Dear Edward,
Thanks for your help.
Dr. Jayashankar Selvadurai
Hannover
Germany
On Fri, Jul 5, 2013 at 6:48 PM, Edward A. Berry ber...@upstate.edu wrote:
Right-click on the shortcut on your desktop, select properties, and see
what folder
it has for start in. Try changing it to C:/CCP4/6.3
:/CCP4/6.3/bin/ ; and open the
windows batch file ccp4i.bat , now after the gui pops-up now the module
shelxcde opens with no complains from the program list.
the problem is similar with when i try jligand.
Thanks
(Jay)
Dr. Jayashankar Selvadurai
Hannover
Germany
Dear Powell,
Isn't it there a way to data mine the PDB or the other repository source
for the time/duration/days of the crystals obtained.
Dr. Jayashankar Selvadurai
Hannover
Germany
On Mon, Feb 4, 2013 at 5:10 PM, Harry Powell ha...@mrc-lmb.cam.ac.ukwrote:
Hi David
try going back
Dear Rex Palmer,
Get monomer---LBT-Save coordinate
HTH
Dr. Jayashankar Selvadurai
Hannover
Germany
On Tue, Oct 23, 2012 at 3:17 PM, Rex Palmer rex.pal...@btinternet.comwrote:
Does anyone know if the alpha lactose molecule LBT coordinates are in the
Coot library. If so how can
Dear All,
I would like to buy the book '' X-ray structure determination'' by
George.H.Stout and Lyle.H.Jensen.
If in any case , somebody has shelved it and want to give away for
reasonable price. I would buy it.
sincerely
Dr. Jayashankar Selvadurai (Jay)
Hannover
Germany
Thanks for the links and suggestions,
actually the second edition is expensive and the prices are comparable to
that of amazon.
sincerely
Dr. Jayashankar Selvadurai
Hannover
Germany
On Mon, Oct 22, 2012 at 8:50 PM, Frances C. Bernstein
f...@bernstein-plus-sons.com wrote:
There is a website
Dear All,
A bit offtopic question,
Does any body know how can I get the PIR output of the aligned sequence
from clustal omega.
I have a full length protein solved, to give weightage during comparitive
modelling, I use domains of the same/similar protein solved before.
I expect an alignment
, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear S. Jayashankar,
have you tried the clustalw options '-convert -output=PIR'? This should
result in a pir-formatted output file.
Tim
On 03/27/12 10:18, Jayashankar wrote:
Dear All,
A bit
: SHA1
Dear Jayashankar,
sorry, you did explain this in your model and I flipped clustalo with
clustalw. Even though when I used the option '-convert', clustalw does
not re-align the input but simply converts it, so in case it can read
the clustalo output, this should do the job, shouldn't
I face exactly the same problem. any advice in this regard would be
greatful.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Wed, Feb 29, 2012 at 2:58 AM, Dialing Pretty hdc123hdc...@yahoo.comwrote:
Dear All,
I want to use CCP4i
Dear friends,
Should I be happy if i get my crystals with one of the condition with a
commercial kit
containing citric acid and 40%MPD+ protein in(hepes+MgCl2)+ADP+VO3
any insights ...
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
Very much appreciable.
thanks
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Fri, Apr 23, 2010 at 4:50 PM, Jawahar Swaminathan jawa...@ebi.ac.ukwrote:
Biobar version 2.0.1 is now available.
Biobar is a powerful browsing and searching
Dear Victor,
I faced the same problem and got the same error for arpwarp solvent module,
and I have even communicated you through my system admin for arp warp
classic module
giving some trouble.
sincerely
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical
Let his soul rest in peace,In our Life we just pass many people and some
sits in our memory because of their deeds and contribution to the world.
with heavy heart
A humble student and a Fan of PyMol.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Dear Hari,
In the first hand , i thank you for this handy tool.
