Dear All,
I would like to add my 5 cents to partly answer Eugene's questions about
the script, and to follow up on Eleonor's mentioning of Zbsyzek and the
rules for placing macromolecular structures in the crystal lattice.
For the last couple of years, we have been routinely using the ACHESYM
;
> On 10 Nov 2019, at 16:55, R. D. Oeffner wrote:
>
> The program phenix.famos (or phenix.find_alt_orig_sym_mate) does exactly
> that for a pair of pdb files.
>
> Robert
>
> *From:* Eugene Osipov
> *Sent:* Sunday, November 10, 2019 11:49 AM
> *To:* CCP4BB@JISCMAIL.AC.U
019 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A grumble
By the way, may be someone has a script to move several isomorphous structures
to the same origin and rename chains according to reference structure?
пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson
<176a9d5ebad7-d
The program phenix.famos (or phenix.find_alt_orig_sym_mate) does exactly that
for a pair of pdb files.
Robert
From: Eugene Osipov
Sent: Sunday, November 10, 2019 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A grumble
By the way, may be someone has a script to move several
There was a paper/comment in Acta Cryst by Zbigniew Dauter "the
asymmetric unit should be close to the origin".
The uncomfortable source is most probably that the result of a
molecular replacement is sometimes an asymmetric unit "elsewhere" ,
origin shifts etc.
Nice weekend
Winfr
Eleanor, whom are you grumbling at? If it's at the depositors, here's a
counter-grumble:
How would a depositor even know
* know that it's "wrong"
* know what definition of "wrong" to work towards
* know that someone somewhere will care about this particular "wrongness"
* kno
Dear Eleanor,
>From PDB files I see that the structures were solved by molecular
replacement using pdbid 1gci as a starting model. It is hard to say
definitely without the linked paper but may be the depositors made the same
error that I did some time ago: they solved both structures using molecul
I have just downloaded two isomorphous coordinates from the pdb
5arb and 5arc deposited by the same team
Tried to compare and they are on different origins.
I know it doesnt affect the crystallography
It is easily corrected
BUT it seems bad practice to me
Eleanor
