On 12/07/2010 09:38 PM, Arnon Lavie wrote:
Hi there:
The situation: We are facing difficult molecular replacement: we believe
we have two molecules in the ASU, but phaser/molrep find only one. Using
the electron density calculated using this single molecule, we have
manually placed the 2nd molec
As far as I know there are no repulsions restraints applied if the sum
of the atoms occupancies is <=1.0. If one atom is fully occupied. and
another partial then there will be a restraint.
Eleanor
On 12/08/2010 04:45 PM, Keitaro Yamashita wrote:
Dear Ed,
These tables were reported by Refmac5
Of course metal ions, So4 etc often lie on special positions - the
insulin hexamer is generated around Zn atoms on the 3-fold axis.
Eleanor
On 12/09/2010 01:29 PM, Ian Tickle wrote:
Of course it's always possible for an asymmetric molecule (or part of
a molecule, such as a side-chain) to lie on
That gap isnt surprising given your resolution - indeed anything smaller
could be suspicious! eg symmetry equivalent reflections labeled
differently..
Eleanor
On 12/10/2010 11:17 AM, Petr Kolenko wrote:
Dear colleagues,
I appreciate any help, or any suggestion with my difficult data. Many
tha
compar does this providing the sequence is the same.
amd you can get lsqkab to give you the full list but only i think for
those atoms you overlap..
eleanor
On 12/29/2010 01:52 PM, Michael Swan wrote:
Dear all,
I am having a bit of trouble finding a program to do an rmsd calculation and
give m
Hmm - there are some hydrogens which are simply not fixable from
chemistry, or electron density at low (ie <1.5A!) resolution - any of us
who have looked in vain for them can testify to that - and I cant think
that it is good to add in scatterers when you dont know where they are.
The ones det
Well - REFMAC and I think other refinement programs simply read in an
atom with occupancy 0.00 and write it out again in exactly the same
place.. All refinement contributions for atoms both Xray and geometrical
are weighted by the atom occupancy so such an atom will not shift.
The assumption i
Does anyone know where to look for an error when PHASER outputs this
message?
Eleanor
.
*
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT
2.1.4 ***
***
If your dataextends to 2A resolution I suggest you run Arp-Warp or
Buccaneer to rebuild the structure. At that resolution the automated
building programd can usually fix errors.
At the end use this option to get the new build back to overlap the original
csymmatch -pdbin-ref MR.pdb -pdbin arp-
On 01/20/2011 01:44 PM, Shao-Yang Ku wrote:
Dear all,
Is there a way to specify (somewhat arbitrarily) a origin for any
molecular replacement package (in a polar space group) without resorting
to phased translation so that one could more easily compare results from
different MR runs?
Thanks,
Sh
I absolutely agree with Phil.
However I think it is very important NOT to remove systematic absences
before scala. There are many cases of mis-assigned space groups where
"systematic absences" are misleading - due to NC translation or bad
measurement or whatever
Eleanor
On 01/24/2011 09
Coot does this seamlessly..
Eleanor
SSM superpose A to B
NCS Maps will generate the map around A over B - or vice versa..
Eleanor
On 01/28/2011 06:15 PM, RONG hui Rong wrote:
Dear All,
I have the problem as follows, but I can not find the corresponding
solution. Can somebody give me some su
Have you checked for twinning? Look at the plots after scala..
Eleanor
On 02/07/2011 10:49 AM, Md. Munan Shaik wrote:
Dear all,
I have a question regarding the refinement and density map.
My protein is 261 amino acids long and crystalize very nicely with very high
resolution . There is no mul
Yees - a translation of 0.5 along x means you must consider SGs P212121
and P2 21 21 since the absences will be present (at least at low
resolution) with either SG.
I dont know how good Phenix would be at distinguishing between z=0.233
and z=0.25
However even if the exact peak is at z0.25, i
Pseudo translation doesnt seem too much of a problem if the model is OK.
MOLREP uses it within the search, phaser seems not to mind too much for
a general translation..
