Hmm - no idea but perhapd=s interesting that 0.83 ~ 1.7/2
Eleanor
On Fri, 7 Jun 2024 at 15:13, Aline Dias da Purificação <
d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear all,
>
> I am currently validating a structure for deposition in the wwPDB and
> encountered the following
Well, REFMAC output a (mislabelled) F SIGF which was detwinned so if you
deposited the REFMAC output I guess that is detwinned..
Do you have the original REFMAC input still?
Eleanor
On Thu, 6 Jun 2024 at 15:18, Ben Bax wrote:
> Hi,
> I am just re-refining an old twinned dataset - which I
Hmm - rather tricky! I would do an MR search with the crystal model v the
EM density,
Steps would be:
1) convert EM density to "structure factors". - there are tools which do
this ..
1a) You need to go back to ccp4i - program sfall to read map to generate
SFs from map - then cad or sftools to
Your pictures 1 3 & 4 don't seem to show multiple occupancy? Maybe the
difference map 2 is saying - too much complexity ??
Eleanor
On Thu, 30 May 2024 at 23:29, Michael Colaneri
wrote:
> Dear All,
> We have alternate conformations for a number of residues in a structure
> and one is a Val that
With that translation (x,1/2,1/2) lots of your reflections with k and l
Odd will be relatively weak and those zones usually have higher r factors.
Look at the plots of reflection zones in hklview and you will probably
notice weak and strong zones.
The translation will make selecting the
But are there two conformations of the disulphide? or one disulphide and
one broken link?
Eleaor
On Mon, 6 May 2024 at 20:42, Dr. Kevin M Jude wrote:
> I have done this in shelxl or phenix refinement, you can define occupancy
> groups (or free variables in shelxl) so that 472A and 384A are one
Well - I turn off occupancy refinement once there is a sort of consensus..
Disulphides often break after long exposures and you see the positive and
negative blobs clearly. I must admit I usually just set 0.5 as occ , fix
the surviving disulphide link and let the B values suggest a better ratio
That result looks really bizarre but it is hard to make a sensible comment
without more details..maybe you could attach the whole log file for the
refmac run.
What input reflection dAta are you using ? You couldn’t have picked up a
Sharpened set by any chance? (It is always good practice to make
If you are using CCP4I2 and use the task "Import merged data" that sort of
reprocesses that data through AIMLESS. You get all the usual graphsv
resolution - completeness, I/SigI , Wilson plot, Second moments etc and
from those can make a sensible decision on where the resolution limit
should be
I like to use difference maps between Fa and Fb ..
It is a bit tricky now to set them up..but they do highlight changes.
Obviously
1) you need to have the same spacegroup and cell, and the same indexing
convention.
(Easy to check this in the data processing task when importing the second
data
It. Will probably take me a. Full year to draft the. Application - is that
too slow?
On Mon, 1 Apr 2024 at 09:22, Frank Von Delft <
bcb385fe5582-dmarc-requ...@jiscmail.ac.uk> wrote:
> Oh dear, your prime number oversupply crashed the crypto Ponzi scheme
> market. Will you accept $10e2
This is best done by calculating the structure factors for the part you
want to fix. (make sure the occupancies are set yo 0.8)
The REFMAC hklout will contain F SIGF etc plus FCALC PHIcalc for that bit
Define this file as your input hkl
Then refine the 20% structure (occs=0.2) with input
LABI
That is extremely likely! - certainly REFMAC will do that..
If 5% missing using DFcalc is a good thing - if 35% is missing not wise..
Eleanor
On Mon, 4 Mar 2024 at 07:53, Ben Bax wrote:
>
> Fcalc maps look fantastic. Are you sure they were not using an Fcalc for
> the missing 35% of the data?
>
Well REFMAC tells you how many reflections are used..
And if you do
mtzdmp data.mtz
that will tell you too..
With such low completeness R factors are pretty meaningless - you must have
many more parameters than observations so that does often give low
Rfactors..
On Wed, 28 Feb 2024 at 16:21,
Well - it is extremely surprising! How many reflections are there in the
"work" set (Rwork) and the "free" set (Rfree)?
