What I did so that I could use the labels command was read the coordinates in twice. One copy was used for display, the second copy had no atoms/representations displays, but instead I attatched labels to the atoms on the second copy and then moved these atoms around (and thusly the labels) till the label were visible and well oriented.
I have to admit though, once you raytrace the labels become almost unreadable and I think I will end up using them only to help me to position the final labels in a picture editing program... Robert PS: Here is an example of what I mean: #read in PDB file with dummy name to move around atom-labels set label_color,black load a.pdb,bbbb label (/bbbb//A/GLN`112/CA) ," %s-%s" % (resn,resi) translate [-1,0,0],/bbbb//A/GLN`112/CA Ingo P. Korndoerfer: > >hello everybody, > >shouldn't it be possible to extract the proper rotation for the cgo >labels >from the view matrix ? > >i have been trying arount a few things, but was not so succesful so far. > >my idea was, to > >- extract the coordinates of the atom i want from the pdb file. either >from within pymol or in an external python script. >- put a label at those positions >- move the label to the origin. >- apply the inverse of the rotational part of the view matrix >- move the label back to were it came from >- and then adjust the wee little offsets for better image clarity >manually (try and error, as in molscript). > >or is that not possible ? > >from what i have seen, i can not apply a matrix directly to the cgo >objects, >but would have to convert the matrix to three succesive rotations around >x, y and z. > >also, moving the label to the origin, rotating and moving it back >afterwards >did not have quite the effect i was anticipating. i.e., it looked the >same, as rotating in place. >in particular, the label got moved a significant way off ... > >would anybody have any insights he would like to share ... > >putting in the labess in illustrator or gimp afterwards is way too >cumbersome ... > >1000 thanks for your help > >ingo _______________________________________________________________ Robert Lucas rlu...@alumni.uci.edu Department of Biochemistry Phone: (206) 616-4510 HHMI & Univ. of Washington Fax: (206) 685-7002 Health Science Bldg., Room K-428 Box 357742, Seattle, WA 98195 _______________________________________________________________