I dont know about pathological cases where the crystal is very near but
not quite C centred, ie the translation is quite spec
Are you sure these are real FP=0 or reflections which werent measured
but have been added for completeness of the h k l list.
The check is whether the SigF is also 0.00 - in that case they are
genuinely missing..
Eleanor
On 02/09/2011 11:34 PM, Ed Pozharski wrote:
I observe under some conditi
On 02/15/2011 04:36 PM, vineet joshi wrote:
Dear CCP4ers,
Is there any specific way that can help me locate the interactions between
ligand (GTP) to any other residue in the protein(GTPase) using CONTACT. And
how do I run CONTACT for a number of .pdb files(around 650) in one single
step and sepa
Well P4 isnt a subgroup of P43212 - you would need P43
MR programs will often let you test several spacegroups. See Phaser MR
or MOLREP - I would try that and choose the best
Eleanor
On 02/16/2011 02:48 PM, Ting-Wei Jiang wrote:
Dear experts,
Sorry for a simple question but confusing me
Another cause of difficulty - nothing really to do with the spacegroup
selection - is when one copy of the model has much higher B factors than
others. Most MR searches assume that the copies contribute more or less
equally to scattering.
If you assign too high a symmetry this will make MR le
On 02/17/2011 09:35 PM, Peter Grey wrote:
Dear CCP4 and XDS users,
I have a P21 case with some strange ratios in the cell dimensions : a, b=a,
c=1.5a, 90, 105, 90. The native patterson shows a strong peak (40% of
origin) at (x,0.5,0) indicating some pseudo symmetry. Such cell dimension
and peak
On 02/18/2011 07:42 AM, Vellieux Frederic wrote:
Arp Warp used to want a blank line between the > MALDH title, and the
first line of the sequence..
Not sure if that still holds.
Eleanor
a> Hi Careina,
Just an example of a pir file which I just generated (using Bart Hazes
program mcfman):
Yes - you are.
-
There are some extra steps.
Download pdbs and mtz files
csymmmatch -pdbin-ref 1.pdb -pdbin 2.pdb -origin-hand -pdbout 2-to-1.pdb
That checks they are on same origin and symmetry equivalent.
refmac for 1.pdb
refmac for 2-to-1.pdb
cad to merge two refmac outputs.
You will hav
I think you have been caught by a new REFMAC "feature" which tries to
design its own TLS groups including linked H2Os and ligands.
Check your tls output records and see what it has clustered into a group..
I am not sure how to disable this - at times I want to override any
automatic selection
On 03/03/2011 06:13 AM, Ting-Wei Jiang wrote:
Dear all experts,
I'm trying to calculate R-value (and free R) specifically which is between
data and the modified structure(refined by myself without help from any
program).I've looked the program for calculating a long while.Actually,I
found one n
No - and I dont think it is accepted practice now either..
I often use I/SigI > 1.5 for refinement..
Look at your Rfactor plots from REFMAC - if they look reasonable at
higher resolution use the data
Eleanor
On 03/03/2011 11:29 AM, Roberto Battistutta wrote:
Dear all,
I got a reviewer com
On 03/12/2011 05:29 AM, Vandu Murugan wrote:
Dear all,
Recently I collected a data for my 20Kda protein in C2 space group, and
ran SFcheck in ccp4 suite. It is giving an indication for
pseudo-translation as 'Pseudo-translation is detected: 17.6%
Pseudo-translation vector: 0.000 0.00
I guess the only real choice is P2 21 21 or P21 21 21 - the absences
alng h00 could be a result of the pseudo-translation.
I cant explain the score - maybe there is something in the documentation?
But I am afraid after refinement in P212121 the resultant model is sure
to give the best score in
I have found it erratic, and sometimes terribly slow, but that may be
due to local network problems..
But it was working last week..
Eleanor
On 03/26/2011 05:28 PM, Miri Hirshberg wrote:
Sat., March 26th 2011
EBI
Dear Dan,
I've just checked (Sat. 17:25 British times), and uploading my
Well - I usually work in confunction with the graphics, so you can look
at the regions which differ.
