Program : ACONIO
Version : 990129
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 : convert PDB files with alternative conformations to/from O
Package : (none; freeby)
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-1999), Uppsala University, Uppsala, Sweden, Unpublished program.
* 2 * G.J. Kleywegt & T.A. Jones, Chapter 25.2.6. O and associated programs, Int. Tables for Crystallography, Volume F (1999 ?).
970818 - 0.1 - first version
980909 - 1.0 - added option to merge ANISOUs back in since O
ignores them at present; serious debugging;
added occupancy filter and main-chain filter;
updated this manual and added worked example;
implemented simple X-PLOR/CNS I/O as well;
first public release
990129 -1.0.1- fixed small bug in reading X-PLOR/CNS files (if only
one residue had an alt. conf., the program refused
to help you)
This program converts PDB files containing alternative conformations from/to O-style multiple PDB files. Anisotropic temperature factors can also be maintained (not for CNS or X-PLOR files).
O treats alternative conformations by reading in separate molecules. The first should contain all atoms which occur in only one conformation, plus the first conformation of those that have multiple conformations. The second file should contain *all* atoms of the second conformation of all residues, etc.
This will work with pure PDB files, as well as those produced by TNT, CCP4 (incl. PROLSQ and REFMAC), and SHELX. It will produce multiple PDB files for O. If at all possible, avoid HETATM cards and use ATOM cards for all atoms in the input file (see the worked example for the type of problems you may otherwise run in to).
The program reads one residue at a time, and when finished will:
- write the atoms with blank alternative conformation flag to
the first O file
- write the atoms with the first non-blank type of alternative
conformation flag to the first O file
- write the atoms with the second type of alternative conformation
flag to the second O file (together with atoms of this residue
which occur in only one conformation !)
- etc. for possible other alternative conformations
When the entire input file has been processed, alternative conformation files to which no atoms have been written will automatically be deleted.
SCALE*, ORIGX*, and CRYST1 cards are echoed to all output PDB files; all other non-ATOM|HETATM|ANISOU cards are ignored.
NOTE that your disordered residues must be numbered sequentially. E.g. if you have a loop with two disordered residues, 54 and 55, in the PDB file they must come in the order A54, B54, A55, B55. (If you have them as A54, A55, B54, B55 it will not work !).
NOTE that the files with alternative conformations will contain ALL atoms of any residue which has an alternative conformation for AT LEAST ONE atom ! This is done so that most of the standard O tools (which expect all atoms of a residue to be present) can be used ! It also means that when the separate files are merged back into one big file, such atoms have to be removed again (see "O to PDB" below) !
NOTE also that NO alternative conformation flags are used in the separate files produced by ACONIO. This is because O does not like them (it appends them to the atom name if possible) and gets terribly confused !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO ***Version - 980909/1.0 (C) 1992-98 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 - Wed Sep 9 20:59:31 1998 User - gerard Mode - interactive Host - sarek ProcID - 970 Tty - /dev/ttyq27
*** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO ***
Reference(s) for this program:
* 1 * G.J. Kleywegt, Uppsala University, Uppsala, Sweden, Unpublished program.
* 2 * 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
*** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO ***
Max nr of atoms per residue : ( 1000) Max nr of alt. confns. : ( 5) Max nr of atoms with alt. conf. : ( 10000)
Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty)
Operation (1,2,3,4,5) ? ( 1) 1
Input PDB file name ? (m1.pdb) 1ctj.pdb
Base name of output PDB files ? (m2) 2ctj
Open PDB file : (2ctj_2.pdb) Open PDB file : (2ctj_3.pdb) Open PDB file : (2ctj_4.pdb) Open PDB file : (2ctj_5.pdb) Open PDB file : (2ctj_6.pdb) Open PDB file : (2ctj_1.pdb)
Residue : ( N AGLU 1) Add insert : (A) Alt. conf. : (B) Residue : ( N AALA 2) Add insert : (A) Alt. conf. : (B) Residue : ( N ASP 3) Residue : ( N LEU 4) Residue : ( N ALA 5) Residue : ( N LEU 6) Residue : ( N GLY 7) Residue : ( N LYS 8) Add insert : (A) Alt. conf. : (B) Residue : ( N ALA 9) Residue : ( N VAL 10)
[...]
Residue : ( O HOH 259) Residue : ( O HOH 301)
Delete unused file : (2ctj_3.pdb) Delete unused file : (2ctj_4.pdb) Delete unused file : (2ctj_5.pdb) Delete unused file : (2ctj_6.pdb)
All done !
*** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO ***
Version - 980909/1.0 Started - Wed Sep 9 20:59:31 1998 Stopped - Wed Sep 9 20:59:38 1998
CPU-time taken : User - 0.2 Sys - 0.1 Total - 0.3
*** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO ***
>>>>>> This program: (C) 1992-98, GJ Kleywegt & TA Jones <<<<<< >>>> E-mail: gerard@xray.bmc.uu.se or alwyn@xray.bmc.uu.se <<<< >>>>>>>>>>>>>>>>> http://alpha2.bmc.uu.se/usf <<<<<<<&l
*** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ACONIO *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This converts PDB files produced by CNS or X-PLOR. Since these programs use the SEGIDs to flag alternative conformations, the program needs some help (otherwise, it wouldn't know if a different SEGID signifies a hetero-compound, an NCS-related molecule, or an alternative conformation). SEGIDs are case-sensitive, and make sure that any spaces are in the correct position (e.g., a leading space in " AC1").
NOTE that the files with alternative conformations will contain ALL atoms of any residue which has an alternative conformation for AT LEAST ONE atom ! This is done so that most of the standard O tools (which expect all atoms of a residue to be present) can be used ! It also means that when the separate files are merged back into one big file, such atoms have to be removed again (see "O to PDB" below) !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty)Operation (1,2,3,4,5) ? ( 1) 2
Input PDB file name ? (m1.pdb) alternate.pdb
SEGID of *main* conformation ? ( AC1) Alt. SEGID (<CR> to end) ? ( AC2) Alt. SEGID (<CR> to end) ? ( ) AC3 Alt. SEGID (<CR> to end) ? ( )
Base name of output PDB files ? (m2) cns
Open PDB file : (cns_2.pdb) Open PDB file : (cns_3.pdb) Open PDB file : (cns_1.pdb)
Residue with alt. conf. : (SER 10) Residue with alt. conf. : (TYR 20)
Nr of residues with alt. confs. : ( 2)
Writing file for SEGID : ( AC2) Writing file for SEGID : ( AC3)
All done ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This will generate a single PDB file that ought to be compatible with the PDB format, TNT, CCP4 (incl. PROLSQ and REFMAC), and SHELX.
The program will first read all the files containing alternative conformations, and store all atoms found in them (while assigning them alt. conf. markers as provided by the user, usually B, C, ..).
Subsequently, the program will process the main PDB file. For every atom it will check the set of alt. conf. atoms to find its mates (these must have the same atom name, column 13-16, and the same residue name and type, column 18-27). However, since O required complete residues, some of the atoms in alt. conf. file(s) may not represent alt. conf. at all (see "PDB to O" above). In order to try and figure out if an atom is simply a duplicate of a main-conformation atom, or whether it is a genuine alt. conf. atom, three heuristics can be used:
- main-chain filter: if your alt. confs. are limited to side-chain atoms, then it must mean that all main-chain atoms in the alt. conf. files can safely be ignored
- occupancy filter: if the main-conformation atom has an occupancy greater than, say, 0.99, its mates in alt. confs. can be ignored
- distance filter: if an alt. conf. atom is very close to its main-conformation mate it can perhaps be ignored
Usually, the occupancy filter is the simplest and safest to use. You will be asked if you want to use the main-chain filter. If you want to use the occupancy filter, use a cut-off of, say, 0.99. If you do NOT want to use it, use a cut-off greater than 1.0. If you want to use the distance filter, use a safe value (e.g., 0.01 A); if you don't want to use it, use a value less than 0.0 A.
All cases where duplicate atoms occur wil be listed by the programme, and the reason for ignoring or accepting the alt. confs. will be printed as well. If an atom has (apparently) genuine alt. confs., the main conformation will get an alt. conf. indicator (usually, A), and all of them will be written to the output PDB file.
Any "orphaned" alt. conf. atoms (i.e., present in one of the alt. conf. file, but not in the main file) will be listed at the end (there shouldn't be any !).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty)Operation (1,2,3,4,5) ? ( 1) 3
Input PDB file from O (<CR> to end) ? ( ) m2a.pdb Input PDB file from O (<CR> to end) ? ( ) m2b.pdb Input PDB file from O (<CR> to end) ? ( ) Nr of PDB files from O : ( 2)
Alt. conf. flags ? (ABCDEF)
Alternative conformations for all main-chain atoms can be ignored if you like. Ignore alt. main-chain conformations ? ( Y) n
An alternative conformation for an atom is ignored if the occupancy of its main- conformation partner is high. Cut-off occupancy ? ( 0.990)
An alternative conformation for an atom is ignored if it lies very close to its main- conformation partner. Cut-off distance ? ( -1.000)
Output PDB file name ? (m2.pdb) m2all.pdb
File # : ( 2) # AC now : ( 105)
AC : (ATOM 1 N GLU 1 4.127 26.179 -7.903 0.49 57.53) : (ATOM 1 N BGLU 1 3.535 25.488 -12.889 0.51 54.52) Alt. conf.: main occupancy 0.49 and main-alt atom distance 5.07 A
[...]
