Dear All,
Thanks everyone for the suggestions. I did go to library to look up some
chapters in books which gave me lot of information about conserved zinc finger
domain. My protein has Cx4C and Cx3C and with very large spacing, so I suspect
it could be zinc finger like protein (though no
Dear All,
I would like to learn how to relate water molecules by NCS and refine them.
When I googled, CCP4 utilities sortwater and watncs showed up. I also found
Applying NCS to a high resolution structure , including water molecules in NCS
restraints on autobuster examples. Some how I got
for information about which waters obey NCS although the output is not standard
nomenclature..
Alternately just use the coot facility to fit chain A over chain B and see
which waters overlap each other in the Copy and original..(Remember to turn
symmetry ON)
Eleanor
On 22 April 2012 16:33, Rajesh Kumar
Dear All,
I have very thin crystals but diffracting. I was not able to handle them easily
for iodide soak. I always lost the crystals during manipulation and other big
crystals obtained after seeding doesn't even give any diffraction. I tried for
co-crystallizing with NaI. The crystals appear
) and hydrogen peroxide VIL (HYPER-VIL)
Worked for me with salt concentration sensitive crystal
and a
derivatization time 10 min.
Good luck,
Florian
Am 03.05.12 15:51, schrieb Rajesh Kumar
Dear all,
Is ligands and metals could also be NCS restrained during the refinement. I
have Na+ and SO4 in my model which are NCS related.
Thanks for the help
Warm regards
Rajesh
Sent from my iPhone
), but the question is whether they should?
Can't you try both options to see which one works best in your specific case?
Pavel
On Sat, May 5, 2012 at 6:02 AM, Rajesh Kumar ccp4...@hotmail.com wrote:
Dear all,
Is ligands and metals could also be NCS restrained during the refinement. I
have Na+ and SO4
Dear All,
This question sounds simple but I dont know the answer.I was preparing a 24
well crystal screen. When I try to use 10 mM ZnSO4 with HEPES (pH 7.6) buffer
it precipitates. I tried both ZnCl2 and Zn acetate the effect is same. I dont
know why this Zn in not compatible with
with
concentrated HEPES. Also it depends what else is in your cocktail.
JPK
On Fri, May 11, 2012 at 11:26 AM, Rajesh Kumar ccp4...@hotmail.com wrote:
Dear All,
This question sounds simple but I dont know the answer.I was preparing a 24
well crystal screen. When I try to use 10 mM ZnSO4 with HEPES (pH 7.6
If there is no cure , then fine.pH may not be the answer as it doesn't Happen
with TRIS buffer pH 7.6.Thanks to every oneRajesh
Date: Fri, 11 May 2012 12:35:45 -0400
From: dj...@cornell.edu
Subject: Re: [ccp4bb] zinc with HEPES
To: CCP4BB@JISCMAIL.AC.UK
There is no
seems a bit too high. I normally used it at 50uM conc.
ray
On Fri, May 11, 2012 at 12:26 PM, Rajesh Kumar ccp4...@hotmail.com wrote:
Dear All,
This question sounds simple but I dont know the answer.
I was preparing a 24 well crystal screen. When I try to use 10 mM ZnSO4
with HEPES (pH
...@hotmail.com
Rajesh,
10mM zinc seems a bit too high. I normally used it at 50uM conc.
ray
On Fri, May 11, 2012 at 12:26 PM, Rajesh Kumar ccp4...@hotmail.com wrote:
Dear All,
This question sounds simple but I dont know the answer.
I was preparing a 24 well crystal screen. When I
Dear All,
My friend needs a help.What is the best way to connect Lys to PLP with covalent
bond.I am sure there are many ways do it. My friend would appreciate if you
could simplify and explain this so that he could learn it without difficulties.
Also I could learn
I appreciate your time and
Dear All,
I am trying to install CNS in ubuntu 10.04 LTS. Even after reading all the
advice on CNS installation on CCP4bb, I have failed to get it working.
Both in bash and tcsh, cns_web works but cns_solve gives error command not
found.
yogesha@yogesha-laptop:~/work$ echo $CNS_SOLVE
terminal window is opened to set
the paths to the executables.
