One can access the database information on an ESV or SGI in a number of different ways:.
% link -s /usr/people/alwyn/o/data odatThen in the program one would use menu.o,
% setenv ODAT /usr/people/alwyn/o/data/Then in the program one would merely specify menu.o. Provided menu.o did not exist in the current directory, it would then come from the correct place.
.odat T 1 40 /usr/people/alwyn/o/data/Then in the program one would merely specify menu.o
In the following, user input is written in boldface.
% ono
O > Use of this program implies acceptance of conditions
O > described in Appendix 1 of the O manual
O > O version 5.9.1 , Fri Jul 30 14:36:38 MET DST
O > Define an O file (terminate with blank): startup.o
O > File is formatted
O > Define an O file (terminate with blank): menu.o
O > File is formatted
O > Define an O file (terminate with blank):
O > File_display_connectivity is not defined.
O > Enter file name [ o.dat] :
Maximum inter-residue link distance = 6.00
There were 22 residues
113 atoms
O > Do you want to use the display? [Y]/N
Read in coords for 2 chains, call them A and B
O > sam_at_in Sam>Name of input file: m17_a.wah Sam>O associated molecule name : a Sam>Type of coordinates assumed from file name. Sam>Is that O.K. ? ([Y]/N) Sam>Is it Wayne s format ([Y]/N) ? Sam>Are there any S-S bridges (Y/[N]) ? O > sam_at_in Sam>Name of input file: m17_b.wah Sam>O associated molecule name : b Sam>Type of coordinates assumed from file name. Sam>Is that O.K. ? ([Y]/N) Sam>Is it Wayne s format ([Y]/N) ? Sam>Are there any S-S bridges (Y/[N]) ? O > dir a* Heap>A_ATOM_XYZ R W 3162 Heap>A_ATOM_B I W 1054 Heap>A_ATOM_Z I W 1054 Heap>A_ATOM_NAME C W 1054 Heap>A_ATOM_WT R W 1054 Heap>A_RESIDUE_NAME C W 132 Heap>A_RESIDUE_TYPE C W 132 Heap>A_RESIDUE_POINTERS I W 264 Heap>A_RESIDUE_CG R W 528 O > save As1> File_O_save is not defined. As1> Enter file name [ binary.o] :
Make an object from molecule a
O > mol O > Current molecule has not been loaded. Mol> Molecule code name []: a O > ca Mol> Ca zone [all molecule]: O > end
That could all have been done in one line:
O > mol a ca ; end
Centre it on the fatty acid
O > cen_atom As3> Define molecule [A ], residue, and atom [CA] : a132 c5
Believe me , it did centre. Now make an object with the fatty acid too
O > ca ; zon a132 ; end
Note the use of `;' in the above line. Make another object with those residues close to the fatty acid:
O > obj sph_a cover a132 ; 2.5 end
After activating On_off, we can click the objects on and off... Now, make mol b...
O > mol b ca ; z b132 end Mol> Second residue not in molecule
Notice the error in the last line. It was trying to find a second residue in the zone called end. Add the desired zone with
O > z b132 ; end
Now compare molecules A and B
O > lsq_ex Lsq >Lsq definition defaults are taken. Lsq >Least squares match by explicit definition of atoms. Lsq >Given 2 molecules A,B the transformation rotates B onto A Lsq >What is the name of A (the not rotated molecule) ? a Lsq >What is the name of B (the rotated molecule) ? b Lsq >Now define what atoms in A are to be matched to B. Lsq >Defining 3 names in A implies a zone and an atom name. Lsq >Defining 2 names in A implies a zone and CA atoms. Lsq >Defining 1 name in A implies the CA of that residue. Lsq >The B molecule requires just the start residue. Lsq >A blank line terminates input. Lsq >Define atoms from A (the not rotated molecule) : a1 a131 Lsq >Define atoms from B (the rotated molecule) : b1 Lsq >Define atoms from A (the not rotated molecule) : Lsq >The 131 atoms have an r.m.s. fit of 0.614 Lsq >xyz(1) = 0.3866*x+ 0.0907*y+ 0.9178*z+ -16.9487 