Hi,
> Anyone please tell me
> the name of programme which can be used to draw enzyme reaction
mechanism (
> like Sn1 and Sn2). Your kind help will be much appreciated
BKChem is also free software.
http://bkchem.zirael.org/
Takanori Nakane
xdrawchem is free and will do this.
On May 31, 2012, at 8:01 PM, Appu kumar wrote:
> Dear ccp4 user,
> Sorry for offset question, Anyone please tell me
> the name of programme which can be used to draw enzyme reaction mechanism (
> like Sn1 and Sn2). Your kind hel
Dear ccp4 user,
Sorry for offset question, Anyone please tell me
the name of programme which can be used to draw enzyme reaction mechanism (
like Sn1 and Sn2). Your kind help will be much appreciated
Thank you
Appu
Leo will probably answer better than I can, but I would say I/SigI counts only
the present reflection, so eliminating noise by anisotropic truncation should
improve it, raising the average I/SigI in the last shell.
F/sigF is expected to be better than I/sigI because dx^2 = 2Xdx,
dx^2/x^2 = 2dx/x,
I am little curious about the anisotropically truncated data for 3RKO:
Percent Possible(All)96.0
Mean I Over Sigma(Observed) 0.8
In the supplementary table of the nature paper it was made clear that this
3.16-3.0A, I/sigmaI=0.8 and Rmerge=1.216 shell was the outer shell of the
a
In the meantime we could follow Phoebe Rice's example and put
the resolution at I/sigma=2 in REMARK 2 "resolution of structure"
but put the actual bleeding-edge resolution we used in the
reduction and refinement statistics (At least if the PDB
will allow us to have different values in these three
> There are things you can expect to learn from a
> 2Å structure that you are unlikely to learn from a 5Å structure, even
> if equal care has been given to both experiments, so it makes sense
> for the title to give the potential reader an idea which of the two
> cases is presented. But for this p
On Thursday, May 31, 2012 02:21:45 pm Dale Tronrud wrote:
>The resolution limit of the data set has been such an important
> indicator of the quality of the resulting model (rightly or wrongly)
> that it often is included in the title of the paper itself. Despite
> the fact that we now want to
Good idea, but how to get it to catch on without publishing in Science?
JPK
On Thu, May 31, 2012 at 4:21 PM, Dale Tronrud wrote:
>
> On 05/31/12 12:07, Jacob Keller wrote:
>> Alas, how many lines like the following from a recent Science paper
>> (PMID: 22605777), probably reviewer-incited, could
On 05/31/12 12:07, Jacob Keller wrote:
> Alas, how many lines like the following from a recent Science paper
> (PMID: 22605777), probably reviewer-incited, could have been avoided!
>
> "Here, we present three high-resolution crystal structures of the
> Thermus thermophilus (Tth) 70S ribosome in com
Alas, how many lines like the following from a recent Science paper
(PMID: 22605777), probably reviewer-incited, could have been avoided!
"Here, we present three high-resolution crystal structures of the
Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or
YfiA that were refined by
Yes! I want a copy of this program RESCUT.
REMARK 200 R SYM FOR SHELL(I) : 1.21700
I noticed structure 3RKO reported Rmerge in the last shell greater
than 1, suggesting the police who were defending R-merge were fighting
a losing battle. And this provides a lot of ammunition to those
A list that you might want to check if it is useful for you.
http://www.caver.cz/index.php?sid=133
Enjoy.
Allan
Quoting "Zhou, Tongqing (NIH/VRC) [E]" :
Dear All,
I am looking for a way to calculate the size of a protein cavity
which is occupied by a loop from a ligand protein. The goal
We used VOIDOO recently and it worked well
Kleywegt, G. J. & Jones, T. A. (1994). Detection, delineation,
measurement and display of cavities in macromolecular structures. Acta
Crystallogr. D Biol. Crystallogr. 50, 178-185.
On Thu, May 31, 2012 at 12:41 PM, Zhou, Tongqing (NIH/VRC) [E]
wrote:
>
Rpim (from the East) just told me "You don't need to be helped any longer.
You've always had the power to go back to Kansas."
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Oganesyan, Vaheh
Sent: Thursday, May 31, 2012 2:27 PM
To: CCP4BB@JISCMAIL
It wasn't doing well lately. So, it was expected.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller
[j-kell...@fsm.northwestern.edu]
Sent: Thursday, May 31, 2012 2:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Death of Rmerge
Meant to include the following link in the previous message:
http://www.youtube.com/watch?v=9Jn8K8EA7-Q
JPK
On Thu, May 31, 2012 at 1:20 PM, Jacob Keller
wrote:
> Dear Crystallographers,
>
> in case you have not heard, it would appear that the Rmerge statistic
> has died as of the publication
Hi,
You could try CASTp (http://sts.bioengr.uic.edu/castp/). If your protein is in the pdb it may well be in their database, if not, just upload it.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Dear All,
I am looking for a way to calculate the size of a protein cavity which is
occupied by a loop from a ligand protein. The goal is to see what's the maximum
length of peptide allowed in this cavity.
Thanks,
Tongqing
Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccin
Hi all,
E3 ubiquitin ligase is responsible for flagging proteins for degradation by
transferring ubiquitin from a donor protein onto the molecule to be degraded.
It is activated by phosphorylation of a tyrosine which promotes a huge
conformational change, swinging its RING domain 180 degrees t
Hi Eleanor,
was there recently an update to beverage ? Could you send me a link to version
2.0 perhaps ?
And more importantly it hopefully was compiled with EtOH and some vitamins :-)
Jürgen
On May 31, 2012, at 7:02 AM, Eleanor Dodson wrote:
Or do something like beverage, and again you will s
Post-Doctoral Research Assistant in Biochemistry
Molecular Diagnostics and Thereputics
*University of Southampton*
*Location: *Highfield Campus
*Salary: * £27,578 to £33,884
Full Time Fixed Term
*Closing Date: * Tuesday 12 June 2012
*Interview Date: * To be confirmed
*Reference
Space groups F23 and P4132 are not subgroups of each other (without
invoking pseudotranslational symmetry) so they cannot be related by
twinning. The end of theoretical analysis.
Zbyszek Otwinowski
> You need to say what the cell dimensions are for these 2 options..
> Eleanor
>
> On 29 May 2
Well - I am not familiar with the PHENIX dictionary but you are right; if
you restrain metal bond distances the structure will reflect the restraints
but if you don't restrain the distances then the respective gradients for a
light atom and a heavy one can produce some very odd and unrealistic
resu
You need to say what the cell dimensions are for these 2 options..
Eleanor
On 29 May 2012 15:59, Andrey Lebedev wrote:
> Hi Mike.
>
> I would be more careful about "incorrect" space group. Yes, sometimes
> auto-indexing gives strange results.
> However, in your case two sets of crystals differ
Do you have the SEQRES residues?
If these are properly generated, that should be a complete list of what is
in the crystallisation, and any missing residues will just not be there in
the pdb.
Any program which displays residue properties by number will show these up.
Try the validation in coot - de
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