I also tried Ca, Ca2+ but no luck.  I added them to the structure with coot. Also, I forgot to say that the refinement works when I use another computer so it's something to do with mine.

Thanks,

Louise

----- Messaggio Originale -----
Da: Louise Gourlay <[log in to unmask]>
Data: Martedi', Agosto 19, 2008 4:26 pm
Oggetto: [ccp4bb] Refmac problems on Mac OS X Leopard
A: [log in to unmask]

>
> Dear All,
>
> I installed CCP4 on my Mac OS X Leopard system using fink. I
> have some problems with Refmac, it doesn't refine calcium or
> chlorine atoms, or any non-protein atom in general.  In the log
> file it doesn't recognize them and says:
> FORMATTED      OLD     file opened on unit  45
> Logical name: ATOMSF, Filename: /sw/share/xtal/ccp4-
> 6.0.2/lib/data/atomsf.lib No match for atom ID CL subtracting
> one character
>  No match for atom ID CA subtracting one character
>
> Thanks,
> Louise
>
>
>
>
> ----- Messaggio Originale -----
> Da: Garib Murshudov <[log in to unmask]>
> Data: Mercoledi', Luglio 30, 2008 2:28 pm
> Oggetto: Re: [ccp4bb] Preventing close contact between protein
> and ligand
> A: [log in to unmask]
>
> > Dear Snageetha
> >
> > 1) Could you check please if specified atoms have zero
> > occupancy. 
> > Atoms with zero occupancy are considered as absent and there
> are
> > not 
> > restraints on them
> > 2) symm y at the end of instructions means that the program
> > check all 
> > possible symmetry operators and finds minimal distance. Most
> > probably 
> > 5.024 is the distance between symmetry related atoms
> > 3) to remove antibumping between different chains there is
> > an 
> > undocumented keyword. It can be used. the keyword is (as an example)
> >
> > vdwrestraints exclude between chains A B
> >
> >
> > Please let me know if this instruction does not work.
> > NB: This option should not be used unless you know what you
> are
> > doing 
> > (that is the reason why it has not been documented). If there
> > are 
> > clashes between chains then there are reasons for that. For example
> > if ligand has half occupancy then it is very likely that
> > surrounding 
> > atoms also have multiple conformation and you should model them.
> >
> >
> > regards
> > Garib
> >
> >
> > On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote:
> >
> > > Dear bb users,
> > >
> > > I am refining a protein-ligand complex (at 1.68 A
> resolution)
> > in 
> > > which the ligand lies on a 2-fold crystallographic symmetry
> > axis. 
> > > The ligand occupancy is, therefore, 0.5 in each asymmetric unit.
> > >
> > > I am almost at the end of the refinement but one problem has
> > me 
> > > stumped. Refmac keeps moving a carbon in the ligand too
> close
> > to a 
> > > serine OG and an oxygen too close to an arginine CD. Given
> > that the 
> > > ligand is at the interface, the density is not perfect.
> > However, I 
> > > rebuild the ligand to eliminate close contacts and still be
> > within 
> > > density and refmac pulls it right back close to the protein.
> > The 
> > > refined position does not even look better than the rebuilt
> > one! It 
> > > almost always looks worse! Would refmac put less weight on
> > close 
> > > contacts with the ligand because it is only partially occupied?
> > >
> > > I tried to use external restraints between the ligand and
> > the 
> > > residues so that they are kept further away.
> > >
> > > Upon searching the net, I found this command line:
> > >
> > > external distance first chain [ch] residue [res] insertion
> > [ins] -
> > > atom [n] [altcode [a]] second chain [ch] residue [res]
> > insertion 
> > > [ins]-
> > > atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n]
> > >
> > > I thought (hoped) that the distance herein is the minimum
> > distance 
> > > of approach between the specified atoms, I added these lines
> > from 
> > > within "Developer options" in refmac interface:
> > >
> > > exte dist first chain A resi 59 atom CD seco chain X resi
> 2001
> > atom 
> > > O1 valu 3.2 sigm 0.02 symm Y
> > > exte dist first chain A resi 27 atom OG seco chain X resi
> 2001
> > atom 
> > > C10 valu 3.2 sigm 0.02 symm Y
> > >
> > > It didn't recognize these restraints at all.
> > >
> > > However, when I change these lines to:
> > >
> > > exte dist first chain A resi 59 atom CA seco chain X resi
> 2001
> > atom 
> > > O1 valu 3.2 sigm 0.02 symm Y
> > > exte dist first chain A resi 27 atom OG seco chain X resi
> 2001
> > atom 
> > > C10 valu 3.2 sigm 0.02 symm Y
> > >
> > > Refmac recognizes the first line but not the second - lines
> > from 
> > > log file:
> > >
> > > Bond distance deviations from the ideal >10.000Sigma will be
> > monitored>
> > > A     59 ARG CA  . - X  
> > 2001 DIE O1  . mod.= 5.024 id.= 3.200 dev= 
> > > -1.824 sig.= 0.020
> > >
> > > This raises two concerns:
> > >
> > > Concern 1: From the first line of output: the restraints
> here
> > don't 
> > > seem to be minimizing close contact at all; it seems to
> think
> > they 
> > > are bonded somehow (the distance between these atoms is not
> > 5.024; 
> > > it is 6.26 A; I don't know what 5.024 A is!).
> > >
> > > I am missing something here. It'd be great if someone can
> tell
> > me 
> > > what that is!
> > >
> > > Concern 2: This command only works when the first atom
> > specified is 
> > > a C-alpha atom (or maybe a main chain atom; I didn't try
> > using 
> > > other main chain atoms). Why is that?
> > >
> > > AND ULTIMATELY,
> > >
> > > is there some way I can tell refmac not to make the ligand
> > and 
> > > protein clash?
> > >
> > > I'd really appreciate any help!
> > >
> > > Thanks,
> > >
> > > Sangeetha.
> >
> >
>
> Louise Gourlay Ph.D Dep. of Biomolecular Sciences and
> Biotechnology, Università degli Studi di Milano Via Celoria 26
> Milano 20133 http://users.unimi.it/biolstru/Home.html Italy
>
>
>

Louise Gourlay Ph.D Dep. of Biomolecular Sciences and Biotechnology, Università degli Studi di Milano Via Celoria 26 Milano 20133 http://users.unimi.it/biolstru/Home.html Italy