Hello Chimera-Users and -Devs, I encountered the following problem when trying to visualise the following purine molecule (Actually, I tried to do something more complex(*) but the same problem can be reproduced with this more simple example). For clarification, the first lines contain the column numbers. 1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012345678 HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00 0.00 N HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00 0.00 C HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00 0.00 N HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00 0.00 C HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00 0.00 C HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00 0.00 C HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00 0.00 N HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00 0.00 C HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00 0.00 N When I load a pdb file containing these coordinates into Chimera, I get 9 non-connected dots (obviously representing the atoms) which can neither be coloured by hetero-atom, nor by element. Note that the atom names are located in the appropriate columns, i.e. between columns 13 and 16, more specifically in columns 15 and 16. I noticed that in other pdb structures 2-character atom names are located in columns 14 and 15 and when I put my atom names there, Chimera displays the purine ring system which then can be coloured by hetero-atom/element. Now it is nice that this workaround fixes my problem, however, according to the pdb file format specification (columns 13-16 are reserved for the atom name), atom names located in columns 15 and 16 are valid(*) and as such should be processible by visualisation tools etc. The behaviour occurs with the latest daily build as well as some older versions I found on my hard disk... (*) The purine is part of a larger cytokinin. I stumbled upon the described behaviour while using the AddHydrogen function on the whole molecule, which lead to the replacement of the purine with a hydrogen. (**) Unless there are some additional rules regarding the placement of atom names shorter than 4 characters, in which case I apologise for bugging you with this. Any comments on this? Best regards, Christian Schudoma -- Christian Schudoma, M.Sc. Bioinformatics Group System Integration Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 331 567-8624 email: schudoma@mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de