Hi Robert,
In addition to the great suggestions you already have received, maybe you
should also consider SIMBAD or similar programs? The behavior you are
describing is typical of, albeit not exclusive to, having crystallized a
contaminant protein.
Good luck!
Nukri
On Thu, Jun 18, 2020, 08:01
: CCP4 bulletin board On Behalf Of Robert S Phillips
Sent: Thursday, June 18, 2020 9:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molecular replacement problem
EXTERNAL EMAIL – Use caution with any links or file attachments.
I've been pulling out my hair with this for a few months now. I have
/david_briggs
> --
> *From:* CCP4 bulletin board on behalf of Robert S
> Phillips
> *Sent:* 18 June 2020 14:00
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Molecular replacement problem
>
> I've been pulling out my hair with this for a few
I managed to solve a structure by MR at 2.4 A with a 27% identity model.
Like you, I had to use a dimer search model to make any headway. To get
usable maps and an initial model, I used Chainsaw to truncate the search
model, Phaser (MR), Parrot (DM) with NCS averaging, then auto building with
Phillips
Sent: 18 June 2020 14:00
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molecular replacement problem
I've been pulling out my hair with this for a few months now. I have data sets
to 2.6 A for a new enzyme in the aminotransferase superfamily. Unfortunately,
the closest structure is only
I've been pulling out my hair with this for a few months now. I have data sets
to 2.6 A for a new enzyme in the aminotransferase superfamily. Unfortunately,
the closest structure is only 25% identity. MR with PHASER using the monomer
was a complete failure. Since the minimum structure of
conformational changes like antibodies and
>>>> calmodulin).
>>>>
>>>>
>>>>
>>>> If molecular replacement fails, you should also look very carefully in
>>>> the space group assignment and in case of ambiguity try all poss
odies and
>>> calmodulin).
>>>
>>>
>>>
>>> If molecular replacement fails, you should also look very carefully in
>>> the space group assignment and in case of ambiguity try all possible space
>>> groups for your MR searches.
&g
Hi All;
I have a native data set of membrane protein at 3.8A. I nearly use all the
options for Molrep. I would like to ask, is some body has some special
strategy which can work for difficult Molrep
Thanks you in Advance
Bashir
--
Muhammad Bashir Khan
Thanks for all the good suggestions. This gives me a lot more things to
try.
Ursula
On Sat, Dec 13, 2014 at 2:44 AM, Claudia Millán Nebot cmn...@ibmb.csic.es
wrote:
Dear Ursula,
If you have a resolution around 2.0 A you can try some of the following:
- Expand the partial solution with
Dear Ursula,
If you have a resolution around 2.0 A you can try some of the following:
- Expand the partial solution with shelxe autotracing feature.
- Do a search with ARCIMBOLDO_LITE using the partial solution. You can fin
the program at http://chango.ibmb.csic.es/arcimboldo_lite. Then,
Dear Ursula
AMPLE is also worth trying, especially but not exclusively for smaller
and predominantly helical targets. It was originally conceived for
novel folds but you may well find ab initio modelling methods get closer
to the real structure of distant homologs than the nearest available
I am trying molecular replacement with a very poor model. The model
consists mainly of 1 long helix and two slightly bent antiparallel helices.
After dividing it into 2 fragments, I was able to find a solution for one
of the fragments ( at least I think so after looking at maps, packing,
Hi Ursula,
I also tried to just superimpose the complete model onto the partial
solution. This results in quite nice packing, but doesn't refine. Is there
a rigid program refinement program with very large convergence?
depending on what you call very large, this may be helpful:
Automatic
Dear Ursula,
18% identity is really in the twilight zone for molecular replacement, where it
may work but there are certainly no guarantees.
However, there’s a feature in Phaser that is useful for this kind of problem,
i.e. the “rotate around” option, where you take advantage of knowing the
What is the resolution of your data? I have been able to get a solution for
my protein with 30% identity but my resolution of data was 1.4 Angs. I
believe to get a solution at 18% identity your search model has to be very
close, like using Robetta to make the 3 mer and 9mer peptides and then work
All:
While Phil Jeffrey attributed to me the trick of aligning the hinge axis of
an Fab along the Z direction, I, in turn, must give credit to Mirek Cygler, who
explained this to me at the Diffraction Methods in Molecular Biology [now
Structural Biology] Gordon Research Conference in 1986.