AC : (ATOM 48 N LYS 8 11.650 32.326 -19.080 1.00 16.64) : (ATOM 20 N BLYS 8 11.650 32.326 -19.080 1.00 16.64) Merged; main occupancy : ( 1.000)
[...]
AC : (ATOM 514 OE2 GLU 70 -5.159 35.424 -19.094 0.49 44.32) : (ATOM 101 OE2BGLU 70 -5.632 35.772 -16.130 0.51 48.51) Alt. conf.: main occupancy 0.49 and main-alt atom distance 3.02 A
Nr of "orphans" : ( 0)
All done ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This will generate a single PDB file that is compatible with CNS and X-PLOR (hopefully).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty)Operation (1,2,3,4,5) ? ( 1) 4
Input PDB file from O (<CR> to end) ? ( ) m4a.pdb Input PDB file from O (<CR> to end) ? ( ) m4b.pdb Input PDB file from O (<CR> to end) ? ( ) m4c.pdb Input PDB file from O (<CR> to end) ? ( ) Nr of PDB files from O : ( 3)
SEGID # 1 ? ( AC1) SEGID # 2 ? ( AC2) SEGID # 3 ? ( AC3)
Alternative conformations for all main-chain atoms can be ignored if you like. Ignore alt. main-chain conformations ? ( Y) n
An alternative conformation for an atom is ignored if the occupancy of its main- conformation partner is high. Cut-off occupancy ? ( 0.990)
An alternative conformation for an atom is ignored if it lies very close to its main- conformation partner. Cut-off distance ? ( -1.000)
Output PDB file name ? (m2.pdb) m4abc.pdb
File # : ( 2) # AC now : ( 18) File # : ( 3) # AC now : ( 36)
AC : (ATOM 64 N SER 10 0.411 25.125 21.340 1.00 15.00) : (ATOM 3 N BSER 10 0.397 25.123 21.326 1.00 15.00) Merged; main occupancy : ( 1.000)
[...]
AC : (ATOM 66 CB SER 10 0.467 26.015 23.570 0.33 15.00) : (ATOM 1 CB BSER 10 0.515 26.082 23.582 0.33 15.00) Alt. conf.: main occupancy 0.33 and main-alt atom distance 0.08 A
[...]
AC : (ATOM 161 O TYR 20 18.052 26.483 15.027 1.00 15.00) : (ATOM 18 O CTYR 20 18.052 26.483 15.027 1.00 15.00) Merged; main occupancy : ( 1.000)
SEGID : ( AC2) Nr of atoms : ( 10) SEGID : ( AC3) Nr of atoms : ( 10)
Nr of "orphans" : ( 0)
All done ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Since at present O ignores anisotropic temperature factor cards, the output PDB files from O will not contain these records. This option provides a quick-and-dirty way to salvage the ANISOU cards by stealing them from an older PDB file of your model. The only prerequisite is that the names and order of the ATOMs and HETATMs is exactly the same in both PDB files.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty)Operation (1,2,3,4,5) ? ( 1) 5
Current PDB file name ? (m1.pdb) 5ctj.pdb
Old PDB file name with ANISOU ? (m2.pdb) 1ctj.pdb
Output PDB file name ? (m3.pdb) 7ctj.pdb
Working ... Nr of atoms processed : ( 918)
All done ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Just to see how all this is now supposed to work, using the PDB entry 1CTJ (so you can try this at home as well !).
