image.
http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/
--- On Thu, 18/8/11, Yuri wrote:
From: Yuri
Subject: [ccp4bb] Sequence Alignm
Dear all,
I am trying to crystallize a protein for which the yield and solubility were
both fine. However, this protein has a severe problem of degradation. When
stored at RT, the protein will degrade madly into pieces, while stored at 4
degree, the degradation is much slower and a relatively
For anything other than the most intensive I/O operations, recent processors
will give you very respectable performance.
I don't encrypt whole drives but I do have some AES-encrypted disk images in
Snow Leopard, and I get about 38 MB/sec throughput copying (using cp) and 60
MB/sec reading (whil
Hi all,
I was wondering with the all of the advances in microbeam technology and
hardware, what is the best methods for cryoprotecting microcrystals? Are
oils better than solutions? How do you address the excess liquid issues? Is
there a way to test the conditions prior to shipping it off to the
s
You can try this site:
http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi
If you have .pdb for one of your sequences, you'll be able to show secondary
structure also.
vitali
On Thu, Aug 18, 2011 at 6:31 PM, Yuri wrote:
> Hello Everyone,
> A little off topic but, what is a good way to show (pub
On 08/18/2011 09:34 PM, Andreas Förster wrote:
Since we're on the subject... I've been tempted on and off to encrypt my
hard drive, but after getting burned once a hundred years ago when
encrypted data turned into garbled bytes all of a sudden I've been
hesitant. I've gone so far as to install Tr
Hello Everyone,
A little off topic but, what is a good way to show (publication
quality) multiple sequence alignment?
I am trying to show conserved regions in related proteins from
different organisms.
Thank you
--
Yuri Pompeu
OS X 10.7 enables you to do whole-drive encryption.
Here is a description from Arse Technica:
http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13
I ain't never tried it myself. 10.7 seems to run slow enough as it is.
-- Bill
On Aug 18, 2011, at 5:34 AM, Andreas Förster wrote:
Dear Colleagues,
Thankyou for your detailed, and prompt, helpful advice on this issue, which I
much appreciate.
I see that I have overestimated my anxieties but should probably still move a
little cautiously.
Thus I will first suggest to my IT encryptors' taskforce, for want of a better
term,
Hi all,
As part of its recent summer update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) introduced PDBeXpress (http://pdbe.org/express), an umbrella
name for a set of easy-to-use yet powerful PDB analysis tools. The first two
modules can be used to answer questions such as "what r
On Thursday, August 18, 2011 08:19:13 am G Y wrote:
> Dear all,
>
> I am a student in crystallography. So not quite familiar with some even
> basic concepts.
>
> In shelx .hkl file or ccp4 .mtz file there is a column SIGF which is related
> to standard deviation of the structure factor. I read t
On Thu, 2011-08-18 at 17:23 +0100, WENHE ZHONG wrote:
> Dear all,
>
> I would like to show the visible metal-residue interaction during the
> Morph movie. Anyone knows how to do that in Chimera? Thank you.
>
> King regards,
> Wenhe
>
IIUC, you have worked out how to generate the morph traject
Hi,
You'd be better off sending this query to the Chimera BB:
chimera-us...@cgl.ucsf.edu
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer
Dear all,
I would like to show the visible metal-residue interaction during the Morph
movie. Anyone knows how to do that in Chimera? Thank you.
King regards,
Wenhe
Check out Theseus: http://www.theseus3d.org/
You will need a sequence based alignment. This alignment can be provided
automatically by muscle if you have it installed
(http://www.drive5.com/muscle/)--this is different from pymol. Pymol seems to
do an SVD to obtain the alignment. I'm not up to d
Dear CCP4
There is a bug in the ccp4i interface to prodrug on both linux and windows.
There is a title line that is read in to the command file which means the
software does not run
Unrecognised keyword.
This can be removed using the run and view com file option
However on windows I then get the
You can do structure based sequence alignments using STRAP. It's java based
and free.
On Aug 18, 2011 5:20 AM, "Suda Ravindran" wrote:
> Dear all,
>
> I would like to know the tools/servers/programs that can be used for
> structure based superposition of two or more proteins. Please help me
> out.
Hi Shilong,
On Thu, Aug 18, 2011 at 5:55 AM, Shilong Fan wrote:
> normaly you can do it in the pymol. In the main interface, on the left menu,
> there is a:"A" button, click it, then looking for "Aliagn". Then you can do
> it.
