On 8 December 2014 at 21:51, Uma Ratu rosiso2...@gmail.com wrote:
Dear All:
I try to import the .sca file from hkl2000.
The data was scaled as P212121 from HKL2000.
In ccp4, I used scalepack2mtz from Scalepack(Denzo) into MTZ format,
run as Ctruncate.
The import stopped at Twin fractione
was processed using xds or mosfilm.
Thank you for advice
Uma
On Wed, Aug 1, 2012 at 2:27 PM, Uma Ratu rosiso2...@gmail.com wrote:
Dear All:
I try to use Phaser to solve the structure by Molecular Replacement.
The data set is collected @180 degree. I process the data using HKL, and
have
:38, Uma Ratu wrote:
Dear All:
I try to solve a structure by using Phaser.
The data set was collected at 3.9 A with 98.1% (95%) completeness. Based
on pointless, the best space group for the data set is P21212. And the data
can be processed with P21, P212121 as well. The I/sigma value
.
(you will have to adjust the path /xtal/Suites/CCP4/ccp4-6.4.0
according to your installation). The file .bashrc resides in your home
directory.
Best,
Tim
On 03/11/2014 10:37 PM, Uma Ratu wrote:
Dear All:
I try to run xds in linux, but have some problems.
With xdsconv
Dear All:
I try to run xds in linux, but have some problems.
With xdsconv, it complains:
f2mtz: error while loading shared libraries: libccp4f.so.0: cannot open
shared object file: No such file or directory
cad: error while loading shared libraries: libccp4f.so.0: cannot open
shared object
Dear All:
Many thanks for your comments and inputs!
Uma
On Sat, Nov 23, 2013 at 7:14 PM, Uma Ratu rosiso2...@gmail.com wrote:
Dear All:
I use Coot to check water molecules in my model.
Most of them are in good coordinates for water.
Some of these waters have unusual coordinates
Hello,
I try to replace one of cysteine residue to CSX using Win-coot.
Here is how I did:
Extensions Modelling Replace Residue... and enter the three letter code.
The program place the CSX residue, but with break bond. The new residue is
no longer linked with other residue and not in the
. It's annoyingly complicated, but it works for me.
Hope that helps,
Bernhard
On Sep 11, 2013, at 12:56 PM, Uma Ratu rosiso2...@gmail.com wrote:
Hello,
I try to replace one of cysteine residue to CSX using Win-coot.
Here is how I did:
Extensions Modelling Replace Residue... and enter
in
you crystallization solution? This is a quite normal feature, you will find
many examples in the PDB.
You could try to model it and see how it fits the density, how your
R-factors behave, etc.
On Thu, May 16, 2013 at 8:45 AM, Uma Ratu rosiso2...@gmail.com wrote:
Dear All:
I
:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Uma
Ratu
*Sent:* Wednesday, February 13, 2013 5:38 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] S-nitrosylation protein
** **
Dear All:
I plan to use X-ray crystallography method to study the S
Dear All:
I plan to use X-ray crystallography method to study the S-nitrosylated
protein structure.
The native protein crystals diffracted to 2A with synchrontron. I now have
the crystals of S-ntrosylated protein.
Since S-NO moiety appears to be unstable to synchrotron radiation, could
you
School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-2926
http://lupo.jhsph.edu
On Oct 24, 2012, at 10:16 AM, Uma
: (315)-228-7935
email: rrowl...@colgate.edu
On 8/1/2012 2:27 PM, Uma Ratu wrote:
Dear All:
I try to use Phaser to solve the structure by Molecular Replacement.
The data set is collected @180 degree. I process the data using HKL, and
have resonable good score: rejection (0.05), Linear R-factor
Dear All:
Thank you very for your comments and advices. '
I am getting to know why are the problems. And will try again.
I appreciate you all for your inputs
regards
Uma
On Thu, Aug 2, 2012 at 4:11 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
An earlier post said the point-group is P2, and
Dear All:
I collected 5 data sets from one crystal and would like to process them
together.
Here is how I did:
In HKL2000, load the all data sets. Index each set. When I try
Intergrate, the program automatically go through the whole data sets
there, and do not go through.
I then process data
to start off a new batch, which is
mostly due to inaccurate goniostats. In that case, you will need to process
the batches individually and them combine them during scaling.
Hope that helps.
MM
On Aug 1, 2012, at 8:50 AM, Uma Ratu wrote:
Dear All:
I collected 5 data sets from one crystal
, but that's
another question (pace, ZO, WM, MM!)
On 1 Aug 2012, at 14:08, Uma Ratu wrote:
The data sets were collected from the same crystal by scan collecting
40 frames from each section. The space group of this crystal is P2.
My guess that I may have to index and integrate each set
Dear All:
I try to use Phaser to solve the structure by Molecular Replacement.
The data set is collected @180 degree. I process the data using HKL, and
have resonable good score: rejection (0.05), Linear R-factor (0.038),
completeness (98.3), resolution (50-1.5).
I then use Phaser to do MR. The
? And
subsequently, can't integrate and scala together. If so, is there a way
that I can fix it?
Thank you for your advice
Uma
On Wed, Aug 1, 2012 at 8:50 AM, Uma Ratu rosiso2...@gmail.com wrote:
Dear All:
I collected 5 data sets from one crystal and would like to process them
together.
Here is how I
] on behalf of Uma Ratu
[rosiso2...@gmail.com]
*Sent:* Monday, May 21, 2012 4:57 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Serine
Dear All:
Some of serine residues in my model have extra positive Fo-Fc density at
the edge of side chain. Some don't have. It is not like from
site that faces
the SOH group to account for a possible hydrogen bond.