But, I am so curious to know how can i rectify the following error.
selva...@pc3241769:~/Desktop/tools/GridZilla_0.1beta_binary ./GridZilla
Traceback (most recent call last):
File
specify the residues involved in the
actal alignment, and the residues to calculate the RMS on
Miri
On Tue, 16 Jun 2009, Jayashankar wrote:
Dear friends,
Is it possible to allign structure of proteins of same class or family
just
based on acive site residues or defined by its volume
Dear friends,
Is it possible to allign structure of proteins of same class or family just
based on acive site residues or defined by its volume of cavity with
preferred deviation.
any suggestions could possibly help me.
sincerely
S.Jayashankar
Research Student
Institute for Biophysical
Dear Folks,
The last novel proteins fold were from the yr 2007(pdb statistics),
From 2007 to till date no novel fold has been identified, this mean the
present 1283 fold are the final or
should I wait, if so , with what criteria do I expect for a new fold..or
what are the expectations ...
If we
, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:
Jayashankar wrote:
Dear Folks,
Dear gmail-user,
The last novel proteins fold were from the yr 2007(pdb statistics),
From 2007 to till date no novel fold has been identified, this mean the
present 1283 fold are the final or
should I wait, if so
information exactly the way
Jayashankar wants.
http://www.sourcecod.com/structure/
I hope their is something like this for Linux/Windows also.
*From:* Jürgen Bosch jubo...@jhsph.edu
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent
Dear Scientists,
It may be too much...
But as a biophysics student I would like to appreciate and feel happy to
have pdb
structures as my computers screen savers than to have some funny and fancy
stuffs.
And it may help me as a motivator to solve my own structures in future
I want to ask is
Hi,
If you could send in stereo mode of the density you want to get suggestion,
it will be convenient for the well trained eyes.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Tue, Feb 10, 2009 at 3:16 PM, ar...@xtals.org wrote:
Hi,
Yes, William I do agree with you,
and in the same line of doubt, I have one more thing to ask you.
Where is this .cvspass resides.
I have problem in updating my fink , with fink selfupdate-cvs.
thanks
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Yes CCP4I, works better,
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Sat, Dec 13, 2008 at 6:43 AM, William Scott
wgsc...@chemistry.ucsc.eduwrote:
Does ccp4i work?
On Thu, December 11, 2008 8:06 pm, Jayashankar wrote:
since its
Paul and William,
since we are end users,
we have to depend on big heads like you.
and i believe that things will be bug free and efficient soon.
If it is a trivial problem, then please do update the FAQs so as to make our
ccp4bb not just to bug with these type of questions .
should i
Here we are dealing with two different state of chemistry,
solid state and solution state, If one of the minima in solid state
resembles
the biological state minimum, then there is a possiblw way to clearly
define
the biology and its significant interaction of that particular 'mer' of a
protein,
since its a same coot problem,
i have one more,
i am using mac 10.5 leopord osx the thing is, i dont get any pop upped
table even after i do a translate and do a real space refinement .
is it a bug or is it a problem in setups of other supportive libraries
S.Jayashankar
Research Student
Dear ccp4bb caretakers,
I am very young for the ccp4bb thread(2007 jan-my thread date of birth).
Is is possible to compile very important issues in a hyperlinked style
of the important problems,discussions and queries with in ccp4 threads.
for example when am reading a query of 2006 regarding
Dear Friends,
I recently followed William Scott page and followed his advice to install
fink and crystallographic softwares...
But out of my curiosity i once tried to install arpwarp as per the
instructions and it was done successfully,
no problem,
but whenever i open a new terminal window,i see
Dear Fransico,
*Salt bridges are close range electrostatic interaction which depend on
conformer population.
*S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Thu, Oct 16, 2008 at 8:21 AM, Chavas Leo [EMAIL PROTECTED] wrote:
Dear
to the
1978 paper of Max Perutz:
Electrostatic Effects in Proteins
Science (1978) 201 (4362), 1187-1191.
Nadir Mrabet
Jayashankar wrote:
Dear Fransico,
*Salt bridges are close range electrostatic interaction which depend
on conformer population.
*S.Jayashankar
Research
Dear Jacob,
You are absolutely right,
I was very much excited and clear when I read Randy J.Read 's paper
Improved Fourier coefficients for maps using phases from partial structures
with errors.
its a must read paper for all students like me.
thanks
S.Jayashankar
Research Student
Institute for
Dear friends and crystallographers,
During One of my lab meeting ,
I told twinning in crystals are ok, because ccp4's recent releases just need
the keyword TWIN to solve them,
As a new generation research student, I am now confused, is that I need to
learn and understand all programs(so
Dear Computational crystallographers and developers,
I still struggle with my mac book pro, to install crystallographic
softwares,
The fink list has cctbx, I want to know whether this cums in unstable or
stable branch of fink distribution.
