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ATOM 6189 O HOH W 63 14.409 51.932 0.124 1.00 46.53 O ATOM 6190 O HOH W 64 26.387 33.040 -0.685 1.00 40.92 O ATOM 6191 CA CA B 1 37.417 44.961 41.022 1.00 12.13 CA ATOM 6192 CA CA B 2 23.027 43.324 21.110 1.00 5.01 CA ATOM 6193 CA CA B 3 52.444 49.349 2.208 1.00 14.66 CA ATOM 6194 CA CA B 4 34.610 74.683 4.564 1.00 10.52 CA ATOM 6195 CL CL C 1 32.966 46.780 3.090 1.00 2.00 CL END 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, Universitą 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, Universitą degli Studi di Milano Via Celoria 26 Milano 20133 http://users.unimi.it/biolstru/Home.html Italy