Thanks to both, in the end I downloaded the new version of refmac and moved the characters, Louise
----- Messaggio Originale ----- Da: Eleanor Dodson <[EMAIL PROTECTED]> Data: Martedi', Agosto 19, 2008 6:00 pm Oggetto: Re: [ccp4bb] Refmac problems on Mac OS X Leopard A: Louise Gourlay <[EMAIL PROTECTED]> Cc: CCP4BB@jiscmail.ac.uk > You need to move the CA and CL names one character to the left > > 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 > > more like this.. > > Eleanor > > Louise Gourlay wrote: > > 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 <[EMAIL PROTECTED]> > > Data: Martedi', Agosto 19, 2008 4:26 pm > > Oggetto: [ccp4bb] Refmac problems on Mac OS X Leopard > > A: CCP4BB@JISCMAIL.AC.UK > > > > > >> 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 > >> > >> > >> > >> > > > > 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
