Michael, PyMOL will only insert TER records when residue identifiers are non-sequential.
Cheers, Warren > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Michael George Lerner > Sent: Monday, March 08, 2004 10:23 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] How do I get PyMOL to keep TER cards? > > > Hi, > > I have a file called test.pdb that looks like this: > > ATOM 13268 O00 U00 1945 -18.065 -4.226 1.590 > ATOM 13269 H03 U00 1945 -17.394 -4.877 1.447 > ATOM 13270 C04 U00 1945 -19.175 -4.837 2.212 > ATOM 13271 H05 U00 1945 -19.963 -4.104 2.383 > ATOM 13272 H06 U00 1945 -18.888 -5.266 3.173 > ATOM 13273 H07 U00 1945 -19.576 -5.633 1.583 > TER > ATOM 13274 O00 U01 1946 -18.452 -3.459 2.224 > ATOM 13275 H03 U01 1946 -17.636 -3.864 1.971 > ATOM 13276 C04 U01 1946 -19.108 -4.290 3.158 > ATOM 13277 H05 U01 1946 -20.055 -3.842 3.462 > ATOM 13278 H06 U01 1946 -18.491 -4.429 4.047 > ATOM 13279 H07 U01 1946 -19.314 -5.268 2.722 > TER > ATOM 13280 O00 U02 1947 -5.561 -17.187 5.362 > ATOM 13281 H03 U02 1947 -5.123 -17.493 6.143 > ATOM 13282 C04 U02 1947 -6.904 -17.622 5.389 > ATOM 13283 H05 U02 1947 -7.428 -17.283 4.495 > ATOM 13284 H06 U02 1947 -7.419 -17.223 6.263 > ATOM 13285 H07 U02 1947 -6.953 -18.711 5.424 > TER > > If I do this from PyMOL: > > delete all > load test.pdb > save test2.pdb > > I end up with a file that is missing TER cards .. like this: > > ATOM 1 O00 U00 1945 -18.065 -4.226 1.590 0.00 > 0.00 O > ATOM 2 C04 U00 1945 -19.175 -4.837 2.212 0.00 > 0.00 C > ATOM 3 H03 U00 1945 -17.394 -4.877 1.447 0.00 > 0.00 H > ATOM 4 H05 U00 1945 -19.963 -4.104 2.383 0.00 > 0.00 H > ATOM 5 H06 U00 1945 -18.888 -5.266 3.173 0.00 > 0.00 H > ATOM 6 H07 U00 1945 -19.576 -5.633 1.583 0.00 > 0.00 H > ATOM 7 O00 U01 1946 -18.452 -3.459 2.224 0.00 > 0.00 O > ATOM 8 C04 U01 1946 -19.108 -4.290 3.158 0.00 > 0.00 C > ATOM 9 H03 U01 1946 -17.636 -3.864 1.971 0.00 > 0.00 H > ATOM 10 H05 U01 1946 -20.055 -3.842 3.462 0.00 > 0.00 H > ATOM 11 H06 U01 1946 -18.491 -4.429 4.047 0.00 > 0.00 H > ATOM 12 H07 U01 1946 -19.314 -5.268 2.722 0.00 > 0.00 H > ATOM 13 O00 U02 1947 -5.561 -17.187 5.362 0.00 > 0.00 O > ATOM 14 C04 U02 1947 -6.904 -17.622 5.389 0.00 > 0.00 C > ATOM 15 H03 U02 1947 -5.123 -17.493 6.143 0.00 > 0.00 H > ATOM 16 H05 U02 1947 -7.428 -17.283 4.495 0.00 > 0.00 H > ATOM 17 H06 U02 1947 -7.419 -17.223 6.263 0.00 > 0.00 H > ATOM 18 H07 U02 1947 -6.953 -18.711 5.424 0.00 > 0.00 H > END > > How can I convince PyMOL to give me the TER cards? > > The only obvious-sounding setting I could find was > pdb_use_ter_records, but that doesn't seem to do what I want. > > Thanks, > > -michael > > -- > This isn't a democracy;| _ |Michael Lerner > it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan > -Torrence, Bring It On| - against HTML email X | Biophysics > | / \ | mler...@umich > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials Free > Linux tutorial presented by Daniel Robbins, President and CEO > of GenToo technologies. Learn everything from fundamentals to > system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
