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Hi Garib, This is a side-question. What you just said writing to Abhinav explains why I have problem of some repulsion between identical ligands with different tail conformations when I try to refine them at 25% and 25% occupancy. In my case the overall occupancy of the ligand is not expected to be 100% (the ligand is naturally partially lost) so in order to have the well behaving refinement I will have to change these occupancies to 50-50, right? And just pay the price with the higher B factors? Or is there any other way to deal with this situation? Aleks On 30 Jul 2008, at 16:15, Garib Murshudov wrote: > If sum of occupancies of atoms is less than or equal to one and atoms > are not in the same residue with the same alt code then they do not > see each other. Otherwise they see each other and there is vdw > repulsion between them. this has not changed substantially since the > first version. > > Waters are not good way of modelling unknown ligands. > If you want to model unknown model then you can use DUM atoms with DUM > residue name (just like the arp/warp uses it). Then atoms can come > much closer to each other (up to 1.2A or so. this value can be > controlled) > > Garib > > On 30 Jul 2008, at 16:05, Kumar, Abhinav wrote: > >> I have had a similar experience. >> >> I was trying to model a bunch of waters to simulate an unknown ligand >> (UNL) in an unmodeled density. The waters were all in different >> alternate conformations of the same residue number. When the >> occupancies of these waters were set to 0.5, the vdw repulsion became >> absent; waters stayed within density at close distances. But, as soon >> as the occupancies were changed to anything but 0.5, waters got >> pushed out of density due to vdw repulsion. >> >> So my feeling is that at 0.5 occupancy the atom does not see vdw >> repulsion (?). Change it to something else and atom should crawl back >> into its density. >> >> I was using refmac5 version 5.2.0019. >> >> >> Thanks >> Abhinav >> >> Stanford Synchrotron Radiation Laboratory >> Joint Center for Structural Genomics >> Mail Stop 99 >> Phone: (650) 926-2992 >> Fax: (650) 926-3292 >> >> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf >> Of Garib Murshudov >> Sent: Wednesday, July 30, 2008 5:18 AM >> To: [log in to unmask] >> Subject: Re: [ccp4bb] Preventing close contact between protein and >> ligand >> >> 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. >> ------------------------------------------------------------------------ -------------------------------------------------- Aleksander W. Roszak, PhD E-mail: [log in to unmask] Protein Crystallography Web: www.chem.gla.ac.uk/~aleks University of Glasgow Fax: +44-(0)141-330 3779 Level 3 Room B 317 Tel (office): +44-(0)141-330 4476 Glasgow Biomedical Research Centre Tel (X-ray lab): +44-(0)141-330 3589 120 University Place Mobile: +44-(0)780 9559996 Glasgow G12 8TA Scotland, UK