Hi,

Still impatient to be able to calculate structures with a ligand and 
reimport the structrues into analysis.

I encountered a few wrinkles as well as the orginal ones reported before.

1. Structure->Structures->Import still fails. This is a cheeky one, 
because Tim has previously said that this requires a bit of a major 
overhaul, but here goes: the next hurdle is that chain naming is not 
preserved for the ligand because MoleculeBasic.findMatchingChains and 
getSequenceResidueMapping don't deal with the case of a single ccpCode, no 
biopolymer so a new, different chain is created every import.

Would a simple fix be to check the length of the chain and skip all the 
sequence matching stuff if it's only length 1?

2. formatConverter is the other route of course. There seems to be a 
problem with the path used for online chemComp search/download from the 
ccpforge site. (the path in the url includes "/~checkout~" which does not 
seem to be correct?). Solution - make sure the chemComp is in the right 
directory of the project or your ccpnmr setup.

3. still with formatConverter - when importing coordinates, if the project 
already includes structures, it does not seem to be possible to create a 
new "structure generation" to accomodate your import - you are forced to 
choose the existing one(s). This leads to problems later if your previous 
structures were without the ligand as analysis can't handle the mismatch 
in number of atoms or something.

So here's my recipe:

Prepare your protein + ligand pdb file by removing any unwanted stuff 
(e.g. ANI, HOH, TIP or whatever).

Put the ligand chemComp into the appropriate directory (see "Add a small 
molecule" howto on the ccpnwiki).

Load a protein only structure with Structure->Structures->Import so you 
have a "structure generation" and then delete the "ensemble" again

Backup your project at this point so that if you run into trouble with the 
import you can get back quickly!

Use formatConverter Import->Coordinates->PseudoPDB to import your tidied 
pdb file - view the additional options as you do so and select the 
existing molecular system. Accept the structure generation you are offered 
and deal with linking any unrecognised atoms (remember to click "show all 
atoms" to get a choice in the drop down menu). Don't worry about running 
linkResonances.

Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
           College of Medical, Veterinary & Life Sciences,
   Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089                        Fax: 0141 330 4600
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