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:
>
&
The pdb seems to have gone so up market I can no longer see how to submit a
simple sequence search or rum SSM
I get offered multiple options to use services I do not want to use!
But asking for
"sequence search" or Search sequences" gives lots and lots of non-intuitive
choices!
Grrr
Eleanor
Any
Sorted - confusion in the conversion to orthogonal format..
Eleanor
>
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
This message was issued
Can you send your command file ?
And how are you displaying the Patterson map ?
>From CCP4I you can request a peak search of the map - check if the peaks
correspond to ones you would expect from your coordinates
Maybe read the map and vector positions into COOT to see?
Eleanor
On Tue, 21 Jun
Partly depends on what you have written! Faux pas would lead to a
question.. but I would probably concentrate on what the structure has told
you about your protein system. I would expect you to know a bit about the
strengths and limitations of the technique.
Eleanor
On Tue, 14 Jun 2022 at 16:58,
mtzdump hklin a.mtz
end
And you get this output
Look at the BOLD bit
Name of file
Cell and spacegroup
Column labels.
In this case the file I downloaded from the PDB only has F and SIGF
Resolution
etc..
mbat:Paul-5ACs eleanor$
*mtzdump hklin
If you run mtzdump hklin your.mtz
the first output is descriptive.
Have you done that?
You will get "header" information about cell, selected symmetry, etc, and a
list of labels for the columns
That will start H K L then maybe F+ SIGF+ F- SIGF-
or I+ SIGI+ I_ SIGI-
or something else.
Can you
How I hate RNA!
However, structures have been solved..
As others say:
Look for twinning
Look for translation non-cryst symmetry.
It seems likely when you have a doubling of the a axis for the Zn
derivative.
I use CCP4I2 and the data processing report will do both these tests.
Then you need to
and shaker who led the establishment of
the many great Indian laboratories now in existence.
It is a privilege to have known him.
Eleanor Dodson
On Mon, 25 Apr 2022 at 05:21, Karthik Selvam
wrote:
> Prof Vijayan preferred to call the book as his memoirs, instead of
> biography or autobio
Well - I would look at the deviants in COOT and see if there is a proper
reason for the angels - water molecules too close? alternate conformation
for some near by sidechain? Any refinement program wants to get good
geometry unless there is an obstacle. If there is nothing obvious to fix
you could
;
> ARN UPR 9002 CNRS
> IBMC Strasbourg
> 2, Allée Conrad Roentgen
> F-67084 STRASBOURG cedex (Google Maps Code Plus: HQH7+VV Strasbourg)
> +33.3.8841.7109
> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
> URLs: https://ibmc.cnrs.fr/, https://ibmc.cnrs.fr/labo
t")
> dataset.crystal_name = "mycrystal"
> dataset.project_name = "myproject"
> dataset.wavelength = 1.44555
> for column in mtz.columns:
> column.dataset_id = dataset.id
> mtz.write_to_file("output.mtz")
>
> Cheers,
> Paul
>
mmCIF reflection files I use.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board On Behalf Of Eleanor
> > Dodson
> > Sent: Tuesday, April 5, 2022 15:47
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] sftools
> &g
Does ANYONE know how to use this useful but ultra-frustrating program??
I have an mtz file which lacks WAVElength AND Dataset name.
I try to follow the sftools documentation, and get an output file which -
lacks WAVElength AND Dataset name.
G
sftools
Hmm - not sure if this would work but it is worth a try.
Refine your model against twinned data to get PhiCalc
Go to
Reflection Data Tools
Calculate unusual map coeffs
Give reflection file with I+ and I- from data processing ( They are twinned
Is but maybe this will work)
Phases from your best
I am sure you have checked this but
A) is there non cryst translation? If so this can make space group
selection tricky . Could it be P3 21 or P31 21 or ...
B ) the twin indicators at data processing are pretty reliable and if that
suggests no twinning it probably isn’t there... you could process
As I am sure you know -
if you generate experimental phases from isomorphous or anomalous
scatterers the differences between the reflection pairs can be equally well
described by sites at (x,y,z) or (-x,-y,-z) .
