Dear Francis,
I am very interested in your work with this.
In the paper :-
A. Mukherjee, J.R. Helliwell and P. Main 'The use of MULTAN to locate the
positions of anomalous scatterers'. (1989) Acta Cryst. *A45*, 715-718.
you will see that missing centric reflections was not limiting. However, the
m
If you ask for Real space R factor from overlapmap it gives you the mean
density for eaxch residue main chain and side chain, or mean density at
atom centre. It is rather confusedly labelled Fobs(mc) etc.
You could convert this to sigma level by just dividing the values.
Eleanor
The Hailia
Some afterthoughts:
Of course avoid the common MR problems - assigning wrong SG, saturating
low resolution data etc etc..
1) Any sequence search tool might have told you there was only a poor
match available. 23% is very marginal for MR and with that degree of
similarity you are very wise to
Hy Mohd,
There was recently a nice review about all the alignment software available.
You might find one you like in there.
Visualization of multiple alignments, phylogenies and gene family evolution.
http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1434.html
By the way there's also a revie
On Tue, May 25, 2010 at 6:22 AM, Frank von Delft
wrote:
> Hi Ian, I read with great interest. But got stumped here:
>
>>> - how you compute sigma(rho)?
>>
>> See my reply to George Sheldrick's post.
>>
>
> I think your reply did not make it out to the BB, certainly neither to my
> inbox nor to th
Thank you all for very helpful suggestions, I used the software STRAP,
Espript is also user friendly and effective. Many recommended ALINE, but
unfortunately I had troubles with the download. Thanks again, Mohd
Dear Paul,
A few options may be of interest:
RCSB PDB Sequence Searching:
Paste your sequence into the sequence search box at:
http://www.pdb.org/pdb/search/advSearch.do?st=SequenceQuery
(also available from Advanced Search and from the Sequence Search of
the left hand menu).
Sequence search
Hi there,
I remember a friend of mine showing me Aline, and it looked very nice.
However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3).
With respect to the instruction I found on the website, I had to change the
export lines to be added to the .bashrc in order not to get error messages
Hi,
When I run UPPSALA rsfit, there are lots of "ERROR --- Serious FRCSYM
error". These atoms/residues are generally around the protein surface, so
I guess the reason is the mask were out of the unit cell. Is there any way
to avoid this?
Thanks!
Best Regards, Hailiang
Hailiang Zhang wrote:
Hi,
When I run UPPSALA rsfit, there are lots of "ERROR --- Serious FRCSYM
error". These atoms/residues are generally around the protein surface, so
I guess the reason is the mask were out of the unit cell. Is there any way
to avoid this?
I've seen that error in averaging/
Hi there,
I just got this working a couple of days ago under Mac OS X 10.6.3. I
manually compiled and installed Perl-Tk from CPAN. Steps taken:
1. Download and ungzip / untar:
http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz(the
newer -503 version didn't work)
2. Change in
Dear All;
Can some body tell me a website for structure based sequence alignment,
which can also pin point the similar and identical residues in different
colors.
regards
Bashir
--
Muhammad Bashir Khan
Department for Biomolecular Structural Chemistry
Max F. Perutz Laboratories
University of
Hi,
I wanted to convert a binary ccp4 map file to a readable format so that I
can retrieve the electron density at each real space grid point. Just
tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not
readable, and I didn't find any documentataion about how to read them.
Could some
http://ww2.cs.mu.oz.au/~arun/Site/mustang.html
http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=EXPRESSO(3DCoffee)::Regular
or maybe what you are searching for is Consurf ?
http://consurf.tau.ac.il/
Jürgen
On May 25, 2010, at 2:39 PM, Muhammed bashir Khan wrote:
I would also recommend STRAP if you haven't tried it (
http://www.bioinformatics.org/strap/)
On Tue, May 25, 2010 at 2:53 PM, Jürgen Bosch wrote:
> http://ww2.cs.mu.oz.au/~arun/Site/mustang.html
>
>
> http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=EXPRESSO(3DCo
Hi, those formats are not intended to be readable other than by the
format exchange programs, and I would strongly advise against trying!
Instead, pretty well all programs read a CCP4 binary map directly and
do whatever they need to with the map array in memory. The
documentation for the Fortran
Hi there
I wonder if anyone can recommend a good review/paper describing crystal
structures that show high energy residues in active sites. By that I
mean residues that may be in a strained conformation and rotate between
conformations, such that they may even switch into unfavoured
ramachandran
On 26/05/2010, at 6:53 AM, Jürgen Bosch wrote:
http://ww2.cs.mu.oz.au/~arun/Site/mustang.html
We have built a web server for this at
http://pxgrid.med.monash.edu.au:8080/mustangserver/
Cheers
Ashley
http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=EXPR
Dear Heng,
Tris forms only a very weak complex with Zn2+. It is unlikely that the
problem arises from Tris. It might be simply that the complex
dissociates in the presence of high imidazol when you elute the complex
from the nickel column. Imidazol is a pretty good Zn2+ coordinating
molecule. DTT i
Sorry, the link was broken (problem with tomcat not restarting properly): Use
http://pxgrid.med.monash.edu.au/mustangmr-server
cheers
Ashley
On 26/05/2010, at 8:08 AM, Dhirendra K Simanshu wrote:
> Hi
>
> It seems the link (the one you send) is not working!
> Can you resend the correct lin
Hi Charlie
I am so sorry I assumed development had halted, but I'm glad one of the
authors of ALINE has stepped in to restore the truth, and even more that
ALINE is still being taken care of.
Hopefully those needed funds will materialize, for your sake and also for
the benefit of all the scient
Hi,
Have seen the real-space correlation used widely judging the map quality.
Generally or empirically, in order to say an map (area) has "good"
quality, how large should the real space correlation coefficient be? Say,
is 0.8 good enough on a residue base? Any references about this will be
greatly
On Tuesday 25 May 2010, Hailiang Zhang wrote:
> Hi,
>
> Have seen the real-space correlation used widely judging the map quality.
> Generally or empirically, in order to say an map (area) has "good"
> quality, how large should the real space correlation coefficient be?
I do not think that the rea
Hi,
I am working on a real space correlation on a specif protein section using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map\
mapin2 ${PDB}-2
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