Re: [ccp4bb]: REFMAC5 and heme

[Laurent Maveyraud <maveyrau@ipbs.fr>]

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"David J. Schuller" wrote:
> 
> hi,
> 
> i am trying to use the latest version of REFMAC5 for a protein which
> contains a heme. i used residue name "HEM", and even corrected the atom
> names of "FE  ", " N_A", " N_B", " N_C" and " N_D" to match the PDB
> standard,  but refmac tells me that it
> does not recognise my ligand.  it says my ligand resembles existing entry
> "MHM" (file mon_lib_10.cif) and that it will create a new dictionary entry
> for me based on that.  i don't know why it doesn't recognise my heme,
> which is surely a commonly used ligand, except perhaps that the dictionary
> entry (defined in file mon_lib_1.cif) contains hydrogens while my
> coordinates do not.

As I can see it, you don't use the right atom names for your HEM residue
: in the 
mon_lib_1.cif entry for heme, I can't see atoms N_A, N_B... that you
have in your PDB file. But these are part of the residue MHM, hence I
guess refmac thinks this is what you really have. If you want to use the
HEM entry, check your atom names.
Don't worry about hydrogen atoms : if they are not present in our
coordinates, refmac will build them, depending on the commands you feed
him with.

Now, all monomers present in the libreary are not fully described :
residue HEM is fully described but MHM is not. In this case, refmac
tries to build a dictionnary file from the connectivity information
provided in the short description of the monomer, from the atom type and
bond type. This is the dictionnary file you have to use in subsequent
runs of refmac. Take care that this dictionnary is most probably not
perfectly correct for your compound : you better have to build
coordinates for your ligand (with some good modelling program, of semi
empirical method), and make the dictionnary from these coordinates.

> 
> i took a look at the documentation and there was a lot about creating new
> dictionary entries by various means (sketcher, etc) but i didn't notice
> anything about using existing dictionary entries, so that i guessed it
> should happen automatically.(?)
> 
> i would like to know
> a) why REFMAC does not recognise my ligand as "HEM"
wrong atom names

> b) should i try to force it to recognise my heme and
yes, because dictionnary for HEM is derived from coordinates observed in
a structure, while dictionnary for MHM will be derived from atom type,
bond type and connnectivity.

good luck


laurent-- 


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Laurent Maveyraud               
Groupe de Cristallographie Biologique  -  IPBS-CNRS

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