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
>
> [log in to unmask] 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
>>>>>>
>>>>>>
>>>
>>>
>>
>>
>>
>
>