As for your second question, whether refining in a lower symmetry affects the
R-factors,
On 7/20/22 10:10 AM, Jorge Iulek wrote:
Related, and a question I mentioned before in this forum: what if a
genuine 2 axis (say , P222 to P2, or even to P1) (I do not mean this is the
case here) is
I have noticed renaming chains in the sequence ID's but not in the coordinates:
2FBW_3|Chains C, G[auth P]|Succinate dehydrogenase cytoch
MATTAKEEMARFWEKNTKSSRPLSPHISIYKWSLPMAMSITHRGTGVALSLGVSLFSL
2FBW_4|Chains D, H[auth Q]|Succinate dehydrogenase [ubiqu
On 06/10/2021 11:19 AM, James Holton wrote:
I'm afraid the only bash command I know is: "tcsh"
I learned csh by studying "elves"
To unsubscribe from the CCP4BB list, click the following link:
)
On 03/05/2021 04:00 PM, Edward A. Berry wrote:
For manually masking out the rings, you can use mtz2various to dump reflections
in resolution ranges without ice in ascii, cat them all together and use f2mtz
to read them into a new mtz file. Example attached.
You might also be able to do it using
For manually masking out the rings, you can use mtz2various to dump reflections
in resolution ranges without ice in ascii, cat them all together and use f2mtz
to read them into a new mtz file. Example attached.
You might also be able to do it using mtzutils to write out mtz files in
limited
On 03/04/2021 10:42 AM, Gerard DVD Kleywegt wrote:
If there is interest I could post a tgz file with -as far as I can determine-
the latest version of all manuals in HTML format (0.8 MB total).)
Yes, I would like to grab a copy of the manuals.
Ed
This came up on phnix BB recently:
On 10/20/2020 01:30 PM, John Berrisford wrote:
Dear Armando and Pavel
During the deposition process we compare two values
_reflns.number_obs
And
_refine.ls_number_reflns_obs
We expect the number of observed reflections to be higher (or the same) as
the
For my own info,
Does microED encompass work with 2D crystals, or only micro-3D crystals?
On 08/15/2020 10:40 PM, Jessica Bruhn wrote:
Hi Alex,
Welcome to the field of microED! From a practical standpoint, microED also
suffers from the phase problem, and somewhat moreso compared to X-ray
There seems to be a list of the 7.0 programs (and documentation!) still
available:
http://www.ccp4.ac.uk/html/FUNCTION.html
I hope this is not going away!
eab
On 07/07/2020 12:09 PM, Tim Gruene wrote:
Dear Kelvin,
the command 'ls $CBIN' lists the majority of CCP4 programs on your
system. This
Now can we get rid of all the superfluous disks in our RAID? Or at least not
replace them when they fail?
On 06/29/2020 06:24 PM, Andreas Förster wrote:
I like to think that the reflections I carefully measured at high multiplicity are not redundant, which the
dictionary on my computer
On 01/26/2020 01:02 PM, benjamin bax wrote:
Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
to produce the crystal.
Happy New Years to all!
delete the ligand you fitted and any water molecules near the ligand and run a
few rounds of refinement to get an unbiased omit map.
The cavity may be filled with bulk solvent by the refinement program, which can
reduce the difference signal from whatever is there.
On 09/16/2019 06:29 PM, Mariana Ajalla wrote:
Dear all,
We tried to use the Rfree set from a lower resolution data with a higher
resolution from the same Crystal. To do so We used aimless at ccp4i with the
option use free flag from another mtz file and extend the data.
I think it worked, but
Sorry- Richard Muller (How could I get that wrong?!)
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Agreed. I support green new deal and I think we should be doing all we can to
combat climate change,
not because I have studied it and concluded it is a problem but because some
very smart people have, and have come to that conclusion. But I would not sign
a letter saying that I have
I would respectfully suggest that higher pixel resolution does not generally help much
in these situations. If an average spot is 10 or more pixels wide then the profile is
defined pretty well. But if the spots overlap, they still overlap with higher pixel
density. It may make profile fitting
I think it is not really the detector, but the strategy. If you decrease
exposure time by a factor of ten and make up for it by 10 x higher redundancy,
then obviously R-merge, which is a measure of accuracy of the individual
frames, is going to suffer. Chi^2 statistics can distinguish this
cture
factors in the center of the excluded zone will be poorly determined, since information
pertaining to them is being excluded. So of course the R-factor calculated from these
reflections will be higher than with randomly absent data. Furthermore, if G-function is
the vehicle by which
will be poorly determined, since information
pertaining to them is being excluded. So of course the R-factor calculated from these
reflections will be higher than with randomly absent data. Furthermore, if G-function is
the vehicle by which R-free follows R, R-free will follow less closely
Revisiting (and testing) an old question:
On 08/12/2003 02:38 PM, wgsc...@chemistry.ucsc.edu wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
On 08/12/2003 06:43 AM, Dirk Kostrewa wrote:
(1) you only
(in case everyone assumes someone else already answered offline, which they
probably have)
In coot go to the region where you want to put the heme and do:
File:get monomer and type HEM in the box that pops up.