Hi Steven,
Thank you for the information and guidance. When you search for all the
ensembles with Phaser do you use “AND” or “OR”
searching?
Cheers,
Scott
While Phil Jeffrey attributed to me the “trick” of aligning the hinge axis of
an Fab along the Z direction, I, in turn, must give
Dear Scott,
By “AND” searching, presumably you mean adding another SEARCH command? (Or
clicking “Add another search” in the ccp4i interface.) For Steven’s strategy,
you want to specify separate searches for separate ensembles, i.e. give several
SEARCH commands in a script or add extra
That document is fairly old and is in dire need of revision to reflect
the modern arsenal of programs.
Nevertheless:
Putting the hinge axis along Z was a trick told to me by Steven Sheriff
back in the days when we worked on Fab structures - which after all are
classical examples of hinged
Hi Phil,
Thank you for the input. I would like to get CCP4ers input. I deal with
multiple domain
cytokine receptors in a manner very similar to antibody molecules.
Have people have more correct solutions searching for 1 domain sequentially and
then other
domains OR searching for multiple
Dear all,
I’m doing molecular replacement using Phaser. My protein is predicted
to have two domain with a “hinge” linking them. The model sequence identity is
0.27. But the MR result is poor. I’ve tried other programme (Molrep, MrBump,
Balbes,,,_.) But no improvement was observed. I
Since there is a hinge, you could try searching with the two domains
separately.
On 10/05/14 03:34, Luzuokun wrote:
Dear all,
I’m doing molecular replacement using Phaser. My protein is predicted
to have two domain with a “hinge” linking them. The model sequence
identity is 0.27. But the MR
-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jan
Félix
Gesendet: Freitag, 18. Oktober 2013 13:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Molecular Replacement using low sequence identity templates
Dear all,
I have a question regarding Molecular Replacement using
Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jan
Félix
Gesendet: Freitag, 18. Oktober 2013 13:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Molecular Replacement using low sequence identity templates
Dear all,
I have a question regarding Molecular
@JISCMAIL.AC.UK
Betreff: [ccp4bb] Molecular Replacement using low sequence identity
templates
Dear all,
I have a question regarding Molecular Replacement using low sequence
identity templates.
I have a 2.7 Angstrom dataset of a heterodimeric protein-protein complex
(space group C 1 2 1
Dear all,
I have a question regarding Molecular Replacement using low sequence
identity templates.
I have a 2.7 Angstrom dataset of a heterodimeric protein-protein
complex (space group C 1 2 1, no twinning detected using xtriage). For
the first component homologs are available, but for
i.e.
continuous crystal contacts in all three dimensions.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jan Félix
Gesendet: Freitag, 18. Oktober 2013 13:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Molecular Replacement
Umm - this is tricky.
First of all you need to reindex the C2221 data into the P21 cell - do you
know the operator?
then expand that data set to spacegroup P21. There is a cad option to do
this..
Then add that FreeR to the re-processed P21 data.
Eleanor
On 24 March 2013 14:37, Appu kumar
Thank you for the quick reply. After molecular replacement , i have done
only few cycle of refinement in refmac. I have not done any solvent
modification or NCS averaging. I have initially indexed the data in C2221
but Rfree was not decreasing so i reindexed the data in data in P121 space
group
I run the phenix.xtriage to evaluate the twining but it suggest no twining.
When i reindex from C2221 to P21, the completeness of data reduced from 95
% to 35% whereas the map is very good and Rwork and Rfree are 26/31 for 2.2
resolution. I do not understand why the completeness of data reduced so
Hello,
Here we deal with symmetry and the unique part of reciprocal space (the
reciprocal space asymmetric unit so to speak).