Lsq >xyz(2) = 0.1155*x+ 0.9826*y+ -0.1458*z+ 25.7526 Lsq >xyz(3) = -0.9150*x+ 0.1624*y+ 0.3694*z+ 66.9966 Lsq >The transformation can be stored in O. Lsq >A blank is taken to mean do not store anything Lsq >The transformation will be stored in .LSQ_RT_ b_to_a O > lsq_obj Lsq >Apply a transformation to an existing object. Lsq >There is an alignment called B_TO_A Lsq >Which alignment [<CR>=restore a transformed object] ? b_to_a Lsq >There is an object called A Lsq >There is an object called SPH_A Lsq >There is an object called B Lsq >Which object ? b
Now they are on top of each other, we can identify them
O > lsq_obj ; b
That removed them. Do a deliberate mistake in LSQ:
O > lsq_e Lsq >Lsq definition defaults are taken. Lsq >Least squares match by explicit definition of atoms. Lsq >Given 2 molecules A,B the transformation rotates B onto A Lsq >What is the name of A (the not rotated molecule) ? a Lsq >What is the name of B (the rotated molecule) ? b Lsq >Now define what atoms in A are to be matched to B. Lsq >Defining 3 names in A implies a zone and an atom name. Lsq >Defining 2 names in A implies a zone and CA atoms. Lsq >Defining 1 name in A implies the CA of that residue. Lsq >The B molecule requires just the start residue. Lsq >A blank line terminates input. Lsq >Define atoms from A (the not rotated molecule) : a1 a125 Lsq >Define atoms from B (the rotated molecule) : b5 Lsq >Define atoms from A (the not rotated molecule) : Lsq >The 125 atoms have an r.m.s. fit of 11.038 Lsq >xyz(1) = 0.2809*x+ 0.0037*y+ 0.9597*z+ -8.7543 Lsq >xyz(2) = 0.2134*x+ 0.9747*y+ -0.0662*z+ 16.6426 Lsq >xyz(3) = -0.9357*x+ 0.2234*y+ 0.2730*z+ 69.5881 Lsq >The transformation can be stored in O. Lsq >A blank is taken to mean do not store anything Lsq >The transformation will be stored in .LSQ_RT_ b_to_a O > lsq_i Lsq >Least squares match by Semi Automatic Alignment. Lsq >There is an alignment called B_TO_A Lsq >Given 2 molecules A,B the transformation rotates B onto A Lsq >What is the name of molecule A [A ]? Lsq >Zone to look for alignment [all molecule A] : Lsq >What is the name of molecule B [B ]? Lsq >Zone to look for alignment [all molecule B] : Lsq >What atom [CA] ? Lsq >Number of atoms in A/B to look for alignment 131 131 Lsq >Search for connected fragments. Lsq >A fragment of 131 1 1 residues located. Lsq >Loop = 1 ,r.m.s. fit = 0.614 with 131 atoms Lsq >x(1) = 0.3866*x+ 0.0907*y+ 0.9178*z+ -16.9487 Lsq >x(2) = 0.1155*x+ 0.9826*y+ -0.1458*z+ 25.7526 Lsq >x(3) = -0.9150*x+ 0.1624*y+ 0.3694*z+ 66.9966 Lsq >Search for connected fragments. Lsq >A fragment of 131 1 1 residues located. Lsq >Loop = 2 ,r.m.s. fit = 0.614 with 131 atoms Lsq >x(1) = 0.3866*x+ 0.0907*y+ 0.9178*z+ -16.9487 Lsq >x(2) = 0.1155*x+ 0.9826*y+ -0.1458*z+ 25.7526 Lsq >x(3) = -0.9150*x+ 0.1624*y+ 0.3694*z+ 66.9966 Lsq >The transformation can be stored in O. Lsq >A blank is taken to mean do not store anything Lsq >The transformation will be stored in .LSQ_RT_ b_to_a Lsq >Here are the fragments used in the alignment Lsq > A1 SNKFLGTWKLVSSENFDEYMKALGVGLATRKLGNLAKPRVIISKKGDIIT Lsq > B1 SNKFLGTWKLVSSENFDEYMKALGVGLATRKLGNLAKPRVIISKKGDIIT Lsq > A51 IRTESPFKNTEISFKLGQEFEETTADNRKTKSTVTLARGSLNQVQKWNGN Lsq > B51 IRTESPFKNTEISFKLGQEFEETTADNRKTKSTVTLARGSLNQVQKWNGN Lsq > A101 ETTIKRKLVDGKMVVECKMKDVVCTRIYEKV A131 Lsq > B101 ETTIKRKLVDGKMVVECKMKDVVCTRIYEKV B131
See it worked
O > lsq_pair Lsq >There is an matched pair called B_TO_A Lsq >Object state ([ON],OFF) : on
That shows some little arrows between matched atoms
O > stop %
This ends the session. Next time O is started up, you don't need to specify the startup.o and menu.o files.