This gives plain old heme b (ferroprotoporphrin 9) like in Hb or cyt b
For heme C
While I agree with testing in lower symmetry (and I'm sure you have), it is
also possible that the asymmetry is too slight or doesn't affect the crystals
contacts, so that the dimer would orient randomly as it packs into the crystal.
In that case, taking the average over all asymmetric units,
What if you have one domain with many B-factors aroun 70 and above, and another
domain with B-factors around 20? The atoms with high B-factor will make
essentially no contribution to the intensty of spots beyond 3 A, and so have no
effect on the slope of the Wilson plot byond that. But they
Also check if the mean value of the map over the ASU is zero. If so, the map
was probably calculated without the 0,0,0 term of the Fourier series, so zero
does not represent zero density but rather the mean density.
On 03/04/2019 12:43 PM, Ian Tickle wrote:
Hi Sen
If you multiply the
and add pi to the phase. So we get 2 possible
phases, separated by 180*. (Or something like that.)
-Original Message-
From: CCP4 bulletin board On Behalf Of Edward A. Berry
Sent: Saturday, March 2, 2019 2:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Confused about centric reflections
:00 PM, Edward A. Berry wrote:
The wiki:
https://urldefense.proofpoint.com/v2/url?u=https-3A__strucbio.biologie.uni-2Dkonstanz.de_ccp4wiki_index.php_Centric-5Fand-5Facentric-5Freflections=DwICaQ=ogn2iPkgF7TkVSicOVBfKg=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA=HENAQrgItEIhnnUZhWe8GMKW5sRX2v7V
The wiki:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Centric_and_acentric_reflections
says:
"A reflection is centric if there is a reciprocal space symmetry
operator which maps it onto itself (or rather its Friedel mate).
. . .
Centric reflections in space group P2 and P21 are
(Another idle post to see if we can hit the record)
One assumes the image is an attachment, and won't be included in the reply.
But no, its inline with the text. Easy enough to delete if you notice that,
but less likely to be noticed as the thread gets longer and longer . . .
On 01/23/2019
So, are there any other common errors of annotation that one should look for?
I've just submitted seven structures (same protein) and there are some
newly introduced LINK records, but all seem correct.
eab
On 11/11/2018 02:31 PM, Robbie Joosten wrote:
Hi Tristan,
Erroneous LINK records happen
In case one wants to play around with openVMS or just recover some
now-unreadable old data,
and doesn't have a vax farm or even a single vax computer,there are
step-by-step instructions for setting up a vax system using the simh emulator:
The fact that chi^2 is approximately 1.0 in all shells says that the deviations
are about what is expected from the error model. The fact that Rpim is much
lower than Rmeas means that you have rather high redundancy. This would seem to
be a case of collecting low dose per image and making up
Hi Melanie,
Mapmask was suggested. The XYZLIM command of mapmask takes values in grid
points or fractional coordinates.
You could make a 300A cube by giving fractional coordinates of 300/(current
cell edge),
But since that doesn't change the grid it won't change the thickness of your
slices.
I
Is it a membrane protein?
Looks like a phospholipid without the phosphate. diglyceride maybe?
But I see not much blue density. Presumably this fills out if you contour
at a lower but still reasonable level?
On 07/02/2018 06:26 AM, Christopher Horne wrote:
Does anyone have any insight into this
On 06/21/2018 03:34 PM, John Berrisford wrote:
From a PDB deposition point of view, I echo Paul’s comment. If possible,
please move your molecule closer to the origin. It helps with the curation
process and is easier for users of your entry as some software struggles with
such extreme
nformation in the dictionary, then actually heme C (HEC) should be the
same
as heme b (protoheme).
