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Small Angle X-ray Scattering Initiative for Europe :: Forum
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PostPosted: 2017.03.10 16:47 
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Joined: 2017.03.10 15:57
Posts: 2
Hey,

I have recently started to use Coral and I just can't set restrains right.

There are 3 pdb files - core_a.pdb and flexible_a.pdb make together one protein and core_b.pdb is another one. I am trying to set K140 from one protein (A) and K113 from another one (B) to be about 12 A apart. However it seems Coral is taking all my pdb files as one chain (see bellow). How can I set it correctly?

Code:
 Contacts conditions file name .......................... : dist.cnd
Condition #  1: Distance  12.000
   Between chain #  1, Residues from GLY   140 to GLY   140
       and chain #  1, Residues from GLY   378 to GLY   378
 Contacts conditions penalty ............................ : 33.54
 Contacts penalty weight ................................ : 10.00


dist.cnd:
Code:
dist 12.0
1 140 140 2 113 113


configuration:
Code:
NTER 8
core_a.pdb
LINK 14
flexible_a.pdb
CTER 20
core_b.pdb
CTER 10


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PostPosted: 2017.03.14 11:31 
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Joined: 2007.08.03 19:16
Posts: 330
Hi,

Internally Coral puts all the input proteins into one "superchain",
therefore the reported numbering is different from the dist.cnd.
Have you checked that the conbdition is fulfilled in the resulting model?


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PostPosted: 2017.03.17 11:53 
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Joined: 2017.03.10 15:57
Posts: 2
I have made 2 models with restrains and sadly no - the gap is about 40 A. However without restrains the models are much better.


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