And i have hard time in updating my fink with fink
Dear Scientists,
Sorry if the mail intervene you scientific thinkings.
Can anybody Share a wonderful site to share jokes on science.
moreover it would be nice if we have a tool to create such jokes.
(And is there any ready made photoshop kind of thing to create a cartoon
character for the
DearAriel,
http://davapc1.bioch.dundee.ac.uk/prodrg/
try this and see,
On Tue, Jul 22, 2008 at 9:42 PM, Ariel Talavera [EMAIL PROTECTED] wrote:
Hi all,
I need to create the coordinates of a small molecule with no structure yet.
Could any one tell me what program can I use to build small
Dear All,
Scott has good point.And the requesting party should reply to these kind
mails very quickly ,so as to avoid of receiving huge number of same paper
from different persons,(such a basic sense is important to avoid of wasting
others time.)
thanks.
(still am confused about how far or how
Dear scientists and friends,
When I try to convert a .cv file to .mtz by f2mtz I got the following
error,what it means ans what should I do to get rid of it.
''Parameter MAXSAVE exceeded''
--
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany
Of Ezra
Peisach
Sent: Thursday, July 03, 2008 11:28 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Parameter MAXSAVE exceeded
I do not know off hand what a .cv file is - unless it is a cns/xplor
reflection file. Instead of using f2mtz - try sftools.
Ezra
Jayashankar wrote:
Dear
Dear Bill,
A person started his career as a Laboratory Technician and raised to a
level of Associate Professor(and still dont know the next highest level) ,
this transitions in Sanskrit called as avatars (every state serve its
purpose of its existence) ,
there is always good reasons for an
Dear Scientists and Friends,
I am not sure, whether organic crystals need to be in cryo stream
necessarily during data collection from an in house
xray machine .
How most of the organic crystals have been solved mostly?
--
S.Jayashankar
(A bit confused new generation researcher).
Dear scientists and friends,
I am much interested to learn things by my own.
There are many guys out there as me.
To fulfill the thirst and quest for more crystallographic practical
knowledge, I need test data set for
SAD,MAD,SIR,MIR,SIRAS,MIRAS.
And I want to remind kevin and Martyn that they
I have received the article,
thanks for all.
On Wed, Jun 11, 2008 at 3:11 PM, bharath SR [EMAIL PROTECTED] wrote:
attached ,...
On Wed, Jun 11, 2008 at 4:48 PM, Jayashankar [EMAIL PROTECTED]
wrote:
*Dear Friends,*
I am a research student , looking for an article mentioned below.
I
Dear friends and scientists,
(A pre-Structural biological question.)
I Have a multidomain protein , I know the domain boundaries,
But am still not that rational to what residues a construct should start or
end?
But I have learned from people that changing one residue changes the fate of
the
-- Forwarded message --
From: Jayashankar [EMAIL PROTECTED]
Date: Tue, May 20, 2008 at 7:34 PM
Subject: Right terminal residues for constructs.
To: CCP4BB@jiscmail.ac.uk
Dear friends and scientists,
(A pre-Structural biological question.)
I Have a multidomain protein , I know
hi Ngo,
Reduce such showering by increasing the reservoir volume, or by increasing
the protein concentration.
On Wed, Apr 16, 2008 at 4:08 PM, Van Den Berg, Bert
[EMAIL PROTECTED] wrote:
Hi Ngo,
your needles actually look like very thin plates. They seem promising to
me. From appearance
Dear Brad,
the flexibility, that is how far a protein is stabilized with cold and heat
denaturation of a protein,
this inturn depends on
1.solvation enthalpy of nonpolar moieties(need more energy,so there needs to
be some randomness)
2.shift in temparature due to the enthalpy associated with
Dear members,
What is the maximum spring constant a protein can have as such.
Is it possible to calculate how stiff a protein molecule is.
What is the correlation between the diffusion coefficient of a protein and
its surface tension during protein-protein interactions?
--
S.Jayashankar
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