(1) Split PDB file into separate files for O
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty) Operation (1,2,3,4,5) ? ( 1) 1 Input PDB file name ? (m1.pdb) 1ctj.pdb Base name of output PDB files ? (m2) 2ctj Open PDB file : (2ctj_2.pdb) Open PDB file : (2ctj_3.pdb) Open PDB file : (2ctj_4.pdb) Open PDB file : (2ctj_5.pdb) Open PDB file : (2ctj_6.pdb) Open PDB file : (2ctj_1.pdb) Residue : ( N AGLU 1) Add insert : (A) Alt. conf. : (B) Residue : ( N AALA 2) Add insert : (A) Alt. conf. : (B) Residue : ( N ASP 3) Residue : ( N LEU 4) Residue : ( N ALA 5) ... Residue : ( O HOH 259) Residue : ( O HOH 301) Delete unused file : (2ctj_3.pdb) Delete unused file : (2ctj_4.pdb) Delete unused file : (2ctj_5.pdb) Delete unused file : (2ctj_6.pdb) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(2) Do your stuff in O
Read in the "main" molecule
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- s_a_i 2ctj_1.pdb m2a Sam> File type is PDB Sam> Database compressed. Sam> Space for 285492 atoms Sam> Space for 10000 residues Sam> Molecule M2A contained 241 residues and 853 atoms mol m2a zo ; end Sam> Current molecule has not been loaded. Mol> No connectivity Db for M2A Mol> Nothing marked for deletion, so no compression. mol connectivity is 1378 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Read in the residues with alternative conformations and draw them. You may want to colour them differently from the usual yellow for carbons, etc., e.g. using the OMAC macro alt_colours.omac
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- s_a_i 2ctj_2.pdb m2b Sam> File type is PDB Sam> Database compressed. Sam> Space for 283549 atoms Sam> Space for 10000 residues Sam> Molecule M2B contained 12 residues and 105 atoms @omac/alt_colours.omac As3> Macro in computer file-system. As3> Which molecule ? m2b Paint> green Paint> cyan Paint> magenta Paint> yellow mol m2b zo ; end Mol> No connectivity Db for M2B Mol> Nothing marked for deletion, so no compression. mol connectivity is 141 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now you can rebuild your molecule (and the residues with alternative conformations) using the regular O tools (rotamers, torsions, real-space refinement, etc.)
When you're done, write out the modified molecules:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- s_a_o m2a.pdb m2a ;;;;; Sam> Coordinate file type assumed from file name is PDB Sam> 853 atoms written out. s_a_o m2b.pdb m2b ;;;;; Sam> Coordinate file type assumed from file name is PDB Sam> 105 atoms written out. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(3) Merge the various PDB files into one file again
Since there are a few residues with alternative main-chain conformations, we cannot use the main-chain filter. So, we will use the occupancy filter to remove atoms without real alternative conformations.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty) Operation (1,2,3,4,5) ? ( 1) 3 Input PDB file from O (<CR> to end) ? ( ) m2a.pdb Input PDB file from O (<CR> to end) ? ( ) m2b.pdb Input PDB file from O (<CR> to end) ? ( ) Nr of PDB files from O : ( 2) Alt. conf. flags ? (ABCDEF)Alternative conformations for all main-chain atoms can be ignored if you like. Ignore alt. main-chain conformations ? ( Y) n
An alternative conformation for an atom is ignored if the occupancy of its main- conformation partner is high. Cut-off occupancy ? ( 0.990)
An alternative conformation for an atom is ignored if it lies very close to its main- conformation partner. Cut-off distance ? ( 0.010) -1 Output PDB file name ? (m2.pdb) File # : ( 2) # AC now : ( 105)
AC : (ATOM 1 N GLU 1 4.127 26.179 -7.903 0.49 57.53) : (ATOM 1 N BGLU 1 3.535 25.488 -12.889 0.51 54.52) Alt. conf.: main occupancy 0.49 and main-alt atom distance 5.07 A ... AC : (ATOM 48 N LYS 8 11.650 32.326 -19.080 1.00 16.64) : (ATOM 20 N BLYS 8 11.650 32.326 -19.080 1.00 16.64) Merged; main occupancy : ( 1.000) ... AC : (ATOM 199 CB HIS 30 18.297 50.130 -11.517 0.35 19.99) : (ATOM 32 CB BHIS 30 18.331 50.149 -11.568 0.65 20.69) Alt. conf.: main occupancy 0.35 and main-alt atom distance 0.06 A ... AC : (ATOM 514 OE2 GLU 70 -5.159 35.424 -19.094 0.49 44.32) : (ATOM 101 OE2BGLU 70 -5.632 35.772 -16.130 0.51 48.51) Alt. conf.: main occupancy 0.49 and main-alt atom distance 3.02 A
