Program : RIGOR
Version : 971201
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : recognition of pre-defined main and side chain motifs
Package : SPASM
Reference(s) for this program:
* 1 * G.J. Kleywegt (1998). Deja-vu all over again. CCP4/ESF-EACBM Newsletter on Protein Crystallography 35, July 1998, pp. 10-12. [http://alpha2.bmc.uu.se/usf/factory_9.html]
* 2 * G.J. Kleywegt & T.A. Jones (1998 ?). Databases in protein crystallography. Acta Cryst D54, in press (CCP4 Proceedings). [http://alpha2.bmc.uu.se/gerard/papers/databases.html]
* 3 * G.J. Kleywegt & T.A. Jones (1998). Databases in protein crystallography. Acta Cryst D54, 1119-1131. [http://alpha2.bmc.uu.se/gerard/papers/databases.html] [http://www.iucr.org/iucr-top/journals/acta/tocs/actad/1998/actad5406_1.html]
* 4 * G.J. Kleywegt (1998 ?). Recognition of spatial motifs in protein structures. J Mol Biol, in press.
950421 - 2.0 - first production version (Uppsala)
951102 - 2.1 - removed some bugs (nothing major, just annoying);
new database from AUTOMOTIF
951110 - 2.2 - new database including ENGINEERABLE motifs;
new parameters: (*) cut-off in/deflation,
(*) selection of residue-specific and/or
engineerable motifs, (*) max nr of hits for
each motif
971201 - 2.3 - removed check-sum requirement for library motifs;
included MAKRIG instructions in this manual
981007 - X - the jiffy program DEJANA (part of the DEJAVU package)
has been changed so it can also be used with O macros
produced by SPASM and RIGOR !
RIGOR does sort of the opposite of SPASM (hence the name). In SPASM you define a motif that occurs in your structure and you check if it also occurs in any other structures. With RIGOR, you feed the program your entire protein and the program will figure out which of a pre-defined set of motifs also occur in your protein.
NOTE: This program is sensitive to the environment variable GKLIB. If set, the name of this directory will be prepended to the default name for the library file needed by this program. For example, in Uppsala, put the following line in your .login or .cshrc file: setenv GKLIB /nfs/public/lib
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! MOT catalytic S-D-H triad in C. antarctica lipase B PRO 1TCA1_CAT PDB /nfs/pdb/full/1tca.pdb PAR 1.0 1.5 n n n n 1 REM also in 1YSC (0.47 A), 4TGL (0.46 A) SER 105 -8.136 21.862 14.832 -7.612 22.938 16.320 ASP 187 2.590 21.835 14.434 0.152 21.475 14.714 HIS 224 -0.921 25.162 13.569 -3.157 24.098 15.511 CHK -280 END ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOT - brief description of the motif
PRO - identifier
PDB - name of the parent PDB file
PAR - parameters for the comparison search. These are values for
some of the parameters that are also used by SPASM, namely:
- max superpositioning RMSD (A)
- max distance mismatch (A)
- allow some substitutions (Y/N)
- preserve sequence directionality (Y/N)
- preserve sequential neighbours (Y/N)
- preserve sequence gaps (Y/N)
- use MC atoms only (2), SC atoms only (0), or both (1)
REM - any number of remark cards (e.g., a more complete
description of the motif, and/or a list of other
known structures in which the motif occurs as well)
... - list of residues that make up the motif (if the residue
type is "XXX" then the type will be ignored [matches any
residue type] and only the MC atoms of that residue will
be used in the superpositioning)
CHK - a check sum
END - end of the motif definition
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note: from version 2.3 on, the check-sum is no longer used; any CHK records are ignored
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOT catalytic S-D-H triad in C. antarctica lipase B MOT catalytic E-D-E triad in T. Reesei cellobiohydrolase I MOT P2 myelin R-R-Y fatty-acid binding motif in human CRABP II MOT charge interaction E-W-R in human CRABP II MOT glutathione-binding residues in human GST alpha 1-1 MOT lipocalin GXW motif in human CRABP II MOT catalytic site in actinidin (sulfhydryl proteinase) MOT calcium-binding site in alpha-parvalbumin MOT Fe4-S4 cluster in E. coli endonuclease III MOT catalytic S-E-H triad in acetylcholinesterase MOT NXS glycosylation site in T. reesei cellobiohydrolase I MOT H-H-H copper 2+ binding site in nitrite reductase (2 mol !) MOT H-C-H-M copper 2+ binding site in nitrite reductase MOT catalytic Y-E-R triad in alpha-momorcharin MOT NXT glycosylation site in alpha-momorcharin MOT catalytic S-D-H triad in trypsin MOT catalytic D-E-D triad in cyclodextrin glycosyltransferase MOT H-H-R-R oxaloacetate-binding site in citrate synthase MOT D-E-D ammonium-binding site in parvalbumin MOT ammonium-binding site in actinidin (sulfhydryl proteinase) MOT phosphate-binding site in BPTI MOT phosphate-binding site in enolase MOT copper(I)-binding site in arthropodan hemocyanin MOT proton relay system in some dehydrogenases MOT glutathione binding site in GRX's MOT adenine base (of rna hairpin loop) binding motif from MS2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Wrote AUTOMOTIF which automatically generates "interesting" motifs. The new database contains ~1,300 entries.