C222(1) has eight asymmetric units (international tables, space group 20);
P2(1) only has two. Assuming that Friedel's law does apply, then the
minimum rotation
Dear Appu,
You want to be sure you have good reason to drop the space group from
C222(1) to P2(1). There may be many reasons why your Rfree may not drop
following refinement, especially if you only have one domain in your
protein located and just in case there are more molecules to locate in the
Sorry for the misconception. Yes i am expanding the space group from merged
mtz file. Actually i have enough number of images collected. when i
indexed, integrate, and scale the data in either C2221 or P 21, it fetches
the overall 98% completeness. But when i am trying to reindex the data
from
Dear members,
I am doing a molecular replacement of a
transcription factor whose ligand binding structure(24000 Da) is available
in PDB but not for the DNA binding(13000 Da). When i am searching for the
two copies from ligand binding domain as a template model, i am
Dear Appu,
I am not sure that I have a complete sense of the issue at hand since some
of the information needed to think your issue through is missing in your
email. For example, to what high resolution cut-off were the data measured?
What resolution limits were used for the MR search? How do the
Dear ccp4 user,
I have problem in finding the phase for the
flexible DNA binding domain of LTTR protein. The unit cell parameters are ,Unit
Cell: 46.92 105.30 47.75 90.00 103.26 90.00, and space-Group P 1 21 1.
Molecular weight of protein is 36000Da. When i am running
to try both options.
Good luck!
Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Appu kumar
Sent: Monday, February 18, 2013 10:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] molecular replacement
Hi All,
Thanks for the all the advice on my previous question regarding the likely
photo-reduction of my crystals.
I've now collected a data set on these crystals. The protein is a chimera of
two domains of known structure (Ferredoxin domain and Colicin domain), what's
the best way to use all
Thank you very much!
Eleanor
On 19 April 2012 19:43, Bret Wallace bretw...@gmail.com wrote:
I noticed this missing when I first installed v. 6.2 as well.
They noted this in the problems page. You just need to replace the
phaser_MR.tcl file with the updated version in the updates page. I
Several possibilities.
1) Phaser is very prone to reject solutions because of packing clashes..
(PS How do you reset the packing limit in the current GUI?)
Running chainsaw before you begin the search can help - it prunes out
patches where the sequences don't match and gives a sensibly truncated
I noticed this missing when I first installed v. 6.2 as well.
They noted this in the problems page. You just need to replace the
phaser_MR.tcl file with the updated version in the updates page. I tried this
earlier and it created a new line in the GUI to specify the packing criterion
under
I always start MR by running chainsaw - you need a pit file or fast or
blast output with the sequence alignment of the template and your new
protein.
chainsaw will edit the template to a) renumber residues taking account of
any insertions and deletions b) prune and rename residues to the given
On Tue, 2012-04-17 at 17:49 -0400, Uma Ratu wrote:
In order to have my target .pdb, I need to mutate the residues using
coot?
Others already recommended CHAINSAW to prepare the model. Note that
coot has a nice feature under Extensions-All molecule... called [Post
MR] Fill partial residues
Ed:
Thank you very much for your advice and inputs
regards
Ros
On Wed, Apr 18, 2012 at 8:44 AM, Ed Pozharski epozh...@umaryland.eduwrote:
On Tue, 2012-04-17 at 17:49 -0400, Uma Ratu wrote:
In order to have my target .pdb, I need to mutate the residues using
coot?
Others already
Hi all,
I am working on an oxidoreductase and having some trouble during molecular
replacement.
The resolution of the crystal is 1.7 A and the space group is I4122 (a = b =
121.086, c =156.93 and alpha = beta = gamma = 90).
The cell content analysis results predicted two molecules in the
36% solvent sounds too low. Most protein crystals are at ~50%. On the
other hand, if you assume one molecule, your solvent content jumps to
68% - not unheard of, but somewhat high for 1.7A resolution dataset.
But you have a good MR solution, just try to refine/rebuild and see what
you have in
Hello,
I have a question about molecular replacement.
I use Phaser or AutoMR to generate models of my target protein. Input
.mtz is from X-ray diffraction. Template is from a known structure. I also
set up seq file using my target protein. The sequence identity between
template and my target
I would say yes. In any case you need to examine each mutated
residue to be sure the correct conformation is chosen, so you might
as well do the mutagenesis in coot or O. The ccp4 chainsaw program
is sometimes used to prepare models for MR, but it truncates the mutated
residues to variable
Thank you very much for your inputs and comments.
I am getting understand what is going on now.
If your resolution is high (2.2 A or better?) and you have ARP/wARP
Yes, the resolution is about 2A. I have ARP/wARP. Will give a try.
