Hi Peter,
I have a P21 case with some strange ratios in the cell dimensions :
a, b=a, c=1.5a, 90, 105, 90. The native patterson shows a strong
peak (40% of origin) at (x,0.5,0) indicating some pseudo symmetry.
Such cell dimension and peak prompted me to think that the actual
space group is
some water molecules have Bfactors at 0
B-factors refining towards zero may be an indication of heavier molecules,
e.g. SO4. You have to model them manually.
Ralf
Hi Gloria,
My hobby is space group symmetry.
My interest phenix development.
so I can't imagine a protein crystallographer
would ever need to apply the modulation function to a protein atom
that happened to be on one.
That's true. Protein residues don't have internal symmetry, therefore
Hi Bernhard,
The bad news is (so much for yesterday): there is no FORTRAN compiler for
Android (sorry
no multi-solution SHELXD applet :-/ )
There is good news: http://cci.lbl.gov/fable/
It'll need a few tweaks to fully support the SHELX programs but I don't
think it is difficult.
Ralf
In the most recent phenix.refine version, the links should be automatic if the
backbone atom names are consistent with the naming for standard RNA residues.
Let me know if you're having problems with phenix 1.6 or 1.6.1.
Ralf
- Original Message
From: William G. Scott
Posted on behalf of Lachlan Cranswick:
The Computing Commission and Teaching Commission has produced a joint
November 2009 newsletter on the theme of Age Concern, which deals with
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Hi Bernhard,
In phenix.refine, the chiral volume is computed from the ideal bond lengths and
angles,
using the unit cell trick pointed out already by George:
uc = uctbx.unit_cell( [bond.value_dist for bond in bonds]
+ [angle.value_angle for angle in angles])
if
Yet another alternative: you can do this with iotbx.pdb. Loop over the
hierarchy in the
standard manner (http://cctbx.sourceforge.net/sbgrid2008/tutorial.html,
v1_loop_over_atoms.py)
and insert chain.id = new_chain_id, rg.resseq = new_resseq into the loops. The
only trick is
to add the
Hi Phil,
If you have a reasonably recent version of the cctbx around (phenix, cci apps,
maybe ccp4), try
this:
import scitbx.math
rotation_matrix = (1,0,0,0,0,1,0,-1,0)
fm = scitbx.math.r3_rotation_axis_and_angle_from_matrix(r=rotation_matrix)
print fm.axis
print fm.angle(deg=True)
The
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This program puts a strong weight on
For those interested in the history of Crystallographic Computing,
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I think CCP4 gives you the option to include the Python sources (v 2.4).
That would be better than to mess with the system python.
BTW: I've fixed the problems you are seeing a long time ago, even before
Python 2.5 was released. In the next CCP4 release it'll probably work
with the system python.
Dear George,
I like your hybrid_ 36 scheme and will implement it and the two character
hain IDs PDB file columns 21 and 22, right justified) when I next update
HELXL. Of course I will need to do some programming because of the SHELX
zero dependency' philosophy, but it seems to me to be
with equivalents of the hy36decode() and hy36encode() functions below.
This file is unrestricted Open Source (cctbx.sf.net).
Please send corrections and enhancements to [EMAIL PROTECTED] .
See also:
http://cci.lbl.gov/hybrid_36/
http://www.pdb.org/ Dictionary File Formats
Ralf W. Grosse-Kunstleve
The Intel Fortran compiler produces code that is indeed significantly faster
than code generated with g77 or gfortran, but recent g++ (and most likely gcc)
versions consistently produce code that is at least as faster or faster than
code generated with Intel's C++ compiler.
Bottom line: it
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