Ccp4's Gesamt (new algorithm, interfaced jointly with SSM in ccp4i) should do
what you want -- Eugene
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Zhijie Li
[zhijie...@utoronto.ca]
Sent: Thursday, October 25, 2012 12:45 AM
To: ccp4bb
Subj
Hi Wenhe,
Superpose allows you to specify residue (as well as Ca/main chain/side chain)
ranges. Also in COOT you can select the range of residues used in the LSQ
superpose calculation.
For superposing parts of the proteins only, a little trick is to cut the
interested fragments from the origi
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.g. 5 residues) which we are interested in. But these two structures do
not have similarity for overall structures. In this case, I can
Hello everybody,
I'm looking for small proteins (up to 150 aa) that are known to express
reasonably in E. coli, are soluble and folded but failed to crystallize.
Can you provide some examples, especially of proteins that might be
interesting for a broad community?
Thanks,
Karolina
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Thank you for correcting me.
The other two ligand inside the tetramer are fited manully now.
Because their geomtry are significantly differed from the NAD PDB file that
I used.
Thank all of you for your comments.
Uma
On Wed, Oct 24, 2012 at 11:23 AM, Bosch, Juergen wrote:
> That's not what I
That's not what I suggested.
you have a tetramer and you have found two ligands within the protein and two
ligands outside your protein - right ?
Now if you merge those 4 found ligands with your protein and then turn on
symmetry mates you will find that the two ligands which were shown outside yo
Dear Giovanna and Bosch:
Thank you for your advices.
I tried the way as you suggested, but not work.
Here is how I did:
1. Center on the ligand density, and "Find ligand" "Right here".
2. Increase Fo-Fc at 3 sigma or reduce 2Fo-Fc maps to 0.8 sigma.
Coot failed to recognize the density.
> Yo
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If you show symmetry mates I'm sure the ones Coot found "outside" your protein
are actually in the sites you are missing.
Nothing to worry, just safe the symmetry mate and read in those coordinates&
merge with your current model.
Jürgen
..
Jürgen Bosch
Johns Hopkins Universi
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Job Details
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