The concentration of oligonucleotide seems much lower than you will ultimately
need for biophysical work. Annealing two strands is a bimolecular reaction and
it will be driven by mass action more to completion at higher total
oligonucleotide concentrations. I also agree with the posts that hav
Having just faced this problem, I used the coot 'symm shift reference
chain here' command (in Extensions / Modelling menu) to assemble the
model from the scattered fragments.
This should be scriptable, but I didn't think it was worth the effort
for the 20 odd fragments I had.
Hope this he
coot, lsq command
i have not checked chimera but it may have too. (I think so)
For coot. I used it recently for a small molecule.
And pymol
Finally the superpose server may do it.
On Jul 8, 2015, at 3:41 PM, Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> Hi Fellows,
>
> I seek advice for a
Hi Bernhard, symmatch in the ccp4 suite comes to mind but also any superposition program will superimpose your scattered pieces onto the relevant part of your reference structure, won't it?
Cheers, Boaz
Original message
From: "Bernhard Rupp (Hofkristallrat a.D.)"
Date:
Two possibilities:
"Cealign" all scraps onto reference in pymol
Achesym server: a generally wonderfully useful way automatically to collect
fragments into one unit cell
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard
Rupp (Hofkris
Hi Fellows,
I seek advice for a trivial but tedious problem: I have rebuilt,
automatically and manually, several parts of a
structure, which of course, are all over the place in different ASUs. I also
have a reference model, where
the parts form a correct ASU.
Is the a program/script that can
Does this look like a suitable solution for those who like dials while
model building?
http://petapixel.com/2015/07/07/review-palettes-modular-photo-editing-controls-are-pricey-but-powerful/
http://www.cnet.com/news/buttons-and-sliders-and-knobs-oh-my-palette-offers-a-more-physical-interface-fo
It's not ccp4, but I've successfully used MultiSeq in VMD to make a
1-dimensional tree from a large group of conformations. Though like you
mention, the big conformational changes might not be handled well in the
STAMP alignment of that package.
ProSMART might be more appropriate if you have rigid
Thanks Jose - I missed that one.
REMARK 2 is somewhat ambiguous with:
_refine.ls_d_res_high
and
_reflns.d_resolution_high
although the former makes more sense and seems to be what corresponds to
REMARK 2. Haven't yet seen an entry with only _reflns.d_resolution_high
and not _refine.ls_d_res_h
REMARK 2 is generated from
_refine.ls_d_res_high
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html
Regards
John
On Wednesday 08 July 2015 15:04:45 Jose Manuel Duarte wrote:
> This looks like the mapping you are after:
>
> http://mmcif.wwpdb.org/docs/pdb_to
Hi all,
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Have you ever searched the PDB and needed to answer questions like these?
* Which structure is the best for the molecule you are interested in?
* How many different human proteins have structures solved?
* Which entries contain your protein bound to DNA?
* How many different macromolecules ha
This looks like the mapping you are after:
http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html
It maps only the structured PDB data items to their equivalent mmCIF
items. For instance REMARK 2 is not there, but REMARK 200 is. The
resolution value should then be in "REMARK 200 RESOLUTI
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Hi Jacob,
Principal component analysis (pca) might work but it will modify the
original dimensions as a linear combination, which might make it difficult
to derive physical meaning out of it. May be, you could use decision trees
which give results that are easier to interpret. Looking at decision
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