gt; opposites you may still be able to try SIRAS.
>
> George
>
>
> On 23.07.19 11:43, Eleanor Dodson wrote:
>
> Well - there are lots of ways to proceed. It doesnt really matter for the
> crystallography theory if the exptl phases are from SAD or SIR. Just harder
> to hand
Well - there are lots of ways to proceed. It doesnt really matter for the
crystallography theory if the exptl phases are from SAD or SIR. Just harder
to handle in some software
I think I would start to refine the poor MR model with the xptl phases as
restraints.
REFMAC will do this. Then see if the
Isnt it most likely that this chain is partially occupied?
Eleanor
On Mon, 22 Jul 2019 at 12:32, wrote:
> Dear Peer,
>
> I did not check, but I expect that atoms with B-factors exceeding 200 Å2
> will not contribute much to the F's at 2.3 Å. A good test might be to
> calculate Rfree's at 4 or 4
Good advice above..
Someting extra - I would look at information about how the molecules might
be arranged.
Is there any non-crystallographic translation? ( One with a coordinate 0f
say z= 0.5 could mean the spacegroup
could be P21212 or P212121 )
Sometimes there is a sub-cell and you can search f
Hmm - MET often has two (or more) conformations..
I would check the anom maps to see where the S atoms are - maybe the CYS S
also is partially occupied?
Eleanor
On Wed, 17 Jul 2019 at 15:03, Stephen Graham wrote:
> Hi all,
>
> We've spotted something very weird in our density that we're struggl
gt; same unit cell by new version of HKL2000, which is better than old version
>
>
>
>
> -Original Messages-
> *From:*"Eleanor Dodson"
> *Sent Time:*2019-07-15 22:08:01 (Monday)
> *To:* "张士军" <21620150150...@stu.xmu.edu.cn>
> *Cc:* "
Do you mean these crystals have different unit cells? If so then DMMULTI is
a useful technique..
Or do you mean you have collected isomorphous data from several crystals
and want to merge that data?
In that case BLEND will help you decide how isomorhous the data sets are..
Eleanor
On Mon, 15 Jul
Are all the trigonal cells related?
Eleanor
If so, you can use your untwinned data set as a guide to pointless to make
sure all others are in the same indexing system, assign all the spacegroups
to P3221
Then just start refinement with the key word twin from your good model.
Eleanor
On Thu, 11 J
Read the log file?
Do you mean MOLREP self-rotation?
Eleanor
On Thu, 11 Jul 2019 at 08:28, Madhurima Roy wrote:
> Dear All,
>
> How do we find the contour levels, peak heights and angles in self
> rotation function ?
>
>
>
> Madhurima
>
>
> --
>
> To unsubscribe from
On Wed, 10 Jul 2019 at 11:32, Lumbini Yadav wrote:
> No I am using ccp4i. I tried doing SAD refinement in refmac and the output
> image is attached below .
> I do not seen density near cysteine that was visible in Fo-Fc map
>
> On Wed, Jul 10, 2019 at 3:40 PM Eleanor Dodson
> w
The key word for refmac is ANOM MAPONLY
Are you using GUI2?
Eleanor
On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav wrote:
> I have soaked my crystals in sodium dithionite a reducing agent. I have
> not done mass spec but sequence is confirmed
>
> On Tue, Jul 9, 2019 at 9:26 PM Bonsor, Daniel
> wr
I am serious about checking the anomalous map!!
(trivial from REFMAC - key word anom map on)
Then do a peak search and just check first that the rogue residue IS CYS
first - you should see the S as a peak..)
Eleanor
On Wed, 10 Jul 2019 at 07:38, Lumbini Yadav wrote:
> Thanks for the reply.
>
Any anomalous diffraction?
On Tue, 9 Jul 2019 at 10:32, Lumbini Yadav wrote:
> Dear all,
>
>
>
> We have found a huge Fo-Fc density close to cysteine residue (see attached
> image) in the structure with resolution of 1.2A. In the crystallization
> condition, we have PEG 3350, Potassium phosphate
Well - i would always do the final refinement to the highest resolution
with CC1/2 > 0.5
There may be other problems with the data - completeness low for current
standards ..