I start with the rms difference. If that is > 2, I think there are
significant changes. So then you have to decide what Q you are asking,
and why. Is it that you want to use a model for Molecul
Yes - that is true.
Any crystal might be split, and give diffraction with overlapping
lattices- ie show non-merohedral twinning. If you are lucky/careful you
might only get a few spots which overlap after integration of one of the
lattices- not enough to be detected as "twinning" from the stat
That translation is interesting - R3 indexed as hexagonal has a
crystallographic translation of 0.667 0.333 0.333, so this one
indicated by SFCHECK is related.
The twinning is not very severe so it should refine OK from the PHASER
solution.
Is that so?
Eleanor
On 04/08/2011 05:50 AM, ka
On 04/08/2011 12:17 PM, krishan wrote:
Dear CCP4BB members,
We are using a script written in python to generate symmetry mates for a
given pdb file using PYMOL. After generating symmetry mates we want to
combine all the symmetry molecules in a single PDB file with all the chains
having uniqu
On 04/08/2011 05:19 PM, Cale Dakwar wrote:
Hello all,
Given a PDB file of a newly solved protein structure, what is the standard
procedure for assigning regions of secondary structure? And by this I mean
to ask, how does one decide which residues form beta strands, which alpha
helices, and so o
On 04/13/2011 09:18 PM, REX PALMER wrote:
Dear All
What is the best program to use for comparing two protein structures which are
very similar both structurally and wrt aa sequence? ie to get the rms
deviations both generally and in selected regions.
Rex Palmer
Birkbeck College
Using CCP4 g
Hmm - I use this quite a bit.
ifier.
You cant start Autoamore for a particular model until that has been
entered into the model database - the first Q you are asked from the GUI
is "Which model?" But you can certainly close the model database once
you have entered the model name with a unique
I dont know - it works for me..
That is under Fedora x
Eleanor
mtz2various HKLIN "./ins_pig_zn_T2_hex-unique_refmac1.mtz" HKLOUT
"./ins_pig_zn_T2_hex-unique_refmac1.hkl"
OUTPUT CNS
labin FP=FP SIGFP=SDFP PHIB=PHIC FREE=FreeR_flag
end
On 04/27/2011 07:26 PM, Kelly Daughtry wrote:
Yes,
I guess one way would be to seperate coordinates..
But doesnt overlapmap do that by default?
Eleanor
On 04/21/2011 10:25 PM, Maher Alayyoubi wrote:
Hi Everybody, I posted a question earlier on the bulletin regarding
how to calculate the map correlation coefficient using Overlapamp or
any othe
This may be too late to be of use, but as one of the authors of the
sfall/overlapmap system..
sfall does generate a coded map which flags every grid point with a
unique ID of the nearest atom, ie one which is unique providing there
are not too many atoms - it is adequate for most molecules tho
On 05/11/2011 10:30 AM, ka...@ssl.serc.iisc.ernet.in wrote:
Dear users,
I have refined a structure in R3 with cadmium bound to it, which
was present in the crystallization condition. There are 2 chains
in the asu. The structure is twinned. R and Rfree is around 22% and
28%. One of the cadmiu
On 05/12/2011 08:13 PM, Fulvio Saccoccia wrote:
Dear ccp4 users,
I need to generate intensities from a model (.pdb). That is, I think that a
correct procedure could be to convert model to structure factor and then obtain
intensities squaring the SF.
Does anyone know how can I do?
Thanks in advan
If you have model coordinates for your CSA, I send those to the PRODRG
server and let it generate a REFMAC style dictionary.
You will need to make sure it is labelled as a peptide - cf the standatd
residue cif files to see how to do that..
Then you need to enter the LINKR record into the pdb fi
I dont think there is an Rfree problem..
At 2.7A you expect quite a big difference between R and Rfree
Reducing the resolution will a) probably makethe Rfree/R difference
greater, and b) degrade the quality of your maps and model.
