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Re: PROTIN/REFMAC



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On Jan 20,  9:41am, Riikka Reitzer wrote:
> Subject: PROTIN/REFMAC
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> I would like to try out REFMAC. First I generated the PROTIN dictionary for
> the ligand with makedict. Have I understand right, I have to add the output
> from makedict to the protin.dic file? If so, how (sorry, I'm sure this all
> is trivial for you)? Also, how should I refere to this ligand in the
> protin.inp file, with CHNNAM and CHNTYP?
>
> I would be thankful for answer in in the style 'PROTIN & REFMAC for dummies'
>


 It is a horrible mess; due to be improved asap!

 But in the meantime:

 Generate your makedict bits.
 You need to chosse a 3 character name for the ligand ( unique) LIG would do..
 and assign it a number in the list. I usually put it just before the END
cards, which at least here means it become entry 62
So PRESERVING the format you add..
                                                 1   61          HOH O
    0.0000    0.0000    0.0000             10         1    0               OW0

.......
                                                 1   62          LIG L
then cordinates..

 and later on the distance list:
PHL          60   40
  1  2 1 3  2  3 1 3  3  4 1 3  3  5 1 3  2  6 1 3  6  7 1 3  7  8 1 3  8  9 1
3
  9 10 1 3 10 11 1 3 11 12 1 3 12  7 1 3  1  3 2 4  1  6 2 4  2  4 2 4  2  5 2
4
  2  7 2 4  3  6 2 4  4  5 2 4  6  8 2 4  6 12 2 4  7  9 2 4  7 11 2 4  8 10 2
4
  8 12 2 4  9 11 2 4 10 12 2 4  1  4 3 0  1  5 3 0  1  7 3 0  2  8 3 0  2 12 3
0
  3  7 3 0  4  6 3 0  5  6 3 0  6  9 3 0  6 11 3 0  7 10 3 0  8 11 3 0  9 12 3
0
HOH          61    0
LIG          62   ??
 etc - cut and pasted from the DICT output
END         100


 then the next entry is for any planes you want to restrain..
PHL 60  7  7   6   7   8   9  10  11  12
                                     60
HOH 61  0  0
LIG 62  7  7   6   7   8   9  10  11  12
                                     60
 ....
 Look in the PROTIN document for formats if needed
 You will have to write this yourself.

Then if you really want to restrain chirality the next entry is for that..
I dont usually use it - it is implicit in the distances and angles, but maybe
it is sensible for sugars - opinions vary!


 Does that help? Send your coordinates if you are still unclear.
Eleanor


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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
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