Hi Philipp,
The two FFTs introduce a scale factor equivalent to the number of grid points. Please try adding this code:
x = abs(new_array).data()
y = abs(very_new_array).data()
lc = flex.linear_correlation(x, y)
lc.show_summary()
lr = flex.linear_regression(x, y)
lr.show_summary()
The correlation coefficient should be 1.0 exactly, and the linear-regression slope is the same as the "total number of grid points" shown in the output:
total number of grid points: 345600
...
is_well_defined: True
mean_x: 43.9292797741
mean_y: 15181959.0899
coefficient: 1.0
is_well_defined: True
y_intercept: 5.1687812285e-07
slope: 345600.0
Ralf
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Hi Celine,
There isn't something like a pdb.output object, but there are a few helper functions for writing certain records. E.g. see section 5.6 of this newsletter:
http://cci.lbl.gov/publications/download/iucrcompcomm_nov2006.pdf
Look for "def format_" in iotbx/iotbx/pdb/__init__.py.
Ralf
----- Original Message ----
From: celine Besnard <celine.besnard(a)epfl.ch>
To: cctbxbb(a)phenix-online.org
Sent: Monday, July 9, 2007 9:02:05 AM
Subject: [cctbxbb] pdb output
Hello
I have a structure object which I want to write a pdb file from. Is
there any function that does the contrary of the pdb.input function in
the iotbx? I have not been able to find one.
Thanks
Celine
--
Dr. Céline Besnard
EPFL - SB - IPMC - LCR2
CH-1015 Lausanne
Suisse
e-mail : Celine.Besnard(a)epfl.ch
Tel : +41(0)21.693.05.41
Fax : +41(0)21.693.05.04
http://lcr.epfl.ch
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Hello
I have a structure object which I want to write a pdb file from. Is
there any function that does the contrary of the pdb.input function in
the iotbx? I have not been able to find one.
Thanks
Celine
--
Dr. Céline Besnard
EPFL - SB - IPMC - LCR2
CH-1015 Lausanne
Suisse
e-mail : Celine.Besnard(a)epfl.ch
Tel : +41(0)21.693.05.41
Fax : +41(0)21.693.05.04
http://lcr.epfl.ch
Hi,
thanks for the help with my asymmetric unit problem again. However I do
have further questions further down my pipeline regarding the backwards
fft from the map to structure factors:
Am I right if I assume that
fft_map = new_array.fft_map(resolution_factor=1/3., symmetry_flags=maptbx.use_space_group_symmetry)
real_map = fft_map.real_map()
very_new_array=new_array.structure_factors_from_map(map=real_map)
#Output1
new_array.show_array()
#Output2
very_new_array.show_array()
Output1 and Output2 should be identical? They are not... Do I have to
consider something, so that they are identical?
Thanks and kind regards
Philipp
--
--------------------------------------------------
Dr Philipp Heuser
Postdoctoral fellow
EMBL-Hamburg
c/o Building 25A, DESY
Notkestrasse 85
22603 Hamburg
phone: +49 40 89902 188
fax: +49 40 89902 149
mail: philipp.heuser(a)embl-hamburg.de
web: www.philipp-heuser.de
--------------------------------------------------
