Hi,
Last couple of times I asked myself the same question (what does it
look like?) I used ssm (or PDBeFold as seems to be called now).
http://www.ebi.ac.uk/msd-srv/ssm/
HTH,
Fred.
Liu Zhao wrote:
The structure of my protein is as shown as the purple one. Another one
,as shown as
You're welcome!
Next time, irrespective of whether your structure is a new one or not,
please upload your images to picasa, flickr, your university's file
sharing server or some such thing and include the link in your email.
Don't flood several thousand inboxes with megabytes of pixels. And
A post-doctoral position is available to join the group of Pr. E.
Pebay-Peyroula at IBS (Institut de Biologie Structurale, Grenoble,
http://www.ibs.fr). The group explores functional and structural aspects
of membrane proteins mainly focussing on the mitochondrial carriers family.
The
Dear CCP4 users:
This email is to encourage you to join the Young Scientist Special Interest
Linkedin Group, as part of the American Crystallographic Association. Anyone
with an interest in promoting the professional development of young
scientists in the field of crystallography is encouraged
Hi Liu,
If I understand your question correctly, youre asking how different
do two structures need to be for one to be new'. If by new you
mean a new fold, then the answer is NO. Your structure and the homolog
have the same fold.
However, if your structure is the first structure of a
On 12/20/10 05:49, Liu Zhao wrote:
The structure of my protein is as shown as the purple one. Another one
,as shown as green,is homologous .But the structure of my protein
can't be obtained by using molecular replacement. And both structures
have much different, especially in B chain. If my
On Sun, 2010-12-19 at 18:58 -0500, Hailiang Zhang wrote:
(1). CTLS=a, CC=b
(2). CTLS=a, CC=0; followed by: CTLS=0, CC=b
In (2), you are doing two separate runs, with the second not using TLS.
If you want to combine TLS and positional refinement, you must have them
included in the same refmac
I would try it with the latest version (5.6.x) in case there's a bug.
That's a very old version you're still using!
-- Ian
On Sun, Dec 19, 2010 at 11:58 PM, Hailiang Zhang zhan...@umbc.edu wrote:
Hi,
I am using REFMAC 5.2.0019 to run the following script:
***
refmac5 hklin a
PS one other thought: in your run 2b you are not reading in (as TLSIN)
the TLSOUT file produced by run 2a. So run 2b is not starting from
the same point that it would have done as in run 1.
I.
On Sun, Dec 19, 2010 at 11:58 PM, Hailiang Zhang zhan...@umbc.edu wrote:
Hi,
I am using REFMAC
Hi All,
Recently I solved a structure in which some water molecules have
Bfactors at 0 and overall wilson Bfactor is 0.654 based on PHENIX
refinement. Is it possible?
Bill Lu
On Mon, Dec 20, 2010 at 7:34 AM, Zhibing Lu billz...@gmail.com wrote:
Recently I solved a structure in which some water molecules have Bfactors
at 0 and overall wilson Bfactor is 0.654 based on PHENIX refinement. Is it
possible?
Very unlikely - it might be worth trying the latest nightly
Dear Hailiang,
I regularly separate TLS refinement from restraint refinement to spead things
up when I try to optimise the restraint weights. Using Refmac 5.6, I do the
following:
- Do TLS Refinement in refmac
- Use TLSanl to change the total B-factors to residual B-factors.
- Load the output
Thanks Ian, but I was using the output from 2a for 2b running. Results are
still different between 2 and 1. More curious is more second question, the
region with identical ADPs still ended up with identical ADPs (although
different from before running) after 1, and that's why I also tried 2.
some water molecules have Bfactors at 0
B-factors refining towards zero may be an indication of heavier molecules,
e.g. SO4. You have to model them manually.
Ralf
On Mon, 2010-12-20 at 13:11 -0500, Hailiang Zhang wrote:
Thanks Ian, but I was using the output from 2a for 2b running.
It's not enough to use the pdb output - you have to make the proper tls
input file for refmac to incorporate the tls correction
--
I'd jump in myself, if I weren't so good at
Hi Liu
Looks like (on the images you show) that you have a nice conformational
difference for some of the helices between the 2 structures...
Happy Hols
Gina
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Justin Hall
Sent: Monday, December 20,
Mg2+ is (almost) aways octahedrally coordinated, usually by oxygen atoms, with
distances of ~2A.
Phil
On 20 Dec 2010, at 21:16, jlliu liu wrote:
Hi All,
I am refining a structure and encountered a problem of modeling a difference
density as water or Mg2+, and would like to hear opinions
what is the .odp file extension?
JPK
On Mon, Dec 20, 2010 at 3:48 PM, Robbie Joosten
robbie_joos...@hotmail.com wrote:
Dear jlliu liu,
Also note that Mg2+ is significantly smaller than water. It fits in places
where water cannot go. This doesn't look like a magnesium site on first
glance.
If it's more than likely Mg and it's easy to grow crystals, try
soaking/cogrowing BaCl2/BaOAc. At least in the RNA world, Mg sites can
easily be displaced by Ba. The latter of course has anomalous signal
on the home sources. Place your divalents using the anomalous diff map.
Have no clue
On 20/12/10 21:48, Robbie Joosten wrote:
Also note that Mg2+ is significantly smaller than water. It fits in
places where water cannot go. This doesn't look like a magnesium site
on first glance.
I tend to agree with Robbie. I wonder what WASP would say... (if you
use Coot, you can try
Sorry, the attachment is in here.
Doesn't look like Mg2+ at all. Distances are too long, Mg is never
coordinated by amides and if it were Mg you would have seen waters around it.
Looks like tightly bound water to me.
- Dima
On Mon, Dec 20, 2010 at 4:16 PM, jlliu liu
On 12/20/2010 10:34 AM, Zhibing Lu wrote:
Hi All,
Recently I solved a structure in which some water molecules have
Bfactors at 0 and overall wilson Bfactor is 0.654 based on PHENIX
refinement. Is it possible?
Bill Lu
Hi Bill,
What resolution are you working with here? An overall Wilson B
Hi Bill,
if you put a water oxygen in place where a heavier atom is, then water
oxygen's B-factor will refine to a value close to zero. This is the feature
that we currently use as one of many criteria to develop automatic
identification and building of metals.
Overall Wilson B-factor of 0.6A**2
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