Does multiplicity fall off with resolution etc?
Is there considerable anisotropy?
both sets of R factors look surprisingl
What are we meant to make of that picture?
Eleanor
On Mon, 1 Jul 2019 at 18:39, De La Torre Marquez, Pedro L. <
delatorremarque...@osu.edu> wrote:
> Hi all,
>
> Highly recommended for people working with HKL2000. Please check the
> attached picture.
>
> By: Jesse Sandhu from Sotomayor Laboratory,
Old program RSTATS would give r factor..
But easist to run 0 cycles of REFMAC - at least then you know what the
scaling algorithm might be
Eleanor
On Mon, 1 Jul 2019 at 14:22, Robbie Joosten
wrote:
> If you are using SFTOOLS you might as well use the CORREL function to
> calculate things.
>
ne, Rwork
> decreases from 0.525 to 0.5175, but Rfree increases from 0.5239 to 0.5381.
> Is the high LLG, low TFZ because of the wrong or bad search model? Thank
> you!
> Cheers,
> Weixi
>
> ----------
> *From:* Eleanor Dodson
> *Sent:* Monday, 10 June
Hardly enough information!
Resolution?
Wrong spacegroup - eg P21212 when it should be P212121 or something?
Wrong estimate of model difference? That can afffect LLG quite a lot?
But there are many reasons..
Does the Rfactor fall when you refine? A change of R=55% to R=47% usually
indicates the
The current Rfree selection is done in the highest possible Laue group - eg
trigonal uses P6/mmm - then the selection is proogated to the chosen Laue
group - eg P3. So IF the ncs reflects a higher Laue symmetry as it often
does the FreeR is sort of buffered against the ncs- effect..
That wont alwa
Hmm - that sym op means you have a near C centred cell with spacegroup C 2
2 2 ?
Maybe some of your protein has been chewed up? That does happen?
How good is the diffraction?
Eleanor
On Sat, 1 Jun 2019 at 17:44, Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
> Does th
I am afraid you need to do it in stages..
Merge 1-9 into temp.mtz,
then give temp.mtz as hklin1 and add the others..
OK? Eleanor
On Sat, 11 May 2019 at 18:17, Phil Evans wrote:
> Pointless won’t do this with merged files - CAD is the thing
>
> > On 11 May 2019, at 15:24, CCP4BB <
> 193323b1
Could CCP4 documentation include a link to both Marjories one and the
MetalPDB
http://metalweb.cerm.unifi.it
Eleanor
On Tue, 7 May 2019 at 08:42, Louise Jones wrote:
> Dear All
>
> The supporting information for Marjorie's article published in Acta
> Cryst. D in 2004 contains a pdf and a zip a
Yes - this area is a mess.
However I got round it to some extent by naming the nucleotide as a
standard one ((in your case C) , then adding the heavy atom, and creating
the LINK records between that C and the additional atom(s).
Probably at deposition the moiety should be renames as 5CM but that
Not a solution to your problem - just a way to avoid it.. I always put the
waters into the original file - you can always delete them or change the
occupancy if there is a clash..
Eleanor
On Tue, 30 Apr 2019 at 21:21, Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
> One t
Can you attach the pointlesslog and maybe also aimless & ctruncate logs?
ctruncate will check for any non-translational vector..
But missing I cemntring shouldnt stop you solving the structure? If it is
real you would hope to find two solutions seperated by 1/2, 1/2, 1/2.
Eleanor
On Fri, 19 Apr
Can one export of project started under linux to a windows system?
Eleanor
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Yes, Christian - that has happened to me. I found it by using the
Validation Density fit., and noticing that a residue number which was not
meant to exist had a Density fit bar. As you say there was a stray atom
with that ID - totally incorrect - in the coordinate file..
