[ defCell | accFunction | gapFunction | I_out | M_out | R_out | R_2out | S_out | S_proteinTags | swissFields | readMolNames | Selection variable | as_out | as2_out | vs_out ]

the real array of the solvent accessibility penalty parameters (as described in Batalov and Abagyan, 1999). It contains the values of a, b, c and E damping parameters for amino acid substitution scores. Generally, if a residue is completely buried ( Area=0), its substitution scores will be used without changes. If it is completely exposed, its substitution scores will be multiplied by the minimal possible value of a. Between these cases the substitution scores are modulated by a smooth ("arctangent") function with a saddle point at Area=c, where the slope will be -b. The fourth parameter is reserved for development.

 
 gapFunction = {2.4 0.15 10. 0.05 20. 0.} 

• gap penalty=2.25+0.15*L for L={ 0..10} (and for L=1 it is 2.4= gapOpen ),
• gap penalty=3.25+0.05*L for L={11..20} and
• gap penalty=4.25 for L>20

The calculations are fastest for the traditional two-element gapFunction. The three- or four-element gapFunction invokes the optimized routines and is 50-70% slower. The general kind gapFunction costs approximately 70-90% additional time for every pair of gapFunction values. If the last gapExtension is zero, it may be omitted. This definition is effectively implemented in the Align , Score functions and find database search command.

Functions returning in R_out:

• Axis # middle point of the axis
• Disgeo # returns error sum of negative scaled eigen values in R[0], and first three 3 scaled eigen values
• LinearFit # residuals
• Xyz( .. ) returns inverse transformation
• learn returns model accuracy and stds.

R_2out

auxiliary rarray. Used in addition to R_out.

S_proteinTags

sarray of sequence patterns that can be used for detection or deleting those tags from a sequence using Trim ( seq S_tags ) function.

If the field name starts from a minus ('-'), this field will be ignored in the feature table list. Also note that variable i_2out (after read sequence) contains the beginning of mature sequence.

Example:

swissFields={"-HELIX ","-COIL ","-STRAND","-TURN "}
# to suppress the FT records with the secondary structure info

 
... 
M  END 
> <CAT_NO> 
R150002 
 
> <NAME> 
(5-OXO-HEXAHYDRO-PYRANO[3,2-B]PYRROL-1-YL)-ACETIC ACID METHYL ESTER 
 
$$$$ 

 
readMolNames = {"<CAT_NO>" "<NAME>"} # useful for Sigma-Aldrich files 

 
readMolNames = {"<CODE>" "<IUPAC_NAME>"} # useful for ACD database 

Examples:

 
 cc = a_//ca                 # created named selection variable cc  
 show cc & a_/3:15           # use it in the expression  

 
 cc = "a_//ca"      # in this case cc is a string, not a selection 
 show $cc & a_/3:15 # $cc is replaced by a_//ca before parsing 

How to store and exchange selections in strings:Examples of using the String ( os|ms|rs [name|number] ) function to return a residue selection:

l_showResCodeInSelection = yes # the default
res_str = String( Res(Sphere( a_H [1] a_A//!h*,ca,c,n,o 3.5 )))  # same as with option String(.. name)
show res_str
 a_2c0cb.b/^T159,^S205,^K209,^Y224,^V248,^Y275,^L305,^M356,^N361
# or 
l_showResCodeInSelection = no 
res_str = String( Res(Sphere( a_H [1] a_A//!h*,ca,c,n,o 3.5 )))  # same as with option String(.. number)
show res_str
 a_2c0cb.b/159,205,209,224,248,275,305,356,361

• Rmsd
• Srmsd
• superimpose
• set tether
• show drestraint
• show tethers
• find chemical

• Rmsd
• Srmsd
• superimpose
• set tether
• show drestraint
• show tethers

• read variable saves a selection of loaded variables;