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 <[EMAIL PROTECTED]> Data: Mercoledi', Luglio 30, 2008 2:28 pm Oggetto: Re: [ccp4bb] Preventing close contact between protein and ligand A: CCP4BB@JISCMAIL.AC.UK > 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