In addition many spacegroups allow coordinates to be related to several
alternative
Well - there are various traps towards a MR solution.
Maybe the data is not very good? What is the resolution and merging r
factor?
Assuming data is ok...
Most common is that the spacegroup is wrong. Have you tested all possible
spacegroups for the Laura group? Both phaser and molrep have options
to us this (pre-SAD
phasing) and again got too much substitution, not too little. Have other
people used it successfully? I would be interested to know..
Eleanopr
On Tue, 25 Jan 2022 at 13:41, Eleanor Dodson
wrote:
> Thank you
> I can look at it and maybe be useful..
> HgI3c was a heav
?
And have you checked the peaks in the anomalous map.
I can explain how to do that, or if you are allowed to send the data I can
show you what to expect.
Eleanor Dodson
On Tue, 25 Jan 2022 at 04:41, Paul Emsley wrote:
>
> On 25/01/2022 04:10, YUVARAJ I wrote:
>
> Respected Prof. Pa
in chains named S were already in that model, then it is a bug
> that I need to fix.
> Cheers,
> Pavel
>
> On Thu, Dec 30, 2021 at 11:05 AM Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> I am not sure whether I have this straight but
examples of this on the PDB-REDO server, but not
> recently. Renumbering is the only solution I'm afraid.
>
> Cheers,
> Robbie
>
> On 30 Dec 2021 20:05, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> I am not sure whether I have this strai
I am not sure whether I have this straight but someone has sent a pdb file
from phenix refinement with these atoms in the pdb file..
ATOM 5580 N GLY S 18 36.182 44.368 56.021 1.00 79.25
N
ATOM 5581 CA GLY S 18 37.168 44.349 57.091 1.00 74.78
C
ATOM 5582 C
Hmm - I think I have found it.
You provide an input pdb , but in the REFMAC log file it complains about
this.
mon_lib.cif
*ERROR : HOH : duplicated atom_name : "O ".
chain: SSS residue: 18
ERROR : HOH : duplicated atom_name : "O ".
Christine - can you attach the relevant log files! Eleanor
On Fri, 17 Dec 2021 at 22:59, Ethan A Merritt wrote:
> On Friday, 17 December 2021 14:04:17 PST Christine Gee wrote:
> > Hi,
> >
> > I recently came across this strange issue. I was using aimless in CCP4 to
> > scale my data and apply
Well - that should not happen!
Are the cell dimensions the same for the new data and the reference set?
E
On Fri, 17 Dec 2021 at 22:04, Christine Gee wrote:
> Hi,
>
> I recently came across this strange issue. I was using aimless in CCP4 to
> scale my data and apply an Rfree from a reference
Well I do this by overlapping one domain of protein A onto protein B - you
can do that in coot - then overlap the second domain of the shifted A onto
the second domain of B. The coot log file tells you omega phi kappa applied
and kappa is your angle of interest... is that clear enough - I could
THis is always a difficult decision. More commonly I have worried about the
best resolution cut off.
Judge on high Rmerges? Keep the overall R value acceptably low?? etc etc..
I always come back to the map - is it sharper with the extra data? Is more
unmodelled solvent showing up? etc..
But
Sorry lande fu- solutions P4 also can also be on different origins. That
is a polar spacegroup and any value along the c axis is acceptable. But
probably the mr search for both models just sets that to zero...
the r factors for two models being are so different is not so surprising.
How well do
You know there are alternative origins for P43212 - and a different MR
search very often will opt for a different origin..
from CCP4 doc
P4(123)2(1)2 - I4(1)22
N*origin*
Xo
Yo
Zo
1
0.
0.
0.
2
0.
0.
0.5000
3
0.5000
0.5000
0.
4
0.5000
0.5000
0.5000
Use
chains and 1 chain on a special position? I would vote for the latter.
> >
> > Best,
> >
> > Herman
> >
> > *Von:* CCP4 bulletin board *Im Auftrag von
> > *Peer Mittl
> > *Gesendet:* Freitag, 27. August 2021 10:17
> > *An:* CCP4BB@JISCM
ATTACHED SOME CORRESPONDENCE WITH David Lawson re these issues/.
