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Re: [ccp4bb]: REFMAC5 and haem (fwd)

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thanks for the responses to my question about refining a haem in REFMAC5.
i am up and running now.

to review:
1) atom names.  the library haem uses " NA ", the library MHM uses
" N_A" and the PDB standard for haem is " N A"
i changed to " NA " and it still didn't run.

i may experiment to see if i can make the program accept "FE+3" in place
of "FE  ". i like to use 4 letter atom names for metals to force certain
old creaky programs to respect column assignments.

this seemed to do the trick!

3) why was it trying to match to MHM?
not completely sure, other than the names of the nitrogens it appears to
have the same atom layout as haem, although i think it may differ in bond
its library header says:
MHM '[7,12-DIETHYL-3,8,13,17-TETRAMETHYL-21H,23H-PORPHINE-2,18-D' non-polymer M
i didn't want to go that route because real haem (Fe protoporphyrin
IX)  has vinyl instead of ethyl groups. not sure what other differences
might have popped up.
perhaps the lack of hydrogens prevented a match to the haem entry.

4) libcheck
looks useful, i will make a note of it.

thanks much,

"Politicians can survive sex scandals or fiscal mismanagement,
but they cannot survive being laughed at."  - Robert Park
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine

---------- Forwarded message ----------
Date: Fri, 27 Oct 2000 10:31:38 +0100
From: Garib Murshudov <garib@ysbl.york.ac.uk>
To: David J. Schuller <schuller@uci.edu>
Subject: Re: [ccp4bb]: REFMAC5 and heme

"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.
> 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"
> b) should i try to force it to recognise my heme and
> c) how would i go about that?
> attached are my REFMAC output, my HEM coordinates, and my script.

Hi David,

Use  (also change N_A ,, to NA ,,)
then program will not check description of monomers and believe in your
With default check option program tries to check coordinates against
dictionary description.
If the program thinks that coordinates are not good then it tries to make new

> ------------------------------------------------------------------
> Garib N. Murshudov, Chemistry Department, University of York, U.K.
> Tel: Home +44 (1904) 42 62 87, work:  +44 (1904) 43 25 65
> ------------------------------------------------------------------