--
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Paul Emsley
> Sent: 28 February 2017 22:57
> To: ccp4bb
> Subject: Re: [ccp4bb] ANODE anomalous map in pymol
>
> On 28/02/2017 22:54, Appu kumar wrote:
> > Hi,
> > I Already did that in COOT, but PY
Hi Paul and Clement,
As suggested by the Paul, Export the map fragment from the COOT, did the
trick. It worked perfectly fine.
Thank for valuable suggestions, indeed helpful.
Appu
On 28 February 2017 at 19:55, Appu kumar <appu.kum...@gmail.com> wrote:
> Hi,
> Yes I tried renam
extension to .ccp4 instead of .map?
>
> Cheers,
> Clement
>
> *From:* Appu kumar <appu.kum...@gmail.com>
> *Sent:* Wednesday, March 01, 2017 7:54 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] ANODE anomalous map in pymol
>
> Hi,
> I Already did that i
Hi,
I Already did that in COOT, but PYMOL does not read it in map format. Pymol
fail to show mesh in isomesh command.
Thank you
Appu
On 28 February 2017 at 16:31, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:
> On 28/02/2017 20:44, Appu kumar wrote:
>
>> Dear CCP4 Use
Dear CCP4 Users,
I ran anode to calculate the anomalous map for heavy atoms in protein.
ANODE output the anomalous map in .pha file, which can be viewed in COOT.
However, I want to get the anomalous map from .pha file to .map or .xplor
file, which can be feed into PYMOL to make maps. Is there a
on that and try to get higher
resolution data from better diffracting crystals and it might be a much
easier experience, (unless you trying to solve a huge ribosomal complex
kind of protein and in that case 4 angs is amazing)
cheers
Ivan
On Wed, Jul 1, 2015 at 5:57 PM, Appu kumar
Dear CCP4 users,
I am refining a structure at 4A resolution. Crystal diffracted
anisotropically and after refinement in both PHENIX and REFMAC, electron
density in one of the domain of protein is represented by discontinuity and
poor maps. Therefore i did the aniosotropy correction using
: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 6/16/2015 11:13 AM, Appu kumar wrote:
Hello,
I have downloaded 'ccp4-6.5 and deleted the older version of ccp4
installed. After installing the new version, it is giving the following
problem on executing the ccp4i command
Hello,
I have downloaded 'ccp4-6.5 and deleted the older version of ccp4
installed. After installing the new version, it is giving the following
problem on executing the ccp4i command.
Error in startup script: couldn't read file
/usr/local/xtal/ccp4-6.2.0/share/dbccp4i/ClientAPI/dbClientAPI.tcl:
Dear CCP4 Member,
I seek your advice on the refinement issues at the low resolution 4A. I am
trying to refine a membrane protein structure after getting the phases from
MR using the PHASER. The soluble domain structure which comprises of 40% of
protein has been used as template (sequence identity
with a fixed spacegroup (scaled merged data) according
to your pointless log. So you can't get another possible solution from
pointless.
Cheers
Am 22.04.2015 um 22:28 schrieb Appu kumar:
Dear CCP4 Member,
I seek your advice on the refinement issues at the low resolution 4A. I
am trying
Hello,
If the homologous protein structure is available, or you have symmetry
information of your crystal, then try engineering surface by putting in
residues which has less entropy like replacing Lys to Arg, Met to Gln. We
are able to fasten the crystal growth from 20 days to 3-4 days by creating
K. Suhre (one of the
developer of el-Nemo server) has done the same very correctly.
best wishes,
Arpita
On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar appu.kum...@gmail.com wrote:
Dear CCP4 Users,
I seek your valuable advice and suggestion in carrying out the normal
mode structure refinement
would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a
try to what Arpita has suggested. I further, warmly welcome any suggestion
on refinement procedure to improve electron density in flexible or
disordered trans-membrane domain.
Appu
On 21 October 2014 07:39, Appu kumar appu.kum
Dear CCP4 Users,
I seek your valuable advice and suggestion in carrying out the normal mode
structure refinement which manifest the dynamics of protein as linear
combination of harmonic modes, used to describe the motion of protein
structure in collective fashion. Studies suggest that it is highly
Hello All,
I am new to low resolution refinement parametrization and regularization.
Crystal diffracted with high anisotropy reaching to 3.5A in one direction
and 4.5A other direction. I am refining a structure at 3.9A resolution.
Protein has two domain connected trhough a linker and is packed as
Hello All,
I have tried MR in Phaser, MRage, Molrep , Mrbump but i
am not getting the true solution which it supposed to be. Although the
resoution of data is 6.1A, but i want to give a try to CNS and see if I can
find right solution. I have read the manual of CNS but i am
Hello everyone,
I request all of you to please help in getting
the source of hole programme which is required to visualize the cavity
running through the channel in protein structures. This programme is
written by Dr. Oliver Smart. Despite of exhaustive search on
-
On 11/21/2013 5:38 PM, Appu kumar wrote:
Dear All,
I seek your valuable suggestion on a MR problem. I am
asking phaser to search for two molecules in ASU, first molecules
phaser searched right but when placing the second molecule, it
orientation has got flipped
Dear All,
I seek your valuable suggestion on a MR problem. I am
asking phaser to search for two molecules in ASU, first molecules
phaser searched right but when placing the second molecule, it
orientation has got flipped by 180 deegree. Is there any way to tell
phaser to fix the
How do you suspect that C2221 is 'pseudo' and P21 is 'real'? You can use
the reindex programme incorporated in ccp4 suit. Reindex programme can
expand symmetry from C2221 to P21.I Hope you will get the result.
