Straw poll:
Are you interested in software to autobuild polysaccarides?
Kevin
p.s. I expect I'll have to spend at least a year working on the problem
before before I spell polysaccharide consistently.
superpose has two options undfer CCP4i.
Choose match numbered residues ( not SSM)
Then you must give two files to match - in your case that means naming
your model twice.
Then say you want to match residues 1 to 20 Chain A to residues 1 to 20
CHAIN B tever span you want to fit.
It will give you
Dear Kim,
I asume that Kevin plans to build in electron density maps. As far as I
can see Sweet will produce a model unhindered by experimental data.
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Kim Henrick
Sent: Tuesday, July 26, 2011
Yes but it is easier to take the sweet model for the required sequence
and fit that to density rather than do it residue by residue
which will lead to glycan structures unknown to the source
kim
Dear Kim,
I asume that Kevin plans to build in electron density maps. As far as I
can see Sweet
Hi Kim and Kevin,
Even then you can have chirality inversions during real-space refinement, which
would destroy the SWEET input model from. There is no substitute for common
sense (and validation) here.
That said, Kevin, something to autobuild carbohydrates (given a sequence) would
be
Hi,
I had a dataset which is P21 but with a pseudo-translational symmetry of
(1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots
of h+K= 2n+1 compared to h+k= 2n. Is that correct?
I would like to have a close look at the reflections. for example, the
average I/sigma for
On Tue, 2011-07-26 at 09:51 -0400, zhang yu wrote:
I would like to have a close look at the reflections. for example, the
average I/sigma for reflections with h+k=2n+1 and reflections with h
+k=2n.
Once you have your reflections listed in a file having h,k,l,f,sigf as
first five columns (e.g.
Yu,
There is a parity analysis in dataman (a USF program) for example.
You have to take into account that the sigmas are generally estimated
assuming a unimodal intensity distribution, which is no longer true in
the pseudo-symmetric case. In practice this means that the sigmas of
the
A smart polysaacharide autobuilder mindful of geometry and biology (no
non-biological sugars and linkages, please) and not based on what is
already deposited in the pdb might cause a significant decrease in ccp4
and phenixbb traffic. So I am for it!
Engin
On 7/26/11 4:28 AM, Robbie Joosten
Hi
Thanks for all the replies. I ran TRUNCATE in CCP4 and got what I want. I
will try other options later. Thank you again.
Yu
2011/7/26 Esko Oksanen esko.oksa...@helsinki.fi
Yu,
There is a parity analysis in dataman (a USF program) for example. You
have to take into account that the
Dear all,
X-ray crystallographer and Project Leader position at Emerald BioStructures
Emerald BioStructures is an integrated gene-to-structure collaborative research
organization specializing in drug discovery services. Our scientists provide
integrated structural biology solutions to
I am trying to refine a protein-DNA structure, and I am having difficulties
refining the DNA using COOT. I used the ccp4i Phaser program to molecular
replace the protein and DNA simultaneously (there are solved crystal
structures of the free protein and a similar DNA bound to another protein),
Hi Brittney,
DNA is pretty standard so the restraints should be in the dictionary. Perhaps
the DNA in your model has non-standard residue names (PDBv2). Are your bases
called DT, DA, etc? Do your atom names have * or '?
Cheers,
Robbie
Date: Tue, 26
I am trying to refine a protein-DNA structure, and I am having
difficulties refining the DNA using COOT. I used the ccp4i Phaser
program to molecular replace the protein and DNA simultaneously (there
are solved crystal structures of the free protein and a similar DNA
bound to another
Dear All,
Is there a simple way (or already an existing list) to extract/parse from
the heterodictionaries or monomer libraries which 3-letter symbols are
actually modified standard amino acids (as compared to bona fide ligands,
solvent molecules etc)?
Thx!!
BR
Does anyone out there have a protocol of growing HEWL crystals that are
all 50-100 microns wide? I gave this project to a summer student
recently, thinking it would be easy, but it is turning out to be more
difficult than I thought. Keep getting sphereulites instead of small
crystals. Yes,
On Tue, Jul 26, 2011 at 10:46 AM, Bernhard Rupp (Hofkristallrat a.D.)
hofkristall...@gmail.com wrote:
Is there a simple way (or already an existing list) to extract/parse from
the heterodictionaries or monomer libraries which 3-letter symbols are
actually modified standard amino acids (as
If you simply want a list of modified residues, here is one that I
compiled a while ago. More details on each can be found at LigandExpo.
'0CS' = 'ALA', '0NC' = 'ALA', 'AA3' = 'ALA',
'AA4' = 'ALA', 'ABA' = 'ALA', 'AHO' = 'ALA', 'AHP' = 'ALA', 'AIB' =
'ALA',
'ALC' = 'ALA', 'ALM' = 'ALA', 'ALN'
On Tuesday, July 26, 2011 10:46:34 am Bernhard Rupp (Hofkristallrat a.D.) wrote:
Dear All,
Is there a simple way (or already an existing list) to extract/parse from
the heterodictionaries or monomer libraries which 3-letter symbols are
actually modified standard amino acids (as compared to
Thanks to all the respondents - that lib-list and the various script
listing suggestions are a perfect start.
BR
-Original Message-
From: Ethan Merritt [mailto:merr...@u.washington.edu]
Sent: Tuesday, July 26, 2011 11:06 AM
To: hofkristall...@gmail.com
Cc: CCP4BB@jiscmail.ac.uk
Subject:
Thanks for the quick response! I downloaded the newer version of COOT, and
it works perfectly now. Thanks for the help!
Brittney
On Tue, Jul 26, 2011 at 1:16 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:
I am trying to refine a protein-DNA structure, and I am having difficulties
refining
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On Thu, 21 Jul 2011 18:36:59 -0700 (PDT)
Michael Thompson mi...@chem.ucla.edu wrote:
I would like to view the intensity-weighted reciprocal lattice for
several data sets that I have collected. (The data have been indexed,
integrated and scaled with Denzo and Scalepack.) I was wondering if
On Tuesday, July 26, 2011 01:59:32 pm Thomas White wrote:
On Thu, 21 Jul 2011 18:36:59 -0700 (PDT)
Michael Thompson mi...@chem.ucla.edu wrote:
I would like to view the intensity-weighted reciprocal lattice for
several data sets that I have collected. (The data have been indexed,
James,
I would have a look at the paper by Judge et al:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300446/pdf/10465769.pdf
Specifically, in this paper you will find that the crystallization behavior of
lysozyme changes drastically with pH. At the time the paper wasn't really
written to
That's a really old paper. You can purchase the lysozyme from Hampton
Research and it's fine. The recipe is available from the Hampton Research
page:
http://hamptonresearch.com/product_detail.aspx?cid=28sid=173pid=524
Grow them a low temp and you can stop them when they are the right size.
I
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