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
> 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
Hi Pu,
Looks like I'm a little late with my reply, but if you have a similar problem
again
you could try "EMMA", e.g. via this web interface:
http://cci.lbl.gov/cctbx/emma.html
Pasting in your unit cell, space group and coordinates, I got the output
below. It means the two sets of heavy atoms a
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
To: CCP4BB@JISCMAI
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 (volum
Save this:
from cctbx.development import random_structure
from cctbx import sgtbx
rs = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info(symbol="P212121"),
unit_cell=(20,30,40,90,90,90),
elements="random",
n_scatterers=10)
rs.show_summary()
rs.show_scatterers()
Th
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 bookkeepi
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 implemen
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The registration deadline for the 2008 Crystallographic Computing
School is in two weeks: *** July 25 ***
The schedule of the program including abstracts from all speakers is
available here:
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This program puts a strong weight on fost
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.
R
Hi Buz,
> Does anyone have a python routine that can be used to calculate the
> moment of inertia matrix and principal axes of a selection of atoms?
If you have Phenix, CCI Apps or just cctbx installed, try the script below.
Example:
mmtbx.python script.py 1NSF.pdb 'resname GLU and resid 73
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 str
See also:
http://cci.lbl.gov/hybrid_36/
http://www.pdb.org/ "Dictionary & File Formats"
Ralf W. Grosse-Kunstleve, Feb 2007.
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Hi George,
> It seems to me that column 21 of an ATOM or HETATM instruction
> is always blank, and column 22 is the chain ID. So if we put a
> two-character chain ID right justified in columns 21 and 22, for the
> vast majority of structures there would be no change, and it would
> be relatively e
> On the handling of atomic anisotropic displacement
> parameters
> R. W. Grosse-Kunstleve* and P. D. Adams
> J. Appl. Cryst. (2002). 35, 477-480
>
> to look up the above relationship. In the paper it is mentioned that
>
> |Ucart - (lambda)I|=0
>
> is solved using Cardan's formula.
After the paper
> > > The approach adopted by Coot, which is GPL'd, is to use the CCP4
> > > 5.0.2 libraries, which are LGPL, along with some patches currently
> > > maintained by Ralph Grosse-Kunstleve to address the more serious
> > > deficiencies of the older libraries.
> > >
> >
> > Are the libraries with the
I found this question interesting, therefore I quickly searched the entire PDB
V3 (http://wwpdb-remediation.rutgers.edu/) for LINK records linking two
standard amino acid residues, excluding chain links and same-chain disulfides.
Here are the results:
http://cci.lbl.gov/~rwgk/tmp/protein_protei
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 makes
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