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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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- References:
- PROTIN/REFMAC
- From: Riikka Reitzer <havukai@balu.kfunigraz.ac.at>