Eleanor
On Wed, 10 Apr
All these monomers listed in the monomer library are HEM look-alikes. Maybe
one of them is useful to you
Eleanor
HAS.cif: HAS NA FEsingle 2.0900.020
HAS.cif: HAS NB FEsingle 2.0900.020
HAS.cif: HAS NC FEsingle 2.0900.020
Or I am quite happy with the words REFINE
E
On Mon, 8 Apr 2019 at 21:02, Paul Emsley wrote:
> On 08/04/2019 20:36, Eleanor Dodson wrote:
> > Words - use WORDS - what does "the T key" mean in plain English!!!
> >
> >
>
> Dear Eleanor,
>
>
> T is
Words - use WORDS - what does "the T key" mean in plain English!!!
Eleanor
On Mon, 8 Apr 2019 at 18:59, Paul Emsley wrote:
> On 08/04/2019 18:40, Hillen, Hauke wrote:
> >
> >
> > Lately I have been having a strange issue with Coot (0.8.9.2-pre on
> > MacOS X). Sometimes when I add residues
ter than
> having very wrong reflections.
>
> Whether that will fix your Rfactor is a different story.
>
> phx
>
>
> On 04/04/2019 11:05, Eleanor Dodson wrote:
>
> You cant exclude one resolution ring in REFMAC - there would be ways to
> fudge the exclusion fr
You cant exclude one resolution ring in REFMAC - there would be ways to
fudge the exclusion from your current file, but much safer to use a data
integration tool
On Thu, 4 Apr 2019 at 10:27, wrote:
> Dear Sam,
>
>
>
> I would remove the ice ring and reprocess the data. Ice rings may wreak
> havo
Look at the plots for Rfactor for your last cycle.
Is there a blip at some resoution?
And also look at the plot of v v resolution-- again are
there blips?
People have put a lot of effort in generating informative graphs so use
them!
You should see ice ring effects in the Wilson plot too..
Ele
Usually externaly provided has pecedent over library routine ..
you need to label any "amino-acid" as a peptide though to generate the
required links in the protein chain.
E
On Wed, 3 Apr 2019 at 16:09, wrote:
> Dear Deniz,
>
>
>
> In the past, I had similar problems caused by the fact that when
Qs..
1) You are using the same dictionaries for both REFMAC and COOT?
2) What happens in refmac if you just use REFI IDEALISE?
And turn on the option for REFMAC to
MONITOR MANY - it might tell you if there is some clash which is overriding
the geometry restraints..
Eleanor
On Wed, 3 Apr 2019 at 1
Yes - I have had cases like that where reducing the spacegroup symmetry
improved the model a lot!
Eleanor
On Wed, 3 Apr 2019 at 09:47, David Briggs wrote:
> Hi,
>
> This doesn't answer your question directly, but I'd be tempted to reduce
> the symmetry and re-refine in a space group lacking that
is there more detail?!
On Fri, 29 Mar 2019 at 23:22, Zing wrote:
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
##
Hmm - I find maprot extremely confusing, but remember a wrkmap does not use
any symmetry so maybe that is why some is lost.
I would have done this, but I havent tested it. And the documentation is
SERIOUSLY confusing!!
Do I understand you want to ADD the density for mol B to that of Mol A
mapma
In Refmac there is a plot of Rfactors v resolution, Could you high
resolution data (or low for that matter) be particularly high?
Eleanor
On Sun, 24 Mar 2019 at 05:06, Lorenzo Briganti
wrote:
> If you’re sure about your refinement parameters and results, I would check
> PDBredo just in case. I’d
Lazy body's solution - read the PDB into pisa, and output the "assembly" .
This will a) move multiple molecule copies in an asymmetric unit to
symmetry versions which make the best biological sense, and
b) if necessary add extra symmetry mates to make up an
assembly.
Example Heamog
This can do done, but I suspect it is much easier using COOT tools - then
you can output a map from COOT. Will check later ..
Eleanor
On Thu, 21 Mar 2019 at 07:28, Zhijie Li wrote:
> Hi Jan,
>
>
> Sorry I didn't read your script earlier. If you change your mapmask
> command to output a map inste
this information ?
Eleanor Dodson
To unsubscribe from the CCP4BB list, click the following link:
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I(+)/I(-)
>
> Best wishes,
>
> пн, 18 мар. 2019 г. в 09:22, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
>
>> Can you find the position of the anom scatterer used SHELXC/D/E or some
>> other tool.There is no need to know the element name to
Can you find the position of the anom scatterer used SHELXC/D/E or some
other tool.There is no need to know the element name to use it for phasing!
