Thanks Nigel. 
The CIF files generated by SKETCHER in ccp4i work fine in both phenix.refine and refmac, but seems they don't work in phenix.autobuild....(they should work the same right?)

I am not sure why, but I will try what you suggested. Thank you so much again!

Matt
 


Matt


> 1. AutoBuild Wizard will use phenix.elbow to generate geometries for 
> any ligands that are not recognized, but how can I find out which 
> ligands that can actually be recognized by phenix? Or to be save, we 


> better run elbow to generate the libraries for every single ligands?
There are a number of tools available.

phenix.pdbtools file.pdb

will tell you if a PDB file has non-recognised ligands.



phenix.elbow --do-all model.pdb

will calculate all the ligands in the PDB file.

phenix.ready_set model.pdb

will calculate all the ligands and check that the atom names are 
correct.  It also adds hydrogens among other things.


> 2. eLBOW can automatically add hydrogens to the input molecules if 
> there are less than a quarter of the possible hydrogens, however this 
> command doesn't work: phenix.elbow input_file.pdb 


> --add-hydrogens=True, and I can't find this option under the elbow manual?
> And actually I would like to remove those hydrogens so it should be 
> "add-hydrogens=false"? I am now using phenix-1.3-rc2.



To get an absolute list of the options you can

phenix.elbow --help

The --add-hydrogens options overwrites the automatic choice by eLBOW.  
If you don't want the hydrogens in your PDB and CIF files use 


--write-hydrogens=False.  This arises because the internal 
representation must have the hydrogens for accurate geometries and 
restraints.

Nigel

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division


Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov

Web   : CCI.LBL.gov