Changed AUTOMOTIF to include "engineerable heterogen-binding sites". These are sites for which only main-chain coordinates are used and for which the residue type is irrelevant. This will tell you if your structure contains residues which could be mutated to form a binding site for cadmium, iron, sulphate, etc. The new database contains 2,087 motifs.
You can make your own motifs for inclusion into the database using the utility program MAKRIG.
If you want to have a motif added to the database, use the "form(at)" below:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOT here_you_give_a_brief_description_of_the_motif PRO identifier_will_be_provided_by_me PDB PDB_file_name_or_PDB_ID_code PAR values_for_the_7_parameters_(eg_optimised_with_SPASM) REM any_remark_and/or_your_name_etc ! followed by the list of residues that make up the motif ! all i need (in fact, want) is PDB file columns 18-27 for ! each residue; if the residue type is irrelevant (as in ! the Asn-X-Ser example here), append a non-blank string ! (e.g., "XXX" in the example below) ASN A 270 THR A 271 XXX SER A 272 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
A real example (actually generated by AUTOMOTIF):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOT Hydrophobic cluster of CYS ILE CYS CYS CYS CYS CYS PRO 125D1 PDB /nfs/pdb/full/125d.pdb PAR 1.40 2.40 n n n n 0 REM Created by AUTOMOTIF V. 951109/0.4 at Thu Nov 9 22:06:45 1995 for user gerard REM CD2-GAL4 (65-RESIDUE DNA-BINDING DOMAIN) (YEAST) (NMR, 22 STRUCTURES) CYS 11 ILE 13 CYS 14 CYS 21 CYS 28 CYS 31 CYS 38 END ! MOT 4 residues within 3.60 A of CADMIUM ATOM PRO 125D2 PDB /nfs/pdb/full/125d.pdb PAR 0.80 1.80 n n n n 0 REM Created by AUTOMOTIF V. 951109/0.4 at Thu Nov 9 22:06:46 1995 for user gerard REM CD2-GAL4 (65-RESIDUE DNA-BINDING DOMAIN) (YEAST) (NMR, 22 STRUCTURES) CYS 11 CYS 14 CYS 21 CYS 28 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Running MAKRIG is easy:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG ***Version - 950421/2.0 (C) 1992-97 Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Mon Dec 1 14:19:41 1997 User - gerard Mode - interactive Host - sarek ProcID - 13661 Tty - /dev/ttyq14
*** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG ***
Reference(s) for this program:
* 1 * G.J. Kleywegt, (Have to think of a title), To be published.
* 2 * G.J. Kleywegt & T.A. Jones, (CCP4 Proceedings 1998), Acta Cryst D, to be published (Sept 1998).
* 3 * G.J. Kleywegt & T.A. Jones, Chapter 25.2.6. O and associated programs, Int. Tables for Crystallography, Volume F (1999 ?).
