Uppsala Software Factory

Uppsala Software Factory - SEAMAN Manual

1 SEAMAN - GENERAL INFORMATION

Program : SEAMAN
Version : 970827
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 : generate search models for Molecular Replacement
Package : X-UTIL

2 REFERENCES

Reference(s) for this program:

* 1 * G.J. Kleywegt (1996). Making the most of your search model. CCP4/ESF-EACBM Newsletter on Protein Crystallography 32, June 1996, pp. 32-36. [http://alpha2.bmc.uu.se/usf/factory_6.html]

* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.

3 VERSION HISTORY

950622 - 0.1 - initial version
950623 - 0.2 - more options
950626 - 1.0 - first production version
951121 - 1.1 - minor changes; write CRYST1 etc. cards if they were in the input PDB file
961121 - 1.2 - fixed a nasty bug which *sometimes* occurred for commands like ALAN, GLYC, MINI, BFAC etc. (thanks to Margareta Ingelman)
970818 - 1.3 - use P-SEA algorithm to determine secondary structure
970818 -1.3.1- small changes to P-SEA parameters

4 INTRODUCTION

SEAMAN is a small program which should making search models for Molecular Replacement calculations a bit easier. It is probably best used in conjunction with LSQMAN (to align multiple copies of a search model and to find the most similar regions) and MOLEMAN (to reset occupancies and to reset, smooth or average temperature factors).

SEAMAN was designed specifically with the aim of coping with multiple search models, e.g. NMR families of structures, or NCS-copies or multiple determinations of a structure. Still, it will work just as well on single models.

SEAMAN can do most things I could think of to mutate a model into a suitable MR probe: you can delete loops, regions with high-temperature factors, do conservative substitutions or an O-like mutate_replace, replace residues by their most-frequent rotamer conformation.

SEAMAN requires a small library file (seaman.lib) which contains the most-frequent rotamer for each of the twenty amino acids (ergo, SEAMAN will be most useful if you work with proteins).

NOTE: some commands are *destructive*, i.e. they may delete some but not all atoms of a residue (e.g., BFAC). Since the MINI, MUTA and ROTA commands need *intact* residues, the destructive commands should be used *last* !!! Destructive commands are BFAC, OCCU and ISOL.

NOTE: you may want to run O simultaneously in a separate window to monitor the effects of your changes, or to identify other regions that need to be deleted (e.g., those with a large conformational spread).

5 STARTUP

When you start the program, you will see the current dimensioning and available commands, after you have provided the name of the library file (use environment variable GKLIB to point to an appropriate directory): 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 % 160 gerard onyx 02:56:47 progs/seaman > setenv GKLIB /nfs/public/lib
 % 161 gerard onyx 02:56:47 progs/seaman > SEAMAN

   
 *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN ***

   
 Version  - 950626/1.0
 (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  - Mon Jun 26 18:08:43 1995
 User     - gerard
 Mode     - interactive
 Host     - onyx
 ProcID   - 26929
 Tty      - /dev/ttyq13

   
 *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN ***

   
 Reference(s) for this program:

   
 *  1 * G.J. Kleywegt
        Uppsala University, Uppsala, Sweden
        Unpublished program

   
 *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN *** SEAMAN ***

   
 Max nr of residue types : (         20)
 Max nr of type atoms    : (         15)
 Max nr of residues      : (      10000)
 Max nr of atoms         : (     100000)
 Max nr of chains/models : (         26)

   
 Name of library file ? (/nfs/public/lib/seaman.lib)

   
 Reading library ...
 Lines read    : (        233)
 Residue types : (         20)

   
 SEAMAN options :

   
 ? (list options)                     ! (comment)
 QUIT program                         $ issue shell command

   
 READ molecule from PDB file          WRITe molecule to PDB file
 LIST molecule statistics             SEQUence of molecule

   
 BFACtor delete                       OCCUpancy delete
 ISOLated atoms delete                ZONE delete
 LOOPs delete                         TURNs delete

   
 GLYCine zone                         ALANine zone
 SERIne zone                          RESIdue type to Gly/Ala/Ser
 MINImalist substitutions             MUTAte replace rotamer
 ROTAmer residue

   
 Command ? (READ)
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6 COMMANDS

6.1 ?