On 05/15/2018 04:35 AM, Eugene Osipov wrote:
Dear CCP4 developers,
please fix errors with heme c dictionary file HEC.cif.
Edward Berry described this problem in detail 4 years ago:
https://www.mail-a
t; On Behalf Of
Eugene
Osipov
Sent: Tuesday, May 15, 2018 10:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problems with HEC in CCP4
Dear CCP4 developers,
please fix errors with heme c dictionary file HEC.cif.
Edward Berry described this problem in detail 4 years ago:
https://www.mail-archiv
For proteins in membranes, or proteins purified in the presence of detergents
and/or lipids, the active site is sometimes surrounded by a hydrophobic mileau.
The actual concentration that the binding site sees is then dependent on
partitioning of the ligand between the water (where its
/2018 06:42 AM, Eleanor Dodson wrote:
No problem with GUI2..
Eleanor
On 13 March 2018 at 22:38, Edward A. Berry <ber...@upstate.edu
<mailto:ber...@upstate.edu>> wrote:
Thanks- that works!
pdb-redo/tools/cif2cif in.cif out.cif
eab
On 03/13/2018 05:47 PM, Robbie Joost
bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Edward A. Berry
<ber...@upstate.edu>
*Sent:* Tuesday, March 13, 2018 10:25:25 PM
I want to work with an mmcif file that has I+,sigI+,I-,SigI-;
in different columns for each reflection (no Imean).
cif2mtz gives those same columns in the output mtz, with or without ANOMALOUS
keyword.
cif2mtz and truncate seem to need the anomalous data as separate reflections
hkl and -h-k-l
On 01/21/2016 05:48 PM, Edward A. Berry wrote:
Also, pubmed commons allows comments on the abstract page for every article.
Whenever you look up an article on pubmed, there is an invitation to
leave comments below, and if a comment is left it is prominently
displayed above the article like
Dear Peng,
The choice of asymmetric unit is somewhat arbitrary. Please forgive me and
ignore this if I am saying something obvious and you already know this does not
apply in your case, but I see most of your previous posts concern EM
structures, so perhaps you are relatively new to solving
symgen x , y-2, z
end
New CoM 0.7 -0.7 -0.2
Eleanor
On 18 December 2017 at 00:19, Edward A. Berry <ber...@upstate.edu
<mailto:ber...@upstate.edu>> wrote:
Neat idea!
And do you have a 1-line command for setting all the coordinates t
ut changed.pdb
symgen x , y-2, z
end
New CoM 0.7 -0.7 -0.2
Eleanor
On 18 December 2017 at 00:19, Edward A. Berry <ber...@upstate.edu
<mailto:ber...@upstate.edu>> wrote:
Neat idea!
And do you have a 1-line command for setting all the coordinates to 1,1,1?
or 0.1,0.
Neat idea!
And do you have a 1-line command for setting all the coordinates to 1,1,1? or
0.1,0.1,0.1 if I still want it near the origin but biased toward the inside of
the positive-going cell?
eab
On 12/14/2017 07:23 PM, James Holton wrote:
What I usually do for this is make a copy of the PDB
In this case you know the protein is closely relaed to whatefer contaminer
found, and you have good sequence data, so I agree the next step is blast.
Maybe it is an isozyme of the structure used.
In cases where you solve an unknown by heavy atom derivatives and have no idea
what it is; and
On 12/14/2017 04:34 AM, Tim Gruene wrote:
Dear Tommi,
1.
if you only need to consider translations, and not other symmetry operations,
you can use moleman2, convert coordinates to fractional ones and add or
substract the integer that brings the centre of mass closest to 0.
2.
In case you
My 2 cents worth:
I think contaminer is an extremely useful service. I may be a sloppy biochemist,
but I am not the only one. There are multiple structures in the database of say
bacterioferritin or AcrB that were solved from crystals that were supposed to
be something else. I remember in a
(set-go-to-atom-molecule 0)
(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")
Would those be also on the command line, or where?
On 11/16/2017 07:19 AM, Paul Emsley wrote:
On 16/11/2017 08:08, Martín Martínez Ripoll wrote:
I am trying to write a long script that, among others, runs
in the region of the deleted subunit to resolve
the contradiction.