One more question about Molecular Replacement. With Phaser, I
Does that mean a different number of molecules in the asymmetric was found,
With Phaser, 4 monomers. With AutoMR, 2 monomers.
did you divide the molecule and find each part separately?
Each monomer (by AutoMR) is composed of two chains. One chain is part
of my target. The other chain matchs to
Hi all,
I have been trying to solve a protein-DNA complex structure using molecular
replacement. I suspect two copies of protein bind one piece of the DNA, and
the angle between the two copies of protein is somewhere between 130 to 180
degrees. I could get molecular replacement solution using a
Dear CCP4 members
I have a confusion with molecular replacement. I wish to solve a monomeric
protein in P21 where there are 2 monomers in asymmetric unit. I have a search
model that also has 2 monomers in asymmetric unit.
First I try using Phaser. I use only one chain of the monomer model
in order to rebuild the surface loops in their correct
positions.
HTH,
Fred.
(there are other possibilities of course, such as incorrect space group
assignment)
Message du 15/03/11 07:41
De : Careina Edgooms
A : CCP4BB@JISCMAIL.AC.UK
Copie à :
Objet : [ccp4bb] molecular replacement solution
On 03/15/11 02:41, Careina Edgooms wrote:
Dear CCP4 members
I have a confusion with molecular replacement. I wish to solve a
monomeric protein in P21 where there are 2 monomers in asymmetric unit.
How do you know that? What would the %solvent be with one monomer, and
with two?
If, using
On Mon, 2011-03-14 at 23:41 -0700, Careina Edgooms wrote:
So I am confused. What am I doing wrong? Please help me with
suggestions
Generally, it may be a good idea to post phaser log-file, etc. when
asking a question. You may be able to get more specific suggestions
then - otherwise, all one
Is there NCS? (How's the self rotation look? How about the native
patterson?)
Does your search model have flexible loops? You may have the right
solution, but the flexible loops may be in a different conformation
and cause clashes. Trim the search model to the conserved / structured
Maybe there is a domain shift of your protein compared to the model. If this
is the case, try to do the MP with successive domains.
2010/9/13 Paul Holland pholl...@umd.edu
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has
very high
On 09:50 Tue 14 Sep , Dirk Kostrewa wrote:
I would spend some time in improving the search model, first. If there
are more than one possible search molecules in the PDB, I usually do a
structural alignment (ssm superposition) to get an idea about the
flexibility of the search molecules.
Dear Paul Holland,
I would spend some time in improving the search model, first. If there
are more than one possible search molecules in the PDB, I usually do a
structural alignment (ssm superposition) to get an idea about the
flexibility of the search molecules. Then I remove all parts that
Two questions.
What is the resolution of your data? what is the percentage sequence
identity?
even if you are confident of C2, try using PHASER with all space groups and
searching for 2-4 monomers.
Ivan
On Mon, Sep 13, 2010 at 7:52 AM, Paul Holland pholl...@umd.edu wrote:
Hello fellow
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high sequence similarity to the search model with several predicted flexible
loop regions; however, all attempts at finding a solution have not produce very
ideal starting solutions
Does your model structure form a dimer? Maybe best to search with that
model..
eleanor
Paul Holland wrote:
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
high sequence similarity to the search model with several predicted
On Mon, 2010-09-13 at 15:52 +0100, Paul Holland wrote:
that has very high sequence similarity to the search model
How high exactly?
--
I'd jump in myself, if I weren't so good at whistling.
Julian, King of Lemurs
Here is how I would approach this:
Use Phaser to search with monomers, or
dimers if you suspect that the biological unit is composed of dimers
and have reasonable guess at a dimer search model.
Also consider searching with N- and
C-terminal truncated search models. Sometimes a
Try balbes from G. Murshudov's website. It will find proper search model
and use proper truncations automatically. In addition, it will put in
your sequence.
Paul Holland wrote:
Hello fellow crystallographers,
I am trying molecular replacement for a protein crystal dataset that has very
Dear All,
I am trying to resolve a protein structure with the use of Molecular
Replacement. However, some part of protein are overlap in the interface of
homodimer. Would someone please give me suggestions? Thank you!
--
Best regards,
WuXH
Hi there,
If there are a few clashes (acceptable - usually surface loops that
enter the surface part of another molecule or subunit) then you can
delete the parts of loops that usually have poor density and that clash,
refine, compute a new map and see if the loop can be traced (usually it
Hmm - that is odd.