Eleanor
On Tue, 31 Aug 2021 at 10:29, Robbie Joosten
wrote:
> Hi everyone,
>
> Thank you for the replies so far on and off list, they are really helpful.
> Feel free to keep them coming.
>
> Cheers,
> Robbie
>
> > -Original
cludes both the possibility of merohedral and pseudomerohedral twinning.
>> In the latter case, the obliquity parameter can be set using the keyword
>> OBL."
>>
>> I wonder since which CCP4 version (or date) this is the default behaviour.
>>
>> best wishes,
&
Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs
in the highest possible symmetry for the crystal class - eh P6/mmm for a
trigonal crystal, and expand the set to fill the actual space group. This
means the Free R assignment is suitable if later the crystal symmetry is
> refinement in P3221 would come up with the same occupancies for the
> > alternative conformations for the "extra" chain on the 2-fold axis. It
> > seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a
> > sublattice with P3221 symmetry and it'
Motto =mitti in predictive text!
On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson
wrote:
> Great, motto. I think you have nailed it! Did you use tefmac for twinned
> refinement? And if so what did it suggest the twin fraction is?
>
> On Thu, 26 Aug 2021 at 16:30, Peer Mittl wro
Great, motto. I think you have nailed it! Did you use tefmac for twinned
refinement? And if so what did it suggest the twin fraction is?
On Thu, 26 Aug 2021 at 16:30, Peer Mittl wrote:
> Yes, the data indeed seems to be twinned and the tNCS has masked the
> twinning statistics, which is why I
I must admit in cases like this, my first thought is - could the space
group be wrong? or is it twinned - quite common in this space group..
the normal twinning tests are sometimes misleading when you have
non-crystallographic translation.
I would reprocess the data as P32, generate a model with
r for the anomalous signal
> for X-ray scattering at http://skuld.bmsc.washington.edu/scatter/ When
> you choose Br instead of Grr, you find
> http://skuld.bmsc.washington.edu/scatter/data/Br.dat, or you read your
> values from the interactive plot
> http://skuld.bmsc.washington.edu/scatter/AS
Grr - stuck at home - what is f' and f' for Br???
All nicely tabulated on my desktop but not here..
So use chooch..
but it grumbles about file name null
How can I make it happy?
Any help gratefully received
Eleanor
eleanor@wombat cysbfull % chooch -e Br -e 0.92
Your self rotation strongly suggests a different spacegroup - I would look
back at the integration and processing before puzzling over cell volumes!
Eleanor
On Mon, 5 Jul 2021 at 16:00, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:
> Rob,
>
>
>
> Wat is the Matthews number, would
Why you have this problem I cannot guess, but your self-rotation clearly
shows 2 2 2 symmetry.
Try another data processing system?
Eleanor
On Mon, 5 Jul 2021 at 14:54, Robert S Phillips wrote:
> I collected data last week on crystals of tyrosine phenol-lyase obtained
> under new conditions.
000
> 0.311 0.345 0.000 0.000 0.025 0.016 0.000 0.000
> 0.345 0.380 0.000 0.000 0.021 0.014 0.000 0.000
> $$
>
>
> Gamma 0.24162
>
> Log likelihood: 2.920853e+04 Log likelihood (free): 0.00e+00
>
> $TABLE :Cycle 1 SigmaA statistics:
The extract from the log file looks OK - can you send the whole log.txt?
Eleanor
On Fri, 25 Jun 2021 at 12:09, Savvas Savvides
wrote:
> Dear colleagues,
>
> I am trying to run Parrot via CCP4-7.1.014 and the CCP4i2 GUI on a
> MacBookPro (OSX 10.15.7) and keep getting the following error report
I know not many will have met Jenny in person but maybe more have read
Crystal Structure Analysis - a Primer by Glusker and Trueblood.
It is an excellent book, and widely plagiarized!
Please send a message if you would like to
Eleanor Dodson
--
*From:* Miriam Rossi
As you know Paul I would like COOT to output a list of peaks into a
"coordinate " file..
