ProFit V3.1 =========== ********************************************************************** * NOTE: This document is rather out of date - it does not describe * * all the current features of ProFit. You should look at the * * ProFit manual at http://www.bioinf.org.uk/programs/profit/doc/ * ********************************************************************** (c) Dr. Andrew C.R. Martin, SciTech Software, 1992-2009 Some features added and bugs fixed while working for University College London. Some features added and bugs fixed while working for University of Reading under consultancy to Inpharmatica, Ltd. Features in V3.0 (c) Dr. Craig T. Porter, UCL, 2008-2009 funded by BBSRC The ultimate protein least squares fitting program! To access the ProFit download page, point your browser at http://www.bioinf.org.uk/software/ ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate least squares fitting program and is written to be as easily portable between systems as possible. It performs the basic function of fitting one protein structure to another, but allows as much flexibility as possible in this procedure. Thus one can specify subsets of atoms to be considered, specify zones to be fitted by number, sequence, or by sequence alignment. The program will output an RMS deviation and optionally the fitted coordinates. RMS deviations may also be calculated without actually performing a fit. Zones for calculating the RMS can be different from those used for fitting. The interface is command driven, but may offer a graphical environment at a later date. This document gives an overview of the features and command language, but isn't regularly kept up-to-date to reflect new features. There is a full comprehensive manual describing all the command in the 'doc' subdirectory of the full distribution. Features: 1. Portability 2. Specify atom subsets 3. Specify zones: a) Numerically b) By sequence c) By auto sequence alignment 4. Output RMS over a) Fitted region b) Any other region 5. Output fitted coordinates 6. Help facility 1. Portability -------------- The code is written in highly portable ANSI-C. A future feature may be a Tcl/Tk-based graphical interface, but this will be separate from the main program. Earlier version of the code supported windowing, but this has been dropped from the release version in favour of a separate GUI layer which will call ProFit with a control script. 2. Atom Subsets --------------- These may be specified for both fitting and RMS calculation. e.g. ATOMS N,CA,C,O 3a. Numeric zones ----------------- These are specified as follows: ZONE * Fits all residues in both structures, clearing other zone specifications. ZONE *:1-100 Fits all in Reference with 1-100 in Mobile ZONE 10-20 Fits 10-20 in Reference with 10-20 in Mobile ZONE 10-20:30-40 Fits 10-20 in Reference with 30-40 in Mobile ZONE -10:50-59 Fits 1-10 in Reference with 50-59 in Mobile If you have multiple chains, the chain name may preceed the residue number (e.g. ZONE L24-L24); if unspecified, the first chain is assumed. If the PDB file has insertions, the zone may include an insert code by placing it after the residue number (e.g. L25B or 50C) Optionally, the chain name may be separated from the residue number by a full stop. Using the full stop also makes the statement case-sensitive. In practice, the full stop separator is used with either numeric or lowercase chain names. 3b. Sequence zone specification ------------------------------- Typing a sequence will search for this seq in both structures and fit these regions. ZONE CAR:VNS Fits first occurence of CAR in Reference with first occurence of VNS in Mobile ZONE CAR,10:VNS,10 Fits 10 residues from first occurence of CAR in Reference with first occurence of VNS in Mobile ZONE CAR,5/2 Fits 5 residues from secon occurence of CAR in both structures ZONE 24-34:EIR,11 Fits 24-34 in Reference with 11 residues from first occurence of EIR in Mobile 3c. Auto sequence alignment --------------------------- Needleman & Wunsch sequence alignment is provided to perform fitting on sequence aligned residues. The keyword ALIGN sets up zones from the matched parts of the sequence alignment. Alternatively, one may read a sequence alignment from a file using the READALIGN keyword. 