Dear, Dale, Lijun, Michael and all,
Thank you all very much for your comment and discussion, from which not only do
I find the answer to my question, but also I have learned a lot.
In my case, both substrates are in the same form, saying 'D'. And I don't
expect extra energy to break the EQ
Date: Sat, 22 May 2010 11:17:41 +0800
From: rh_ibp2...@hotmail.com
Subject: [ccp4bb]
To: CCP4BB@JISCMAIL.AC.UK
Dear all,
Recently, I am working on a complex which includes two protein subunits. The
interaction was based on the Zinc Finger motif of one protein. I co-purified
the complex
Dear all,
Recently, I am working on a complex which includes two protein subunits. The
interaction was based on the Zinc Finger motif of one protein. I co-purified
the complex by nickel affinity column with one protein bearing a C terminal His
tag and the other without any affinity tags. Ho
Hello,
I was just wondering whether there is some other tools in eg CCP4, Phenix or
CNS to calculate real-space R in the general way in absolute values.
related to your question: in PHENIX you can get a table of map CC
(computed between model and 2mFo-DFc maps), and the value of mFo-DFc a
Hello all,
I'm forwarding a question from my labmate Hailiang Zhang regarding
OVERLAPMAP and real-space R factors.
Thanks in advance for your suggestions.
Nasos Dousis
Rice University
P.S. Can someone please add haili...@bcm.tmc.edu to the CCP4BB listserv?
Original Message
I think we are having a problem with the definition of "reversible"
and "irreversible". By Lijun's definition the reaction is irreversible
because it proceeds from far from equilibrium toward equilibrium. That
situation is more a property of the system than the enzyme. If you make
the enzyme
If I understand what you are saying, I think it is too.
You imply that asymmetry in the enzyme results in two isomerase
pathways. This may be true, but it has no consequence on the
prospects for irreversibility. To avoid confusion, let's call these
pathways "D" and "S". Both the "D" and "S"
Hi Shiva,
Not directly related to the problem you reported, but I wanted
to warn you that in refmac 5.5.0072 the default is for the keyword
TLSD WATERS ADD
to be applied. This keyword tells refmac to assign all of
your water molecules to existing TLS groups. (It does this quietly
without any n
On May 20, 2010, at 1:39 PM, Lijun Liu wrote:
I think this is somehow tortured, especially by a quick reading of
Dale's explanation.
If I understand what you are saying, I think it is too.
You imply that asymmetry in the enzyme results in two isomerase
pathways. This may be true, but it
Dear Filip, CCP4BB, 3DEM, and PDB-L list members,
Thank you for your enthusiastic showing of community support for mandatory
deposition of cryoEM maps to EMDB and for their timely release.
The two year hold is available to EMDB depositors for just one practical
reason: it encourages deposition
Try ESPript..
Gauri
I may be a pessimist, but I'd focus my efforts on getting
experimental phases. It can be hard to tell a correct
molecular replacement solution from garbage with that kind of
data, and it can be a real time sink because its hard to know
when to quit.
If you can get an SeMet data set, even it it doe
Dear All,
Thank you for the several responses. Please see the summary below.
1. Several of them: complain to Qiagen (two or three said: protests loudly).
Unfortunately, my e-mail to the Qiagen marketing manager never got any reply. I
e-mailed to him on 5-12-10. Let me know if you need his e-m
Dear All,
I'm trying to prepare an alignment figure of 2 proteins that highlight
conserved and similar residues and probably secondary structures; I will
greatly appreciate it if anybody can recommend a software that I can
use. Thanks, Mohd
Also check if you have correctly estimated no. of molecules in asymmetric
unit.
On Fri, May 21, 2010 at 4:58 PM, Tim Gruene wrote:
> Dear intekhab,
>
> a few suggestions:
> - are you sure of the space group or might there be alternatives?
> - is you protein globular or modular, i.e., is it wort
Any recommendations for WELL-MADE refrigerated shakers? Our 1980-vintage New
Brunswick Psycrotherm* is getting creaky, and the repair people claim that
parts are not available. Hence, we're looking at the cost-effectiveness of
replacing it with a new one.
Probably best to reply off-list, and
Dear Phil,
Your observation that the refinement details in PDB format REMARKs
are difficult to interpret and compare is well taken. Each refinement
package produces its own set of refinement results calculated in its
own way. Both the calculation and presentation of this information in
PD
Dear intekhab,
a few suggestions:
- are you sure of the space group or might there be alternatives?
- is you protein globular or modular, i.e., is it worth running MR with stable
subdomains one after the other?
- try a poly-alanine model (e.g. chainsaw can do this for you, pdbset probably,
to
Hi all
I am trying to do molecular replacement with low resolution (4Å) using
Molrep and Phaser.
Overall R-factor is 11.3%, completeness 95.4%, I/sigma 2, and Chi^2 0.95.
Identities between my protein and templates were more than 80%.
I couldn’t get correct solution.
Rotation function, translat
Dear Jürgen,
The road to perfection is a long one ... . Thank you for the feedback!
With best wishes,
Gerard.
--
On Thu, May 20, 2010 at 10:31:37PM -0400, Jürgen Bosch wrote:
> I don't like the site finding option in autosharp, takes too long in most of
> my
Dear All,
Not only for beginners, but also for experts who want to solve
structures in hurry at the beamline and who want to complete model
starting from X-ray data at resolution better than 3.0 A resolution.
Santosh
Quoting "Ulrich Zander" :
Hi Qing Lu,
try Autorickshaw: http://www.
That was a bug in TLSANL, introduced in 6.1.0 and fixed in 6.1.2.
So you need to update your CCP4, or at least extract a newer tlsanl
binary. Apologies for that.
Martyn
On Fri, 2010-05-21 at 04:46 +0100, Shiva Kumar wrote:
> Dear Crystallographers
>
> I am trying to print out my total B factor
Hi Karin,
I find PROFESSS by Kevin Cowtan very easy to use:
professs xyzin hatom.pdb xyzout professs.pdb <
>Dear all,
>
>Does anyone know if NCSFIND is still available or how I can get it. If
>not is there another program that I can use to determine
>noncrystallographic symmet
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