I suspect that somehow all the reflections are in both sets??
Eleanor
On Wed, 28 Feb 2024 at 15:11, Justin Cruite
wrote:
> Hi everyone,
>
>
>
> What does it mean if your
Hmm - that is pretty confident that the spacegroup for this cell is P2 21
21 (72.61 73.73 147.23 90 90 90 ..)
There are some strong reflections along the "a" axis
*From pointless log*
Lattice unit cell after reindexing: deviation 0.88 degrees
72.61 73.73 147.23 90.00 90.00 90.00
$TABLE:
Various (all depressing) possibilities..
You don’t say what the sequence ID to the models us
Your protein is flexible with poor fit to the available models. How well do
those overlap?
The bioinformatics tools in i2 give you pictures showing this. Look at them
and see if there are sensible places
the easiest way to resolve this
> unambiguously is to solve in P1, and let that uncover the true symmetry.
>
> Best wishes,
>
> Randy
>
> > On 21 Feb 2024, at 13:56, Pedro Matias wrote:
> >
> > But curiously, all the 4 best solutions correspond to a SG with a 21
Lots of comments, but it would be easier to actually look at your
integrated data!
Some of the stats look a bit ropey -
621 reflections labelled as outliers by PHASER?
Very anisotropic
Moments go mad at the highest resolution..
The good news - extremely strong signal from the rotation function
Hmm - I can't help with the scripting question, but it solved easily from
the I2 interface?
This is run on a Mac.
CRANK2 called SHELX - found SE with weak signal..
Some difference between hand
It traced ALA - R factor 41%
Then BUCCANEER or MODELFIR quickly built and sequenced the rest..
Eleanor
Isnt this what you want? output of CCP4I2 fitting buccaneer to the other..
On Fri, 16 Feb 2024 at 09:46, zx2...@connect.hku.hk
wrote:
> Dear all,
>
> Following the advice provided by Paul and Yi Min, the "*Symm Shift
> Reference Chain Here*" function has proven successful!
>
> I am deeply
That pxmaths document was put together by Maria Turkenburg, with a bit of
input from me long long ago, but then the theory hasn't changed much in
that time.
My old reference was Srinvasen & Parthasarathy
>From crystallography in India..
Influential books by him and his associates (R. Srinivasan,
If I remember for coefficients with FOM and a precise PHI calculated, A =
FOM*cos(phi) B = FOM*sin(phi) C=D=0
If you have a probability curve for PHI. 0 to 360 such as you get from
experimental phasing, A B C D mirror this bimodal curve better ..
On Fri, 9 Feb 2024 at 09:58, Nitin Kulhar <
Did you make the original deposition ? If so the pdb accepts
re-depositions...
If it was done by someone else I guess the courteous thing is to notify
them and maybe talk to the pdb- redo team?
Cheers Eleanor
On Sat, 27 Jan 2024 at 01:53, Lucas Souza
wrote:
> Dear all,
>
> After auditing and
I give MOLREP am input mtz with space group R32:H or R32 or H32
(entered as R32:H)
But MOLREP claims the SG is
default_PST_limit : 0.250 of origin peak
PST will not be used.
If you like to use PST, use keyword PST = Y
* Space group : H 3*
No: 146 Sett: 2
Cell:
THere must be some error in the calculation of the CC - or you are over
optimistic about what constitutes a fit!
What does the COOT density fit show?
Eleanor
On Wed, 10 Jan 2024 at 09:54, Martyn Winn - STFC UKRI <
7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> wrote:
> You can also try the
I thought it was possible to stop B values on bonded atoms from fluctuating
wildly?
But I am quite unable to follow the newly formatted documentation..
To unsubscribe from the CCP4BB list, click the following link:
Hmmm - I am not sure about the value of this - one expects the longer
floppier side chains to have very different B values for the CB than the
OE2..
The program BAVERAGE gives you a plot of mean B value residue by residue..
