Dear Garib, Thank you very much. I will try the keyword.
> Your case: Do you see some sort of modulation of intensities in your images? > Something like weak strong intensities along c axis? Or do you see elongated > peaks in the images. Sorry I'm not sure what "modulation of intensities in image" is. Do you mean something like described in this paper? http://scripts.iucr.org/cgi-bin/paper?S0021889808010716 direct link to figure: http://journals.iucr.org/j/issues/2008/03/00/he5398/he5398fig4.html My diffraction images don't have such reflections. But in some frames, severely elongated peaks along c* were observed. Moreover, I found split peaks at high resolution (about 2.5A) area in frames without elongated peaks. I think my diffraction image is similar to what was discussed recently in ccp4bb: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1011&L=CCP4BB&F=&S=&P=312247 you can see the attached files of that archive. Yours truly, K. Yamashita 2010/12/9 Garib N Murshudov <[email protected]>: > Dear Yamashita > > Refmac indeed does not apply vdw repulsions (antibumping restraints) if the > sum of occupancies is less than 1 and atoms do not belong to the same residue > with the same alt code. It means that if you have two or more molecules each > with occupancy less than 0.5 then there will be no intramolecular antibumping > restraints also. It is not what you would like. In these case you may want to > apply antibumping restraints within molecule. For this reason using keyword > > (if you have three copies and chain names are A B and C) > > vdwrepulsions exclude between chains A B C > > would be better. Then the program would apply antibumping restraints within > molecule but not between them. > > Your case: Do you see some sort of modulation of intensities in your images? > Something like weak strong intensities along c axis? Or do you see elongated > peaks in the images. > > regards > Garib > > > > > On 9 Dec 2010, at 01:11, Keitaro Yamashita wrote: > >> Dear Garib, >> >> Sorry I'm a little confused. >> >> As Eleanor said, Is it true that Refmac doesn't apply vdw restraints >> if the sum of the atoms occupancies is <= 1? >> >>> If you want to deal with translational disorder (e.g. you have a modulated >>> crystal then there is another way. >> In my data, there are crystallographic 4-fold axis on c-axis (P4 21 2) >> and pseudo-translation vector (0.1, 0.1, 0.5), which is indicated by >> native patterson peak with 22% height of the origin. >> >> I can see very clear density at certain position around the 4-fold axis. >> And around the shifted position (+0.1, +0.1, +0.5), there's definitely >> the same density but they are superposed with their symmetry mates -- >> I think they are statically (packing) disordered. >> >> Is my case "translational disorder" as you said? >> If so, how can I solve it? >> >> >> Yours truly, >> >> K. Yamashita >> >> 2010/12/9 Garib N Murshudov <[email protected]>: >>> In refmac you can remove vdw interactions between chains using the >>> following command >>> >>> It is an example: >>> >>> vdwr exclude between chains A B >>> >>> or between resdues: >>> >>> vdwr exclude between residues first residue 123 chain A second residue 155 >>> chain B >>> >>> >>> Regards >>> Garib >>> >>> >>> On 8 Dec 2010, at 16:09, Keitaro Yamashita wrote: >>> >>>> Dear all, >>>> >>>> I'm refining complex structure against X-ray diffraction data with >>>> packing disorder. >>>> (Some domains overlap with their symmetry mates (4-fold), so their >>>> occupancies are set to 0.25) >>>> >>>> I'd like to know whether refinement programs can exclude any >>>> interaction among symmetry mates from geometric term in target >>>> function. >>>> Can it be done only for specific chains? >>>> >>>> I was thankfully taught phenix.refine could do that with the option >>>> pdb_interpretation.custom_nonbonded_symmetry_exclusion in phenixbb. >>>> >>>> I'd very much like to know whether Refmac5, CNS or other programs can do >>>> that. >>>> >>>> (When I tried to refine using Refmac5, the output told many vdw >>>> repulsions with symmetry mates.) >>>> >>>> >>>> Thank you very much in advance, >>>> >>>> K. Yamashita >>> >>> > >