Eleanor
On 05/21/2011 02:28 AM, Seema Mittal wrote:
Hi Ethan,
The default output for REFMAC
Missing Data: For those reflections where the FP are missing, mFo is set
equal to dFc. Hence the terms become FWT=dFC and DELFWT=0.0.
the Rfree reflections are counted as "missing" hence there shouldnt be
any bias intoroduced towards those Fobs assigned as free
How very odd!
I have no ideas on the Zn phenonema - what do the R factor plots look
like against resolution - is there some aberrant reflection which was
part of the FreeR set? The theory is that excluding 5% of the data
should not affect the model seriously at all..
Re the 2nd point. Two
I havent used maprot for years. COOT does it very quickly and
automatically.
But it is tricky to get the matrices correct - can you give some more
details and I will try to help
Eleanor
On 05/27/2011 11:33 PM, Francis E Reyes wrote:
Hi all
I was just fiddling around with ncs and maps, so I tr
Use the GUI
Just feed the 2 sca files into pointless - choose one as the reference -
it really shouldnt match which..
pointless will check the indexing is consistent, then give you an output
file with the two sets merged and sorted together, with different batch
numbers assigned.
scala wil
Simplest is to submit your current structure to PDBe - they have software
which moves all waters to lie close to protein. However the waters IDs
don't help you know if A OH 123 matches B OH 123 for example.
The very old utility water tidy tries to give meaningful names to your
waters, but those nam
Two points.
1) the fit to ideal geometry as flagged in coot validation does not
guarantee a correct model - the best model should be the one that fits the
experimental data best, without having unlikely geometry. You could easily
get a model with perfect geometry which was incorrectly placed in the
What I would do - not net ideal!
1) the ASP looks in the wrong place - shift it into green density and one
OE is probably a water..
2) MET notoriously hard to model - I suspect there often are multiple
conformations.. And of course at some wave lengths the S contribution
should be down weighted by
I think you will find the dictionaries for coot and refmac are different..
REFMAC default dictionary will $CLIBD/monomers/n/NAD.cif
Good knows where coot finds its dictionaries - Paul?
1) check the REFMAC restraints in that dictionary are sensible - spec, are
the planes and chiral centres as
Well - I have found lots of molecules but usually not in a single run.
The first thing to think about is: is this likely to be a dimer? trimer?
tetramer?
Things to consider - a) any non-cryst translation? b) tthe self rotation
might give a clue - c) is the model a multimer, c)what do the biochemist
Is there a fix for this? It has been a perennial request for some time..
eleanor
On 9 May 2012 10:53, sonali dhindwal wrote:
> Dear All,
>
> I want to take the backup of all my data which i have refined using CCP4.
> Can you please guide if I copy all the ccp4 data folders and then transfer
> to
I would proceed in I422 and refine to get a decent model anyway. I presume
you have one molecule in that asymmetric unit?
You don't give the pointless stats on the merging of symmetry equivalents.
That would help decide whether the I point group is the more likely. The
pseudo translation peak in P
Baverage gives you a plot of B value against residue number and chain ID -
that would allow you to visually see which parts of each structure are best
ordered.
If you have run TLS refinement and NOT used TSLANL to add the anise and
individual contributions to B then the plot will give you the devia
Those error messages are warnings - not fatal errors - there must be
something else reported in the log file to cause that.
But as Garib says DNA "standard" names vary according to program and year -
see if your atom names are those in the $CLIBD/monomers/g/GUA.cif
That is where REFMAC will find
It is a long time since I did this, but don't you need just one master mask
- then that is converted using your rotation matrix to mask the related
part of the structure ?
Eleanor Dodson
On 15 May 2012 15:56, Yu Feng wrote:
> Dear De-Feng Li,
>
> Thank you for your reply. Actua
Yu
>
>
> On Wed, May 16, 2012 at 8:26 AM, Eleanor Dodson > wrote:
>
>> It is a long time since I did this, but don't you need just one master
>> mask - then that is converted using your rotation matrix to mask the
>> related part of the structure ?
