Along those lines, one of the things you can do with PyMOL is color map
density based on the color of the nearest atom (if any):
Example image at: http://delsci.com/img/map_color.jpg
Example script:
load ref.pdb
load map.xplor
isomesh mesh, ref, 1.0
ramp_new ramp, ref, [0,1.5,2], [-1, -1, grey70
On behalf of Prof Wei-Jen Tang
Postdoctoral training fellow
Macromolecular crystallography of ion channel and amyloid beta-degrading
enzymes.
Ben-May Institute for Cancer Research,
The University of Chicago
Chicago, USA
One post-doctoral fellow position is immediately available at the Universit
Division of Structural Biology, University of Oxford, UK.
Two MRC DPhil Studentships in Structural Biology starting October 2008.
Applications are invited for two 3-year PhD Studentships to join the groups of
Radu Aricescu and Christian Siebold, in the Division of Structural Biology at
the Well
The crystallographic model-building and display program MIFit can read mmCIF
diffraction data directly and compute the map internally i.e. you don't need
any other software. There is a tutorial (lesson 16) on this exact
application.
MIFit runs on Windows and Linux and is free to academics users. T
Dear friends and scientists,
I want to ask about for an integration of modeller in the ccp4i
interface. The interface in ccp4i is designed for modeller Version 6.2,
we have by now modeller 9.2 , which is a lot different.
Nevertheless I tried to enter the necessary data in ccp4i. I could not
try
Thank you all.
I think I have know how to deal with this situation.
Best Regards.
On 11/1/07, [EMAIL PROTECTED] <
[EMAIL PROTECTED]> wrote:
>
> Dear Jiamu,
> This is a matter of debate, but I prefer to publish something as close as
> possible to the "true" situation. Publishing a structure with
Dear Herman:
It is due to the occupancy obviously.
Previously, someone mensioned that in this resolution it is not suitable to
refine the occupancy.
So I think it is better for me to keep the occupancy to 1.
Do you have some case for this situation in the PDB bank?
Thanks.
On 11/1/07, [EMAIL PRO
Dear All:
I am refining a protein structure with a soaked substrate.
The resolution is 2.5 A. The B factor of protein is around 40, while the B
factor of the soaked substrate is as high as 80.
The density looks fine.
Is this structure acceptable? Or is there anyone who can give me an example
of thi
Having put the "make my density look publishable" (mapcover) command in
BobScript, my conscience wouldn't ever let me use it as it gives a false
impression of experimental maps!
It is useful, though, in a couple of cases: where the map is not representing
electron density but calculated from th
Use the CCP4i Reflection utilities
Convert to MTZ and say you are importing mmCIF
It will sort it out for you
Eleanor
Zheng Zhou wrote:
Hi,
Could anyone give a quick hint for the Fortran format for the following
structure factor mmCIF file? or Is there any easy program or better way to
conver
The first 3 cif columns are not the problem. cif2mtz will happily skip
these along with any other items it doesn't explicitly deal with.
The problem is simply the extra columns F(+) etc, yes?
This bug has been seen on Windows. The same job should work fine on
Linux or Macs. Or you should be able
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