Dear All,
I am able to do the superposition of the ligand with suplig.f program and
superpose also do the same.
Thank you for your valuable suggestions.
regardsvijay
Vijay
On Tuesday, 26 May 2015 6:11 PM, vijay srivastava
vijaytec...@yahoo.co.in wrote:
Dear All,
I want to
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de vijay srivastava
[vijaytec...@yahoo.co.in]
Envoyé : mardi 26 mai 2015 14:41
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Hi
Dear All,
I want to superpose the nucleotide form one GTPase on to the nucleotide of
other GTPase
Dear All,
I want to superpose the nucleotide form one GTPase on to the nucleotide of
other GTPase in order to study
the interaction in the nucleotide binding pocket. I tried to superpose but it
is superposing on the basis of secondary structure as aresult both the
nucleotides from two
On 26/05/15 14:41, vijay srivastava wrote:
Dear All,
I want to superpose the nucleotide form one GTPase on to the
nucleotide of other GTPase in order to study
the interaction in the nucleotide binding pocket. I tried to superpose
but it is superposing on the basis of secondary structure as a
Hi vijay,
I think the pymol-based program “legalign” will do what you want:
http://compbio.cs.toronto.edu/ligalign/
http://compbio.cs.toronto.edu/ligalign/
Hope this can help,
Marco
Il giorno 26/mag/2015, alle ore 05:41, vijay srivastava
vijaytec...@yahoo.co.in ha scritto:
Dear All,
Dear Vijay,
Your problem sounds like a job for LigAlign:
http://www.pymolwiki.org/index.php/LigAlign
Regards,
Dmitry
On Tue, May 26, 2015 at 8:42 AM vijay srivastava vijaytec...@yahoo.co.in
wrote:
Dear All,
I want to superpose the nucleotide form one GTPase on to the nucleotide of
other
I would suggest biopython.
http://combichem.blogspot.com/2013/08/aligning-pdb-structures-with-biopython.html
On Tue, May 26, 2015 at 10:25 AM, Dimitry Rodionov d.rodio...@gmail.com
wrote:
Dear Vijay,
Your problem sounds like a job for LigAlign:
http://www.pymolwiki.org/index.php/LigAlign
]
Envoyé : mardi 26 mai 2015 14:56
À : FOOS Nicolas
Objet : Re: [ccp4bb] Hi
Dear Nicolas,
I ahd tried in superpose but it is not alligning and simultaenousli I had given
only the pdb
containing only the nucleotide but both of them dosen't work.
regards
Vijay
On Tuesday, 26 May 2015 6:22 PM, FOOS
of them (or model a “fresh” one), although I
guess for GTP/GDP this should not be a frequent problem.
Zhijie
From: vijay srivastava
Sent: Tuesday, May 26, 2015 8:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Hi
Dear All,
I want to superpose the nucleotide form one GTPase
vijaytec...@yahoo.co.in
*Sent:* Tuesday, May 26, 2015 8:41 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Hi
Dear All,
I want to superpose the nucleotide form one GTPase on to the nucleotide of
other GTPase in order to study
the interaction in the nucleotide binding pocket. I tried
Hi Vijay,
In addition to the suggestions you've already received, the pair_fit
command in PyMol is also an easy way to align based on specific atoms. You
could use the C-alphas of relevant active site residues, or atoms of the
ligand itself, for example. Just be mindful of the bias introduced
Dear All,
In coot is there is any option so that we can change the colour of atoms. As in
ball and stick model in default
it is showing sulphur as green.
could we change the colour of atoms to show carbon in gray, oxygen in red and
suphur in yellow.
regards Vijay
Dear All,
Sorry to disturb you all it can be easily done in ccp4mg.
regards Vijay
On Saturday, 9 May 2015 4:36 PM, vijay srivastava
vijaytec...@yahoo.co.in wrote:
Dear All,
In coot is there is any option so that we can change the colour of atoms. As in
ball and stick model in
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sanjit Roy
Sent: Thursday, July 24, 2014 15:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] hi
Hello to every one
Can any body send me the information in concise form about
history of protein crystallization along with what
: vendredi 25 juillet 2014 10:59
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] hi - history of protein crystallization
Dear Dr. Sacha,
it is giving following error after typing the command
…
Hello to every one
Can any body send me the information in concise form about
history of protein crystallization along with what is the properties of
protein crystal in lattice parameters.
Thanks In advance
Sanjit Kumar
Hello to every one
Can any body send me the information in concise form about
history of protein crystallization along with some idea about the
properties of protein crystal in lattice parameters.
Thanks In advance
Sanjit Kumar
.
HTH
Raghu
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sanjit
Roy
Sent: Thursday, July 24, 2014 15:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] hi
Hello to every one
Can any body send me the information in concise form about
history of protein
Yes - is it rot mat? at home so can't check but look at the documentation - I
remember it turned any rotation definition into all the other likely ones…
Eleanor
On 21 Jul 2014, at 05:01, vijay srivastava wrote:
Dear All,
Is there is any program to convert euler angles into theta, phi and
:01
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Hi
Dear All,
Is there is any program to convert euler angles into theta, phi and kappa?
regards
Vijay
Dear All,
Is there is any program to convert euler angles into theta, phi and kappa?
regards
Vijay
http://divinewisdomatwork.com/ydmqi/xctcmtjcilhcnmmthiljueaugrhxf
Sun Hur
7/21/2013 4:35:14 PM
@JISCMAIL.AC.UK] Im Auftrag von Wei Shi
Gesendet: Montag, 10. Juni 2013 20:57
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Hi
Hi all,
I was trying to solve the structure of a protein in several different datasets
using xds and phenix. I could solve the structure from one dataset in space
group P4
Hi all,
I was trying to solve the structure of a protein in several different
datasets using xds and phenix. I could solve the structure from one dataset
in space group P4. For another dataset, I could solve the structure using
the monomer of the structure I got from the first dataset as search
I don't really understand what your space group is? space group mC???
