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Re: [ccp4bb] Refmac problems on Mac OS X Leopard |
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- Protein crystallographyMain steps:- Protein purification- Crystallisation Special:- Programs for crystallography- X-ray detectors Basic tutorials:- Chemistry- Protein - Peptide - Amino Acids Xtal community:- CCP4BB |
CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Refmac problems on Mac OS X Leopard From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2008-08-20 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 > 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 >> 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 > > > > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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