SHELXD writes the heavy atom coordinates both as a SHELX format .res file (useful for spotting special positions as well as inputting into SHELXE) and a .pdb file. Unfortunately you need to edit the name of the space group into the first line of this PDB file (leave one space after the last cell dimension, and a space between each part of the space group symbol) so that most CCP4 programs can read it. This is because SHELXD only knowns the symmetry operators, not the name of the space group. I hope to find a fix for this in the next version of SHELXD but using the symmetry operators instead of the space group name has the advantage that non-standard space group settings can be handled completely unambiguously (see the recent CCP4bb discussion on this topic). Note that Coot can read the .res file directly and so if you just want to display the heavy atoms in Coot you don't need to edit the .pdb file.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Tue, 20 Mar 2007, yang li wrote: > Hi: > Now I need to input a heavy atom pdb file in the ccp4 interface, does > ccp4 has a special format for all the programs in the package? I used > heavy atom file from shelxd but it seemed not right. where can I get a > model of such pdb file? Thanks! >