All done ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(4) Salvage ANISOU records
Now steal the old ANISOU cards and merge them into the new model's PDB file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty) Operation (1,2,3,4,5) ? ( 1) 5 Current PDB file name ? (m1.pdb) m2.pdb Old PDB file name with ANISOU ? (m2.pdb) 1ctj.pdb Output PDB file name ? (m3.pdb) m2u.pdb Working ... ERROR --- ANISOU card not found ! For atom : ( OE2BGLU 48) Order/names of atoms differ ??? FATAL ERROR --- ANISOU card not found ! - execution aborted ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Oops ! What went wrong here ? Check out this residue in the original 1CTJ file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ATOM 389 OE1AGLU 48 4.664 39.738 -3.496 0.60 37.58 O ANISOU 389 OE1AGLU 48 4398 6201 3327 1416 2837 1504 O ATOM 390 OE1BGLU 48 4.223 42.919 -3.223 0.40 37.99 O ANISOU 390 OE1BGLU 48 5524 4869 3686 2025 1198 2721 O ATOM 391 OE2BGLU 48 3.739 41.355 -1.834 0.40 29.72 O ANISOU 391 OE2BGLU 48 3278 4237 3499 282 2215 1265 O ATOM 392 OE2AGLU 48 2.819 39.905 -2.380 0.60 33.01 O ANISOU 392 OE2AGLU 48 4577 3632 4021 1247 3110 557 O ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The OE2 atoms are sorted B-A here, which confuses ACONIO since it expects the same order as in our file "m2.pdb", which is A-B. So, edit the file 1ctj.pdb to reverse the order and run again:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty) Operation (1,2,3,4,5) ? ( 1) 5 Current PDB file name ? (m1.pdb) m2.pdb Old PDB file name with ANISOU ? (m2.pdb) 1ctj.pdb Output PDB file name ? (m3.pdb) m2u.pdb Working ... ERROR --- ANISOU card not found ! For atom : ( OE1BGLU 70) Order/names of atoms differ ??? FATAL ERROR --- ANISOU card not found ! - execution aborted ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Same problem again, now for Glu 70. Fix in 1ctj.pdb and same player shoots again:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Supported operations: (1) PDB, SHELX, CCP4, TNT ---> O (2) X-PLOR, CNS ---> O (3) O ---> PDB, SHELX, CCP4, TNT (4) O ---> X-PLOR, CNS (5) Re-associate ANISOU cards (quick-n-dirty) Operation (1,2,3,4,5) ? ( 1) 5 Current PDB file name ? (m1.pdb) m2.pdb Old PDB file name with ANISOU ? (m2.pdb) 1ctj.pdb Output PDB file name ? (m3.pdb) m2u.pdb Working ... ERROR --- ANISOU card not found ! For atom : (FE HEM $ 91) Order/names of atoms differ ??? FATAL ERROR --- ANISOU card not found ! - execution aborted ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This problem has to do with the fact that O doesn't like HETATM cards (it writes them out as ATOM cards and uses a "$" sign as the chain identifier). However, the output file "m2u.pdb" contains all of the protein, and the rest can be added either by cut-and-paste, or by renaming the HETATMs to ATOMs in 1ctj.pdb, and replacing the "$" signs by spaces in m2.pdb and re-running ACONIO. However, normally I suspect all your HETATMs will be called ATOMs to begin with, so this problem wouldn't arise in the first place.
The output PDB file should start like this approximately:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMARK Written by O version 6.2.3 REMARK Wed Sep 9 15:47:09 1998 CRYST1 40.430 40.430 40.430 80.25 80.25 80.25 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.024734 -0.004251 -0.003674 0.00000 SCALE2 0.000000 0.025097 -0.003674 0.00000 SCALE3 0.000000 0.000000 0.025364 0.00000 ATOM 1 N AGLU 1 4.127 26.179 -7.903 0.49 57.53 7 ANISOU 1 N AGLU 1 9336 7394 4591 4 2737 2771 N ATOM 1 N BGLU 1 3.535 25.488 -12.889 0.51 54.52 7 ANISOU 2 N BGLU 1 8406 5015 6783 -887 3093 161 N ATOM 2 CA AGLU 1 5.490 26.607 -8.207 0.49 52.50 6 ANISOU 3 CA AGLU 1 9283 5563 4611 -256 2331 1241 C ATOM 2 CA BGLU 1 2.754 26.395 -12.051 0.51 51.27 6 ANISOU 4 CA BGLU 1 7663 5124 6212 -653 2258 184 C ... ATOM 31 N ALA 5 10.452 27.940 -17.673 1.00 25.52 7 ANISOU 45 N ALA 5 3717 2003 3736 -373 183 681 N ATOM 32 CA ALA 5 10.822 27.868 -19.105 1.00 24.02 6 ANISOU 46 CA ALA 5 3151 1934 3815 -179 147 403 C ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Good luck !!!
None, at present ("peppar, peppar").
Does not compute.
Created at Wed Feb 24 01:44:12 1999
by MAN2HTML version 971024/1.6