Dear Hailiang,
While apparently no response came, here my 2 cents:
Even if there would be an automatic utitility to generate links based on
distances, I would never use it. Either the sugars have been properly
refined and then the link cards are present in the pdb file, or the
sugars have been
Dear Hailiang,
as Herman Schreuder already wrote sugars are quite likely to contain errors. We
are developing the PDB CArbohydrate REsidue check tool (pdb-care) in our group
to help crystallographers locating problems in sugars. There will be an update
soon, which includes checks for
Dear prospective PhD students,
Ten competitive PhD fellowship are available at the Centro Nacional de
Biotecnologia in Madrid, Spain (www.cnb.csic.es).
The webpage
http://www.cnb.csic.es/content/about/lacaixa/index.php?l=0
explains how to apply, although the limit is NOT 13 Feb 2011 as the
Does anybody know the pdb codes with proteins with O-linked
sugars on THR.
I support a program to help interpret sugars in poor electron density
by stabilizing links. Coot helps a bit but branching poses a problem.
Rather than based on distance like coot operates at present it should be
best
Dear Enrico,
you can find information on PDB entries with carbohydrates in the
GLYCOSCIENCES.de database:
http://www.glycosciences.de/database/index.php
To find entries with O-Glycans linked to Thr you can use the substructure
search at
Dear CCP4BB
I have been refining a structure in Refmac and I would like to report an
average B value for the solvent, ligand and DNA chain seperatly. However, I
cant this information in the Refmac log or .pdb file. Is there a
program/option I can use to calculate the B factors for parts of the
Hi James,
You can do this with MOLEMAN / MOLEMAN2 quite easily (see the manual here:
http://xray.bmc.uu.se/usf/moleman2_man.html)
Best
Matthias
Date: Thu, 10 Mar 2011 14:19:21 +
From: james.pearce.h...@gmail.com
Subject: [ccp4bb] Reporting average B values for solvent, chain, ligand
Hi all -
Two of the grad students in our structural biology course are having similar
problems installing Coot on their Mac computers using the stand-alone
packageshttp://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot
from Bill Scott's Crystallography on OS X website. I've pasted
Hello Jared,
Two of the grad students in our structural biology course are having
similar problems installing Coot on their Mac computers using the
stand-alone packages from Bill Scott's Crystallography on OS X website.
I did the same thing about 2 months ago. I tried out the package on
They're both getting Python magic number errors, which from what I know
result from one Python version trying to run a .pyc file created with another Python
version, but I'm not sure exactly how to work around it in the context of the stand-alone
package. The students aren't planning to do
Hi Pete,
Usually python will regenerate pyc files as needed (assuming the source
files are available). So find $COOTDIR -name *.pyc -exec rm {} \;
might be worth a try.
This is true, but the import error is being generated by Coot trying to
read the _system_ .pyc files:
ImportError: Bad
Hi all,
As part of its recent winter update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) released a new widget, called PDBportfolio, that we hope will
find widespread use. It displays a slideshow of images that convey important
information about the entry (or entries). Every image
Ben Eisenbraun wrote:
Hi Pete,
Usually python will regenerate pyc files as needed (assuming the source
files are available). So find $COOTDIR -name *.pyc -exec rm {} \;
might be worth a try.
This is true, but the import error is being generated by Coot trying to
read the _system_ .pyc
Hi there,
I want to found some bad geometry for my ligand (sugar rings). The
procheck .out file seems only shows the bad bond length or angles for
protein. Is there any way we can get these information for sugar rings?
Thanks in advance!
Hailiang
Hi James,
(...) Is there a program/option I can use to calculate the B factors for
parts of the model?
phenix.model_vs_data model.pdb data.mtz
will do this: report B-factor statistics for macromolecule, water and
ligands.
Pavel.
Hi Ben and Pete - I did think about deleting (or moving) the .pyc files, but in
the newer of the two students' computers (3 weeks out of the box), there wasn't
a site.py file in that directory, only .pyc and .pyo, so I figured I'd better
not mess with it.
Thanks for the suggestions so far.
Hi Halliang,
If the ligands are in the pdb het dictionary I think MolProbity will
look at bonds and angles...maybe even dihedrals.