>&
I am not familiar with CNS restraints, but whatever the program restraints
are - if you do a omit map, or just set the occupancies of the metal and
its surroundings to 0.00 and do a few cycles of refinement, I believe any
model bias will disappear and what you see will be pretty accurate
descriptio
On 17 May 2012 21:27, Eleanor Dodson wrote:
> I am not familiar with CNS restraints, but whatever the program restraints
> are - if you do a omit map, or just set the occupancies of the metal and
> its surroundings to 0.00 and do a few cycles of refinement, I believe any
> mod
lovely density - i would like to know what % of series have multiple
conformations - it would need a survey I guess of PDB depositions, not just
coordinates, but checking maps..
Eleanor
On 21 May 2012 22:21, Uma Ratu wrote:
> Thank you All for you inputs.
>
> Uma
>
> On Mon, May 21, 2012 at 5:
Do you have the SEQRES residues?
If these are properly generated, that should be a complete list of what is
in the crystallisation, and any missing residues will just not be there in
the pdb.
Any program which displays residue properties by number will show these up.
Try the validation in coot - de
You need to say what the cell dimensions are for these 2 options..
Eleanor
On 29 May 2012 15:59, Andrey Lebedev wrote:
> Hi Mike.
>
> I would be more careful about "incorrect" space group. Yes, sometimes
> auto-indexing gives strange results.
> However, in your case two sets of crystals differ
Well - I am not familiar with the PHENIX dictionary but you are right; if
you restrain metal bond distances the structure will reflect the restraints
but if you don't restrain the distances then the respective gradients for a
light atom and a heavy one can produce some very odd and unrealistic
resu
Why would anyone ignore the anomalous data they had collected? It will always
help the phasing, and decide the hand for you..
Eleanor
On 6 Jun 2012, at 03:55, Stefan Gajewski wrote:
> Hey!
>
> I was just wondering, do you know of any recent (~10y) publication that
> presented a structure sol
Well - I guess you need to check the input mtz file.
do mtzdmo this.mtz and check that the columns you have selected are present and
have non-zero values. You need a FOM there.
Eleanor
On 14 Jun 2012, at 12:58, Appu kumar wrote:
> Hello Dear all
> I am trying running
If you use the " superpose mo;lecules" task, using LSQKAB , and fit
molecule A over molecule B say, asking for all atoms to be fitted, you
will get a list of large deviations for main and side , which should
include all those residues with side chains in different rotamers.
Eleanor
On 20 June
Beware do ing this - you may just find the coordinates are on a different
origin or a different symmetry equivalent.
Eleanor
On 20 June 2012 09:20, Mark J van Raaij wrote:
> LSQKAB ("superpose" in CCP4i GUI) also outputs in its log-file the
> translation parameters and rotation matrix it used to
You can View input command file, when working from the GUI.
Could you cut and paste this into your message - obviously some inmportant
parameter is not set, but I cant tell which without seeing that file.
Eleanor
On 20 June 2012 05:25, Appu kumar wrote:
> Thank you for your reply,
> I am run
Try emailing ebi - they have some sophisticated search tools to do things
like this..
Eleanor
On 19 June 2012 17:26, stanley5101 wrote:
> Hi,
> Is there such a database that will allow me to search for particular
> structural motifs involved in protein interactions. For example: search
> for
, then the input data IS sorted, and converted to the standard
asymmetric unit.
Eleanor Dodson
On 18 June 2012 14:28, Eleanor Dodson wrote:
> Well - I guess you need to check the input mtz file.
> do mtzdmo this.mtz and check that the columns you have selected are
> present and have
I wonder if this could have happened here?
Some one in the lab has yet again been trapped by a "feature??" of REFMAC.
Say your MR solution is found to be in P21212 after you searched various
orthorhombic SFs,
but the input MTZ file has the space group still listed as P222 (i.e. the point
gr
I suspect you didn't request the FreeR assignment on the TRUNCATE interface?