*baverage* - averages B over main and side chain atoms
SYNOPSIS¶
Back to the value of an anomalous map - IF the anomalous data is good
enough to give a significant peak at a sulphur position, you might expect
to get a peak at a well ordered phosphate- if no sulphur peaks not much
hope...
On Mon, 25 Dec 2023 at 19:51, Tom Peat <
Well - are any of our names worth pricing?!
Very very suspect..
Eleanor
On Fri, 15 Dec 2023 at 14:41, Robbie Joosten
wrote:
> Hotel booking scammers for instance.
>
> Cheers,
> Robbie
>
> On 15 Dec 2023 15:34, Frank von Delft wrote:
>
> I mean, who'd actually want that list anyway?!
>
> On
Very very interesting analysis - Thankyou!
On Fri, 1 Dec 2023 at 18:01, Tom Terwilliger <
b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi Roberto,
> Thanks for the link to the DeepMind site! I hadn't seen that and now I
> read it and the paper that they link to. It looks to me as
Pavel has listed the papers that describe the underlying maths but unless
you have high resolution data (> 1.9A say?) unscrambling results from
occupancy plus B factor refinement is problematic to say the least..
Think about residues such as ARG or LYS where the termini are often
extremely wobbly
Q0. Echoing Randy - how accurate is your starting model - Xray structure at
resolution 1.5A or high quality EM or NMR??
Q1. Are the solutions the same? There is a CCP4 tool in ccp4i2 - Match my
model which will check this taking into account symmetry and origin shifts.
On Tue, 21 Nov 2023 at
Sorry - the simplest answer - is get higher resolution data!
But there are some improvements possible.
How clear is your MR solution.
What is the similarity between model and your sequence?
Etc.
On Tue, 21 Nov 2023 at 12:03, Yahui Liu wrote:
> Dear all,
> I got a protein crystal dataset of 4.3
You seem pretty near to having solved your structure!
Ignoring the data problems..
Extra steps I might have used.
1) Self rotation function. (in CCP4I2 the task is under data analysis ..)
Does it suggest a NCS operator?
If so is this a two fold? which might mean you have a dimer..
2) Now you
Are there some atoms with occupancies < 1.0 ?
You would need to weight those Bs by occ
On Sun, 5 Nov 2023 at 11:34, Ian Tickle wrote:
> The arithmetic mean B value from the structure as quoted everywhere is
> pretty meaningless anyway and 10 Ang.^2 either way is probably not
> significant.
Hmmm - r 50% rather suspect..
do the MR solutions from phaser and molten agree?
Eleanor
On Mon, 6 Nov 2023 at 05:10, Sam Tang wrote:
> Dear all
>
> Thanks for all the input. I will definitely try out in the coming couple
> of days. To provide more information:
> - the data was checked in
IF your MR solution is correct ( ie r factor falls on refinement to 40%
say) and your protein A is roughly 50% of the complex, and IF your data is
good to 1.9A (assumed SG correct etc) I would do my best to correct any
obvious rebuilding needed for protein A, ( r factor should fall further if
this
Favored (%)*
>
> 97.83
>
> *Allowed (%)*
>
> 1.38
>
> *Outliers (%)*
>
> 0.79
>
> *Average B-factor (Å)*
>
> 28.0
>
> *macromolecules (Å)*
>
> 28.65
>
> *ligands (Å)*
>
> 48.98
>
> *solvent (Å)*
>
> 18.44
>
> On
Am I confused? I would accept an I/SigI of 1+, and a CC1/2 of 0.5 as pretty
acceptable?
E
On Thu, 2 Nov 2023 at 15:03, Dr. Kevin M Jude wrote:
> As suggested by the (conflicting) observations of Eleanor and Nicholas,
> it’s not clear whether you are showing data collection statistics for the
>
Well - you probably could use data to a higher resolution I/SigI and CC
1/2 are quite high.
The better the resolution the better the model usually.
On the other hand your Rmerge is high-ish. Hard to comment without seeing
the data processing results. Look at the plots of 2nd moment, wilson plot,
Hmm - I can give you scripts to use SHELX?
