Ok - I have tracked down where it is coming from.
The value being reported is sum(I)/sum(sigma_I). This is not the same
as Mean(I/sigmaI) - as I interpret the later as (Sum(I/sigma))/n.
Where I comes from is the intensity_meas, intensity_meas_au, or
intensity column - whichever is present (
currently serve the older dsn6 format, only ccp4, I think.
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent from Proton Mail Android
Original Message
On 31/05/2024 16:36, Ezra Peisach
<d150cd71a251-dmarc-requ...@jiscmail.ac.uk> wrote:
In fall of 2024,
In fall of 2024, electron density map coefficients will be available in
the public PDB archive for all X-ray structures. These map coefficients
will be the same as used in wwPDB Validation Reports.
The new map coefficients files will replace the electron density maps
and combined map coefficie
May I point you towards the shape similarity search available at the
rcsb.org site?
https://www.rcsb.org/news/feature/63933da0e543b6038c4fc5dd
The news suggests that you need to upload via URL - but there is a file
upload option in the source pull down.
On 5/22/24 5:03 PM, Das, Abhinaba wro
If you take a look at
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
you will see the following:
77 - 78 LString(2) element Element symbol, right-justified.
Going by atom name will get you in trouble. As you stated calcium vs
Calpha. The elem
bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Ezra Peisach
Sent: 26 January 2010 16:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Crystal rescue
First you need to establish if it is your cryo conditions or the
crystals. Depending where you are - they might have the equipment
to d
Howdy,
Within the last few years - I remember a paper discussing an examination
of disorder in the termini of structures found in the PDB. Does anyone
know the citation?
Thanks in advance,
Ezra
First you need to establish if it is your cryo conditions or the
crystals. Depending where you are - they might have the equipment to do
a wet mount - without freezing. Yes the crystal will not last - but
then you know if the problem is in the
crystal. If it is - you need better crystals. If
A number of years ago - we were asked to setup an ftp site a particular
reviewer could see the coordinates... I could have looked at the logs to
figure out where they were coming in from but chose not to. Some
journals also allow the author to upload additional info - that would be
available t
Matthew Franklin wrote:
Once again, I'd like to get the community's thoughts: should we ask the PDB to
stop using 0 and 1 in its IDs?
I'll get off the soapbox now.
I would be all for it... Having tried to downloade 1o08 and gotten it
screwed up Especially when journals use a sans-ser
Sivaraman Padavattan wrote:
Dear all,
I am performing an assay to screen for the inhibitor molecules. One of
our compound shows inhibition at 100 μM and activation at 500μM conc.
What could be the possible reason for the compound work differently in
two different conc.
Thanks
Sivaraman
Maybe... Depending on the energetics - it could stall the translation -
or prevent initiation if it is at the start of the ORF. If it is in the
middle - you might be ok... Usually the gene synthesis company can
recommend alternate sequences that do not run into this problem or rare
codon issues
Artem has already responded - but I believe you will pull down the
cellular debris with the IB.
In my prior experience, post centrifugation, you can wash the IB/debris
with increasing amounts of urea in you solubilization - and you may find
that the other cellular debris stays in solution befo
Regarding concentrating detergents w/ MWCO concentrators - may I suggest
the following reference:
Refractive index-based determination of detergent concentration and its
application to the study of membrane proteins
Pavel Strop and Axel T. Brunger
Protein Sci. 2005 August; 14(8): 2207–2211.
Have you considered seeing if anyone has an anaerobic chamber you can
work in?
