Hi Chen,
I also tried the "Superpose maps" utility in PHENIX, however, since they
> are nucleic acid structures, it seems that the sequences cannot be
> recognized.
>
I'm not aware of such problem. If it does exist and you want me to fix it
please send me the files and I'll have a look.
Pavel
If I understand your question correctly, you have a couple of atoms which you
could align to get the rotation & translation then you can use these values
with maprot (CCP4) or mama (USF) to actually superimpose maps.
Jürgen
On Mar 21, 2013, at 11:29 PM, Chen Zhao wrote:
Dear all,
Does anybody
Dear all,
Does anybody know some softwares for aligning electron density maps?
I tried transforming map by SQL model fit extension in COOT, which turned
out to be not working: the map it transformed is the one supposed to be
fixed. If I switch the moving model with the reference model, I only got
Hello Theresa,
Maybe a functional assay (if possible) is better than determining the
oligomeric state?
Why is finding out the oligomeric state (which is unknown anyway and the
answer can be compared to nothing), the answer to "is having a tag ok?"
"will the protein crystallize"?
What if the analysi
I have successfully used modeller (standalone software; Sali lab) to generate
multimeric complexes up to 24-mers
Hope tis helps
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudipta
Bhattacharyya
Sent: Friday, 22 March 2013 5:00 a.m.
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Subject: [c
Dear Theresa,
Although I haven't yet done the experiment myself, I am told that
microscale thermophoresis (MST) is another useful method for
oligomerization measurements, especially since it is designed to work for
membrane proteins in presence of detergents etc. If you want to quickly
learn more
Dear all
I received off-board replies on this subject. Most people use standard
desalting for all cloning and mutagenesis experiments regardless of length. One
reply recommended desalting for up to 40 bases and HPLC for longer oligos
because of larger ratio of (n-1) contaminants. For crystalliz
Dear all
I have a His-tagged membrane protein with unknown oligomerization state. But I
am worried that tag addition may induce different state than in native and
affect its crystallizability.
Is there a single method that can determine the oligomerization state with
nearly 100% accuracy? I ha
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Dear all,
My question concerns the Extension-> modelling-> Rigid body fit residue
ranges function in Coot. Although it works well through the interface, I
cannot have it to work in a python script, does somebody know the
correct syntax?
Thanks in advance,
Nicolas
Dear All,
Could annyone please suggest me any program or server that can build
homology based models of dimeric/oligomeric proteins? Previously I have
used many software/servers which can build the monomer of my target
proteins but not the dimers. Self docking of homology based monomer is not
work
Respected All,
Thanks for your valuable suggestions and inputs.
with regards,
Harsh
On Thu, Mar 21, 2013 at 7:38 AM, Bosch, Juergen wrote:
> Yep,
>
> mostly you should stay away from Tris as this is the worst buffer system
> when playing with temperature changes. Tris for example has a ∆pKa/1
I was a little provokative. A GUI with a viewer would actually be an excellent
idea since it allows one to see what one is doing, which would be of great help
for difficult data sets. Nevertheless, since XDS is part of many automated
pipelines, the possibility to run XDS offline with a command f
On Thu, 21 Mar 2013 08:28:27 +, herman.schreu...@sanofi.com wrote:
>Dear Tim,
>
>It could be that COLSPOT does not rely on experimental setup parameters.
>However, XDS must have reasonably close starting values for distance, direct
>beam position etc., otherwise the autoindexing would fail,
Dear Herman,
some pros and cons are documented at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Wishlist#Would_be_nice_to_have
, and the workaround is at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings . These
XDSwiki articles are old, and nobody has contribut
Dear Tim,
It could be that COLSPOT does not rely on experimental setup parameters.
However, XDS must have reasonably close starting values for distance, direct
beam position etc., otherwise the autoindexing would fail, so the information
to calculate an approximate TRUSTED_REGION is available.
Or, seeing that this is the CCP4BB , you could use the Xia2 pipeline
from CCP4i - which will also use XDS if installed on your system.
> My recommendation would be to process with XDS. By using the autoProc
> procedure from Global Phasing this is very easy, even for people who are
> normally no
Dear Kyriacos,
Just one thing to add to this suggestion from Herman:
I personally view and study the plots generated by the SCALA/TRUNCATE or
AIMLESS/TRUNCATE route after XDS processing (in particular the plot of
Rmerge values as a function of Batch number) to eliminate deviating
batches from
Dear Kyriacos,
What kind of high-resolution data do you have?
In my experience, while Scala usually produces excellent results, it often
fails miserably or even crashes due to too negative intensities in case of low
redundancy data. E.g. if one does a second high-resolution scan with a high
sw
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