On 10/11/2017 04:47 PM, Edward A. Berry wrote:
This is hard to understand/impossible, at least in terms of
simple 2fo-fc and fo-fc maps.
We can think of a difference map as the difference between two maps,
like fo-fc map = fo map - fc
This is hard to understand/impossible, at least in terms of
simple 2fo-fc and fo-fc maps.
We can think of a difference map as the difference between two maps,
like fo-fc map = fo map - fc map.
There is no model in the region, since you deleted it,
so Fc=0, and Fo-Fc negative => Fo<0, so 2fo-fc
exposing themselves with out of date browsers.
With best wishes,
Guillaume
On Oct 11, 2017, at 10:34, Edward A. Berry <ber...@upstate.edu> wrote:
Is it because of this? Its been coming for a while now:
https://blog.mozilla.org/security/2015/04/30/deprecating-non-secure-http/
I see no
Is it because of this? Its been coming for a while now:
https://blog.mozilla.org/security/2015/04/30/deprecating-non-secure-http/
I see no reason why a website, dedicated to providing information
available to everyone, should be required to use https.
The web is too focused on e-commerce, where
On 10/05/2017 11:01 PM, ameya benz wrote:
Hi,
I want to convert HKL file to mtz. I tried using F2mtz but somehow the output
mtz is not working. What parameters should I set during conversion. Or can
anyone suggest alternative to F2mtz?
regards,
Ameya
National chemical laboratory, Pune, India
Look at CCP4 "compar"
By default it averages RMSD over all atoms in mainchain and sidechain
of the residue, but if you first awk out only CA (or use pdbset to pick CA)
foreach structure, the mainchain value will presumably be the
Euclidian CA distance (This may require identical sequences,
at
Thanks for spelling it out!
Would that advice still hold if the mosaicity of the crystal is 0.7 degrees?
(I know, I should go read the paper., but . . .)
eab
On 07/13/2017 03:00 PM, Gerard Bricogne wrote:
Dear Gerd,
I can assure you that I have no shares in Dectris nor any
commecial
e. But when micro crystals only give off a handful of
photons each before they die, low multiplicity might be all you have.
-James Holton
MAD Scientist
On 7/7/2017 2:33 PM, Edward A. Berry wrote:
I think the confusion here is that the "multiplicity correction" is applied
on each reflectio
I think the confusion here is that the "multiplicity correction" is applied
on each reflection, where it will be an integer 2 or greater (can't estimate
variance with only one measurement). You can only correct in an approximate
way using using the average multiplicity of the dataset, since it
I second the use of LSQMAN.
The command for calculating wo aligning appears to be:
rmsd_calc (abbreviated rm).
http://xray.bmc.uu.se/usf/lsqman_man.html#S59
If you have multiple chains, use the option "chain_mode original"
before loading the pdb's to avoid renaming chains:
(di)Sodium D,L-malate is available from Sigma-Aldrich (# CDS023113) and
probably dissolves to give a 3M solution which is slightly alkaline.
If pK2 is 5.1, then an insignificant amt of malic acid should bring the
pH down to 7 (If you have to add a significant amount, just add more
water to dilute
On 06/07/2017 10:46 AM, Bonsor, Daniel wrote:
It will either be two things. DNA or residual Triton-X-100.
Actually Triton X-100 absorbs more at 280 than 260 - in fact the hydroxyphenyl
in TX-100 looks remarkably like tyrosine in RNase A. I long ago gave up hope of
resolving triton from
Easiest way is to line up molecule pairs or chain pairs in COOT and see if
there are equivalent waters.
If the number of waters is too large to inspect manually,
save the superposed structures to disk, grep out the waters from each into a
separate files,
and use a program like
That is beautiful!
The pins-and-holes approach might be useful also for space-filling models
of multi-subunit complexes- both for holding the subunits together, and in
cases where one subunit partially encircles another, the subunit would be sliced
in half and pins could hold the halves
Couple of wuestions:
What is the procedure for updating an entry? Start a new submission, or mail
revised coordinates along with an explanation of changes to deposit@rcsb?
"unchanged experimental data" - does this mean the exact same structure
factors, or will newly reduced data from the same
Actually this is taken care of in the BIOMOLECULE definition.
If the artist had used the principle biomolecule, it excludes the Fv fragments.