Cheers,
-bob
On Thu, Mar 10, 2011 at 12:23 PM, Hailiang Zhang zhan...@umbc.edu wrote:
Hi there,
I want to found some bad geometry for my ligand (sugar rings). The
Hi,
Swiss-pdb viewer works well for small peptides, you can check if it serves
your objective too...
Even WHAT IF provides clues to bond angles, bond length and torsion angles.
Gauri
On Thu, Mar 10, 2011 at 3:56 PM, Robert Immormino immorm...@gmail.comwrote:
Hi Halliang,
If the ligands are in
Hi all,
I was intrigued by the recent question of whether glycerol had any adverse
effects on the final purity of protein isolated by chromatography. Glycerol
certainly helps to solubilize some proteins. Does anyone know of any negative
effects of glycerol in protein purification, on protein
Hi Ray
I have seen glycerol at less than 5% in the protein buffer prevent crystal
growth completely and when removed from the buffer has resulted in very nice
crystal growth of the glycerol free protein.
Best
Gina
From: CCP4 bulletin board on behalf of
Glycerol is just another additive to crystallizations and a reasonably good
cryoprotectant. Sometimes it helps to grow crystals, sometimes it has no
effect, and sometimes it interferes with crystal growth. Have I covered all
the possiblities?
One thing is the glycerol often makes a protein
Hi Ray;
In case of my protein 5%-10% of glycerol help to increase the solubility
both of the soluble domain as well as the trans-membrane domain,improve
crystal quality dramatically and even prevent radiation damage to some
extent.
Best of luck
Bashir
On Thu, March 10, 2011 23:04, Ray Brown
I think adding 5% glyecrol has a big effect on the solubility, so
conditions would have to be re-optimized if glycerol is included.
In the case i am aware of also solubility was increased, but that
could be compensated by higher PEG and/or lower salt concentration
(in the salting-in region).
Dear All,
I apologize if the questions has already been asked on this forum.
We are purifying a membrane that seems prone to proteolysis. Although we use
Protease Inhibitor cocktails during lysis and the first step of purification
we get rid of them after and only keep PMSF and EDTA as general
Sorry about this.
Issue the command
sudo perl -pi -e
's|/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6\:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5\:||g'
/Library/Coot/bin/coot
and that will fix it.
I'll make a new one.
Bill
On Mar 10,
Hello,
What are the good software to do this?
I already know of Pymol and Jmol.
Both can export the result to a .obj file, which is interesting for
later processing.
However, Pymol's algorithm is not exactly what Connolly described,
cf.
Hi Ray,
Beyond what has already been mentioned and anecdotal evidence, at least
one structural genomics consortium
solves a substantial number, if not most, of its proteins from crystals
grown in the presence of 5-10% glycerol.
You can search crystallization conditions as well as protein
Sorry,
I forgot to mention about what is the .obj file I need.
It is a pure ASCII geometric description of a polyhedra.
Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file
It looks rather easy to parse compared to some VRML file, for example.
Thanks,
F.
Francois Berenger wrote:
Hello,
Regarding adding inhibitors. I'm not sure the effect on crystallization but if
you use too much you will get covalent modification of your protein from one of
them (I can check my notes as to which one). We searched many MS databases of
protein modifications to realize why our protein was the
Dear all
We are trying to combine a protein crystallography with computational
chemistry for a metalloprotein.
Does anyone know whether it would be possible to convert a ccp4 electron
density map to an electron density plot in a format of a 'cube' file as in
Dear Ray,
The solubility and stability effect of glycerol is protein dependent and
highly concentration dependent. When used at the wrong concetration or
molar ratio to protein, preferential interaction could result in adverse
effects. Likewise at concentrations higher than 15% in drops for
Hi,
MAPMAN can read and write a number of formats - see:
http://xray.bmc.uu.se/usf/mapman_man.html#H8
While it doesn't write cube format, it can produce maps in various ASCII
formats (e.g., NEWEZD, CNS, X-PLOR) that you should be able to convert into
something that suits your needs.
Hello,
One can use PARST to check the geometry of the molecules.
The idea is to compare geometries with a standard molecule.
-Divya
On 3/11/11, gauri misra kamga...@gmail.com wrote:
Hi,
Swiss-pdb viewer works well for small peptides, you can check if it serves
your objective too...
Even WHAT
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The Laboratory of Shee-Mei Lok
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