Dear Everyone,
I have to work at home because of the budget cut. However, I still want to do
some research at this difficult time.
I have been used to viewing the crystal structures with stereo view with
program O. I want to find out is it possible to install the stereo option in my
labtop. I
From: Eleanor Dodson
To: Sun Tang
Cc: CCP4BB@jiscmail.ac.uk
Sent: Wednesday, July 8, 2009 10:06:41 AM
Subject: Re: [ccp4bb] Why NCS doesn't help?
There are many reasons why this could have ocurred.
One is that your NCS operator is very close to being a crystallographic
one.
But you need to
the refinement?
Thank you very much for your suggestions?
Best wishes,
Sun Tang
Dear All,
Thank you very much for all your suggestions. They are very helpful in my
further refinements. I am adding some more information about the problem:
1) The Z-score is 11.2 and LLG is 125.
2) The model has 390 aa while my structure has about 440 aa.
Please let me know of any further su
Dear All,
Recently I solved a structure at 2.5 A with PHASER, with two molecules in
assymetric unit. There are no short contacts in the solution. However, the
Rfree stays at about 50% after the refinement of rigid boby and restrained
refinement in CNS. The sequences homology is about 30%.
Wha
[ccp4bb] question about getting rid of model bias in refinement
To: [EMAIL PROTECTED]
Date: Thursday, July 31, 2008, 11:41 AM
Sun Tang wrote:
> Hello Everyone,
>
> I have a question about getting rid of model bias in refinement with
refmac. I solved the structure with molecular replacement.
NS,
with the residues in question omitted. CNS also allows you to make a
composite-omit map. I haven't seen that in phenix yet but presumably it is
doable.
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Jul 25, 2008, at 10:53 PM, Sun Tang wrote:
He
Hello Everyone,
I have a question about getting rid of model bias in refinement with refmac. I
solved the structure with molecular replacement. After final refinement of the
structure, I found out some key amino acids in the structure and wanted to make
sure their conformations are correct. I
downloaded the input files from the CNS website and I tried true and false
for the renaming segid but all did not work.
Thank you very much!
Best,
Sun Tang
-
Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
e wavelength of 1 A. Do I need to adjust the
wavelength to maximize the anomalous signal from Mn or Ca?
Any ideas and suggestions are greatly appreciated!
Sun Tang
-
Never miss a thing. Make Yahoo your homepage.
your suggestions!
Best wishes,
Sun Tang
-
Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
0.186/0.267 (FOM=0.807) for wa=0.2, respectively. It seemed that increase in wa
decreases both R and Rfree with R more than Rfree.
Which wa value is the best one in this case?
Thank you very much for your valuable help.
Best,
Sun
Ian Tickle <[EMAIL PROTECTED]> wrote:
Hi Su
Hi Anastassis,
Thank you very much for your suggestions. I answered the questions as follows.
I used NCS before rigid body refinement. After that I did not put NCS
restraints in the restrained refinement and TLS+restrained refinement because
it raised the R/Rfree quite a lot.
The resolution is
Goettingen
GPG Key ID = A46BEE1A
On Mon, 4 Feb 2008, Sun Tang wrote:
> Hello All,
>
> I refined a structure with Refmac in CCP4i and the R/Rfree is 0.215/0.277.
> The difference between R and Rfree is too much even though I used 0.01 for
> weighting term in the refinement (the
amachandran outliers, etc., map) are OK you should
just be happy with your structure.
Cheers,
Boaz
- Original Message -----
From: Sun Tang <[EMAIL PROTECTED]>
Date: Monday, February 4, 2008 18:41
Subject: [ccp4bb] an over refined structure
To: CCP4BB@JISCMAIL.A
.
What may be wrong with the over-refined structure? What is the reason for
leading to an over-refined structure? How to avoid it?
Best wishes,
Sun Tang
-
Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
Hi James,
I did check teh B-factors and they are similar to the flanking regions (about
40). The difference density appeared at the later stage of refinement (TLS and
restrained in CCP4i).
What do you think and how to do it?
Best,
Sun Tang
James Irving <[EMAIL PROTECTED]> wrote: Hi
nearby residues. This
confused me. Any ideas?
Thank you again for your suggestions.
Best,
Sun Tang
Eleanor Dodson <[EMAIL PROTECTED]> wrote: Hard to say without more information.
Have you refined the B factors for these residues? Most building
software gives some arbitrary b value,
occupancy for those residues?
Thank you very much for your opinions and suggestions!
Best wishes,
Sun Tang
-
Never miss a thing. Make Yahoo your homepage.
the TLS and restrained
refinement in CCP4i. It is hard to tell from the R-factor because they are only
a very small part of the whole structure. Can anyone tell whether it is the
correct way to do?
Any suggestions are greatly appreciated.
Thank you very much!
Sincerely,
Sun
the second one, the
density is much worse than the first one. Are there any ways to improve the
density of the second molecule, such as some kinds of averaging? Why that
happens?
Thank you very much for your help!
Sincerely,
Sun Tang
[EMAIL PROTECTED
21 matches
Mail list logo