Eleanor
PS However the existence of an "anom signal" just meand that I+ differs
systematically from I- and there can be other experimental reasons for
Sorry to plug MOLREP to a Phaser Q, but it does have some simple tNCS
functions which work well for
straightforward cases.
Something to consider:
tNCS can make spacegroup determination based on axial reflection absences
tricky so set a flag to test all SGS in the pointgroup.
For example: (A transl
You need to set the occupancy to 0.5 though..
Eleanor
On Mon, 11 Mar 2019 at 16:17, Phil Jeffrey wrote:
> Hello Firdous
>
> You are seeing two because you are displaying crystallographic symmetry
> and you are seeing its symmetry mate. Coot only places one (check the
> PDB file) but displays th
Both REFMAC and COOT have an option to regularise (coot) or idealise
(refmac) a structure. These options will correct bad gemetry if possible,
but pay no attention to the fit to density.
In general i think it is sensible to inspect the map for regions where
there are serious errors high lighted. H
Yes - I think you do need to assign the space group in the mtz file to be
the same as that in the coordinate file header. I believe that REFMAC will
stop with an error message if there is inconsistency between the two sets
of header information.
It is easy to change the spacegroup.
In GUI2 there i
mtzdump hklin my.mtz
That reads the header and the first 10 lines
or if you want all as ASCII
mtzdump hklin my.mtz > mine.hkl
nref 1
end
and that will list the first 1 reflections to an ascii file..
On Thu, 7 Mar 2019 at 12:52, Sanaz Asadollahpour <
sanaz.asadollahp...@
I tend to use PISA for suggesting biologically relevant complexes. And you
can modify the MR solution to replace a molecule with any symmetry
generated copy of it..
But check Phaser has put your molecule reasonably close to the origin.
On Mon, 4 Mar 2019 at 19:52, Randy Read wrote:
> Dear E
What happens if you use REFI BREF Overall with a Boverall of 0.0?
It might just keep the given atomic B factors and add 0.0 to them?
Eleanor
On Wed, 20 Feb 2019 at 12:06, Pearce, N.M. (Nick) wrote:
> But no way to fix to a set of refined/parametrised Bfactors and refine?
> (That’s the one I wan
Well - I try to quantify the relative anom peak heights by checking those
over MET or CYS S sites with similar B values v the disputed one.. The
expected difference between P and S isnt very big, but it might give you a
crystallographic clue.
Eleanor
On Sun, 17 Feb 2019 at 17:31, Keller, Jacob
The keywords are:
SCALE TYPE SIMPLE
SOLVENT NO
I always use for a completed sctructure
SCALE TYPE SIMPLE
SOLVENT YES
and then a set of 4 numbers for scale and Bfactors are output .
There is an option to give these as a FIXED SCALE.
Forgotten the exact keywords but they will be in the manual..
P
contains a rotation matrix and a translation
> vector that should correspond to the same solution.
>
>
> Thanks everyone!
>
> Erik
>
> --
> *From:* CCP4 bulletin board on behalf of Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jisc
Well - you have one of many examples where your 4 chains do not form the
biological tetramer, but as you say there are two half tetramers in the
asymmetric unit, I would expect that Pisa has already told you there is an
interface between AC and it’s summetry equivalent and told you the symmetry
ope
Mlphare still exists! It gives you all that infirmatoon🕹... or just Argue
that the map is good?
On Fri, 1 Feb 2019 at 13:54, McCoy, Jason (mccoyj5)
wrote:
> Dear CCP4bb members,
>
> I am compiling a rebuttal for a manuscript that utilized experimental
> SIRAS phasing in order to generate coordin
u might be interested in Chimera too (--> Tools --> Structure Analysis
>> --> Thermal ellipsoids)
>>
>>
>>
>>
>> On 23.01.2019 16:17, Eleanor Dodson wrote:
>> > Is there any easy way to do this?
>> >
>> > Coot? ccp4mg?