Eleanor
On Wed, 11 Oct 2023 at 11:02, fuxingke wrote:
> Dear Colleagues,
> Reacently, for SAD experiment, I find SOLVE and SHARP can refine the
> variables
> of heavy atoms, such as occupancies, coordinates and thermal parameters.
> But how to
Well - some outliers are infix able! There are various reasons - floppy
residues like arg or lys
In multiple positions; strain due to protein folding constraints, etc.
I use the validation report to check for obvious modelling errors but if
you can’t find any, you have to just submit the results
I am afraid most scientists will use the most straightforward technique!
If SAD is available the PHOSPHATE backbone of DNA will provide sufficient
signal to allow SAD to work, and you get an unambiguous answer to whether
it is A-DNA or B or Z...
MR will usually work of course as well
Eleanor
On
-zero value and vice versa if it is the only conformation present
> it will be less than unity.
>
> I will take a look at the references! Very much appreciated.
> Matt
>
> On Wed, 6 Sept 2023 at 02:08, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk
Well - occupancy refinement is particularly imprecise, and highly
correlated with temperature factors.
Also the population for a surface ARG or LYS may well have more than two
conformations, whereas some internal residue is better defined.
There is also the Q of solvent - dual occupancies will
I dont know what it is - but thats a beautiful map! What was in the
crystallisation pot, do you know?
Eleanor
On Tue, 29 Aug 2023 at 18:22, Bijelic, Aleksandar <
abae22057430-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear CCP4 members,
>
> I found the attached density in some of my structures
THank you - it is on a two fold axis you said?
That means it could be a sort of average of a molecule..
Eleanor
PS Any anomalous peaks?
On Mon, 14 Aug 2023 at 10:32, Yue Li wrote:
> Hi everyone,
>
> Thank you for your replies. I have uploaded the figures to a website. The
> link is here:
>
>
Hmm - I cant see a picture..
Your email has this..
img
You need to tell us more details - is this a deposited structure?
Eleanor
On Wed, 2 Aug 2023 at 15:42, Thomas, Leonard M. wrote:
> Hello All,
>
> A general questions though phenix.refine is being used for refinement. A
> student I am working with has a structure that was solved and initially
>
Hmmm -are the two ano maps contoured at the same level?
You can check this by setting the SCROLL option to the ano map.
The 2mFo-DFc maps look pretty identical..which suggests the two input mtz
files are similar.
You can get more information by viewing the inputs to make sure the values
are the
You would hope it would show some hydrogen positions..
Eleanor
On Mon, 24 Jul 2023 at 13:47, Ankur Kumar Singh wrote:
> Dear Prof. Eleanor Dodson,
> Thank you for the response. I will try generating difference map as told
> and will update.
>
> -
> Regards,
> Ankur K
hy not calculate structure factors without hydrogen atoms and look at the
difference map?
Eleanor
On Mon, 24 Jul 2023 at 12:36, Ankur Kumar Singh <
a8e375e16ee1-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear Members,
> I am trying to generate an experimental residual electron density map for
>
No attachments Lande Fu?
Your C2221 cell is pretty obviously related to the orthorhombic one.
(a b c )-C2221 ~ (2b 2c a)P212121
The cell volume of C2221 cell is ~ 4 x P212121 cell. -
8 symmetry related copies for C2221 and 4 for P212121
so if there are 2 molecules in P212121 ASU you expect 4 in
Well - it is hard to comment without more information, but many crystals do
have tNCS and yield perfectly satisfactory solutions..
How many molecules do you expect in the asymmetric unit? Look at
the Matthewscoefficient suggestions to guess that.
What are the fractional coordinates of the
C2 Cell :
Average unit cell: 119.05 84.31 107.99 90.00 91.50 90.00
Space group: C 1 2 1
C2 shift ( if I have read your image correctly..)
60.32 2.137. 0.088 In fractions 60.32/119.05 2.137/84.31 0.00. = 0.504
0.023 0.00
See this site C121 has alt origin 1/2, ?,0 so your
WELL - with such high LLG and translation NCSthe high R factors are a bit
surprising..
