James Holton wrote:
> Looks like you have already gotten several good suggestions,
Many good ones indeed, I tried both csymmatch and origins.com
for the moment.
This mailing list and all its people is extremely helpful.
Thank you very much,
Francois.
> but I also
> wrote a jiffy program for doing this that does not require the two PDB
> files to have the same atom names:
>
> http://bl831.als.lbl.gov/~jamesh/pickup/origins.com
>
> Which you run like this:
> origins.com right_origin.pdb wrong_origin.pdb P212121 correlate nochains
>
> The bottom of the script file contains a list of allowed origin shifts,
> which are each applied in turn and the resulting symmetry-expanded atom
> constellations compared. If you use the word "correlate" on the command
> line the atoms will be converted to an electron density map using sfall
> and the correlation coefficient used as the "match" score. By default,
> the program breaks up the PDBs into their "chains" (segids) and searches
> each one separately. You can turn this off by using the word "nochains"
> on the command line.
>
> I think "emma" should give you similar results, but the algorithms are
> certainly different.
>
> -James Holton
> MAD Scientist
>
> Francois Berenger wrote:
>> Hello,
>>
>> 1) In the case I know the true structure (I am verifying I use Phaser
>> correctly), is there a program to do so?
>>
>> Some other questions, if I am to write this program by myself:
>>
>> 2) is there a list somewhere of the translation ambiguities for
>> each spacegroup?
>> For example, in P1 it would say me any translation on any axis
>> is fine.
>>
>> 3) is there a list of permissible origins for each space group?
>> For example, in P212121 it would say me there are 8 possible choices
>> and list them for me.
>>
>> I already know of symop.lib, but I don't think it has some of the
>> information I am looking for.
>> I also know the csymmatch example program of the clipper library, it
>> does part of what I intend to do.
>>
>> Thanks a lot,
>> Francois.
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