You may have the wrong SG in the mtz file. Try MOLREP or PHASER with the
option to try all spacegroups consistewnt with the pointgroup.
Eleanor
intekhab alam wrote:
Hi all
I am trying to do molecular replacement with low resolution (4Å) using
Molrep and Phaser.
Overall
Hi all
I am trying to do molecular replacement with low resolution (4Å) using
Molrep and Phaser.
Overall R-factor is 11.3%, completeness 95.4%, I/sigma 2, and Chi^2 0.95.
Identities between my protein and templates were more than 80%.
I couldn’t get correct solution.
Rotation function,
Dear intekhab,
a few suggestions:
- are you sure of the space group or might there be alternatives?
- is you protein globular or modular, i.e., is it worth running MR with stable
subdomains one after the other?
- try a poly-alanine model (e.g. chainsaw can do this for you, pdbset probably,
Also check if you have correctly estimated no. of molecules in asymmetric
unit.
On Fri, May 21, 2010 at 4:58 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Dear intekhab,
a few suggestions:
- are you sure of the space group or might there be alternatives?
- is you protein globular or
...@gmail.com
Subject: Re: [ccp4bb] molecular replacement
To: CCP4BB@JISCMAIL.AC.UK
Also check if you have correctly estimated no. of
molecules in asymmetric unit.
On Fri, May 21, 2010 at 4:58 PM, Tim Gruene
t...@shelx.uni-ac.gwdg.de wrote:
Dear intekhab,
a few suggestions
Dear All;
We have solved a crystal structrure of protein at 1.8 A. I have now
another crystal of the same protein in aother unit cell,for the new
crystal type resolution is 3.6 A but when I use our structure as a seach
model It does't give any solution.
Any suggestion would be highly
Dear Muhammed,
that's not uncommon. Your protein might undergo domain movements or
contain flexible parts.
if your structure contains any loops / floppy regions (with high
B-values), you can exclude them from the search model.
If it is composed of domains, chop it into pieces and search
Dear Muhammed,
In case you have used phaser for MR you could try to either decrease
sequence identity or increase the rmsd of the search model (both ways
are equivalent). This allows also to account for flexibility/movements
in your target protein like Tim explained.
Cheers,
christian
Muhammed
Hi all,
I got one data about 3.0 A, belong to C2 space group. There are two protein
molecules and one 18-nt dsRNA per ASU. The structure of last 100aa
(C-terminal) has been reported, and 400 aa at N-terminalhe has homology
structure with sequence identiy 30%. I try to solve it by MR with phaser.
Hi Lisa,
There are many things you can try and the phaser manual gives a lot of
useful information what to do in difficult cases. From my experience, it
is quite difficult to find solutions for MR with nucleic acids. I
recommend to search only for protein. As a side effect you can use this
the software because
the DNA is denser.
Of course, every case has its own idiosyncracies.
Phoebe
Original message
Date: Tue, 10 Nov 2009 14:19:43 -0500
From: Christian Biertuempfel biertumpf...@niddk.nih.gov
Subject: Re: [ccp4bb] molecular replacement in phaser
To: CCP4BB
Dear all,
when searching in Molecular Replacement
against say perfectly merohedrally twinned data (i.e. an alpha=0.5 twin)
do I understand it right that I should expect two sets of solutions
that are equivalent under the twin operator (bar xtal symmetry and/or
origin shifts)?
Yes, but if the twin fraction deviates even slightly from 1/2, you may
only get one solution from the search. If you want, you can generate
the other one and see how happy the program is.
Regards,
Randy
On 11 Sep 2009, at 15:12, Pietro Roversi wrote:
Dear all,
when
My first time posting to the CCP4BB board and I am very sure it will not be
my last. I have a general and specific question concerning molecular
replacements of protein-protein complexes. I have a good dataset (2.5A, 98%
complete), which has been integrated and scaled. Pointless suggested the
Dear Allen, Sue,
we also have had some luck with ACORN, but as our peptide did not have
alpha-helical structure, the postdoc on the project used a 4-aa
beta-turn fragment instead. I can put you in contact with him for more
details. As I understand it, ACORN uses a mixed MR/direct methods
If you have 1.1A data and your structure is not too large, ab initio
direct methods (e.g. with SHELXD) will probably solve the structure. I
would be happy to advise if you wish to try this.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr.
