[Chimera-users] Docking of PDB data

Alexander Solodukhin as4j at virginia.edu
Wed Sep 19 08:50:09 PDT 2007

Dear Listers,


I have got the CCP4 3d map of PKC created from tilted series of 2d crystals grown on lipid monolayers. Unit cell: a=b=53A, alpha=beta=90 deg and gamma=120 deg. X-rays 3d structures of three fragments: C1b, C2 of the regulatory domain and catalytic domain are available from PDB data bank. When I try to dock PDB files or their maps created with SPIDER or SITUS programs by the use of 'fit models in maps' or 'fit maps in maps' in CHIMERA, programs place this fragments into one only place around the point that looks like a 'center of gravity' of CCP4 model. If I cut off the part of model where this point is, anyway program places these fragments into the same point out of the selected subregion.


How can I fix this problem? I understand that I have to assign the same origin of coordinates for my model and fragments, but I do not know how to do this.


Alexander Solodukhin, Ph.D.

Department of Anesthesiology

University of Virginia Health System

P.O.Box 800710

Charlottesville VA 22906-0710

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