>>
Is there any easy way to do this?
Coot? ccp4mg?
Eleanor Dodson
To unsubscribe from the CCP4BB list, click the following link:
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Donghyuk - testing your "twinning" in a lower symmetry space group can be
misleading.
Many checks look to see if twin related reflections are similar.
But the twin laws are often the same as the symmetry operators, so if you
have ignored the true symmetry, you will wrongly assume you have twinning.
data in a cell with the a b axes halved, choosing
only the strong reflections not affected by the non-cryst Patterson vector,
but in fact the MR programs take such a translation into account during
structure solution .
Eleanor Dodson
On Fri, 11 Jan 2019 at 10:54, Randy Read wrote:
> Hi,
>
Excellent!
And now you can test Xtal averaging with models??
Eleanor
On Thu, 10 Jan 2019 at 12:38, Andrew Lovering wrote:
> Dear all,
>
>
>
> Thanks to Vincent, Eleanor, herman and others! It turns out I’ve managed
> to sort it out a different way – the initial TFZ of 10 with cutout density
> a
Hmm - You say you have the Se positions in the P3121 form, plus some
roughly placed helices, so you should be able to get the matrices which
interconvert the three P3121 molecules. (there are superpose coordinate
programs. GESANt or LSQKAB, which will give these..)
and PHASER output gives you the
I think any decision depends on the resolution of your two data sets. If
they are very different I would choose the higher resolution one.
If that is the Anom data then I would use the anom signal at least in the
first cycles to improve the phases..
Eleanor
On Thu, 3 Jan 2019 at 14:59, Piotr Wil
potential
problems. But this sort of online guideance needs user response too - is it
comprehenible? Is it accurate? etc etc.
It will be interesting if you can stimulate debate about these issues.
Thank you
Eleanor Dodson
On Mon, 17 Dec 2018 at 19:01, Robbie Joosten
wrote:
> Hi Marie-Hél
Looks as though the column types have been run together.. Xia3 writers?
It should read "F Q D Q" I believe..
Eleanor
On Sat, 15 Dec 2018 at 15:56, Robson-Tull, Jacob <
jacob.robson-tul...@imperial.ac.uk> wrote:
> Dear all,
>
>
> Has anyone encountered the error "Invalid MTZ column_types for the
It is very common for a trigonal spacegroup H 32 to masquerade as C 2 2 21
Here is the log file for other cell.
Note that it is possible to reindex it with two cell dimensions equal and a
beta angle of 63 -
And the self rpotation shows a large rotation at 120 degrees
So go back to the data process
What is the cell difference? Space group difference- surely not??? Between
the two data sets.
At lowish resolution the maps can tolerate more cel difference of course
than at high resolution..
Eleanor
On Wed, 21 Nov 2018 at 13:09, Almudena Ponce Salvatierra <
maps.fa...@gmail.com> wrote:
> Dear
There is a CCP4 basic program rwcontents
Run it as
rwcontents xyzin rna.pdb
It lists no_of_C m no_of_O etc.. and sums their mass
If you have the H atoms in the pdb that will give you the total mass.
If not you will have to estimate the no of H yourself..
Eleanor
On Fri, 16 Nov 2018 at 16:46,
You are all extremely informed and clever!!
This file is part of an old archive of haemoglobin structures from the
1990s.
I suspect they are all generated on a VAX from lcf files when I was
"updating" the archive..
So now if I have the character I can update them all again, in the unlikely
event
#x27;s more likely that the programs for reading and writing the
> MTZ format changed (and the MTZ format itself changed as well) and are no
> longer capable of dealing with "MTZ file mark 1"...
>
> If I can actually get the VAXes to which I referred to read an old DAT
> tape,
Hard to comment on PHEIX refne but check these things: such results must
either mean your molecular replacement solution is wrong or there is
something wrong with the data.
Refinement packages will always try to match the Mean B factor to the
Wilson plot B so I think the problem must be before refi
Anyone any idea what to do about this?? Created in 1992!!
Seems unreadable..
No CTYP lines input for file: 1
Indices output even if all data items flagged "missing"
Warning, NOT all LABOUT data lines given
Warning: Machine stamp corrupted? Assuming native format.