Cheers,
Roger Rowlett
On 07/28/2012 12:40 PM, Rajesh Kumar wrote:
Dear All,
I am trying to install CNS in ubuntu 10.04 LTS. Even after
Hello Ben,
Thanks a lot. After your mail, I looked up your suggestions in old thread on
cnsbb.
Installed gfortran and built as you suggested.
It worked very well.
Thanks
Yogi
Date: Sat, 28 Jul 2012 17:18:09 -0400
From: b...@hkl.hms.harvard.edu
Subject: Re: [ccp4bb] CNS installation
To:
I have slightly different problem. I have windows 7 Enterprise. I don't get any
shortcuts on my desktop after installation.I work with admin account. If I try
to execute /ccp4-6.2.0/ccp4i/bin/ccp4i.tcl I get the following error. please
see attachment.I installed
Dear all,
mtzdump shows my space group as 'C 2 2 21' (number 20)
pointless gives error Space group is not in library. part of the log file is
following.
I appreciate all the help.
Thanks
Raj
**
*
Thanks to Harry Powell, Phil Evans, De-Feng Li for suggestions and special
thanks to Charles Ballard looking in to my data.
The summary is
Harry Powell and Phil Evans-Pointless needs update as newer version is up to
version 1.6.8 - the latest copy is at
Dear All,
We have an anisotropic dataset of 3.3 A and it was solved (not by me) with
P6522 with R/freeR
29.1/37.3.
I got the corrected
mtz file by plugging in the .HKL (P6122) file to anisotropy diffraction server
at
2.04 A. I reindexed this p6122 to p6522 and extended the resolution
Dear All,
I have connected to unix server of the lab through ssh/xming/x11. I can run
open phenix and CCP4 GUI.
I am trying to adxv to see images but I am unable to do so.
I have got two files adxv and adxv.i686FC2 sitting in my work/adxv/.
when i run adxv in bash
bash: adxv: command not
there is a fair chance.
Cheers,
Tim
On 11/19/2011 05:53 PM, Rajesh kumar wrote:
Dear All,
I have connected to unix server of the lab through ssh/xming/x11. I can
run open phenix and CCP4 GUI.
I am trying to adxv to see images but I am unable to do so.
I have got two
] http://sbgrid.org/news/newsletters/2009/06 (search for the string adxv)
On 20 November 2011 19:45, Rajesh kumar ccp4...@hotmail.com wrote:
Dear Tim,
Thanks. Your suggestion of adding to PATH works and its not completely
functional may be due to the Ximg/ssh or some thing to do
] adxv
To: CCP4BB@JISCMAIL.AC.UK
yum install lesstif ?
but wouldn't the motif stuff be required for the X-server, i.e. your
terminal, not for the
server running adxv?
Rajesh kumar wrote:
Dear Mark,
$ locate XKeysymDB - didnt come with any thing suggests probably openmotif
lib
can do..
I think I would make sure the apo structure is as good as it can be,
then fit that to the 3.3A data set, and only use that 3.3A data to
deduce whatever features differ from the APO structure.
Eleanor
On 11/19/2011 12:09 PM, Rajesh kumar wrote:
Dear All,
We have
-connection and not the respective windows-binaries?
I am not familiar with windows and the possible existence of
X11-clients, but I would think that most suggestions to you assumed that
your client computer was also a linux-machine.
Cheers,
Tim
On 11/22/2011 02:27 PM, Rajesh kumar wrote
Dear Ian,
I installed the fonts from the link
http://www.scripps.edu/~arvai/adxv.html.Everything works now on my linux
system.There was no need of extra fonts on my xming (I had already installed
extra fonts from the link you have suggested) and it works just fine.
Thanks to your time to
Dear All,
Any of you know if the Bias removal server at
http://tuna.tamu.edu/ works?My friend says that 'may be the server doesn't
exist' as he never heard back from them about login info.
ThanksRajesh
building pretty much the same can be achieved nowadays (pus benefit of a
model), the ARP/wARP server in Hamburg is a well-working and up-to-date
alternative. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Rajesh kumar
Sent: Tuesday, December 20, 2011 10:19 AM
To: CCP4BB
May be this one helps
The current study presents the design, engineering, and characterization of two
E. coli BL21(DE3) derivatives, NiCo21(DE3) and NiCo22(DE3), which express the
endogenous proteins SlyD, Can, ArnA, and (optionally) AceE fused at their C
terminus to a chitin binding
Dear All,
I am trying to use probe and reduce with coot new version. I tried as
suggested in coot FAQ page-
1. renamed probe.exe and reduce.exe were put in C:\WinCoot\bin- didnt show
validate/probe clashes as active n coot
2. made changes to group settings.py in wincoot/share/coot/python
Dear B,Yes its working. Thanks for your help.