This gives the list of options again.

6.2 !


A line starting with an exclamation mark is ignored.

6.3 QUIT


Stop the program.

6.4 $


Issue a shell command (e.g., ls -al *.pdb).

6.5 READ


Read a PDB file into memory. All HETATMs, hydrogens and other non-recognised atoms (including OXTs) are *stripped* on reading ! Hence, you don't have to edit the PDB file in advance to get rid of waters, ligands, metal ions etc.
After the structure has been read, SEAMAN runs a variant of YASSPA to figure out the secondary structure, and to define loops and turns (a turn is simply a stretch of 1-4 consecutive residues which connect two secondary structure elements).

NOTE: from version 1.3, SEAMAN uses the P-SEA algorithm to figure out secondary structure elements (Labesse et al., CABIOS 13, 291 (1997)). Since the default ranges they quote do not always lead to correct delineation of helices and strands, you can set a "sensitivity factor" by which the ranges will be multiplied (typical values ~1-1.5). 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (READ)
 PDB file name ? (m1.pdb) /nfs/pdb/full/1ldn.pdb
 Cell : (  84.900  118.200  135.500   90.000   96.070   90.000)
 Old chain |A| becomes chain A
 Old chain |B| becomes chain B
 Old chain |C| becomes chain C
 Old chain |D| becomes chain D
 Old chain |E| becomes chain E
 Old chain |F| becomes chain F
 Old chain |G| becomes chain G
 Old chain |H| becomes chain H

   
 Nr of lines read from file  : (      21617)
 Nr of atoms in molecule     : (      19584)
 Nr of chains or models      : (          8)
 Nr of hydrogens stripped    : (          0)
 Nr of HETATMs stripped      : (       1132)
 Nr of non-AA atoms stripped : (          0)

   
 Doing some book-keeping ...
 Running YASSPA ...
 Nr of ALPHA : (       1019)
 Nr of BETA  : (        380)
 Nr of TURN  : (        271)
 Nr of LOOP  : (        858)
 CPU total/user/sys :       5.2       5.0       0.2
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.6 LIST


List some information about the current molecule(s). 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (?) list

   
 Model read from file : (/nfs/pdb/full/1ldn.pdb)
 Last saved to file   : (not_saved_yet)
 Nr of atoms in molecule     : (      19584)
 Nr of chains or models      : (          8)
 Nr of residues              : (       2528)
    B-factors : Ave, Sdv :    26.12   13.68
                Min, Max :     0.50   68.32
  Occupancies : Ave, Sdv :     1.00    0.00
                Min, Max :     1.00    1.00

   
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.7 SEQU


List the sequence (residue type, name, secondary structure, average temperature factor and number of atoms). 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 ...

   
 Type      :  ARG    PHE    HIS    HIS    SER    ALA    ALA    THR    LEU    LYS
 Name      :  H313   H314   H315   H316   H317   H318   H319   H320   H321   H322
 Structure :  ALPHA  ALPHA  ALPHA  ALPHA  ALPHA  ALPHA  ALPHA  ALPHA  ALPHA  ALPHA
 <Bresi>   :   31.8   27.9   42.8   32.0   22.9   23.2   29.7   28.7   24.9   30.4
 # atoms   :  11     11     10     10      6      5      5      7      8      9

   
 Type      :  SER    VAL    LEU    ALA    ARG    ALA    PHE    THR
 Name      :  H323   H324   H325   H326   H327   H328   H329   H330
 Structure :  ALPHA  ALPHA  ALPHA  ALPHA  ALPHA  LOOP   LOOP   LOOP
 <Bresi>   :   39.2   28.9   22.3   34.3   42.5   34.9   47.3   33.0
 # atoms   :   6      7      8      5     11      5     11      7