>> CCP4 library signal l
As you say, the two are related but look different, and the intensity on
the subsequent images look different too
However there are some default scaling parameters, and I have no idea what
they are..
Any alternating strong/weak pattern should generate a strong off-origin
peak in the native Patters
I do think at times the Rfree is a bit of a sacred cow . At one level if
the maps look OK not much can be wrong..
Is the Ramachandran plot OK?
You dont say what the R factor is but does this mean there is a large
difference between the Rfactor and Rfree?
If you are using REFMAC look at the plots
A lot of ways to kill a cat..
Mine:
Read in both PDBs -
SSM superpose to get the best fit of old over new
Then
Copy ligand fragment to a new model
Merge new pdb and fragment
Real space refine fragment
save merged pdb
E
On Mon, 8 Oct 2018 at 09:37, Georg Mlynek wrote:
> Dear Nicola,
>
> Exte
That is a serious bug in the deposition task.
You can find the refmac command script if you search in the Job list
directories. If it does not invoke TLS when there are TLS records provided
that is a fixable bug..
Eleanor
On Wed, 3 Oct 2018 at 10:51, Antonio Ariza
wrote:
> Hi Christian,
>
>
> Y
*Q to ccp4i2dev..*
Hello,
I’m not sure whether this is a refmac issue or a ccp4i2 issue but we have
recently solved the structure of a protein which appears to be twinned in
the space P43 with 10 molecules in the asymmetric unit. When we run refmac
normally it proceeds happily and refines the s
oli one is now rotated by ~ 90 degrees and fits quite well..
There is a lot of unmatched stuff of course for the Ecoli one but that
shouldnt prevent the fit..
Eleanor
On 10 September 2018 at 12:53, Eleanor Dodson
wrote:
> Hmm - when I try to read Therm_tRNA into the CCP4I2 GUI it says
>
ou can see, even though the residues are, as far as
> I can tell correctly indicated, the rotated file is off by about 90 degrees.
>
> Many thanks for any help.
>
> Charlie
>
>
>
> On Sep 10, 2018, at 5:36 AM, Eleanor Dodson > wrote:
>
> Charlie - I will try to c
s do use the charges to modify the scattering
> factors and write them out again. One hopes that this problem is solved
> soon.
>
> Sorry for straying off topic.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board On Behalf
N1+
ANISOU 22 NH1 ARG A 415732 10019 13448 1911785
-419 N1+
On 10 September 2018 at 10:36, Eleanor Dodson
wrote:
> Charlie - I will try to check this, but cant read your pse file - can you
> find another format?
>
> Thanks Eleanor
>
> On 8 Septe
In cases like this I use PISA for the first analysis - it will give buried
surface area - h bonds, salt bridges etc, then work up from there.
Eleanor
On 28 August 2018 at 14:43, Anastassis Perrakis wrote:
> Dear Jorge,
>
> The “coiled coil” has a formal definition - not all interacting helices
>
75% solvent is not uncommon, and such crystals often only diffract to 3A.
Eleanor
On 20 August 2018 at 10:24, SUBSCRIBE CCP4BB Zhu Qiao wrote:
> Hi All
>
> My protein is dimer both in protein buffer and crystallisation reservoir,
> which is confirmed by calibration column Supderdex 200 10/300 in
rent cells) and P222 data.
> > I agree that MR seems very good (in all cases), but the final density
> maps are always bad. Maybe the data has problems that I am not dealing
> with.
> >
> > Kind regards
> >
> > Marcelo
> >
> > Em sáb, 11 de ago de 2018
e log files from aimless, MR and refmac
>> for P2 (in two different cells) and P222 data.
>> I agree that MR seems very good (in all cases), but the final density
>> maps are always bad. Maybe the data has problems that I am not dealing
>> with.
>>
>> Kind
arch select the most likely spacegroup of the 8 possible.
You cant even limit the b axis to be a screw axis .
Your refinement behavior looks OK, but the maps will look bad with spurious
reflections in the list..