>
> But I prefer to use CCP4, in CCp4 there is a tool : Superpose. Y
Dear all,
Thanks a lot helping me out. I shall try it out... :)
-Suda
On Thu, Aug 18, 2011 at 3:52 PM, Phil Evans wrote:
> ... and in ccp4mg
>
> On 18 Aug 2011, at 10:55, Shilong Fan wrote:
>
> > normaly you can do it in the pymol. In the main interface, on the left
> menu, there is a:"A" butt
Dear all,
I am a student in crystallography. So not quite familiar with some even
basic concepts.
In shelx .hkl file or ccp4 .mtz file there is a column SIGF which is related
to standard deviation of the structure factor. I read through many text book
for crystallography, there are many formulas
What software do people on the bb use for encryption? What can be
recommended without hesitation?
I've had no problems with TrueCrypt, which I've been using on linux and
OS X for ~4 years (for personal systems, not lab ones). But I haven't
used it for storing files I've been doing anything I
Since we're on the subject... I've been tempted on and off to encrypt
my hard drive, but after getting burned once a hundred years ago when
encrypted data turned into garbled bytes all of a sudden I've been
hesitant. I've gone so far as to install TrueCrypt (on a MacBook), but
I haven't put i
John,
Since so many people have said it's flawless, I'd like to point out this is not
always the case. The particular version of the particular package that we have
installs some system libraries that caused a program I use on a moderately
frequent basis to crash every time I tried to open a f
On 18 Aug 2011, at 09:29, Eric Karg wrote:
> Thanks Huw. Unfortunately I have the same problem when using the new
> libraries. Maybe it has something to do with the pdb file (output from
> Phaser) I'm trying to refine. Do I have to rename the residues in the pdb
> file or is there another trick
The Schaffitzel laboratory at the European Molecular Biology Laboratory (EMBL)
Grenoble, France seeks to recruit outstanding postdoctoral scientists in
structural biology. We study the structure and function of large macromolecular
complexes in gene expression. The project involves structure de
On 18 Aug 2011, at 09:29, Eric Karg wrote:
> Thanks Huw. Unfortunately I have the same problem when using the new
> libraries. Maybe it has something to do with the pdb file (output from
> Phaser) I'm trying to refine. Do I have to rename the residues in the pdb
> file or is there another trick
... and in ccp4mg
On 18 Aug 2011, at 10:55, Shilong Fan wrote:
> normaly you can do it in the pymol. In the main interface, on the left menu,
> there is a:"A" button, click it, then looking for "Aliagn". Then you can do
> it.
>
> But I prefer to use CCP4, in CCp4 there is a tool : Superpose. Y
Dear All
The following is part of a pdb file for a protein containing two galactose
molecules.
In this form programs like Accelerys using the Hierarchy facility selects the
two galactoses
in the same operation. Does anyone know how they could be labelled so that they
can be selected individuall
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello Suda,
You can use
- - lsqkap
- - lsqman
- - tools available in coot
- - pymol
- - probably something like phenix.superpose ...
Cheers, Tim
On 08/18/2011 11:10 AM, Suda Ravindran wrote:
> Dear all,
>
> I would like to know the tools/servers/pr
normaly you can do it in the pymol. In the main interface, on the left menu,
there is a:"A" button, click it, then looking for "Aliagn". Then you can do it.
But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine any
region you want to do superpose.
Dear all,
I would like to know the tools/servers/programs that can be used for
structure based superposition of two or more proteins. Please help me
out..!!
Thanks,
-Suda
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Eswar,
you can not only alter the protein concentration but also the
precipitant concentration. If your protein really is soluble before you
set up the crystallisation trials, you are bound to find a condition
without crystals by lowering the pre
Dear All
I was working two domain protein and i have an hexagonal
look like crystals from additive screen, now i am facing problem these
crystal are growing in 2 minutes even in cold room even at lower protein
concentration @2mg/ml . and i have an smeary data of 7 Å, and we
Thanks Huw. Unfortunately I have the same problem when using the new libraries.
Maybe it has something to do with the pdb file (output from Phaser) I'm trying
to refine. Do I have to rename the residues in the pdb file or is there another
trick?
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Or a USB-stick with the key, but in this case don't get your laptop
being stolen with the USB-stick near-by ;-)
Tim
On 08/18/2011 03:26 AM, Francois Berenger wrote:
> [...]
> Another minor drawback is that you will possibly need a password to boot
>
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear John,
encrypted disks are completely transparent once the system is up and
running. The only issue will be a slow-down for disk I/O intense
operations, e.g. copying a large amount of data takes noticably longer
on an encrypted disk - but not too
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