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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