Dear Lakshmanan Govindasamy,
I cannot find the related information in refmac5 document. Could you
please help me?
Thanks.
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
**from thunderbird**
On 08/01/2012 04:43 AM, Lakshmanan Govindasamy wrote:
re
Thank you all for quick replies. The issue has been solved by using
sortwater and a little manual editing. Using PDBe could be a easier
way. Next time I may try it.
Best,
Zhiyi
On 7/31/12, Eleanor Dodson wrote:
> The old fashioned water tidy will try to assign matching (non-standard)
> names to
Folks
The latest issue of the Computational Crystallography Newsletter is
available on-line at http://www.phenix-online.org/newsletter for
download. The articles are of general interest to protein
crystallographers and are listed below.
Enjoy
Nigel Moriarty
Articles
---
cctbx tools for
Resending for posting.
From: Marshman, David (TSD)
Sent: Tuesday, July 31, 2012 9:00 AM
To: ccp4bb@jiscmail.ac.uk
Subject: Principal Scientist, Crystallography at Takeda California (San
Diego)
Principal Scientist, Crystallography at Takeda California (San Diego)
Summary
Plays a leading
Dear all,
When we are running the rigidbody refinement of refmac5, if we do not
assign the rigidbody group in CCP4i GUI, what's the default rigidbody group
in refmac5?
Is it a rigidbody for each chain?
Thanks a lot.
HKL2000 does not have an "observed criterion sigma (F)" since Scalepack
deals with intensities. Leave that entry blank. Scalepack uses
observed criterion sigma (I) = -3
On question #2 you always want to quote the statistics (completeness,
Rsym, I/sigI etc) for the highest resolution shell bu
Hi Uma,
In HKL2000, if you go to Report menu (near to Help menu) you will see
the option for generation of tables.
Hope this helps.
With regards
S. Karthikeyan
On 7/31/2012 6:57 PM, Uma Ratu wrote:
Dear All:
I process my data using HKL2000.
After scale, the program generates several fi
Hi Uma,
The scale.log file contains all of those values. They're all near the bottom of
the file. Also, once you refine your structure, refmac will print out most of
those numbers in the .pdb file.
---
Greg Costakes
Hi folks
First off, apologies to all who are not members of the BCA, since this is a
question for the BCA members amongst you - I asked BCA to send out an advert
for this course, and their admin people say they have done so - but I haven't
received it, so I was wondering if anyone had got it?
Dear Ian,
Yes, the expression "lattice mode" I used is synonymous with "centring
type". The choice of a rhombohedral vs. a hexagonal cell would be a choice
of centring type, whereas the choice of obverse vs. reverse would be a
choice of setting. A clear operational difference between the two
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
Dear all
i have two basic queries
1) i have processed my data in HKL 2000 and during pdb submission i need to
know the value of observed criterion sigma (F) and observed criterion sigma
(I).
2) during entering data in category resolution shell whether one needs to
mention the statistics of each
Hi,
The second Patterson peak is twice the first (considering lattice translations,
where 1 is equivalent to 0 modulo 1), and then if you triple the first vector
you'll get minus the first vector (again considering lattice translations, i.e.
3/4 is equal to 1 - 1/4 which is equivalent to
-1/4)
It's a P212121 dataset. I have used phaser to find four solution in ASU.
This is the phaser log file:
PEUDO-TRANSLATIONAL NCS VECTOR
--
Space Group : P 21 21 21
Pat
Dear Gerard
Your point concerning my admittedly somewhat cavalier usage of the
term 'setting' in the R23:r vs R23:h context is well taken, however I
would point out that a) I'm not the first to use this terminology
(e.g. the CCN article I referred to talks about "triple-cell
settings"), and b) ITC
My understanding is that ML functions in the presence of pseudo-translational
symmetry are suboptimal (see a very short discussion in Acta Cryst. (2011).
D67, 355–367. Acta Cryst. (2008). D64, 99–107 is also a good reading).
Having said that if your crystal/dataset exhibits twinning on top of
ps
Dear all,
Can I use the "twin refinement" to refine the pesudo-translational symmetry
dataset?
Thanks a lot for your help.
Best wishes,
Qixu Cai
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