   
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.8 BFAC


Delete atoms with too low or too high a temperature factor. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (LIST) bfac
 Provide B-factor limits for atoms to KEEP
 Limits ? (   1.000   60.000) 5 50
 Nr of atoms marked for deletion : (       1824)
 Delete them ? ( Y)
 Nr of atoms now : (      17760)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.9 OCCU


Delete atoms with too low or too high an occupancy. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (BFAC) occu
 Provide occupancy limits for atoms to KEEP
 Limits ? (   0.990    1.010)
 NO atoms marked for deletion
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.10 ZONE


Delete a zone of residues in any or all chains (models).
Zone selection works as follows:
- 0 0 => all residues
- 0 132 => all residues up to 132
- 133 0 => all residues beginning with 133
- 132 146 => all residues in [132,146]
- a chain ID or "*" (the latter meaning: "in all chains/models")

NOTE: if you run the program in batch mode (-b flag), the question "Delete them ? ( Y)" will *NOT* be asked !!! 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (OCCU) zone
 Select zone (0 0 = all residues)
 Zone ? (          0           0) 325 0
 Select chain (* = all chains)
 Chain ? (*)
 Nr of selected atoms : (        286)
 Nr of atoms marked for deletion : (        286)
 Delete them ? ( Y)
 Nr of atoms now : (      17474)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.11 LOOP


Delete all residues marked as LOOP. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (?) loop
 Nr of atoms marked for deletion : (       5630)
 Delete them ? ( Y)
 Nr of atoms now : (      11844)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.12 TURN


Delete all residues marked as TURN. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (LOOP) turn
 Nr of atoms marked for deletion : (       1798)
 Delete them ? ( Y)
 Nr of atoms now : (      10046)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.13 ISOL


Delete all atoms which are not connected to at least one other atom in the same residue. It is best to only do this at the very end, since it may delete atoms necessary for MUTAte, MINImalist or ROTAmer. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (?) isol
 Nr of atoms marked for deletion : (        669)
 Delete them ? ( Y)
 Nr of atoms now : (       9622)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.14 GLYC


Change a zone of residues to glycines. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (?) glyc
 Select zone (0 0 = all residues)
 Zone ? (        325           0) 10 30
 Select chain (* = all chains)
 Chain ? (*)
 Nr of selected atoms : (        231)
 Nr of atoms marked for deletion : (        109)
 Nr of atoms now : (       9513)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.15 ALAN


Change a zone of residues to alanines (glycines are left intact). 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (GLYC) alan
 Glycines left intact
 Select zone (0 0 = all residues)
 Zone ? (         10          30) 30 50
 Select chain (* = all chains)
 Chain ? (*)
 Nr of selected atoms : (        716)
 Nr of atoms marked for deletion : (        245)
 Nr of atoms now : (       9268)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.16 SERI


Change a zone of residues to serines (glycines and alanines are left intact). 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (ALAN) seri
 Glycines and alanines left intact
 Select zone (0 0 = all residues)
 Zone ? (         30          50) 50 70
 Select chain (* = all chains)
 Chain ? (*)
 Nr of selected atoms : (        756)
 Nr of atoms marked for deletion : (        176)
 Nr of atoms now : (       9092)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.17 RESI


Change all residues of a certain kind to Gly, Ala or Ser. For example, this can be used to replace all lysines by alanines, or all tryptophans to glycines (if you want to have an independent check on the correctness of a Molecular Replacement solution: Trp side-chain density should come up in the maps). 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (?) resi
 Glycines and alanines left intact
 Residue type ? (LYS)
 Nr of selected atoms : (        352)
 Change to Gly/Ala/Ser ? (ALA) ser
 Nr of atoms marked for deletion : (         88)
 Nr of atoms now : (       9004)
 Doing some book-keeping ...
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.18 MINI


