[ccp4bb] The 10% Gap between R-factor and R-free

[Wenhua Zhang]

Good Morning to ALL,

   I encountered large gaps between R-factor and R-free, eg. 10% and 
11%,  during refining several structures with either Refmac or 
Phenix.refine.
  The data were reduced and scaled at resolution with I/SIGMA higher 
than 2.3.
  The model fits and density pretty well despite a few side chains 
missing density.


  I may ask for the reasons that result in such large difference 
between R and R free and some ways to examine and improve the refinement.


 Thanks in advance

Wenhua

Univ. Paris-Sud XI, Orsay


On 11/25/2013 6:03 PM, Beatrice Vallone wrote:
Please check the announcement for 2014 ESRF Users' Meeting & 
Associated Structural Biology Workshop.


Invitation to the 2014 ESRF Users' Meeting & Associated Workshops to 
meet and discuss with fellow users, get inspired, establish new 
scientific collaborations and learn about future opportunities offered 
by the ESRF for your research.


Workshop on*"Structural Biology at ESRF: Past, Present & Future 
"*

3 - 5 February

The Plenary Meeting  will feature:

  *5 plenary lectures by world leading scientists covering a large
spectrum of ESRF activities;
  * a presentation on the status of the facility and on the progress
of the Upgrade Programme;
  * a talk by the winner of the prestigious "ESRF Young Scientist Award";
  * a poster session;
  * a banquet, with awards to the ESRF Young Scientist Award and for
the best poster

Programs for the Meeting and Workshops are available at:

http://www.esrf.eu/home/events/conferences/um2014.html

   Regards to all,

   Beatrice Vallone
ESRF User Organization Committee

[ccp4bb] drawing topology digram

[Wenhua ZHANG]

Dear all,

  Could anyone recommend me an easy program to draw the secondary topology 
digram of protein structure? The PDBsum seems working only for deposited 
structures.

  Thank you.

Wenhua ZHANG 

Re: [ccp4bb] Requesting old data sets

[Wenhua Zhang]

Dear Juergen,
  That's a practically important approach to recheck the details of structures. 
I refined from the structure factor files of two published structures related 
to my subject and already found some key information that was missing in the 
published ones. So it would be more confident if original images could be 
retrieved. I would offer upon request.


Thank you for posting the topic!

Wenhua Zhang
--- Mail sent from my iPhone ---

On 3 juil. 2012, at 04:39, "Bosch, Juergen"  wrote:

> Dear CCP4 community,
> what's the general opinion regarding sharing old published data sets ?
> Would you be offended if I asked you for your raw images from say a 5-10 year 
> old structure ?
> And then the more tricky question, what if I find something you overlooked 
> and I would perhaps be able to use that information ?
> 
> Any suggestions and advice are welcome on or off board.
> 
> Thanks,
> 
> Jürgen 
> 
> ..
> Jürgen Bosch
> Johns Hopkins Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Phone: +1-410-614-4742
> Lab:  +1-410-614-4894
> Fax:  +1-410-955-3655
> http://lupo.jhsph.edu

[ccp4bb] practical protocol to remove cell culture derived Threonine from the protein

[Wenhua Zhang]

Dear ALL,

   The threonine is found in the active site of my protein structure 
from the crystallization in the absence of any threonine containing 
chemicals. I presume that's why there was no signals detected with the 
ITC experiment in which I titrate my protein with Threonine. In the in 
vitro biochemical assay, threonine is one of the substrates in the 
reconsitituted system.
   So could anyone offer me a practical protocol to remove the 
threonine from the protein for further experiment to confirm the binding 
of Threonine to my protein by ITC.


  Thank you all.

Wenhua

Ph. D student in structural biology

Paris-Sud XI,  France

Re: [ccp4bb] Sad News, Defend our CCP4BB community

[Wenhua Zhang]

Dear all,

  I see that the CCP4BB community is becoming less pure due to our 
failure to post structure determination-oriented inquiries and questions 
that can't be answered by googling them.

  Let's filter our questions before attempting to post.

  Wenhua

On 2/28/2012 4:16 PM, Gerard Bricogne wrote:

Dear Smita,

  For me, your story mostly illustrates the grave dangers of wanting to
own a BMW while still in high school ... ;-) .


  With best wishes,

   Gerard.

--
On Tue, Feb 28, 2012 at 09:02:42AM -0600, Smita Mohanty wrote:

Yes, this is of course a scam.  My husband was almost duped by someone
who wrote in the name of a close friend saying that he got mugged in
Europe and to send money to return to USA. My husband of course was
ready to send for his colleague but just gave a call to his friend to
make this not a scam.  Of course, it was a scam.

Only last night we saved ourselves from another scam.  I think it is
good share with the group.  My son (in high school) found a 2005 BMW X5
on an internet site.  The car's blue book price is $26,000 but the
asking price by the seller is $2775.  Sounds too good to be true.   But
when my son (who dreams to own a BMW) contacted the owner (Amanda
Stone), she replied him immediately saying her son died two months back
in an automobile accident hit by a drunk driver while riding his
fiancee's car.  She simply wants to sell the car so that someone else
can use it and she is not interested in making money.  She said that she
has a deal with e-bay and that the car will be shipped by e-bay to the
buyer once the buyer pays the price that will be hold by e-bay.  The
buyer has 5 days to check the car out and if decides not to buy, the car
will be shipped back to e-bay at seller's cost and buyer gets back his
money.  She sent an invoice that was from e-bay with e-bay logo and
exactly looking genuine.

She sent car pictures and Vin and my husband checked the car out with
car fax.  She wanted the money to be sent to a e-bay financial expert
through moneygram although she sent name and address of an e-bay expert.
  That is when my husband called up e-bay just to make sure before he
send the moneygram out.  That is when e-bay told him this is a scam and
that e-bay never asks for moneygram.  That all transactions are done on
e-bay site only and that e-bay does not get any contract like the one we
had.  E-bay told us that their logo has/can be copied to make an invoice
appears to have come from them.  Of course, we went all communications
and invoice to e-bay.  We lost only $35 for car fax.

Lesson: we need to be aware of any advertisements on internet or
unsolicited e-mails.  Here is a site to read about different scams-

http://www.fbi.gov/scams-safety/be_crime_smart

Thanks,

Smita


Vellieux Frederic  2/28/2012 7:01 AM>>>

From: regnicat@, reply to: regniica@...

Somehow I don't believe someone in such a situation would write to
ccp4bb instead of calling the family back home. Using Skype since there

is apparently internet access !

And I rather view with my mind's eye someone sitting in an internet
cafe
in (say) Lagos, or the Paris suburbs or Kingston or...

Fred

Catherine Regni wrote:

I'm writing this with tears in my eyes,my family and I came over here
to Madrid,Spain for a short vacation. unfortunately,we were  mugged

at

the park of the hotel where we stayed,all cash and credit card were
stolen off us but luckily for us we still have our passports with

us.

  We've been to the Embassy and the Police here but they're not

helping

issues at all and our flight leaves in few hours from now but we're
having problems settling the hotel bills and the hotel manager won't
let us leave until we settle the bills. Well I really need your
financial assistance..Please, Let me know if you can help us out? Am
freaked out at the Moment.

Catherine Regni..

Catherine Regni, Ph.D.