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=1470alloc_id=3638op=click
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
