Re: [ccp4bb] Cif file in coot

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: harry powell harry {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-24

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Date: 2007-11-24

Subject: Re: Cif file in coot
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-11-24

Dear Yang Li,

What to do depends on whether what you call ABC is the same thing as is
in the Refmac dictionary. Refmac thinks ABC is for 'MODIFIED ACARBOSE
HEXASACCHARIDE '. If that is what you have - and the atom names
match, then simply Get Monomer -> ABC. That will run libcheck and
refmac to produce a full cif dictionary and read it. Now your all set
to tug around your own ABCs.

If your ABC is not the same as Refmac, then let Refmac have a bash at
your ABC, as Virgile suggest.

The CIF description from ligand-depot is pretty useless - less than
"minimal" - and not particularly helpful to Coot or Refmac as it stands.

Paul.

Virgile Adam wrote:
> Dear Yang Li,
> you probably can download your library file (CIF) from the Hic-up website:
> http://xray.bmc.uu.se/hicup/
> Infact an heterocompound named "abc" is already existing there... that's a
> "modified acarbose hexasaccharide". Is that the one you were looking for? In
> this case, here it is:
> http://ligand-depot.rutgers.edu/pub/ABC/ABC.cif.html
>
> Or you can try to let refmac write one for you thanks to a refinement although
> this one will probably not be an idealised ligand because derived from what's in
> your structure. But you still will be able to modify it later.
>
> Hope this helped,
> Virgile
>
>
> Quoting yang li :
>
>> Hi All,
>> If I have a pdb with some residues named "abc" in it, coot can read
>> it and display it well,
>> but I cannot do real space refine to such residues. The tips asks me to
>> import a CIF file,
>> I wonder what is the format of this CIF file? How can I create it and let
>> coot recognise these
>> residues? Or there are some other ways to solve it?
>>
>> Thanks!
>>
>
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: To bathe or not to bathe.
From: harry powell harry {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-24

Next message:
Subject: Re: To bathe or not to bathe.
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-11-24