The Patterson info does not give the relative height of the origin peak to
the off origin one..
Questions which I would check.
Look at the data processing carefully. Are there bad batches? Could the
space group
and the waters
Good luck Eleanor
On Mon, 26 Jun 2023 at 21:44, De La Torre Marquez, Pedro Luis <
pedro_delatorremarq...@meei.harvard.edu> wrote:
> Thanks Eleanor.
>
> Yes, only refine waters.
>
> Best regards,
>
> Pedro
> ----------
> *From:* Eleanor
Do you mean only refine waters? In a general refinement run the waters will
be refined along with protin/ligands etc..
Eleanor
On Mon, 26 Jun 2023 at 20:54, De La Torre Marquez, Pedro Luis <
pedro_delatorremarq...@meei.harvard.edu> wrote:
> Dear all,
>
> I hope everything is going well.
> Back
Very interesting one from Katherine Lonsdale- thank you
On Thu, 25 May 2023 at 21:21, CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> I found these audio clips on the BBC website - might be of interest -
>
> https://www.bbc.co.uk/archive/dame_kathleen_lonsdale/z6v8kmn
>
>
>From Louise Jones - Acta cryst editor
We put together an obituary for Alexei with contributions from his friends
and colleagues in Moscow and the UK
L*ouse says: I am hoping to put the obituary online this afternoon.*
*The page numbers have not yet been assigned but it can be cited with the*
As Robbie says, in such a case I just blindly refine with local NCS
restraints - this should improve the greater part of the model and thus
provide you with clearer maps. It is quite common for different copies of
the monomer to have differences - after all the crystal environment will be
Ha ha!
On Sat, 1 Apr 2023 at 05:34, James Holton wrote:
> Anyone who has ever had to lecture a student for writing their unit cell
> lengths to dozens of decimal places is going to love the new PDB
> format. It is more compact, more realistic, and less misleading to the
> poor, downstream
Alexei certainly contributed in MANY ways to Study Weekends!
Fun memories..
Eleanor
On Sun, 26 Mar 2023 at 20:00, Jurgen Bosch wrote:
> Sorry to hear, he helped me a very long time ago during my PhD time when I
> was running into troubles with some of his programs.
>
> The York CCzp4 weekends
Thank you Eugene for letting us know. He contributed so much to
crystallography, and was a good friend too.
MOLREP is such a well designed program, and he kept up his innovative ideas
- a true behind-the-scenes shaker and mover..
Eleanor
On Sun, 26 Mar 2023 at 19:29, 'Eugene Krissinel - STFC
ur help !
>
> GIA
>
>
>
>
> Le 22/03/2023 à 07:10, Eleanor Dodson a écrit :
>
> You have tried all spacegroups within point groups? P2 p21 c222 c2221?.
>
> On Wed, 22 Mar 2023 at 03:01, Lijun Liu wrote:
>
>> If data processing to be ok and all possibl
You have tried all spacegroups within point groups? P2 p21 c222 c2221?.
On Wed, 22 Mar 2023 at 03:01, Lijun Liu wrote:
> If data processing to be ok and all possible monoclinic and orthorombic SG
> gave unreasonable high Rs, maybe good to give a try with p1 space group?
> Since
> the
cell 66.3 66.3 83.9 90.2 90.1 98.7. P2 or P21 cell
Cell volume:364551.812
Data line--- cell 86.4 100.6 83.9 90.0 90.2 90.0. Cell volume double
- C2 or C222 or C2221 cell
Cell volume:729240.938. ie
How many residues in your model?
It is hard to decide much without
Thank you for such a careful analysis of modelling a "true" structure. You
should publish this James.
It shows amongst other things, how R factors depend on our modelling of
solvent which is not represented as individual atoms (And also I think on
how the scales are derived between observation
dependent of i2, you have to
>>> dig around a bit to find which output file contains the columns you need.
>>> >
>>> > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>> >
>>> > Sent from Proton Mail mobile
>>> >
fIf you are using ccp4I2 for some forgotten reason the final output has one
reflection with I+ and I-, another with Imean, another with Fmean - aagghh
On Mon, 13 Mar 2023 at 19:40, Ian Tickle wrote:
>
> Hi Gottfried
>
> AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default.