On 05/09/2017 01:08 PM, Edward A. Berry wrote:
In line with this, there are a number of pictures in the literature of the
mitochondrial
electron
ation damage a subject of your manuscript), but this is going to lead to
headaches for people who want to make use of the resulting coordinates to study
the actual biology of your protein. Personally, I'd strongly prefer the latter
approach.
Tristan
On 2017-05-09 16:06, Edward A.
to study the
actual biology of your protein. Personally, I'd strongly prefer the latter
approach.
Tristan
On 2017-05-09 16:06, Edward A. Berry wrote:
On 05/09/2017 06:18 AM, Ian Tickle wrote:
We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (y
On 05/09/2017 06:18 AM, Ian Tickle wrote:
We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (yes
exactly the size of CO2!) where the carboxylate group would be and absolutely no density for the CG-CD bond. So
it's indeed very tempting to
at 100K).
If the residual density is due to partial de-carboxylation, then I would have
expected density for the CG-CD bond, which is not present (at your chosen
contour level).
Do many of your Glu side chains have the residual density?
Best wishes,
Andrew
On 3 May 2017, at 22:19, Edward
On 05/03/2017 02:46 PM, Gerard Bricogne wrote:
Dear Ed,
Have you considered the possibility that it could be a water
stepping in to fill the void created by partial decarboxylation of the
glutamate? That could be easily modelled, refined, and tested for its
ability to flatten the
than a zebra making your hoofprints?)
Matthew Merski
Crystallochemistry Laboratory
Univ. of Warsaw
On Wed, May 3, 2017 at 6:29 AM, Edward A. Berry <ber...@upstate.edu
<mailto:ber...@upstate.edu>> wrote:
I'm finishing up refinement of a 1.8A structure (R's 0.17, 0.20) , and among
People who would know (and know whether such a strain would even be viable)
are Gary Cecchini at UC San Francisco/VA and Bob Gennis at Univ of Illinois
at Urbana. In case you are not already talking with them.
It has been reported that an assembly factor (SDH5 or SDHE or SDHAF2)
is required for
On 03/30/2017 08:10 AM, mesters wrote:
If the pI of the protein is below the pH of the buffer (net negatively charged
protein), optimum stabilization (salting out; lower solubility) of the
macromolecule is achieved by combining a kosmotropic anion with a chaotropic
cation, e.g.
Thanks!
On 03/25/2017 03:36 PM, Paul Emsley wrote:
On 24/03/2017 03:39, Alex Lee wrote:
Dear All,
Is there a tool or software which can give Ramachandran information of
individual residues
in a plot?
I used Coot to check for Ramachandran plots, but it shows all the residues in a
coordinate
On 03/23/2017 11:39 PM, Alex Lee wrote:
Dear All,
Is there a tool or software which can give Ramachandran information of
individual residues in a plot?
I used Coot to check for Ramachandran plots, but it shows all the residues in a coordinate I put in
Coot, not individual one. I also use
On 03/09/2017 11:45 AM, Alice Dawson (Staff) wrote:
you can find a paper model of GFP at the RCSB PDB
https://cdn.rcsb.org/pdb101/learn/resources/gfp-model.pdf
Hmm- that seems to involve quite a bit of cut-and-pasting too - or rather
cut-and taping!
2D topology diagrams are really
Yes, CM-Sephadex expands and contracts incredibly. For other than batch methods
you will be much better using CM-Sepharose. I guess it is cross-linked
sepharose, and doesn't swell up much even in distilled water.
What is happening is the negative charges of the carboxy groups repel each other,
Speaking specifically for succinate dehydrogenase, there are a number of
assembly factors required for insertion of flavin, iron-sulfur clusters
(SDHAF1,2,3 . . .). Since E. coli or Pischia make their own SDH, there is
a possibility the endogenous assembly factors and co-factors would work
with
Does this count as an example?
grep SSBOND /a/pdb/pdb4e9m.ent
SSBOND 1 CYS A 39CYS B 39 1555 1555 2.05
SSBOND 2 CYS C 39CYS D 39 1555 1555 2.04
SSBOND 3 CYS E 39CYS F 39 1555 1555
As I understood the problem, it is that automatic assignment comes out
differently for different structures of the same protein or proteins so close
that they should have the same secondary structure, due to differences in
quality of the structures. The question then is not how to determine
Uma's use of quotes around "di" suggests a related question about PDB
convention. It was my (perhaps not very good) understanding that ligands should be
identified by what is actually present in the crystal, and not by what can be modeled.
