I agree with Paul: use the standard dictionary if at all possible.
It's strange: I've not had any trouble with NADPH (NDP) in refmac
recently---as long as I had the correct atom names.
Is there a typographical error in the standard NAD dictionary entry?
Dave
David Borhani, Ph.D.
D. E. Shaw Rese
Hi,
The details of the experiment are a bit sketchy. Is this a transmembrane
protein or an associated one? What percentage of the structure is expected
to associate with the lipid bilayer? Do you know the correct orientation of
the protein with respect to the bilayer (i.e. what's inside and what's
Put the His-tag at C-terminus.
Remove rare codons
Optimize sequence for translation
You probably got truncations not degradations.
Chun
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kn Ly
Sent: Thursday, March 19, 2009 4:53 PM
To: CCP4BB@JISCMAI
Hello everyone,
I am expressing a 100 KDa eukaryotic membrane protein in E coli. The protein
is fused to 6His-MBP in the N terminus and the resulting mass is ~ 150 KDa.
However, the protein get severely degraded so after putting through a Ni-NTA
column, the protein came out with a lot of contamin
St. Jude Children's Research Hospital in Memphis, Tennessee has an opening for
a Computing and X-ray Scientist in the Department of Structural Biology.
The manager would be responsible for administering computing infrastructure
within the department and maintaining the X-ray facilities. The ide
Eleanor Dodson wrote:
Even for NAD I think I would make my own "new" dictionary.
I must say that I would not (in the general case that is, there may be
an argument for doing so for NAD). There will be a price to pay at
deposition time.
To address your particular problem (and Ignoring the p
Dear CCP4 developers,
The same job ImportScaled on ccp4-6.1.1 failed with
/ccp4-6.1.1/ccp4i/scripts/import_scaled.script: can't read "dataset_name": no
such variable
but finished if run it on ccp4-6.1.0.
Your help is much appreciated.
Thanks,
Jun
Is there a chance that ThDP (TDP or TPP in the ccp4 dictionary) is restrained
differently in 6.1.x than it used to be in 6.02 or even earlier versions (e.g.
5.2) ?
Boaz
- Original Message -
From: Eleanor Dodson
Date: Thursday, March 19, 2009 11:17
Subject: Re: [ccp4bb] nad
Rob, Thanks for the tips of wisdom. Is the 3 letter code for NADH something different, or is it NAD as well? Ditto for FMN and its reduced form. Thomas Edwards-CCP4 bulletin board wrote: -To: CCP4BB@JISCMAIL.AC.UKFrom: Rob Meijers Sent by: CCP4 bulletin board Date: 03/19/2009 01:01AMSubjec
For your amusement/outrage:
A user of our synchrotron shipped samples in a deWar from overseas. The
deWar was held up by U.S. Customs, and we received the following from a
FedEx employee:
---
This shipment is delayed with US Customs. We need to know the amount of
salt in the shipment in kilogram
Hi folks
The real problem here is that the "imosflm" you run by default after
installing the latest CCP4 is a shell script in $CBIN (i.e. where all
the compiled programs are), which doesn't actually set things up
properly. This has been addressed by the guys in Daresbury and the fix
will
On behalf of Prof. S.X. Lin:
Postdoctoral and graduate positions are available at Laval University
Hospital Research Center, for the study of structural biology and
function of important enzymes. These include sex steroid synthesizing
enzymes involved in breast and prostate cancers, as well as
Dear Martin,
this should be fixed in the latest refmac version
http://www.ysbl.york.ac.uk/~garib/refmac/latest_refmac.html
Please let us know if it is not!
Pavol.
--
Sent from: Leiden ZH Netherlands.
Hi Frank,
I would have assumed that the purpose of the experiment would have
been defined in the publication associated with the deposition - not
to trivialize your point, which is very important, but to put it in
context. I would also assume that the sequence and ligands are as per
the associated
On Wed, 2009-03-18 at 18:19 +, Frank von Delft wrote:
> Maybe, but images without experimental context (sequence? ligands?
> purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!!
> relationship to the other 15 similar datasets) are as good as no
> images. And as far as I know,
imosflm also takes the command line switch --startdir so you could try
an alias of
alias imosflm='imosflm --startdir $PWD'
Mark
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
William G. Scott
Sent: 18 March 2009 17:17
To: CCP4BB@JISCMAIL.AC.UK
Jacob,
Just for the fun, and for historical exactness...
I would rather invoke Laplace for such an argumentation, whereas
Poincaré should better be invoked for a very strong warning against it.
Therefore, ignoring the warning and following Laplace, we could even
readily extend your suggestion fr
Even for NAD I think I would make my own "new" dictionary.
If you go to the ebi site ( now pdbe) ask for Msdchem ( is it PDBeChem
now?)
Get the idealised NAD coordinates with the remediated nomenclature
Submit the coordnates to the ProDrg server.
Retrieve the REFMAC dictionary
Use PDB and dict
Dear Bernhard,
Thank you for this suggestion. The question is: who outside the US can
be "in"? I would be most happy to contribute to arguing the scientific case
(in the broadest sense) for the benefits of such an initiative, and to play
whatever role I can in getting (other people to put ...
I can confirm this: I see the following running times for the exact same
job under linux with no other work being done on the machine:
ccp4.6.1.1
Refmac_5.5.0072: End of Refmac_5.5.0072
Times: User: 176.1s System: 78.2s Elapsed: 4:15
ccp4.6.0.2
Refmac_5.4.0062: End of Refmac_5.4.
Hi Jan,
at low occupancy (and I suppose a resolution that does not extend beyond 2.0 A),
you have to rely on your restraints. I think the consensus is that the adenine
ring
should be planar. The pyridine ring of the nicotinamide should be flat if the
ring
is oxidized (NAD+), and can be distorted
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