I am inclined to agree with Gerard. Of course if there is a specific
question to CCP4bb about SHELX, I try to answer it. Since I am too
lazy to maintain my own bb, this is very convenient. However I have
stopped 'poaching', for example for the thread in question I resisted
the temptation to point out that SHELXE has a convenient way of
making
such anomalous maps, because that would not have been a direct answer
to the question and CCP4 provides similar facilities (and SHARP would
be even better). We use the CCP4 programs (especially REFMAC and
COOT)
extensively and are very grateful for all the support we get. In
particular, we should not underestimate the unique role CCP4bb plays
in crystallographic education.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Fri, 19 Feb 2010, Gerard Bricogne wrote:
Dear all,
This is a remark I have wanted to make for a long time but
managed so
far to repress. However, this case is absolutely clear: Ivan was
not asking
for general advice on how to carry out a general task, but how to
perform a
specific task with the CCP4 software.
In response we get (surprise, surprise, ...) another instance
of the
relentless touting for Phenix on the CCP4BB, which has long been an
expected (or tolerated?) feature of this BB. Contributions from
Phenix
developers are of course much appreciated when questions are about
general
crystallographic matters where their expertise and experience is
valuable;
but when people ask specifically how to do something with CCP4
programs,
could they please not be grabbed by the sleeve and enticed to buy
their
sweets from the shop next door?
In this case, for instance, Ivan thanks "guys" (plural) for the
answers
he got ("All of your suggestions were great"). Perhaps one of
those was a
CCP4-based answer, but if so it has not even been communicated to
the rest
of the CCP4BB subscribers - so not only is this touting in bad
taste after a
while: it even interferes with the sharing of expertise in using
the CCP4
software, which after all must be one of the main missions of this
BB.
I have long wondered whether anyone on the CCP4 side been
assigned the
task of answering every question to the Phenix BB by describing
how to do it
with CCP4 programs ... .
With best wishes,
Gerard.
--
On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote:
Hi Ivan,
two ways (at least) to do it in PHENIX:
- phenix.refine always computes anomalous difference Fourier map
(provided
that your input data file contains Fobs(+) and Fobs(-)). The
command below
will do it:
phenix.refine model.pdb data.mtz strategy=none
main.number_of_macro_cycles=0 output.prefix=maps_only
- you can use phenix.maps that is a general tool to compute a
broad variety
of maps. Type "phenix.maps" from the command line for usage
instructions.
You need to have the latest development (or one of) PHENIX
nightly build
for this.
All this is available from the GUI too.
Pavel.
On 2/18/10 3:34 PM, xaravich ivan wrote:
Hello,
I wanted to make an anomalous difference fourier map of a
structure with
zinc bound to it. However I have not been successful in making
the map and
I would really appreciate your help if anyone could suggest me
where I am
going wrong.
I solved this zinc bound structure, by molecular replacement
from a
calcium bound structure (1.4 angstrom) that I solved. I want to
show that
the zinc binds to the identical site by the anomalous difference
fourier
map.
I am using CCP4i and the steps that I have been taking are,
(names of the
files are arbitrary)
1) generating structure factors and phases from the solved
coordinates by
SFALL
Input files
zinc bound pdb
original zinc .mtz data from synchrotron
output file
XXXXsfall.mtz
2)merging the XXXXsfall.mtz containing the PHICalc and FCalc
columns with
the original synchrotron .mtz file containing DANO and SIGDANO
by running
CAD.
input files
XXXXsfall.mtz and zinc synchrtron .mtz
output file
CAD.mtz
3) Running FFT to make anomalous map, selecting labels from
CAD.mtz as
input files.
There is an output map file but nothing in it. all the values
are 0 and
the map is not recognized by coot. There is no error message in
the log
file.
I must be missing something or doing something wrong/stupid.
Thanks,
Ivan
--
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