Eleanor
On 10 August 2018 at 19:02, Eleanor Dodson
wrote:
> Actually
Actually Marcelo - Refinement to an R of 41% is pretty good for an MR
solution!
On 10 August 2018 at 18:42, Eleanor Dodson
wrote:
> Can you attach the refinement log?
>
> Eleanor
>
> On 10 August 2018 at 16:57, Marcelo Liberato
> wrote:
>
>> Dear Randy,
&g
Can you attach the refinement log?
Eleanor
On 10 August 2018 at 16:57, Marcelo Liberato
wrote:
> Dear Randy,
>
> Thank you very much for answering. I followed your suggestions but,
> unfortunately, I couldn't get a reasonable electron density map after MR
> and refinement.
>
>
> First I would l
These problems are a pain!
My (half-baked) thoughts
0) Yes - get rid of all junk images etc and inspect the frames - we have
had a case where MR would not work for the "best" crystal as processed by
XDS, but when we looked at the images there was clear streaking and other
technical problems. t
I wouldnt have thought so.
There is a B factor plot as part of CCP4I2 - does that show any pattern of
differences between ligand and environ,ment?
Eleanor
On 9 August 2018 at 10:54, Santhosh Gatreddy
wrote:
> Hi all,
>
> I have to compare the B-factors of three of my ligand bound structures of
Well that is pretty obviously P 2 21 2 - h 0 0 and l 0 0 are obviously
present..
The 0 k 0 absences could be generated by a nc translation of x, 1/2, z - do
you have that?
Twinning is unusual in P2/mmm but possible of course - can you send the
pointless log file?
Eleanor
On 9 August 2018 at
l quality in some
> directions - overall data is not great...
>
> Best,
> Tommi
>
>
> Kohteesta: Eleanor Dodson
> Lähetetty: keskiviikko 8. elokuuta klo 17.46
> Aihe: Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions
> Vastaanottaja: Kajander, Tommi A
&
How many molecules in the asymmetric unit? and is there a
non-crystallographic translaton?
Eleanor
On 8 August 2018 at 15:29, Kajander, Tommi A
wrote:
> Hi,
> Any clues why the followting happens: pointless (and just looking at the
> XDS output) clearly tells there is one screw axis in P-ortorh
I am not sure if you gave your wave length but it is always worth doing an
anomalous map, and looking at relativr peak heights for your known S
positions and the putative sulphate or phosphate.
There are small differences in the expected f" at most wavelengths.
Chemical arguments are doubtless bet
in Xray if we
> have good crystals. It does not matter, however, how many local
> conformations we observe. It is just one salt bridge, and its energetic
> contribution to protein folding remains (very roughly, and this is
> practical experience for which no good theory exists) about 1kCal
How do people decide on what is a salt bridge within a molecule and how to
count them for those Tables?
I have been looking at 2z2f - paper claims some score..-
But there are several residues in alternate conformation
with NZ A to OE1Aand NZ A to OE1B and NZ B to OE1B etc
Is that one salt
FreeR flags are a bit of a pain - there is the number you should select,
then how to compensate for non-crystallographic symmetry and putative
twinning.
Vilmos has written a useful Rfree assignment tool which covers possible
twinning problems. It selects FreeR flags for the highest Laue symmetry
c
Hmm - the "S" atoms look too close - S=S bond ~ 2A
Eleanor
On 4 July 2018 at 07:26, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:
> Hi all
>
> I got a structure which has COA in it, and the SH in the tail of COA
> is very close to the SH side chain of Cys in the structure. I don't know
> whether it
Hmm - is the refinement complete? Maybe the GLU on the right could be moved
to use some of that greenness?
I try to make all sensible corrections, then check blobs..
Eleanor
On 3 July 2018 at 04:22, zaigham mahmood khan
wrote:
> Uma, that is not something that we see regularly in the crystal
> s
And so does MOLREP..
Phaser too please?
E
And Paul - yes; please cut and paste..
E
On 21 June 2018 at 20:00, George Sheldrick
wrote:
> For small molecules, programs such as SHELXT move the structure to be as
> near as possible to the center of the unit-cell, not the origin. Failure to
> do so
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