Is the prototype shown Figure 1 from
U. W. Arndt, J. N. Champness, R. P. Phizackerley and A. J. Wonacott
A single-crystal oscillation camera for large unit cells
J. Appl. Cryst. (1973). 6, 457-463
http://dx.doi.org/10.1107/S0021889873009210
Hi Elise,
Not exactly what you are asking for, but
lsqman will compare waters between structures with a
cut-off. (However, it will not renumber the
waters as you wanted)
http://xray.bmc.uu.se/usf/lsqman_man.html#S71
If you want to look at waters related by NCS in a
single PDB file with
Hi Martyn,
I too was puzzled by the statement that unmerged data
cannot be handled properly as part of a PDB deposition.
We have deposited the unmerged original index intensities
for the refinement wavelength (and for additional wavelengths
used for phasing in the case of MAD) since 2005.
Hi Ronnie,
I have not tried it, but a quick google search for
protein ribbon 3d printer
turns up the following in the results list--
http://ironchefsynbio.wordpress.com/tag/3d-printer/
http://www.lib.ua.edu/sites/default/files/rodgers/Rodgers%203D%20Printing%20Molecular%20X-ray%20Data_V1.pdf
, Mitchell D. [mailto:mmil...@slac.stanford.edu]
Gesendet: Donnerstag, 20. Juni 2013 16:18
An: Schreuder, Herman RD/DE
Betreff: RE: Twinning problem
Hi Herman,
Have you considered the possibility of your crystals being tetartohedral
twinned. That is more than one of the twin laws may apply to your
Have a look at sortwater.
http://www.ccp4.ac.uk/html/sortwater.html
If you want to use it for non-water ions
in addition to waters, you would need to run
it a second time for each of the atom types
using the water keyword to define the residue
type and atom name. Also, it won't work for
Hi Ed,
Chapter 18.3 of international tables vol F includes values designated
EH99 which are from a more recent CSD release than the original 1991
Engh Huber paper.
R. A. Engh and R. Huber. Structure quality and target parameters.
International Tables for Crystallography (2012). Vol. F, ch.
I too like the idea of reporting the table 1 stats vs resolution
rather than just the overall values and highest resolution shell.
I also wanted to point out an earlier thread from April about the
limitations of the PDB's defining the resolution as being that of
the highest resolution
The PDB requires that a single poly peptide have single chain id.
See page 5 of the wwPDB annotation / processing procedures guide
http://www.wwpdb.org/documentation/wwPDB-A-2012May30.pdf
One thing you could do would be to number the second domain
starting a 1170 which would sort-of preserve
We (JCSG) too have been depositing multiple data sets (including unmerged
original index intensities for each wavelength and even for multiple crystals
when one was used for phasing and another for refinement, and MAD phases
and DM modified map coefficients) since 2004 without problems. These
I too believe that the value is set from the
high resolution limit form data collection or refinement.
All three numbers (high resolution limit in remark 2, remark 3
and Remark 200) are supposed to be consistent and are
defined as the highest resolution reflection used.
I have not tried it, but the latest version of the rcsb
program sf-convert is supposed to support it
(see version 1.2 released March 23)
http://sw-tools.pdb.org/apps/SF-CONVERT/index.html
http://sw-tools.pdb.org/apps/SF-CONVERT/doc/V1-2-00/documentation.html
(Version 1.2 is not yet available as
Hi Afshan,
in Coot select calculate -- other modeling tools -- find ligands
In 0.6.2, there is a message that ligands are limited to 400 atoms or less.
Regards,
Mitch
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Afshan
Begum
Sent: Wednesday,
Hi Catarina ,
For your final refmac refinement job, you need to include
the keyword
TLSO ADDU
to have the TLS contribution added to the residual B-factors.
This keyword can also be set from the recent version of the ccp4i
GUI by checking the checkbox for Add TLS contribution to XYZOUT
in the TLS
of the effect of
TLSD waters exclude vs TLSD waters add on determining
whether or not tlsanal would be able to properly
convert the file.
Regards,
Mitch
-Original Message-
From: Boaz Shaanan [mailto:bshaa...@exchange.bgu.ac.il]
Sent: Wednesday, August 03, 2011 1:40 PM
To: Miller, Mitchell D
Another option is to use the recursive feature of chmod to
change the permissions on the files. E.g.
chmod -R a+rX .
which will recursively add read for all users to files (and directories) and
will
also add execute if the file is a directory or if it already has at least one
execute
bit
Hi Bei,
For the extracellular protein I worked on in graduate school, I
typically purified it from 4 L preps in LB media. The standard
protocol was to do a crude low cut with ammonium sulfate cut followed by
precipitation of the protein with a high cut. The pellet was then
resuspended,
Hi Careina,
There are several places on the web that describe the
PIR format (also called NBRF) E.g.
http://www.ebi.ac.uk/help/formats.html#pir
http://www.bioinformatics.nl/tools/crab_pir.html
etc.
The program readseq -- either via command line or
webserver -- e.g.
I find the phenix.explore_metric_symmetry utility to be useful
for cases like this.
phenix.explore_metric_symmetry --unit_cell=50.48 74.14 149.51 90. 94.16 90.
--space_group=p2 \
--other_unit_cell=96.792 74.052 154.271 90. 90.060 90. --other_space_group=p2
It shows that the volume ratio
I had good audio for the Buster talk. However, early during
Jeff Headd's talk, the audio level dropped to a level that
with maximum amplification could still not really be understood-
sort of like the wrong microphone was turned on. Later near the
end of the talk and during the question/answer
Hi Peter,
If the lysine is dimethylated, the monomer code needed is MLY.