Hi Allen,
With such low solvent content (and corresponding tight packing), you may
want to give 'Queen of spades (Qs)' a try. The reason being that Qs is not
(at least directly) a Patterson-based method (and does not assume that
intra-molecular vectors are topologically segregated). If you
I am trying to do molecular replacement on a small peptide (less than 40 AA)
and have not had any success using phaser. Are there any tricks or better
programs for really small peptides?
The data is great 1.1 A, ~35% solvent, and two molecules in the ASU. I have
tried all the standard stuff,
Have you tried acorn in ccp4? I've had it work well at this resolution,
especially if the protein/peptide has some alpha helical content. We used
acorn to solve a small cro protein that we couldn't get molecular replacement
to work with by using a 5-residue ideal poly-ala helix as the starting
I've had good luck using Phaser on test cases like that, but haven't
had access to a case that was previously unsolved. But in principle
it should work, if the model is good enough.
It sounds like you've thought about the resolution already, so this is
probably redundant. Anyway, the
Dear all,
we have crystals that nicely diffract to 1.7 A (sharp spots), with the
following characteristics and findings:
a) the data appear as P212121, with axes 117.2 133.6 138.3 (if reduced
in P1, the largest deviation of any angle from 90° is 0.2°); the odd
screw-axis reflections are
You dont mention any twinning tests?
The L test, now part of the newest ctruncate is pretty good at detecting
twinning even with the NCS translation.
And SFCHECK does a good job too.
If these are inconclusive I would not assume twinning.
Usually you can get solutions for MR with twinned data,
Eleanor Dodson schrieb:
You dont mention any twinning tests?
sorry, I forgot to mention that the twinning tests do not show twinning.
Rather, the actual curves in the Cumulative distribution of H lie on
the not-twinned-at-all (i.e opposite) side of the alpha=0 curve (see
plot below). But
Well - there s nothing there to indicate twinning, although as you say
it is hard to be sure with a pseudo translation...
The contrast doesnt look brilliant, but then it often doesnt..
What about phaser? If it gives a contrast between one spacegroup and the
others I always think that is a good
are allowed.
Best regards,
Herman
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
Behalf Of Mo Wong
Sent: Monday, January 19, 2009 5:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molecular replacement using a partial
Hello,
My problem: I have poorly phased 3.5A data which suggests 6 molecules per
ASU, and using MolRep with the experimental phases (search for model in the
map) I have good solutions 3 of them. There is a lot of empty electron
density which needs to be filled with more copies of the molecule. I
Wong,
did you look for pseudo-symmetry? For example for pseudo-translation,
which you can deduce from a native Patterson.
Good luck,
Klaus
Mo Wong wrote:
Hello,
My problem: I have poorly phased 3.5A data which suggests 6 molecules per
ASU, and using MolRep with the experimental phases
Hi Junyu
It is possible at 6 Å resolution, what I would try is to cut your data
and try searching in different resolution ranges 20-7 or 25-6.5 , if you
are uncertain about your search model, try with a higher RMS value try
going up to 2.0. If you have any data, even at very low resolution,
Hi,
Does anyone have experience with molecular replacement at low
resolution? I have a 6Å dataset with probably 3-4 monomers per ASU.
Phaser doesn't seem to give me clear results. Can I get some advice?
Any comment will be appreciated.
Thanks a lot,
Junyu
I've had a very good experience with MrBump:
http://www.ccp4.ac.uk/MrBUMP/
Not only because of the program itself, which was able
to find an unexpected template for the problematic
chain (the first one was straightforward in Phaser),
but also because of great support from Martyn Ron.
It's
EPMR (now Open-EPMR, http://www.epmr.info) is an excellent alternative
for finding difficult, high-dimensional MR solutions. Experiment with
various resolution limits. We solved an asymmetric unit with 3
difficult-to-place dimers of low sequence homology by gradually
increasing the
,
Pete
-Original Message-
From: CCP4 bulletin board on behalf of Anjali Mehta
Sent: Thu 3/6/2008 7:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molecular replacement of a multidomain protein
Dear All,
I am working with a Bifunctional protein of molecular weight ~60 kDa.
I have a 3.3
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