Best regards
Savvas
On 04 May 2012, at 20:24, Uma Ratu rosiso2...@gmail.com wrote:
Dear All:
Thank you very much for your advices and comments.
Following your instructions, I am able to change the CYS to CSX
Dear All:
I try to convert the .cif files (the structure factor files from PDB) to
mtz file.
From ccp4i, I chose convert to/modify/extend mtz for this purpose.
But program keep complanining:
no cell information in keywords or files
I open the .cif file in text, and could not find any
copy the cell information from the PDB
web page into the ccp4i interface before running.
HTH
Martyn
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma
Ratu
Sent: 17 May 2012 20:04
To: ccp4bb
Subject: [ccp4bb] Covert Structure Factor to mtz
Dear All:
I try
Dear All:
I use Refmac5 to refine my model. After the run, I check the model quality
by Coot.
Here is the problem:
In Coot, the ligand - NAD, has bad geometry as indicated by a big red bar.
While the geometry of NAD fit nicely with the electron density.
If I use refine tools (i.e. regularize
your model to both describe the data and have
reasonable geometry.
Regards
Rob
On 26 Apr 2012, at 21:26, Uma Ratu wrote:
Hi, Alex:
Which sigma do you mean?
The one for automatic weight, not for Jelly-body refinement.
I did not turn the Jelly-body refinement on.
Thanks
Ros
Dear All:
I use Refmac5 to refine my structure model.
When I set the sigma value to 0.3 (as recommended from tutorial), the
resulted model has many red-bars by coot validation (geometry, rotamer,
especially, Temp Facotr).
I then lower the sigma value to 0.1, the resulted model is much improved
?
J-B sigma=0.01 means very small fraction of the gradient will be used in
each step. It is used usually with very low resolution (less then 3A)
Alex
On Apr 26, 2012, at 11:38 AM, Uma Ratu wrote:
Dear All:
I use Refmac5 to refine my structure model.
When I set the sigma value
Ed:
Thank you very much for your advice and inputs
regards
Ros
On Wed, Apr 18, 2012 at 8:44 AM, Ed Pozharski epozh...@umaryland.eduwrote:
On Tue, 2012-04-17 at 17:49 -0400, Uma Ratu wrote:
In order to have my target .pdb, I need to mutate the residues using
coot?
Others already
Hello,
I have a question about molecular replacement.
I use Phaser or AutoMR to generate models of my target protein. Input
.mtz is from X-ray diffraction. Template is from a known structure. I also
set up seq file using my target protein. The sequence identity between
template and my target
and the correct sequence. Not only will it build
most of the mutated residues correctly, but in its role as a model bias
remover it will fix or remove incorrect parts of the structure that may
not be obvious in the initial maps.
Uma Ratu wrote:
Hello,
I have a question about molecular replacement
and
whether the tetramer is crystallograhic or all in the asymmetric
unit, and some expert may be able to provide suggestions.
Uma Ratu wrote:
Thank you very much for your inputs and comments.
I am getting understand what is going on now.
If your resolution is high (2.2 A or better?) and you
:21 PM, Uma Ratu rosiso2...@gmail.com wrote:
Dear Roger:
Thank you very much for your comments. I use them as guideline and
remove many 'false waters.
Still, I am not clear of some of these 'waters' are real or not. I have
the pic attached.
In Pic-W11-1, the 'water' is connected
Dear All:
I try to add water to my model.
Here is how I did:
Coot: Find Wates
Map: FWT PHWT; 1.8 rmsd; Distances to protein atoms: 2.4
min/3.2 max
Coot found 270 water molecules.
I then examed these waters. Most of them had ball shape. Some had two or
more balls together.
:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Uma
Ratu
*Sent:* Thursday, 8 March 2012 10:22 a.m.
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Water
** **
Dear Roger:
Thank you very much for your comments. I use them as guideline and remove
select the best output from PHASER or REFMAC to
calculate maps. The columns FWT and PHWT are used to generate a
2mFobs-DFcalc map The columns DELFWT and PHDELWT generate a mFobs-DFcalc map
Eleanor
On Feb 29 2012, Uma Ratu wrote:
Hello,
I have a question about .mtz files used in model building
Hello,
I run my model in Coot to do Temp Fact Variance Analysis.
There are red bars from the B-factor Variance graphy.
I click each red bar to exam the residues in Coot. Many of these residues
do not have the electronic density on their side chains, especially Lys
residues.
Here is my questions:
***
On Thu, Mar 1, 2012 at 9:26 AM, Uma Ratu rosiso2...@gmail.com wrote:
Hello,
I run my model in Coot to do Temp Fact Variance Analysis.
There are red bars from the B-factor Variance graphy.
I click each red bar to exam the residues in Coot. Many
as you build and refine.
HTH,
Fred.
Uma Ratu wrote:
Hello,
I have a question about .mtz files used in model building.
Here is how I did:
Diffraction data - HKL 2000: .sca
CCp4i: scalepack2mtz: .mtz (1)
Phaser: In: template pdb .mtz(1)
Out: model .pdb(1) .mtz(2)
Refmac5
Dear All:
I am having trouble with Coot.
The program keeps crashing when I click on rotamer analysis. Other
functions, sych as geometry analysis all worked fine.
It runs normal before, and only happened when I added the ligands into the
model.
I am using WinCoot_0.7_pre-1-revision-3772, and
39 matches
Mail list logo