ThanksYogi
Date: Sun, 26 Feb 2012 22:49:08 +0100
From: bernh...@chem.gla.ac.uk
Subject: Re: [ccp4bb] coot with probe and reduce
To: CCP4BB@JISCMAIL.AC.UK
Dear Raj,
please follow exactly what is written in the FAQ
Dear All,
I have a 3.3 A data for a protein whose SG is P6522. Model used was wild type
structure of same protein at 2.3 A. After molecular replacement, first three
rounds of refinement the R/Rf was 26/32.8, 27.1/31.72 % and 7.35/30.88 %
respectively.In the fourth round I refined with TLS
: Rajesh kumar ccp4...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, March 2, 2012 10:54 AM
Subject: [ccp4bb] sudden drop in R/Rfree
Dear All,
I have a 3.3 A data for a protein whose SG is P6522. Model used was wild type
structure of same protein at 2.3 A. After molecular replacement
Dear All,
Thanks for all the suggestion. Data is anisotropic. Since anisotropic
correction with the UCLA server didnt give any good Molprobity scores and
didnt reduce the R/Rfree at 2.1A, I am using ~3.3A data for further refinement.
Using Tom's suggestion of target restrains reduced the gap
http://www.neb.com/nebecomm/products/productP8070.asp
Date: Mon, 12 Mar 2012 09:38:22 -0400
From: elias.fernan...@utk.edu
Subject: [ccp4bb] recombinant enterokinase
To: CCP4BB@JISCMAIL.AC.UK
Dear all,Would anyone know of a source for recombinant enterokinase? Best,Elias
Mahesh,
You should always use output_1.mtz for refinement.
Dont use output_2. mtz for further refinement instead use some ccp4 utilities
to change output_1.mtz (C222) to say output1_mod.mtz (C2221). This will become
your master file for all further refinement. What ever remaining 2.mtz,
This sentence in my previous posting may or may not be correct technically-
May be make sure about this as it says reindex because only you need to rescale
it like in HKL2000. It its wrong I am Sorry in advance.
Date: Wed, 14 Mar 2012 07:43:15 -0500
From: ccp4...@hotmail.com
Subject: Re:
Dear All,
I have few papers in hand which explain me about microseeding, matrix
microseeding, and cross seeding.I have also read few earlier threads and some
more literature in google.Using Phoenix robot, I did a matrix micro-seeding and
matrix cross seeding. I have few hits with this.In 96
Dear All,
I have a structure of a protein and peptide complex, in which peptide has
modified residues ( phosphoserine and phosphothreonine). During refinement
these both gets disconnected with adjacent residues and its hard to connect
them.Could you please suggest me some options.
Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh
kumar
Sent: Thursday, 22 March 2012 12:00 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034 From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar
Sent: Thursday, 22 March 2012 12:00 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] refining
Dear All,
I am trying to crystallize a protein, so far I got no diffraction though I have
large crystals.It has few cystines and a histidine near by at N-terminal. I
dont have much literature on biochemistry of this protein available in pubmed
(5 papers only).Is there a way if I could check
Of Rajesh kumar
Sent: Tuesday, April 03, 2012 10:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] zinc fingre
Dear All,
I am trying to crystallize a protein, so far I got no diffraction though I have
large crystals.
It has few cystines and a histidine near by at N-terminal. I dont
Dear Rohit,
Try to run sfcheck or XTRIAGE and check, if your data is fine. Check for
twinning or pseudo-translation. You can send your processed mtz to me and I
would be more than happy to help you.
You can look into cumulative intensity distribution (if you processed with
XDS, it will be in
Hi Chenjun,
Few suggestions from my side. Process the data with XDS and look into
acentric intensity distribution (it indicates any twinning possibility).