This calls amongst other programs, CAD and CAD makes sure that the reflection
list is unique and that it is in a standard asymmetric unit. Most people do it
by default so don't hit these problems...
I suggest you just
I use the GUI with most of the defaults , and just ask for SCALES constant
And anomalous on of course but that is by default in SCALA ..
Eleanor
On 3 Jul 2012, at 16:43, Phil Jeffrey wrote:
> I'm not exactly a Scala veteran so am looking for advice as to what would be
> the best way to run Sc
On 11 Jul 2012, at 03:36, dengzq1987
don't understand the question really. What DELPHI do you mean?
Many programs output DELPHI (refmac, SigmaA etc ) and they are usually used as
input to a difference map using FFT
Eleanor
> Hi all,
> recently，I want to use DelPhi to calculate the Electros
Well - the problem may well be here - in the REFMAC dictionary (see
$CLIBD/monomers.s.SO4.cif ) the chiral volume calculation uses at the order
of the O numbering around the S atom .
So if your O numbering is not right handed you will have the chiral volume
calculated as positive, not negative.
T
All this is best done from the GUI - pointless will sort out batch numbers,
check indexing etc..
But you still have to identify any rogue batches, and decide on when to
jettison the data st..
The Sigma level is related to the number of observations of each reflection, so
this will decrease as th
It isn't that your space group is wrong, but are you sure that your mtz file
has that space group in its header?
MR will test all possible alternatives - in this case P3121 or P3221 - but
won't change the symmetry information in the input mtz.
You need to do that with a utility like
mtzutils h
Don't forget you will need to adjust the contour level to see something with
occupancy 0.3 - easily done with coot
eleanor
On 27 Jul 2012, at 11:25, Steiner, Roberto wrote:
> Or refine the occupancies with Refmac...
>
> Roberto
>
> From my iPhone
>
> On 27 Jul 2012, at 11:04, "Tim Gruene" wro
The old fashioned water tidy will try to assign matching (non-standard) names
to matching H2Os which is useful for analysis of structural waters, but cannot
be deposited.
I think coot has a tool to move waters to be near the protein but maybe that
isn't all you want. Why not start deposition and
What do you mean - running REFMAC directly on the output file?
Are you sure you have the same space group given in the mtz file and the PDB
file? If the MR has placed your structure in P32 say, nd the input mtz has SG
P31, you need to change the mtz header to include the now-known SG. There are
l not be applied
> >
> >
> > PS: I have used phenix.xtrige and found the p-value of
> > pseudo-translational ncs is very little, which indicates the exist of
> > the pseudo-translational ncs. And no twin found in this dataset.
> >
> > Now the problem is two in t
Brilliant illustration - even in 3D!
eleanor
On 3 Aug 2012, at 14:01, Laurie Betts wrote:
> I couldn't resist this shot. It might not make the cut.but
>
>
I am surprised if the numbers are wrong, maybe your chosen superposition isn't
the same as that used for superpose - there are 2 methods available - are you
using the secondary structure matching, or the assigned residue match?
Eleanor dodson
On 5 Aug 2012, at 15:17, Zhou, Tongqing (NI
Lijun Liu 's suggestion is sensible. And is there any possibility of
twinning?
But I always thought that at least in REFMAC all A conformations were
restrained as a set, and ditto for B C etc.
So if the documentation is to be believed an A chain would be restrained as a
unit. I don't think
Like Ian, I tend to use as much data as is reasonable - but it is useful to
look at the Rfactors plot again resolution in REFMAC output. If this shoots sky
high at the limit, the data is probably not very useful in refinement or map
calculation (and will automatically be down-weghted by the M
Before any further attempts you must check that the crystals have the same unit
cell volume. I usually do this using matthewscoeff from the GUI
( By the way why isn't the volume automatically written into the mtz header
asap!!!)