Eleanor
On 10 Jun 2013, at 19:57, Wei Shi wrote:
Hi all,
I was trying to solve the structure of a protein in several different
datasets using xds and phenix. I could solve the structure from one dataset
in space group
Hi Eleanor,
C2 - this was XDS lingo or Bravais talk :-)
Jürgen
** LATTICE SYMMETRY IMPLICATED BY SPACE GROUP SYMMETRY **
BRAVAIS-POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS
TYPE [SPACE GROUP NUMBER,SYMBOL]
aP [1,P1]
mP [3,P2] [4,P2(1)]
mC,mI
The other obvious conclusion would be that dataset #3 is a different protein
perhaps ?
How about pointless for your third dataset ?
Jürgen
On Jun 10, 2013, at 2:57 PM, Wei Shi wrote:
Hi all,
I was trying to solve the structure of a protein in several different datasets
using xds and phenix. I
I guess Wei means just the lattice symbol, taken from the indexing program?
br
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Eleanor Dodson
Sent: Monday, June 10, 2013 10:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Hi
I don't really
Hi
I am refining my 2 angstrom strucutre using phenix windows based software.
After many refinements my clashscore is not at all reducing and showing a
value of 12. Can anybody suggest how to reduce the clashscore. Is there any
technique to do it. Or i have to deal with each individual clashes
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Supratim,
I am afraid so, yes, you'll have to do it manually. Model building is
the other half of creating a model, and time-wise surely the more time
consuming one. On the other hand it is also the more scientific one
where you feel less
Subject: [ccp4bb] Hi clashscore
Hi
I am refining my 2 angstrom strucutre using phenix windows based software.
After many refinements my clashscore is not at all reducing and showing a
value of 12. Can anybody suggest how to reduce the clashscore. Is there
any
technique to do it. Or i have
Dear all
A mtz output from mosflm when fed to SCALA gives information about total no
of reflection, uique reflection, R merge, redundancy etc.
i have two questions.
1. is there anyway to use sca files from HKL2000 with SCALA.
2. SCALA gives two multiplicity, one along with binary reflection and
Hope you get this on time, I made a trip to Aberdeen in Scotland and had my
bag stolen from me with my passport,cash and credit cards in it. unfortunately
for me,I have made contact with my bank but they are not providing a fast
solution. I need you to lend me some money to sort my self out
Hi all , thank you for being new member in this group. i also just stated with
my PhD in structural biology at Hamburg University (DESY) . i have no Idea
about crystallography . I just go step by step. so please help me to find my
way for excellence in structural biology. i appreciate your
Your question is way to broad to be answered in a reasonable time/space.
As for books (plenty of options exist beyond these)
There is a 1976 classic
http://www.amazon.com/Protein-Crystallography-Molecular-Biology-Series/dp/0121083500
And of course there is a more recent highly recommended
Hi,
Two educational softwares which might help you (off course in conjunction
with books and articles) are
1) XrayView
2)SpacegroupViz
Best
Arko
On Wed, Jun 27, 2012 at 6:22 PM, Ed Pozharski epozh...@umaryland.eduwrote:
Your question is way to broad to be answered in a reasonable
wow this is crazy you should give it a look
http://www.wa15news.net/biz/?employment=5773947
~*Advertisement
What are the buffer pHs (first and second run), what is the
isoelectric point of your protein, have you tried Q column?... You
have to give more experimental details to be more precisely helped.
Nevertheless, you can find helpful advices in GE healthcare life
science Handbooks:
We have a hi prep SP column from GE. We try to load ~14 mg protein but all
goes to FT. We lowered the pH and changed the buffer but no luck. We would
appreciate all suggestions. Mike Colaneri
hi
i am facing problem in cloning,getting my insert and vector at the
correct position after digestion but after ligation colony is not
coming and if how it is coming than i am not getting my insert
Add more friends to your messenger and enjoy! Go to
vijay srivastava wrote:
hi
i am facing problem in cloning,getting my insert and vector at the
correct position after digestion but after ligation colony is not
coming and if how it is coming than i am not getting my insert
That sux. phx.
PS. Sorry, couldn't resist. But seriously, for those new to the list:
if you want someone to spend time writing a useful answer, then you need
to spend time formulating a useful question.
Good: specific questions with sufficient background given
Bad: general questions which are best answered
details to suggest
something reasonable.
Artem
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Frank
von Delft
Sent: Saturday, August 30, 2008 7:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] hi
PS. Sorry, couldn't resist. But seriously, for those
srivastava [EMAIL PROTECTED] schrieb am Sa, 30.8.2008:
Von: vijay srivastava [EMAIL PROTECTED]
Betreff: [ccp4bb] hi
An: CCP4BB@JISCMAIL.AC.UK
Datum: Samstag, 30. August 2008, 13:04
hi
i am facing problem in cloning,getting my insert and vector at the
correct position after digestion but after
before you click on the send icon on your computer with derogatory
remarks.
Thanks
Sridhar Prasad
-Original Message-
From: CCP4 bulletin board on behalf of Jan Schoepe
Sent: Sat 8/30/2008 8:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] hi / cloning stuff
Hi, I think your
textbooks).
Good luck!
Jan
--- vijay srivastava [EMAIL PROTECTED] schrieb am Sa, 30.8.2008:
Von: vijay srivastava [EMAIL PROTECTED]
Betreff: [ccp4bb] hi
An: CCP4BB@JISCMAIL.AC.UK
Datum: Samstag, 30. August 2008, 13:04
hi
i am facing problem in cloning,getting my insert and vector at the
correct
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