>
> Cheers
>
>
Does Superpose or GESAMT align multiple structures?
And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L
2 etc?
Eleanor
On Mon, 6 Mar 2023 at 14:53, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Or you could use Gesamt - also in CCP4.
>
> Harry
>
>
See the answer last week to my query about aligning nmr structures - use
Theseus .
I wonder if it could be used for this task too?
Eleanor
On Mon, 6 Mar 2023 at 07:35, Armando Albert wrote:
> Dear all,
> I want to align several structures we obtained from a fragment screening
> campaign and
I have been looking at 1hiq - an NMR structure with 20 models.
I had always assumed that an attempt had been made to overlap the first
with the second, third etc, but this does not seem to be so for this
structure..
Have I been labouring under a misapprehension?
Eleanor Dodson
Well - I made a copy of a ligand A 2001 and called it B 2001; gave each of
the "Ligands" occupancy 0.5, mangled the B molecule a bit and ran REFMAC .
It notes these atoms are too close but carries on refinement happily
enough..
But when I read the structure into COOT and try to refine the A
I thought that REFMAC tolerated dual occupancies if the sum of the two
conformers was <= 1.0?
Eleanor
Will test..
On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie <
974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:
> I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some
>
Usually you can bully coot into doing it but by bit. Say you need to
renumber A 1-8. I often have to change the chain id to Z say then renumber
Z. And so on . Then go back once you have finished and reset chain id fir
Z1-8 to A. Tedious but possible!
Or just run a few cycles of buccaneer with
The tool must have sharpened your data - sometimes enhancing the outer data
does improve the electron density..
So I wouldnt worry about that "negative" B factor - it is doubtless a
result of the "careless" run, and not presumably the one you got at the
data processing step..
Eleanor
On Fri, 6
d. Is there a way to do MR to predict where the
> missing domains will go in the rest of the chains, based on my
> solved structure?
>
>
>
> Thanks for all the helpful suggestions!!
>
>
>
> M
>
>
>
> On Wed, Nov 9, 2022 at 3:11 PM Eleanor Dodson <
&
Well you could just try the buccaneer pipeline. It would use the phases
from your solved domain and try to fit the missing sequence. What are your
twin fractions? And what is the resolution?
Eleanor
On Wed, 9 Nov 2022 at 21:06, Tim Gruene wrote:
> Dear Medhanjali DasGupta,
> unless the
How to deal with poor data is a challenge. Look at the images - see at what
resolution there is detectable diffraction.
Then run a self rotation function.Do you expect a trimer? dimer? etc and
does the self rotation give any clues?
Are your models dimers? trimers? etc.
Eleanor
On Wed, 26 Oct 2022
- Those reflections are equivalent:
- P6/mmm
- reflections h,k,l k,-h-k,l -h-k,l. all due to 3 fold
- hkl equiv to -h,-k,l because of 6 foldnes
h,k,l equiv to k,h,-l. due to t extra 2 fold
So -1,3,1. 3,-2,1 and -2,-1,1 equiv
Also 1,-3,1 -3,2,1. 2,1,1
Etc.. etc
OK?
Eleanor
There have been several discussions lately where anisotropy has been an
issue.
I have always believed weak unreliable data does little harm to refinement
or maps because it is given a very low weight in any calculation.
Weighting, in REFMAC anyway. is set partly using the Rfree for that
Dear Matt,
Your data past 2.5A is awfully weak, and wont contribute much to any map
you calculate. Each term at the outer resolution will have a very low
weight.
I sometimes cling to the belief that the weak data may help the B factor
refinement, but there isnt much evidence of that. There is a
We probably need more detail to help you.
Have you looked carefully at the data processing? Is the Rmerge or Rpim
reasonable for all batches? Is there any suggestion of twinning? Does the
wilson plot look linear? (These hexagonal SGs can be twinned)
How many copies of your molecule do you
Is that the right way round? Atomic no K 19, Na 11
Call something K when it should be NA - B factor will shoot to reduce the
atom contribution.