For example endogenous ubiquinone is likely to be UQ50
When faced with a program requiring HL coefficients, and having
phases from a (partial) model, I used to run a ccp4 program called
sigmaa to generate the HL coefficients. I'm not sure if this is
theoretically a good idea, but at least it allows the program to run.
On 01/19/2017 11:10 PM, Vikram
On 11/30/2016 10:16 PM, Keller, Jacob wrote:
If you fine slice and everything is then a partial, isn't that *more* sensitive
to lack of synchronization between the shutter and rotation axis than the
wide-frame method where there's a larger proportion of fulls that don't
approach the frame
On 11/17/2016 08:36 AM, herman.schreu...@sanofi.com wrote:
Dear Shijun,
The reject.hkl file is the file with all rejected reflections. The first three
numbers are h, k and l. For the other items you have to consult the HKL manual.
As I said, I am not familiar with HKL2000. However, in your
What about China? Singapore?
On 11/09/2016 12:45 AM, Tom Peat wrote:
I don't know about Europe, but it is very tight Down Under...
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William
G. Scott
Sent: Wednesday, 9 November 2016 4:38 PM
To:
, Tobias.
On Fri, Jun 19, 2015 at 4:54 PM, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
A number of superposition programs allow to superimpose specified atoms
(such as CA).
Once you get the operator, comparing two different operators is not a job
I think it is part of ccp4:
$CCP4/bin/topdraw
On 07/05/2015 10:30 AM, Faisal Tarique wrote:
Dear all
Can anybody provide me the link to download or install TopDraw a topology
drawing interface in CCP4..?
Thanks
--
Regards
Faisal
School of Life Sciences
JNU
Another criterion for cutoff, also requiring the structure to be solved,
is the agreement between data and structure, e.g. Rfree or CCfree.
I think it is very unlikely that you could get Rfree =.2493 in a shell
which contains only noise. So I would suggest doing paired refinement
to 2.2 and 2.1 A
: *Edward
: Edward
I can't imagine a journal doing that can you? When I work on my
supplementary material in a paper I don't expect that the journal will
take a bit out and publish it separately to support the work of my
competitors. Not out of spite that I was beaten - but because I don't
want to take the
You raise some good points, but as far as better confidentiality
pre-publication goes. unreleased entries are not secret in any case- if the
second group is at all nervous about competition, they will be searching the
unreleased entries database
A number of superposition programs allow to superimpose specified atoms (such
as CA).
Once you get the operator, comparing two different operators is not a job
for a conventional superposition program, since you are superimposing a
line on a line which has the extra degree of freedom- rotation
Neat! It's true the PDB will choose a unique code for you,
but they will use what you supply if it is already unique,
and it is nice to be able to choose something that can help
you remember what it stands for.
Gone are the days when we could choose meaningfull pdb ID's
(like 1PRC, 2PRC, 3PRC etc
In other words, the free set for each complex must be
such that reflections that are also present in the apo dataset retain
the FreeR flag they had in that dataset.
A very easy way to achieve this- generate a complete dataset to ridiculously
high resolution with the cell of your crystal, and
Is it possible to distinguish P64 from P62 without having basically solved the
structure?
Given that it is P64, is the +ive direction of the c axis arbitrary? A
left-hand helix is left hand either way you point it, and the molecules in the
asymmetric units could be pointing the opposite way.
-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A.
Berry
Sent: Friday, May 15, 2015 3:08 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Two kinds of solvent-accessible-surface ?
If I remember correctly, there are two different ways to calculate a surface by
rolling
:
Good points. But also, the traditional isomorphous difference map is not as susceptible
to model bias issues compared to a real space difference map (or a vector
isomorphous difference map).
On Tue, May 12, 2015 at 11:37 AM, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote
Thanks, these are great! I installed the ttf font on a windows box, and the
symbols are available in MSWord and Photoshop (and presumably powerpoint and
everything else). No more designing my own symbols in photoshop!
eab
On 05/08/2015 02:43 PM, Mooers, Blaine H.M. (HSC) wrote:
Hi Nick,
On 05/02/2015 12:23 PM, Imre Berger wrote:
Dear Edward -
Would you be so kind and explain why you went ahead to post that comment
about Alex Rich on CCP4, in a thread which announced the sad news of his
passing away?
Yes- I realized after posting it that it was inappropriate. If there is any
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