4a. RMS over fitted region -------------------------- The program will report the RMS deviation over the fitted region once fitting has been performed with the command FIT. The RATOMS keyword has the same syntax as the ATOMS keyword and will cause the specified atoms to be included in the RMS calculation. 4b. RMS over other regions -------------------------- The keyword RZONE has the same syntax as the keywords ZONE, but causes the RMS to be calculated over the specified residue zone. 5. Output fitted coordinates ---------------------------- WRITE causes the fitted coordinates to be written to file. 6. Help facility ---------------- A comprehensive VAX style help facility is provided. Type HELP once in ProFit to enter the help facility. Running ProFit ============== profit [-h] [reference.pdb mobile.pdb] Optionally you my specify the reference and mobile PDB files on the command line. Otherwise you may use the REFERENCE and MOBILE commands once in the program. The -h flag causes the program to read HETATM records from the PDB files. The default is to ignore them. This may be changed using the (NO)HETATOMS commands. Keywords ======== Basic commands -------------- REFERENCE file.pdb Specify the reference structure MOBILE file.pdb Specify the structure to be fitted FIT Causes the structures to be fitted on the current residue/atom selection. The RMS deviation will be reported over the fitted selection. Specifying atoms ---------------- ATOMS atm[,atm]... Specify atoms to be considered in fitting. BVALUE cutoff [REF|MOB] Ignore atoms (in fitting and RMS calculation) if B-value greater than specified cutoff. Optional REF or MOB causes calculation to be restricted to the specified structure. A negative cutoff may be used to ignore atoms with B-values less than the absolute (i.e. unsigned) value of the cutoff. Specifying zones ---------------- ZONE CLEAR|((*|(X...[,n][/m])|(j[-k]))[:(*|(X...[,n][/m])|(j[-k]))]) Specify the zone to be fitted either numerically, or as a sequence. Repeating the specification after a colon refers to the mobile structure. X represents a residue type or ? wildcard. n represents a number of residues. m represents the m'th occurence of the sequence. j and k represent residue numbers. DELZONE CLEAR|((*|(X...[,n][/m])|(j[-k]))[:(*|(X...[,n][/m])|(j[-k]))]) Delete fitting zone. This command uses the same syntax as ZONE. SETCENTRE CLEAR|(*|j[:j]) Specifies a single residue as the centre of fitting. NUMBER (RESIDUE|SEQUENTIAL) Specify zones based on residue numbering or sequential numbering ALIGN Perform N/W alignment. Set the fitting zones based on the sequence aligned residues. GAPPEN penalty [extend_penalty] Specify gap penalty and extension penalty for ALIGN command (default: 10 and 2 resp.) READALIGNMENT file.pir Read a PIR alignment file and set zones from that. Calculating RMSD over different atoms/zones ------------------------------------------- RATOMS atm[,atm]... Specify atoms to be considered in RMSd calc. Then reports the RMSd. RZONE CLEAR|((*|(X...[,n][/m])|(j[-k]))[:(*|(X...[,n][/m])|(j[-k]))]) Specify zone to be considered in RMSd calc. Then reports the RMSd. DELRZONE CLEAR|((*|(X...[,n][/m])|(j[-k]))[:(*|(X...[,n][/m])|(j[-k]))]) Remove zone for RMSd calculation. Obtaining output ---------------- WRITE file.pdb Writes the fitted mobile coordinates MATRIX Displays the rotation and translation matrices for fitting. STATUS Shows information on the current selections. RMS Redisplays the RMS calculated over the current zones. RESIDUE [filename] Display a by-residue RMS over current RATOMS and RZONES (ATOMS and ZONES if RATOMS and RZONES are not specified) NFITTED Report number of atom pairs fitted Reading non-protein atoms ------------------------- HETATOMS Read HETATOMS (default if started with -h) NOHETATOMS Do not read HETATOMS (default unless started with -h) Weighting the fit ----------------- WEIGHT Weight the fitting by the B-value BWEIGHT Weight the fitting by the inverse of the B-value NOWEIGHT No weighting (default) Miscellaneous ------------- HELP [keywd] Gives help on keywd if specified; otherwise lists valid keywords. IGNOREMISSING Ignore missing atoms during fitting NOIGNOREMISSING Restore default of generating an error if there are any missing atoms QUIT Exits the program. Not yet implemented: ==================== GRAPHIC Start graphical alignment