t, and trying again
> Eleanor
>
>
>
>
>
>
>
> On 8 December 2014 at 21:51, Uma Ratu wrote:
>
>> Dear All:
>>
>> I try to import the .sca file from hkl2000.
>>
>> The data was scaled as "P212121" from HKL2000.
>>
>>
rnal
> Academic Editor of PLoS One
>
>
>
>
>
>
> On 30 Jul 2014, at 18:38, 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
&g
was processed using xds or mosfilm.
Thank you for advice
Uma
On Wed, Aug 1, 2012 at 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
> h
pe it each time you want to use ccp4.
>
> (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 Al
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 file:
Dear All:
Many thanks for your comments and inputs!
Uma
On Sat, Nov 23, 2013 at 7:14 PM, Uma Ratu 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 coordin
ack to the
> original chain ID. It's annoyingly complicated, but it works for me.
>
> Hope that helps,
> Bernhard
>
>
>
> On Sep 11, 2013, at 12:56 PM, Uma Ratu wrote:
>
> Hello,
>
> I try to replace one of cysteine residue to CSX using Win-coot.
>
>
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 cha
t; 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 wrote:
>
>> De
Good luck
>
> ** **
>
> Thierry
>
> ** **
>
> *From:* 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
&g
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 advic
igands.
> Next you open your set of coordinates and only import those ligands which
> are in the right position. You will end up with your tetramer and 4 ligands
> sitting in the right position. If not then I misunderstood your original
> post.
>
> Jürgen
>
> On Oct 24, 2012
+1-410-614-4894
> Fax: +1-410-955-2926
> http://lupo.jhsph.edu
>
> On Oct 24, 2012, at 10:16 AM, Uma Ratu wrote:
>
> Hello,
>
> I have problems to find the ligand using WinCoot.
>
> The protein was purified with NADH, and crystallized. Data diffraction is
&g
ssor
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: rrowl...@colgate.edu
>
> On 8/1/2012 2:27 PM, Uma Ratu wrote:
>
> Dear All:
>
> I try to us
y *
> *East Lansing, MI 48824-1319*
> *Office:** **(517) 355-9724 Lab: (517) 353-9125***
> *FAX: (517) 353-9334 Email: rmgarav...@gmail.com*
> **
>
>
>
>
> On Aug 1, 2012, at 4:37 PM, Uma R
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 wrote:
> An earlier post said the point-group is P2, and these reported cells d
? 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 wrote:
> Dear All:
>
> I collected 5 data sets from one crystal and would like to process them
> together.
>
&g
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
ess.
> >
> > Of course, I'd use Mosflm/Pointless/Aimless rather than HKL, 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&
doesn't work, the parameters at
> the end of one batch may not be accurate 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.
>
&
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 dat
Dear All:
I process my data using HKL2000.
After scale, the program generates several files, including .out, .log and
.sca.
Is there a way that I can generate a summary report file from the .out
file, such as Rmerge, total number of observation, and completeness so on.
XDS give a nice report wi
ulletin board [CCP4BB@JISCMAIL.AC.UK] 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
opy 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
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 info
e active 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 wrote:
>
> Dear All:
>
> Thank you very much for your advices and comments.
>
> Following your instr
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 Zo
ry low sigma will cause geometry
>> to be more tightly restrained towards "ideal" values, which is why you
>> observe improvements in Coot validation. Note that strengthening the
>> geometry weight causes the observations (data) to be less influential in
>> refinement. T
nement?
> 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
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 b
Ed:
Thank you very much for your advice and inputs
regards
Ros
On Wed, Apr 18, 2012 at 8:44 AM, Ed Pozharski wrote:
> 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
; dimer a heterodimer? Provide more details like space group 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.
>>
>&
odel", giving it
> your current model 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
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
Hello,
One of my crystal diffracted to 20A. I collected 4 snaps and would like to
get the information on space group and cell dimensions.
I opened the images in iMosflm. The files are .cbf
Is there way I can find such information in iMosflm?
Thank you for advice.
Ros
ard has an option to search for
>> "hihgly-coordinated waters" like the one you have pictured.
>>
>> Hope this helps,
>> Partha
>>
>> On Wed, Mar 7, 2012 at 4:21 PM, Uma Ratu wrote:
>>
>>> Dear Roger:
>>>
>>> Thank you
ra Taiwhanga Putaiao
> Te 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
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. Some
stry Department
> Duke University
> Alex H. Sands, Jr. Building
> 303 Research Drive
> RM 250
> Durham, NC 27710
> P: 919-684-5178
> ***
>
>
>
> On Thu, Mar 1, 2012 at 9:26 AM, Uma Ratu wrote:
>
>> Hello,
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
master mtz as input..
>
> coot will automatically 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 29 201
ing
> introduced... Thus the maps improve seen that your model should reflect
> more and more what is present in the crystal as you build and refine.
>
> HTH,
>
> Fred.
>
>
> Uma Ratu wrote:
>
>> Hello,
>> I have a question about .mtz files used in model bui
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: model .pdb(2) & .mtz(3)
Here is the question:
1. Coot check
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
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