Call something Na when it should be K - B factor will become very small..
As you say - check which fits best with the surrounding atoms..
On Thu, 8
Hmmm - very puzzling..
One expects the for the atoms to more or less match the Wilson B for
the data sets..
There are some mini bugs which can mislead you.
Is your average a mean or an RMS value? RMS ones can be hugely inflated if
you have a few crazily high Bs and the refinement programs can
The high peak is to be expected if the B factor is ludicrously too high.
I think the problem is in the behavior of the B factor refinement.
Try setting all B factors for the CYS to some sensible value (you can do
that in COOT - ) then see what happens after more cycles of refinement..
Eleanor
Is it spam? It is from a contributor to CCP4BB and I guess it says
something like - received your message - my Chinese rather rusty..
Eleanor
On Mon, 1 Aug 2022 at 18:26, Andrew Leslie - MRC LMB <
and...@mrc-lmb.cam.ac.uk> wrote:
> Every time I send an email to ccp4bb, I get a spam email from
>
I cant see how the C2 cell can be reindexed to the P/mmm one?
Am I right to assume these are different processing of the same
diffraction?
And how many molecules do you have in each cell?
Eleanor
On Thu, 28 Jul 2022 at 12:52, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:
> Dear
a sets can show up if the Rfactor is greater than
> about 1%.
> Greetings,
> John
> Emeritus Professor John R Helliwell DSc
>
>
>
>
> On 26 Jul 2022, at 11:40, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Not only doe
Not only does SCALEIT do the job - it presented useful plots and an
informative log file..
Eleanor
(You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the
columns from each Xtal will need different labels..)
On Tue, 26 Jul 2022 at 09:45, Phil Evans wrote:
> If you give
eleanorOh dear - why don’t crystals behave better!
Re twinning - do the data processing Plots indicate twinning? ( L test?2nd
moments?)
It sounds rather more like overlapping diffraction where only some of the
observations are Affected.
Eleanor
On Thu, 21 Jul 2022 at 10:50, Flaig, Ralf
rlap between
> individual data sets. And the data quality is often low.
>
> In my posting I forgot to say that CrystFEL also has a facility to
> overcome indexing ambiguity.
>
> Best wishes,
> Kay
>
> On Fri, 22 Jul 2022 19:02:19 +0100, Eleanor Dodson <
> eleanor.dod...
Surely once you have indexed one crystal, you can use the facility to check
the next ones indexing against the reference - aka pointless?
On Fri, 22 Jul 2022 at 16:20, Kay Diederichs
wrote:
> Hi Monika,
>
> in June we had a summer school at MaxIV, and one of the topics was serial
>
Most molecular replacement programs allow you to search in all possible
space groups consistent with a given point group.
Eleanor
On Fri, 22 Jul 2022 at 11:18, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:
> Hi Monika,
>
>
>
> I would process the data using the point group
Hmmm - is there a smaller lattice which might fit the density? As Andrew
says there are examples of pseudo emptiness in crystals but there are more
examples of wrong lattices!
Check for non-crystallographic translation?
You could attach the pointless/aimless/etc log files..
Eleanor
On Fri, 22 Jul
Sorry to go back in time but distang is useful.
You set radii
Example:
distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb
RADI CA 1
end
will give all CA withion 2A of each other
distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb
end
Will give all C N O S
Did you check anomalous difference peaks? They would show zn very clearly.
On Sat, 2 Jul 2022 at 08:08, Sayan Saha wrote:
> Dear all,
> As suggested by most people, we modeled Zn2+ ions coordinated with
> three water molecules.
> Thanks for everyone’s response.
>
> With best regards,
>
work. Be careful about the url characters either
> side of the sequence.
>
> Sameer
>
> On 24 Jun 2022, at 15:41, Eleanor Dodson
> wrote:
>
> PDBe server - my long term favorite website...
>
> On Fri, 24 Jun 2022 at 15:40, Sameer Velankar wrote:
>
&
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