By mass spec we found most sites to be dimethylated. However,
looking at the structures we found a few sites to be protected
from methylation. These had clear density for the NZ atom, no
density for methyl groups and a
FYI --
The :h suffix for R3 is described in the IUCr symmetry cif (intl tables vol G
chapter 4.7) under _space_group.reference_setting where it states For the
space groups where more than one setting is given in International
Tables, the following choices have been made. For monoclinic
space
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
The decrease in missing reflections are due to the fact that
the output file does not include the missing reflections that
are lower resolution than the lowest resolution observed
reflection. Thus, this file is no longer uniqueified and
then refmac reports a higher completeness since it
no
Hi Kyle,
Are you refining with TLS? If so, then the default output will
be the residual B-factors. To get the full B-factors you need to
add the TLS component to the residual B's. This can be done
by re-running your refmac job with the keyword
TLSO ADDU
Note that this version of refmac will
If you want even more confusion on the labeling -- take a look at
the PDB to mmCIF correspondence mappings for conversion between
PDB and mmCIF format.
In the PDB file format under REMARK 200
http://www.wwpdb.org/documentation/format32/remarks1.html#REMARK%20200
there is a line written as
Hi Bernie,
We had a case recently which was a dimer in the crystal (with 2
Ca binding sites in the symmetric dimer interface) but anSEC gave
monomer under standard conditions ( 20mM Tris, 200mM NaCl,
0.5mM TCEP at pH7.5, Temperature at 8C ).
The crystals had 0.2 M Ca Acetate. We had a
Hi Alun,
The material we use is cross linked polyethylene/EVA foam. We use the 4 PCF
(pounds per cubic foot) variety it has tradenames of youngboard, artilon and
epilon.
(see
http://smb.slac.stanford.edu/facilities/hardware/cassette_kit/dewar_schematics.pdf
and
Hi Jane,
Qingping Xu wrote a python script that will extract the
sequence from the PDB file and align it with a fasta file.
The script depends on biopython and clustalw.
Regards,
Mitch
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Miller, Mitchell
Hi Yusuf,
You need to run the uniqueify script to expand the input
file to include all possible reflections (observed and missing
from your data set). I have not run xdsconv with the
GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05
However, generally after running xdsconv without that command,
it is
Hi Bernhard,
Google books is your friend...
It returns 2 hits for
Although the hydrogen bond is not strong it has great significance in
determining the properties of substances. Because of its small bond energy
Both are essays / chapters by Max Perutz
I Wish I'd Made You Angry Earlier:
Another new school cloning reference:
Klock, H.E., Koesema, E.J., Knuth, M.W. Lesley, S.A. Combining the
polymerase
incomplete primer extension method for cloning and mutagenesis with
microscreening
to accelerate structural genomics efforts. Proteins (2008) 71, 982-994.
published online 14
You could also try cns2mtz?
http://www.ysbl.york.ac.uk/~cowtan/cns2mtz/cns2mtz.html
Regards,
Mitch
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ezra Peisach
Sent: Thursday, July 03, 2008 11:28 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb]
I would like to also add that depending on what you want to
use the test data for, you may find that the data JCSG has deposited
with the PDB is sufficient.
The JCSG crystal structures include the following data sections in
the structure factor file deposited with the PDB (since spring 2004).
There is a resolve script that will allow you to shift the origin of phases to
match another set ---
http://solve.lanl.gov/Resolve/html_resolve_manual/resolve_sample_scripts.htm#offset_phases
Regards,
Mitch
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Hi Martyn,
When the rcsb processes files, that line is stripped form the PDB file.
We have taken an effort in the last few years to copy it into the
REMARK 3 OTHER REFINEMENT REMARKS: field so that it is retained in
the PDB file. Sometimes you can find out if that line was in the
original
Hi Juergen,
I found that if I follow the link for the Jan 4 talks
on the http://extrplay.dl.ac.uk/
http://extrplay.dl.ac.uk/CCP4/20080104-1/
It appears that they did not update the link page
and are using the same URL for the streaming today
that they used yesterday
Regards,
Mitch
P.S. I
I was using real player v 8 with Ie v 6 and I also
tried it with IE 6 and real player v 10.5 on another
system and it worked. Currently the site gives me the
error file not found for rtsp://extrplay.dl.ac.uk/broadcast/CCP4.rm
but this is only since the live streaming session ended. I did not
Hi Petra,
You can use sftools, to set the FreeR_flag column
to be the old ((FreeR_flag - 1)*-1 ) e.g.
sftoos eof
read myfile.mtz
calc col FreeR_flag = col FreeR_flag 1 - -1 *
write free-R-swap-1-0.mtz
quit
eof
Regards,
Mitch
-Original Message-
From: CCP4 bulletin board
What about Ton Spek's Platon / System-S package?
http://www.cryst.chem.uu.nl/platon/pl00.html
It does not have precompiled mac OSX binaries (only
linux and windows), but it does have source code
and instructions for compiling under unix and states
that it will compile without changes under
Hi Ethan,
I have been wanting a way to instruct refmac to accept a user-defined
f' term since about forever.
According to Garib's latest release notes, a command was
added to refmac 5.3.0015 and later to allow f' to be specified.
I have not tried it myself yet.. see
The SSBOND record does not allow the specification of
an alternate location indicator. The PDB practice is to
list the SSBOND record if any confirmation is in an SS-bond.
I think that refmac has problems with this since it will
try to apply the SSBOND patch to both confirmations. The
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