==> For manuals and complete references, visit: ==> http://alpha2.bmc.uu.se/usf/
*** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG ***
Pre library file ? (rigor.pre) test.pre New library file ? (rigor.newlib) test.newlib
NEW MOTIF > (MOT Hydrophobic cluster of CYS ILE CYS CYS CYS CYS CYS) Protein : (PRO 125D1) File : (PDB /nfs/pdb/full/125d.pdb) Parameters : (PAR 1.40 2.40 n n n n 0) Remark : (REM Created by AUTOMOTIF V. 951109/0.4 at Thu Nov 9 22:06:45 1995 for user gerar) Remark : (REM CD2-GAL4 (65-RESIDUE DNA-BINDING DOMAIN) (YEAST) (NMR, 22 STRUCTURES)) > (CYS 11) > (ILE 13) > (CYS 14) > (CYS 21) > (CYS 28) > (CYS 31) > (CYS 38) Nr of residues : ( 7) Processing : (/nfs/pdb/full/125d.pdb) Nr of atoms : ( 346) Residue : (CYS 11) Residue : (ILE 13) Residue : (CYS 14) Residue : (CYS 21) Residue : (CYS 28) Residue : (CYS 31) Residue : (CYS 38)
NEW MOTIF > (MOT 4 residues within 3.60 A of CADMIUM ATOM) Protein : (PRO 125D2) File : (PDB /nfs/pdb/full/125d.pdb) Parameters : (PAR 0.80 1.80 n n n n 0) Remark : (REM Created by AUTOMOTIF V. 951109/0.4 at Thu Nov 9 22:06:46 1995 for user gerar) Remark : (REM CD2-GAL4 (65-RESIDUE DNA-BINDING DOMAIN) (YEAST) (NMR, 22 STRUCTURES)) > (CYS 11) > (CYS 14) > (CYS 21) > (CYS 28) Nr of residues : ( 4) Processing : (/nfs/pdb/full/125d.pdb) Nr of atoms : ( 346) Residue : (CYS 11) Residue : (CYS 14) Residue : (CYS 21) Residue : (CYS 28)
*** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG ***
Version - 950421/2.0 Started - Mon Dec 1 14:19:41 1997 Stopped - Mon Dec 1 14:19:49 1997
CPU-time taken : User - 0.1 Sys - 0.0 Total - 0.1
*** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG ***
>>>>>> This program: (C) 1992-97, GJ Kleywegt & TA Jones <<<<<< >>>> E-mail: gerard@xray.bmc.uu.se or alwyn@xray.bmc.uu.se <<<< > http://alpha2.bmc.uu.se/usf/gerard_manuals.html <
*** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** MAKRIG *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The new file looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by MAKRIG V. 950421/2.0 at Mon Dec 1 14:19:49 1997 for user gerard MOT Hydrophobic cluster of CYS ILE CYS CYS CYS CYS CYS PRO 125D1 PDB /nfs/pdb/full/125d.pdb PAR 1.40 2.40 n n n n 0 REM Created by AUTOMOTIF V. 951109/0.4 at Thu Nov 9 22:06:45 1995 for user gerar REM CD2-GAL4 (65-RESIDUE DNA-BINDING DOMAIN) (YEAST) (NMR, 22 STRUCTURES) CYS 11 1.118 3.206 -5.622 -0.488 2.651 -4.488 ILE 13 -1.684 6.580 -3.188 -3.876 6.238 -3.150 CYS 14 0.915 5.301 -0.735 0.819 3.300 -0.464 CYS 21 2.673 0.751 1.004 2.511 0.761 -1.034 CYS 28 -3.285 -2.101 -1.674 -2.236 -0.294 -1.307 CYS 31 -7.259 1.845 -2.088 -5.677 2.241 -3.315 CYS 38 -4.153 2.541 -6.913 -3.572 0.891 -5.893 CHK -143 END ! MOT 4 residues within 3.60 A of CADMIUM ATOM PRO 125D2 PDB /nfs/pdb/full/125d.pdb PAR 0.80 1.80 n n n n 0 REM Created by AUTOMOTIF V. 951109/0.4 at Thu Nov 9 22:06:46 1995 for user gerar REM CD2-GAL4 (65-RESIDUE DNA-BINDING DOMAIN) (YEAST) (NMR, 22 STRUCTURES) CYS 11 1.118 3.206 -5.622 -0.488 2.651 -4.488 CYS 14 0.915 5.301 -0.735 0.819 3.300 -0.464 CYS 21 2.673 0.751 1.004 2.511 0.761 -1.034 CYS 28 -3.285 -2.101 -1.674 -2.236 -0.294 -1.307 CHK 18 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Mail your motif to "gerard@xray.bmc.uu.se" and it will be added to the public domain version of the RIGOR library).