Ezra
On 10/05/2009 11:39 AM, Roger Rowlett wrote:
Of these, typically TCEP>DTT>BME in terms of effectiveness in
maintaining reduced Cys groups. Some proteins, when purified, require
obscenely large reducing agent
We used to use a needle to crush the crystals - and then make serial
dilutions
ucbccka wrote:
sonication
Dear CCP4bbers,
Can anyone suggests how to make seed-stocks if one is not having
seed-beads... Is there any other methods to crush the crystals for the
same
purpose. What if it is
On 09/10/2009 12:17 PM, Sean Seaver wrote:
Hello Sylvia,
Two issues I would consider:
1) recheck the space group
2) make sure that I had selected a good model for my MR search
All the Best,
Sean
Hi Sylvia,
If you have just used rigid body refinement - the Rfactor might be high
until y
William G. Scott wrote:
On Sep 8, 2009, at 4:29 PM, Ezra Peisach wrote:
If you want to gamble - go w/ P6122... Data from the PDB indicates
that there are 1.5x as many proteins w/ P6122 vs P6522...
So if you believe in the overall anisotropy of the universe
(neglecting the weak interaction
Rafael Couñago wrote:
Hi,
I am in doubt between the enamtiomorph space groups, p6522 and p6122.
Is there a way to distinguish the correct one in the absence of a
molecular replacement model?
Cheers.
Rafael.
You cannot distinguish by absences. How do you plan to phase? I would
say choose o
A little tangental You mentioned lowering the temperature - how
low... Stratagene markets a call line - Arctic Express - that adds
chaperones that are more active at lower temps. I know someone who
overcame inclusion body problems by expression at 16 using these cells.
(I know someone els
Been there, done that, got the T-shirt.
I do not believe there is a protease like 3C in E. coli.
That said - do you have any rare codons in your protein - that might
cause the stall/termination in expression - leaving you a large amount
of tag. Have you followed through with purifictaion to s
Vesna Serrano wrote:
Dear all,
I am using Refmac_5.5.0088 in CCP4 6.1.0, linux version. The program runs
well normally, but all of a sudden it failed with the following message:
Refmac_5.5.0088: Open failed: File: /tmp/vesna/refmac5_temp1.06489.txt.
Here is the log file of the run:
#CCP4I VERS
They are SigmaA weighting coefficients. See the sigmaa documentation -
and references there in by Read. (I think the 1986 reference is the
correct one).
Ezra
Mayer, Mark (NIH/NICHD) [E] wrote:
Hi,
What do m and D indicate in the Fourier coefficients for a 2mFo-DFc map?
I've dug a bit in w
I do not know off hand what a .cv file is - unless it is a cns/xplor
reflection file. Instead of using f2mtz - try sftools.
Ezra
Jayashankar wrote:
Dear scientists and friends,
When I try to convert a .cv file to .mtz by f2mtz I got the following
error,what it means ans what should I do to
I saw that toy - Personally, I do not like the idea of encouraging
children to aim a light (low powered led) directly at one's eye...
Ezra
P Hubbard wrote:
I took my 5 year old niece to a McDonald's (in England) for a happy
meal today - Spiderwick Chronicles promotion. The toy's light effect
You may wish to look at the occp4-pm perl package by E. Courcelle and
J.P. Samama (formerly available from ftp://ftp.ipbs.fr/pub/occp4 - but
this no longer works...) I no longer have a copy but someone might...
Ezra
[EMAIL PROTECTED] wrote:
Dear CCP4 users,
I am writing a PERL script to ex
It depends on your path environment variable... It used to be that "."
was by default in your path - then the more security conscious removed
the current working directory from the default list of paths to search
for commands.
Try ./scalepack2mtz.exam
The ./ gives a path
U Sam wrote:
I
The file format is definitely machine byte order dependent. (see
$CDOC/plot84.doc) A few years ago I was toying with the idea of making
library code deal with swapping if need be...
Never did it though
William Scott wrote:
Did you make your plt file on the intel mac? I've noticed that one
I have never worked at 3.2A - but I suspect that the overal temperature
factor is being determined from the slope of a Wilson plot. However,
Wilson plots only really "work" at higher resolution (2.8 or better). Look
at the output from truncate and see what it is predicting - and look at
the pl
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