Carry out some "minimalist" substitutions. Implemented are at present:
- anything except Gly, Ala --> Cys
- Ile or Val --> Thr
- Ile or Thr --> Val
- Arg --> Lys
- Asp <--> Asn
- Glu <--> Gln
- Trp --> His
- Tyr --> Phe
Note that *no rotamers* are involved; i.e., a Tyr --> Phe will give a phenylalanine with the same conformation as the tyrosine had !!
Note that this option *only* works if the residues are still intact ! 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (READ) mini
 Residue number ? (          1) 238
 Select chain (* = all chains)
 Chain ? (*)
 Nr of selected residues : (          8)
 Change to type ? (VAL) phe
 MINI : (A238)
 Nr of atoms marked for deletion : (          1)
 Nr of atoms now : (      19583)
 Doing some book-keeping ...
 MINI : (B238)
 Nr of atoms marked for deletion : (          1)
 Nr of atoms now : (      19582)
 Doing some book-keeping ...
 MINI : (C238)
 Nr of atoms marked for deletion : (          1)
 Nr of atoms now : (      19581)
 Doing some book-keeping ...
 MINI : (D238)
 Nr of atoms marked for deletion : (          1)
 Nr of atoms now : (      19580)
 Doing some book-keeping ...
 MINI : (E238)
 Nr of atoms marked for deletion : (          1)
 Nr of atoms now : (      19579)
 Doing some book-keeping ...
 MINI : (F238)
 Nr of atoms marked for deletion : (          1)
 Nr of atoms now : (      19578)
 Doing some book-keeping ...
 MINI : (G238)
 Nr of atoms marked for deletion : (          1)
 Nr of atoms now : (      19577)
 Doing some book-keeping ...
 MINI : (H238)
 Nr of atoms marked for deletion : (          1)
 Nr of atoms now : (      19576)
 Doing some book-keeping ...
 CPU total/user/sys :       1.7       1.7       0.0
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.19 MUTA


Same as Mutate_replace in O. Note that this option *only* works if the residues are still intact ! 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (MINI) muta
 Residue number ? (        238) 324
 Select chain (* = all chains)
 Chain ? (*)
 Nr of selected residues : (          8)
 Change to type ? (PHE) trp
 MUTA : (A324)
 RMSD (A) : (   0.025)
 NO atoms marked for deletion
 MUTA : (B324)
 RMSD (A) : (   0.006)
 NO atoms marked for deletion
 MUTA : (C324)
 RMSD (A) : (   0.012)
 NO atoms marked for deletion
 MUTA : (D324)
 RMSD (A) : (   0.008)
 NO atoms marked for deletion
 MUTA : (E324)
 RMSD (A) : (   0.014)
 NO atoms marked for deletion
 MUTA : (F324)
 RMSD (A) : (   0.008)
 NO atoms marked for deletion
 MUTA : (G324)
 RMSD (A) : (   0.006)
 NO atoms marked for deletion
 MUTA : (H324)
 RMSD (A) : (   0.048)
 NO atoms marked for deletion
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.20 ROTA


Replace a residue by the most-frequent rotamer of its kind (i.e., same as Lego_auto_sc in O). Note that this option *only* works if the residues are still intact ! 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (MUTA) rota
 Residue number ? (        324) 314
 Select chain (* = all chains)
 Chain ? (*)
 Nr of selected residues : (          8)
 ROTA : (A314)
 Identical residue types; replace by rotamer
 ROTA : (B314)
 Identical residue types; replace by rotamer
 ROTA : (C314)
 Identical residue types; replace by rotamer
 ROTA : (D314)
 Identical residue types; replace by rotamer
 ROTA : (E314)
 Identical residue types; replace by rotamer
 ROTA : (F314)
 Identical residue types; replace by rotamer
 ROTA : (G314)
 Identical residue types; replace by rotamer
 ROTA : (H314)
 Identical residue types; replace by rotamer
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

6.21 WRIT


Save the current model in a PDB file. 

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 Command ? (?) writ
 PDB file name ? (not_saved_yet) q.pdb
 Number of atoms written : (       9055)
 CPU total/user/sys :       2.6       2.6       0.1
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----

7 KNOWN BUGS

None, at present.

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