Note that a motif is any arrangement of main-chain and/or
side-chain atoms that *you* think is biologically and/or
crystallographically and/or protein-scientifically important.
A motif can be a metal-binding site, a ligand-binding site,
a strange turn or loop, or even a small arrangement of
secondary structure elements (helix-turn-helix, for instance).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----*** RIGOR *** RIGOR *** RIGOR *** RIGOR *** RIGOR *** RIGOR *** RIGOR ***
Version - 950421/2.0 (C) 1993-5 Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Fri Apr 14 23:49:16 1995 User - gerard Mode - interactive Host - ALPHA/OSF1 ProcID - 18223 Tty - /dev/ttyqf
*** RIGOR *** RIGOR *** RIGOR *** RIGOR *** RIGOR *** RIGOR *** RIGOR ***
Max nr of atoms in pattern file : ( 10000) Max nr of residues in ,, ,, : ( 2500) Ditto, in database proteins : ( 100)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- RIGOR database file ? (/nfs/public/lib/rigor.lib) ./rigor.lib ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Supply the name of the local RIGOR library file.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- List contents of database ? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Do you want to see which motifs are in the library ? If so, you'll see the following flash over your screen:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- List contents of database ? (N) y > (! Created by MAKRIG V. 950419/1.0 at Thu Apr 20 02:05:40 1995 for user gerard) ... >>> NEW MOTIF: > (MOT catalytic S-D-H triad in C. antarctica lipase B) > (PRO 1TCA1_CAT) > (PDB /nfs/pdb/full/1tca.pdb) > (PAR 1.0 1.5 n n n n 1) > (REM also in 1YSC (0.47 A), 4TGL (0.46 A)) > (SER 105 -8.136 21.862 14.832 -7.612 22.938 16.320) > (ASP 187 2.590 21.835 14.434 0.152 21.475 14.714) > (HIS 224 -0.921 25.162 13.569 -3.157 24.098 15.511) > (CHK -280) > (END) > (!) >>> NEW MOTIF: > (MOT catalytic E-D-E triad in T. Reesei cellobiohydrolase I) > (PRO 1CEL1_CAT) ... > (CHK -5520) > (END) > (!) Nr of lines read : ( 318) Nr of motifs read : ( 23) CPU total/user/sys : 0.2 0.1 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Which PDB file ? (0xyz.pdb) /nfs/pdb/full/1lid.pdbNr of atoms : ( 1017)
Nr of residues found : ( 131) Nr of residues okay : ( 131) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The name of the structure you want to screen against the library.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Four-character ID for this run ? (1LID) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
An identifier for this run of the program.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may multiply the matching cut-offs by a factor (>0) to reduce (<1) or increase (>1) the number of hits. Use a value of 1.0 for "factory settings". Factor (>0) ? ( 1.500) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use stricter or more relaxed cut-offs.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may opt to check only residue-specific motifs (0), or only engineerable motifs (2), or both (1). Option (0,1,2) ? ( 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Select which motifs to use.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may limit the number of hits to be generated for any single motif. Max hits per motif (>0) ? ( 5) 3 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You may limit the number of hits per motif (if you don't want to do that, enter a very large number).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may want to see the MC/MC and/or SC/SC distance matrices of each search pattern and that of any hits found in your protein, to help decide if the hit is good enough for your purposes. Matrices are *only* printed if the search pattern contains 10 or fewer residues. Print distance matrices ? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You may want to see the distance matrices.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- If you are not an O user, you may want the best superpositioning operator to be printed. Print operators ? (N) n ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You may want to see the operators.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- For debugging purposes, you may request extensive output, listing *all* database motifs which are tried. Extensive output ? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Not normally used.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may want an O macro plus LSQ operator file for easy inspection of the hits. O macro and operator file ? (N) yO macro file ? (1lid.omac)
O operator file ? (1lid.odb) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You may want to get an O macro which will read and draw the "hit"
structures and superimpose the graphics objects with your own
structure.