If the cell volumes differ by as much as 5% no reindexing or any
Begin forwarded message:
> From: Eleanor Dodson
> Subject: Re: [ccp4bb] CC1/2, XDS and resolution cut off
> Date: 8 August 2012 10:10:55 GMT+01:00
> To: Marcus Fislage
> Cc: CCP4BB@JISCMAIL.AC.UK
>
> Like Ian, I tend to use as much data as is reasonable - but it is use
These are the atom names you should have in your monomer. No mention of H_N4
there..
NH4 HN4HH 0.000 0.0000.0000.000
NH4 N NNT1.000 -0.5810.302 -0.782
NH4 HN3HH 0.000 -1.2321.041 -
The ensemble should be a set of coordinates
Eleanor
On 15 Aug 2012, at 04:42, 李华 wrote:
> Dear ccp4er,
> I try to use Phaser MR to solve a structure. A mtz file from oasis was
> used as a ensemble. All of the parameters containing protein MW, nucleic acid
> MW, extent of X, Y, Z and center
I haven't seen that message, but I think you could provide Arp/Warp with the
model, plus the original data, and it would probably work.
Eleanor
On 25 Aug 2012, at 16:38, Ben wrote:
> I recently processed a dataset in HKL2000, imported the scaled data to mtz
> format in CCP4, and obtained a mol
I wish I could give a sensible explanation, but this feature is very common
with heavy atoms.
Possible problems. The default wavelength for all atomic scattering functions
is Cu Ka - you can see the formula used and details in the file
$CLIBD/atomsf.lib.
The atomic scattering values are much t
Like Tim says SORTMTZ expects a different format used for unmerged reflection
lists.
And I think this space in the filename causes the SCALEIT problem - linux
operating systems often treat spaces as filename terminators..
But the " … " marks around a file name are meant to override the space
Why don't you calculate the FFT over the whole asymmetric unit? That is the FFT
default I think
Eleanor
But I think the COOT option works too, but it will also require that your input
map covers the asymmetric unit.
Eleanor
On 19 Sep 2012, at 23:25, Niu Tou wrote:
> Dear colleagues,
>
> Is
You could use COOT to do the map rotation - then the parameters seem to work
The conventions should be the same. I thought but I can't really speak for COOT.
If you look at the CCP4 documentation for MAPROT, and use the Superpose
molecules GUI task to fit A to B using lsqkab - that gives you a ma
This is interesting. In principle m and D should provide an optimum map, and
at high resolution they do a reasonable job.
The answer about occupancy is a good point.
You don't say what resolution your data is at, but maybe it is rather low?
I suspect that below ~ 3A the estimates of both m and
, and I would hesitate to alter those
unless yu have special knowledge.
Eleanor Dodson
On 15 Oct 2012, at 12:36, Danilo Belviso wrote:
> Hi! Does anybody know which is the range is used by REFMAC to vary bond
> distances, angles, and torsions of a ligand molecule during a refinement
> pr
Or put all files into pointless..
It will read XDS and do the indexing checks
Eleanor
On 19 Oct 2012, at 12:45, vellieux wrote:
> Well, the first thing I note is that P6(3) is a polar space group.
>
> Hence what I would do myself is the following:
>
> take your crystal 'number 1' (as a referen
You can use superpose LSQKAB to fit various residues by number..
Eleanor
On 24 Oct 2012, at 23:59, WENHE ZHONG wrote:
> Dear members,
>
> I have one difficult task on hand and would like to ask for your advice.
>
> I want to superpose two enzyme structures just based on several residues
> (e
You don't say whether you have any indication of non cryst translation or
likely dimer NC axes? The self rotation can help sometimes to select likely
pairings - for instance if one (or both) domain(s) is forming a dimer.
Eleanor
On 26 Oct 2012, at 13:43, Bosch, Juergen wrote:
> We had rece
I don't quite understand this - you can use an editor to add any coordinates
you like in the correct "atom" format to a pdb. (Don't think you can deposit
them though!)
Then a program like coot can be tricked into thinking the monomer CUB say is
to be displayed in any style it supports.
Elean
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