Thank you
Appu
On 2 October 2013 21:43, wtempel wtem...@gmail.com wrote:
Hello,
I
Deal Xiang,
You can think of GFP/YFP protein attached with any protein would be good
for your experiment. These can be easily cloned and expressed.
Alternatively one more approach is mentioned below.
Chose a protein which has only one cysteine, that too at the surface then
you can think of
Deal CCP4 member's
Sorry for asking Off topic question.
Please correct me if i am doing wrong measurements. I am determining the
double stranded concentration using the absorbance spectrophotometer
reading at 260A and extinction coefficients for individual
Dear John,
You can you the Prosmart
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/prosmart/documentation.html
and also pdbsum can give what you asking for.
Thanks
Appu
On 27 April 2013 02:57, Mike John perturb-w...@hotmail.com wrote:
Hello, Every one,
I am preparing a ppt
have to crystallize the protein
in presence of DNA.
Good luck!
Raji
On Sat, Mar 23, 2013 at 2:26 PM, Appu kumar appu.kum...@gmail.com wrote:
Dear members,
I am doing a molecular replacement of a
transcription factor whose ligand binding structure(24000 Da
) 1865 287547
Email matth...@strubi.ox.ac.uk
Website http://www.strubi.ox.ac.uk
-
On 3/24/2013 7:46 AM, Appu kumar wrote:
Thank you for the quick reply. After molecular replacement , i have done
only few cycle of refinement in refmac. I have not done any
!
HTH,
Fred.
On 24/03/13 11:20, Appu kumar wrote:
I run the phenix.xtriage to evaluate the twining but it suggest no
twining. When i reindex from C2221 to P21, the completeness of data reduced
from 95 % to 35% whereas the map is very good and Rwork and Rfree are 26/31
for 2.2 resolution
Dear members,
I am doing a molecular replacement of a
transcription factor whose ligand binding structure(24000 Da) is available
in PDB but not for the DNA binding(13000 Da). When i am searching for the
two copies from ligand binding domain as a template model, i am
Dear ccp4 user,
I have problem in finding the phase for the
flexible DNA binding domain of LTTR protein. The unit cell parameters are ,Unit
Cell: 46.92 105.30 47.75 90.00 103.26 90.00, and space-Group P 1 21 1.
Molecular weight of protein is 36000Da. When i am running
Dear Users,
I am refining a enzyme structure with ligand. I
want to make the simulated annealing omit map of ligand including with 4
Angestron radius around the ligand. I am seeking your valuable advice to
help me out. I know how to make omit map but i have not come
Dear all,
Please guide me on right track in weired confusion. I
have model structure(available in pdb) and a structure solved by molecular
replacement as a dimer . Our structure does not giving correct tetramer by
symmetry mates. Strangely when i am aligning our structure on
Dear all ccp4 users,
I have solved the structure of a protein
which is a dimer. On comparison with the other structure from PDB data
bank, i found that structure solved by us show a tiltness in
monomer-monomer arrangement of a dimer. May you please help me in
On 24 August 2012 08:52, Appu kumar appu.kum...@gmail.com wrote:
Thank you Sir for your kind eply. I will follow your instruction to
calculate the angle.
On 24 August 2012 00:38, Nikolina Sekulic nikolina.seku...@gmail.comwrote:
Dear Appu,
I had similar issue once. You can use Coot
the GUI.
Could you cut and paste this into your message - obviously some inmportant
parameter is not set, but I cant tell which without seeing that file.
Eleanor
On 20 June 2012 05:25, Appu kumar appu.kum...@gmail.com wrote:
Thank you for your reply,
I am running Malphare through CCP4
Dear CCP4 user,
I am facing problem in running Mlphare
for *HEAVY
ATOM REFINEMENT and PHASE CALCULATO. It is running successfully but in
output log file i am not getting any FOM for acentric. Log file output of
one of the cycle is
** * *** Finished refinement
:
It's not clear without looking at your input script, but it appears that
you've got a problem with either your LABIN, ATREF or ATOM lines. It might
be helpful to check out some of the example scripts distributed with ccp4.
Pete
Appu kumar wrote:
Dear CCP4 user
Hello Dear all
I am trying running dm (density modification)
programe for density modification, but it giving error complaining about
density map. It says, dm: (WFO) No density in map! Check input FOM
present and nonzero.
Please suggest me how to overcome this
To generate this input file, I used scalepack2mtz, TRUNCATE, and then
MLPHARE. The test.com script runs DM. And yes, it did take me a while
to figure this out.
-James Holton
MAD Scientist
On 6/14/2012 4:58 AM, Appu kumar wrote:
Hello Dear all
I am trying running dm
Hi peter,
I agreed with Kelly, You should try indexing your data in
different program. I recently collected a diffraction data which showed
problem in indexing in HKL2000, but data indexed very fine in imosflm
giving right cell parameter. So it is worthfull to index your data in
Dear ccp4 users,
Would you please guide me how to calculate
the RMSD of side chains alone without considering C-alpha backbone.
Is/are there any program/programs availble which do this job. I want
to know the RMSD of side chains for protein comparison.
Thank you in
...@u.washington.edu wrote:
On Friday, 13 January 2012, Appu kumar wrote:
Dear ccp4 users,
Would you please guide me how to calculate
the RMSD of side chains alone without considering C-alpha backbone.
Is/are there any program/programs availble which do this job. I want
Hello every one,
Sorry for asking off topic question, I have
purified different subunit of RNA polymerase, now i want to assemble it.
Can you give me valuable suggestion regarding the gel filtration column and
ion exchange column which will facilitate the purification
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