The jiffy program DEJANA (part of the DEJAVU package) can be used
to sort the hits in the O macro produced by SPASM !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Searching ...==> HIT : (1CBS1) Motif : (P2 myelin R-R-Y fatty-acid binding motif in human CRABP II) File : (/nfs/pdb/full/1cbs.pdb) Residues : ( 3)
MATCH with RMSD 0.38 A for 6 pseudo-atoms ARG 111 <---> ARG 106 * ARG 132 <---> ARG 126 * TYR 134 <---> TYR 128 *
==> HIT : (1CBS3) Motif : (lipocalin GXW motif in human CRABP II) File : (/nfs/pdb/full/1cbs.pdb) Residues : ( 3)
MATCH with RMSD 0.17 A for 5 pseudo-atoms GLY 5 <---> GLY 6 * XXX 6 <---> THR 7 TRP 7 <---> TRP 8 *
Nr of motifs found : ( 2) Total number of hits : ( 2) CPU total/user/sys : 0.4 0.3 0.1
Run again ? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
So, RIGOR found two (not unexpected) motifs in this structure.
The O macro looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by RIGOR V. 950421/2.0 at Fri Apr 21 23:56:32 1995 for user gerard ! Scanned PDB file /nfs/pdb/full/1lid.pdb read 1lid.odb sam_atom_in /nfs/pdb/full/1lid.pdb 1LID PDB mol 1LID pa_case atom_z 4 6 7 8 16 green cyan magenta yellow object 1LID zone ; end centre_xyz -42.36 69.66 -6.08 ! ! HIT 1CBS1 ! P2 myelin R-R-Y fatty-acid binding motif in human CRABP II sam_atom_in /nfs/pdb/full/1cbs.pdb 1CBS1 PDB ! Hit nr 1 ! RMSD 0.38 print P2 myelin R-R-Y fatty-acid binding motif in human CRABP II ! ARG 111 <---> ARG 106 * ! ARG 132 <---> ARG 126 * ! TYR 134 <---> TYR 128 * mol 1CBS1 delete 1CBS11 ; object 1CBS11 zone 111 ; zone 132 ; zone 134 ; end lsq_obj 1CBS11_to_1LID 1CBS11 ! HIT 1CBS3 ! lipocalin GXW motif in human CRABP II sam_atom_in /nfs/pdb/full/1cbs.pdb 1CBS3 PDB ! Hit nr 1 ! RMSD 0.17 print lipocalin GXW motif in human CRABP II ! GLY 5 <---> GLY 6 * ! XXX 6 <---> THR 7 ! TRP 7 <---> TRP 8 * mol 1CBS3 delete 1CBS31 ; object 1CBS31 zone 5 ; zone 6 ; zone 7 ; end lsq_obj 1CBS31_to_1LID 1CBS31 on_off bell message Done ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
And the O-style operator file looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by RIGOR V. 950421/2.0 at Fri Apr 21 23:56:32 1995 for user gerard
.lsq_rt_1CBS11_to_1LID r 12 (6f12.6)
-0.388958 -0.843127 -0.371278 -0.084088 0.433823 -0.897066
0.917410 -0.317701 -0.239636 -59.400398 84.781677 26.675573
.lsq_rt_1CBS31_to_1LID r 12 (6f12.6)
-0.378108 -0.826017 -0.418008 -0.064208 0.473840 -0.878267
0.923532 -0.305240 -0.232199 -59.534931 82.519150 28.120340
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now start O, type "@1lid.omac", go and have a cup of coffee if you have many hits, and admire the result ...
The O macros will *only* work if the PDB file names in the RIGOR database file actually point to the corresponding PDB files on your local file system. To this end, your local system manager should do something like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix> sed -e 's%/nfs/pdb/full%/your/pdb/directory/%' rigor.lib > local.lib ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Fri Dec 18 19:42:24 1998
by MAN2HTML version 971024/1.6