Dear James: This is really the easiest and a very smart way to get around this problem. I generated a PDB only only my interest region, which serves to produce a mask encomprassing only this region. The last "Total" line in the output should be it. Everything is cool except that some terminal residues in my region is a little bit different from the complete PDB results, which I think should be due to changing of flag labels on the map grids around the terminal residues. Anyway, I think this issue has been solved based on your suggestion. Thanks a lot!
Best Regards, Hailiang > The easiest thing to do is to make a PDB file that contains ONLY the > residues you are interested in and set all the residue numbers to "1". > Use this PDB file to calculate the "MODE ATMMAP" and the "MODE ATMMAP > RESMOD" maps with SFALL. Then OVERLAPMAP (in "correlate residue" mode) > will give you a CC and RSR for "resiude 1", which is your > region-of-interest. > > -James Holton > MAD Scientist > > zhan...@umbc.edu wrote: >> Hi James: >> >> Actually I did OVERLAPMAP calculation in this way. I first flagged the >> map >> grid points by using the provided pdb information, which serves as >> "mapin3" for the OVERLAPMAP calculation. However, the calculated CCs or >> RSRs are either based on each individual atom, residue or map section, >> but >> it didn't calculate a single CC or RSR by integrating over the whole >> region encomprassed by a group of residues as I wanted. >> >> Maybe there is something I didn't discovered in OVERLAPMAP to do this? I >> appreicate if you could point out which key word I need to use. This >> will >> save me lots of time in coding on the map:-( >> >> Thanks a lot! >> >> Best Regards, Hailiang >> >> >>> OVERLAPMAP will do this, but you need to calculate a "label map" with >>> SFALL first and provide that to OVERLAPMAP as "mapin3", as MW and >>> others >>> have pointed out already. >>> >>> RTFM: >>> http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3 >>> http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resmod >>> >>> -James Holton >>> MAD Scientist >>> >>> Hailiang Zhang wrote: >>> >>>> Dear Eleanor: >>>> >>>> Yes, this is something I want to do (RSR and CC). But I just want to >>>> do >>>> the calculation based on a group of residues or atoms, and it seems >>>> OVERLAPMAP doesn't do it, so I think I have to find other ways. >>>> >>>> Hailiang >>>> >>>> >>>> >>>>> mapdump does this if you select the right flags. But as Ian says you >>>>> will get a LOT of numbers. You dont say why you want this >>>>> information, >>>>> but if it is to find the electron density at an atom site overlapmap >>>>> will do that if you ask for "real space rfactor" >>>>> >>>>> eleanor >>>>> >>>>> Hailiang Zhang wrote: >>>>> >>>>> >>>>>> Hi, >>>>>> >>>>>> I wanted to convert a binary ccp4 map file to a readable format so >>>>>> that >>>>>> I >>>>>> can retrieve the electron density at each real space grid point. >>>>>> Just >>>>>> tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not >>>>>> readable, and I didn't find any documentataion about how to read >>>>>> them. >>>>>> Could somebody give me any hint? Thanks a lot! >>>>>> >>>>>> Best Regards, Hailiang >>>>>> >>>>>> >>> >>> >> >> >> > >
