The biannual Gordon Conference on Diffraction Methods in Structural
Biology will be held at Bates College in Lewiston, Maine from 18-23rd
July. The program covers all aspects of macromolecular structure
solution
from crystallization to structure solution and refinement and includes
sessions on
Dear all,
I am wondering if there are publications, where it is shown
that a ligand/substrate was not able to bind in one crystal
form of a protein, but was found in another crystal form.
In other words:
is there a case where the crystal packing interactions are
proofed to be responsible for
Dear All,
this is a reminder on the EMBO Practical Course on Solution Scattering
from Biological Macromolecules, which will take place in Hamburg on
Oct, 25th - Nov 1st, 2010.
The deadline for applications is 31st July 2010. The information
and on-line registration for the course are available
Dear All,
there are two positions available in SAXS methods development at the
biological SAXS group (EMBL, Hamburg Outstation).
1. A PhD position in the frame of a Marie Curie Initial Training Network
IDPbyNMR. The topic of the thesis work will be the joint use of SAXS and
NMR as well as
Hi all,
I need to create a cif file for a new ligand that does not exist in the pdb,
so far. Normally refmac created such a cif file when I merged the ligand to
the structure, but this time it stops with a fatal error. I think the
alternatives are sketcher and the prodrg server. Can anybody tell
Hi Paul,
Usually I just Sketch the molecule, I make sure that the bond types are
OK (single, double, aromatic etc.) and I do an idealization in Sketcher,
then use the resulting .cif file in RefMac.
Flip
Paul Lindblom wrote:
Hi all,
I need to create a cif file for a new ligand that does
There is an option in Phenix to generate the necessary cif file for
Phenix refinement. But that's a Phenix file, not a REFMAC file (I think,
I never tried taking the cif file generated by Phenix to use it in
REFMAC). As an example, I am enclosing a cif file that was generated by
Phenix for
Hi Paul,
you can use PRODRG server at Dundee university (
http://davapc1.bioch.dundee.ac.uk/prodrg/ )
It generates libraries in different formats... you just need to
copy/paste in your preferred text editor.
HTH
Marco
Paul Lindblom wrote:
Hi all,
I need to create a cif file for a new
Received from Peter Zwart:
Original Message
Subject:Re: [ccp4bb] creating new ligand cif file
Date: Mon, 21 Jun 2010 07:08:18 -0700
From: Peter Zwart phzw...@lbl.gov
To: Vellieux Frederic frederic.velli...@ibs.fr
References: 4c1f4f26.2070...@ibs.fr
it is
Hi Paul,
the command
phenix.ready_set model_with_unknown_ligand.pdb
will create a CIF file for all novel ligands in your input PDB files.
You can do it from the command line or using the main GUI.
phenix.elbow will do this too.
Pavel.
On 6/21/10 3:40 AM, Paul Lindblom wrote:
Hi all,
I
Wasnt there recently a similar discussion(?):
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg16099.html
Maybe try JLigand (www.ysbl.york.ac.uk/mxstat/)
B
Hi all,
I need to create a cif file for a new ligand that does not exist in
the pdb, so far. Normally refmac created such a cif
Prodrg does very good job in guessing atom types and bond orders. Once
it guessed things right it does extremely good job in generating bond
lengths, angles etc.
But it still depends on accuracy of coordinates. You need to check
carefully bonding orders before using them in refinement.
You
Dear all,
Is there any possible of twining for a normal P212121 spacegroup and
what is the twin law, say no equal cell dimensions?
Some people said there is no twin law for such symmetry but I am not very
sure. Thanks a lot.
Best
Yang
Hi,
I suggest you check the following publication: Morales, R. et al. (2000),
Crystallographic studies of the interaction between the ferredoxin-NADP+
reductase and ferredoxin from the cyanobacterium Anabaena: looking for the
elusive ferredoxin molecule, Acta Cryst. D56, 1408-1412.
Here is
Hi there:
Is there any easy to convert a colume in mtz file (say fom) into a fixed
value? I tried to convert to ascii first, but mtz2various only takes 1
single FP colume (unfortunately I have 2). Thanks!
Hailiang
There are probably multiple ways to do this. sftools makes this very
easy. From the command line type
sftools
read input.mtz
calc col 6 = 0.9
write output.mtz
stop
Just change the file names, column number and the fixed value to
whatever you need.
Bart
On 10-06-21 03:23 PM, Hailiang Zhang
Yang,
There are not any merohedral twin laws, but there are several
pseudomerohedral twinning possibilities. The most common would be a
monoclinic cell with a beta ~90, so it appears orthorhombic. Going the
other way, you could have an orthorhombic cell look tetragonal if A and
B are
Is there any easy to convert a colume in mtz file (say fom) into a fixed
value? I tried to convert to ascii first, but mtz2various only takes 1
single FP colume (unfortunately I have 2). Thanks!
Can't think why you might want to do this, but sftools will do it.
shellscript:
#!/bin/bash
sftools
A postdoctoral position to study membrane protein structure
One postdoctoral position is available immediately at the Center for Membrane
Biology, Department of Biochemistry and Molecular Biology, University of Texas
Health Science Center at Houston. (http://www.uth.tmc.edu/cmb/)
The
Got it! Very handy!
Hailiang
There are probably multiple ways to do this. sftools makes this very
easy. From the command line type
sftools
read input.mtz
calc col 6 = 0.9
write output.mtz
stop
Just change the file names, column number and the fixed value to
whatever you need.
Bart
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