Thanks, Tom.
Ps Someone told me that the second link doesn't work, it is probably
because of the missing ´index.html´. (It works for me with or without it
o_0' ). Anyway, the first link redirects to the paper titled "Tapping the
Protein Data Bank for crystallization information" and the second lin
Hi,
> On 26 Nov 2020, at 17:59, Nikolas wrote:
>
> I am trying to prepare and export the files for a structure solved in CCP4i2
> but so far the only tasks available are the "Prepare and validate" and "Merge
> experimental data .." tasks.
Yes the first of these "Prepare and validate files for
Hello Murpholino,
OpenEye Scientific Software may still have a working version of the BDP, but
you would need to inquire with them.
Best of luck, tom
Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
___
Hello, if you are depositing the structure, a workaround might just be to use:
https://pdb-extract.wwpdb.org/
I suspect that was obvious, sorry!
Cheers, Jon. Cooper
Original Message
On 26 Nov 2020, 17:56, Nikolas wrote:
> Hi all,
>
> I am trying to prepare and export the file
Do you know if the BDP (
https://journals.iucr.org/d/issues/2005/12/00/en5128/index.html) and/or the
CCPD (https://journals.iucr.org/d/issues/2006/06/00/cy5030/) are still
available?
Thanks
To unsubscribe from the CCP4BB l
Dear Nikolas
I have the exact same problem
Joel
On Nov 26, 2020, at 20:00, Nikolas wrote:
Hi all,
I am trying to prepare and export the files for a structure solved in CCP4i2
but so far the only tasks available are the "Prepare and validate" and "Merge
experimental data .." tasks. I have t
Hello Anamika,
>From the information you gave, you have two different promoters- araC and the
>lac promoter. LacI is the lac inhibitor. The lac promoter is a two part
>system- when lactose is not present, the inhibitor sits near the promoter and
>blocks transcription of genes downstream.
Almost
Hi all,
I am trying to prepare and export the files for a structure solved in
CCP4i2 but so far the only tasks available are the "Prepare and validate"
and "Merge experimental data .." tasks. I have tried to look for the
tutorial but both the icon and the input page illustrated are different
from
Hi all,
I am trying to prepare and export the files for a structure solved in
CCP4i2 but so far the only tasks available are the "Prepare and validate"
and "Merge experimental data .." tasks. I have tried to look for the
tutorial but both the icon and the input page illustrated are different
from
Hi Prasun,
Apparently, when you just mixed the peptide solution with the reservoir
solution, crystals formed. After equilibration, the crystals were gone.
1) what I would try: just mix peptide and reservoir solution, but do not
equilibrate, e.g. do not use a reservoir solution. This is called b
A postdoctoral position is immediately available at the Paul Scherrer Institute
in the group of Dr. Richard A. Kammerer. The successful candidate will have a
strong background in recombinant protein production and the biochemical and
biophysical characterization of proteins. Expertise in X-ray c
Hello, yes, I tangled with this about a year ago so my memory is a bit vague. I
think you can get the mean protein B-factor from the refmac log file, but for
ligands, etc, I had to write a script. I can dig it out this evening if that's
any use.
Best wishes, Jon Cooper
Sent from ProtonMail mob
Answer to self: the number of non-H atoms per chain can be found in the PDB
validation report! Duh! I guess I’ll trust the average B values reported by
Refmac.
/Julia
--
Dr. Julia Griese
Assistant Professor
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsal
Hi Julia,
For a table 1 you should make a sensible split of the atoms over which you
calculate the mean. You might need to pool certain chains. There is not really
convenient tool for that because the choice depends on the biology/biochemistry
of your system. In practice, the easiest way is usi
Hi all,
I’m writing a Table 1 and getting a bit confused when it comes to number of
atoms and average B factors. Refmac has these in the table in the GUI, but the
atom numbers in that table seem to include H, and I’m only interested in non-H
atoms.
As an example, the PDB file says:
REMARK 3
Hi Group:
I have a peptide that got crystallized within 20-25 minutes after putting down
the tray.
The condition has 1.8M Ammonium Salt, 0.01 Cobalt (ii) Chloride hexahydrate and
MES (0.1M) pH 6.5.
I dissolved my peptide in 25 mM Sodium Accetate (pH=5).
PI of my peptide is 10.2
When I checked
BL21(DE3) pLysS using 5X KCM and heat shock transformation worked for me.
Crissy L Tarver
Postdoctoral Researcher
Department of Structural Biology
Stanford University School of Medicine
From: CCP4 bulletin board on behalf of Hughes, Jonathan
Sent: Thursday, Nove
Bl21Pro
j
Von: CCP4 bulletin board Im Auftrag von Anamika Singh
Gesendet: Donnerstag, 26. November 2020 11:07
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] OFF TOPIC question
One correction to the previous question: I have two constructs having different
ori, p15ori and M13 ori, different pro
*One correction to the previous question:* I have two constructs having
different ori, p15ori and M13 ori, different promoters *araBAD promoter*
and LacI, and different antibiotic resistance chloramphenicol and
Ampicillin respectively. I would like to know which E. coli host cells will
be good for
Hi all,
I have two constructs having different ori, p15ori and M13 ori, different
promoters araC and LacI, and different antibiotic resistance
chloramphenicol and Ampicillin respectively. I would like to know
which *expressing
E. coli host cells* will be good for the co-transformation of these
con
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