You can do it laboriously by hand using Add atom at peak position but that
gets tedious...
Eleanor
On Thu, 10 Jun 2021 at 22:14, Edward A. Berry wrote:
> On 06/10/2021 11:19 AM, James Holton wrote:
> >
> >
peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" <
wrote:
> Paul was a little too terse, perhaps.
> In script form
>
> peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx
> keywords in here
> EOF-pmx
>
> at least that's what works for me in Csh. Bash proselytizers will
First spacegrouop - trigonal spacegroups can also be indexed as C2 so it
isnt so surprising that a P6/mmm should masquerade as C2.
I would look very carefull at the POINTLESS symmetry scores and see if some
are more convincing than others.
But how I hate RNA & DNA - molecular replacement
James - could you send me a few examples to add to the documentation?
Lockdown means I cant easily access my own examples - all trapped on the
lab desktop..
Eleanor
On Mon, 7 Jun 2021 at 17:18, James Holton wrote:
> I wrote a script for auto-generating occupancy refinement relationships
> for
In GUI2 the Advanced box allows you to do that
eg RESO 10 3 say if you wanted to restrict resolution..
Eleanor
On Mon, 7 Jun 2021 at 11:35, Marina Gárdonyi <
marina@pharmazie.uni-marburg.de> wrote:
> Hi,
>
> I didn't know that I can also enter keywords without a file! That is a
> good note,
here is an extract from the documentation.
is it a help?
i will try to find examples.
eleanor
This keyword defines number of cycles of refinement.
Occupancy refinement (version 5.6.0037) from Tidied up
occupancy group id chain ... residue
atom alt
or
occupancy group id chain ...
esn't necessarily imply a 4-fold axis (i.e.
> a closed group). It could simply be 2 (or even 3) subunits related by a 90
> deg. rotation (i.e. not a closed group). A 4-fold axis gives rise to
> multiple overlapping peaks on the chi=90 and chi=180 sections (so the peak
> heights wo
rotation system - they could be relating distant monomers..
Cheers Eleanor
On Sat, 22 May 2021 at 17:50, Ian Tickle wrote:
>
> Hi Eleanor
>
> On Sat, 22 May 2021 at 14:55, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> And several stron
Yes - contacts or distang gives you a list of distances. PISA a list of h
bonds and salt bridges - all with associated sym ops.
But none produce a complete table - PISA output prob the best.
Eleanor
distang gives you this sort of information but i guess it is far too
detailed?
R 125 NA R
Where did you find the tutorial files??
Eleanor
On Tue, 11 May 2021 at 10:24, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hello, just to double check, I assume that you input the correctly
> oriented and positioned structure of each domain from successive runs as a
>
Finding a solution will be very difficult then.
Eleanor
On Fri, 23 Apr 2021 at 21:11, Swati Gupta wrote:
> My data is moderate anisotropic also with a high Wilson b factor greater
> than 200
>
> On Sat, 24 Apr, 2021, 01:19 Eleanor Dodson,
> wrote:
>
>> If you were luc
If you were lucky the new crystal might have the same cell and
spacegroup as your model, but otherwiseThis is a case for molecular
replacement.?
My course of action using CCP4I2
Process data carefully and look for any warnings.
Align your new sequence with the model using clustalw
Edit the model
hough.
>
> Cheers,
>
> Dirk.
> On 07.04.21 11:46, Eleanor Dodson wrote:
>
> Well - I use COOT for this sort of task, and dont trust the automated
> tools.
> my procedure is
> load COOT - probably after a refinement cycle
> set occupancy of ligand(s) to 0.00 (
Well - I use COOT for this sort of task, and dont trust the automated tools.
my procedure is
load COOT - probably after a refinement cycle
set occupancy of ligand(s) to 0.00 ( Measures - residue information -
change occupancy)
Look at the environment critically . eg if an ARG or other bulky side
Agree with Herman except re using refined model as search model. This will
almost always return the answer you started from..
Eleanor
On Thu, 1 Apr 2021 at 13:49, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:
> Dear Sam,
>
>
>
> The first thing that would come to my mind would be
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