Run XTRIAGE and SFCHECK to understand any twinning or pseudo translation
possibilities. Twinning can confuse the program and suggest you
Dear Meytal,
PHENIX-REFINE has an option for Ramachandran outlier refine. If you check
this on, it will do the work. But after this refinement, you must check
every residues to make sure residues are in the density.
Thank you
Rajesh
---x
With regards
Rajesh K. Harijan, Ph.D.
Schramm
Dear Rik and Joel,
This is really great. Thank you very much. I will follow it from New York.
Have a great workshop.
regards,
Rajesh
---x
With regards
Rajesh K. Harijan, Ph.D.
Schramm Laboratory
Albert Einstein College of Medicine
1300 Morris Park Ave., Bronx, NY 10461
Tel:
Dear Rik and Joel,
Thank you very much for organizing this great workshop for students. I
followed it online from New York. It was nice to see some familiar faces as
the speaker.
Hoping to see you all in coming future.
regards,
Rajesh
---x
With regards
Rajesh K. Harijan, Ph.D.
;
>
>
> With best regards,
> Ivan Shabalin, Ph.D.
> Research Scientist,
> Department of Molecular Physiology and Biological Physics,
> University of Virginia,
> 1340 Jefferson Park Avenue
> <https://maps.google.com/?q=1340+Jefferson+Park+Avenue=gmail=g>,
> Pinn Hall,
it looks well coordinated - could be
> cacodylate? Or water, am not sure.
>
> Cheers,
> Hussain
>
> > On 7 Mar 2018, at 9:19 am, Rajesh Kumar <rajesh.p...@gmail.com> wrote:
> >
> > Dear All,
> >
> > Have you had experience with this kind of de
Dear All,
I just had installed new SSD and latest macOS High Sierra 10.13.3 into my
macbook pro.
It seems my macbook is much faster but running COOT is a bit problem.
When I open COOT, screen becomes gray for a second and then it opens. When
I try to move from one residue to next, it does not
Dear Paul,
It seems that XQuartz 2.7.7 is working in my macbook and I can run COOT a
bit faster.
Thank you for the help.
-Rajesh
On Wed, Feb 28, 2018 at 5:42 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:
> On 27/02/2018 21:11, Rajesh Kumar wrote:
>
>>
>> I ju
Dear Paul,
Thank you very much. Only COOT is giving problem. Other programs work very
well.
I will change XQuartz to 2.7.8 and see if COOT works.
regards,
Rajesh
On Wed, Feb 28, 2018 at 5:42 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:
> On 27/02/2018 21:11, Rajesh Ku
I totally agree with Berry. Please consider Rpim, CC1/2 and I/sigI for
cutting the data. Rmerge is old approach as it is data redundancy dependent.
Thank you
Rajesh
---x
With regards
Rajesh K. Harijan, Ph.D.
Schramm Laboratory
Albert Einstein College of Medicine
1300 Morris Park Ave.,
Hi Amala,
In addition to Limbini´s suggestions.
1. You can always do MALS, SLS, Native Page or cross linking experiments to
check whether your protein is monodisperse in the solution or not. This is
very important step.
2. When you set up crystallization and if you have 40-50% drops
/wissenschaftliches-personal/institut-fuer-biochemie-nr-07b51.html
As mentioned in the advertisment, the deadline for applications is
15.10.2007.
With best regards
Rajesh Kumar Singh
--
Rajesh Kumar Singh, PhD
Institut fur Biochemie
Universitat Greifswald
Felix-Hausdorff-Str. 4
D-17489 Greifswald
in 760D6a0***.img
do
mv $i ${i%760D6a0***}760D6a0_${i#760D6a0}
done
Rajesh
On Wednesday 12 March 2008 02:32, Raja Dey wrote:
CCP4BB@jiscmail.ac.uk
--
Rajesh Kumar Singh, PhD
Institut fur Biochemie
Universitat Greifswald
Felix
wUI/Search/home/HomeWithPreLoad?PageType=JobDetails=0=169=5140=798102#jobDetails=798102_5140>
Best regards,
Rajesh Kumar P
gt;
32911BR - Biophysical assays - SPR - Sr. Associate Scientist
<https://sjobs.brassring.com/TGnewUI/Search/home/HomeWithPreLoad?PageType=JobDetails=0=169=5140=795658#jobDetails=795658_5140>
Thank you.
Best regards,
Rajesh Kumar Prakash
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