disulb¹ identify disulphide bridges

firstp¹ identify atoms with poulation parameters to be refined

spcpep¹ identify the C and N terminus groups for each chain

altchn¹ identify alternate chains

restrm^2,3 identify and idealize terminal and main residues

reslnk³ identify and idealize linkage residues

residu³ identify and idealize standard chain residues and other groups

reside³ identify and idealize the last standard residue at ends of chains

distrm⁴ characterize terminal chain residue interatomic distances

dislnk⁴ characterize linking chain residue interatomic distances

disres⁴ characterize normal chain residue interatomic distances

plares⁵ identify planar groups in standard residues

plapro⁵ identify multi-planar prosthetic planar groups

platrm⁵ identify terminal planar groups

plalnk⁵ set up the four linking planar groups

plalnl⁵ specify restraining pairs for linking planar groups

chiral⁶ characterize ideal chiral centres

vdwdis⁷ set van der Waals diameters by atomic species

vdwtrm⁷ number of non-bonded contacts for specified terminal residue

vdwlnk⁷ number of non-bonded contacts for specified linking residue

vdwres⁷ number of non-bonded contacts for specified residue

vdwcon⁷ van der Waals contact codes for vdwtrm, vdwlnk, or vdwres

tortrm⁸ identify atoms defining ideal torsion angles in terminal residues

neighb⁸ identify neighbours in torsion groups

chidis⁸ set neighbour distance identification

torres⁸ identify atoms defining ideal torsion angles in chain residues

chiwgt⁸ set weighting codes for torsion angles

secstr⁸ characterize secondary structure features by ψ and φ values

elltrm⁹ set ellipsoid specifications for terminal groups

ellres⁹ set ellipsoid specifications for main chain groups

interd^10,11 set up blocks of inter chain special distances

intrad¹¹ set up blocks of intra chain special distances

spcdis¹¹ set up special inter-group distances

spcpla¹² specify special planar groups

excon¹³ specify distance identifiers for contact exclusion

secsel¹⁴ specify elements of secondary structure for backbone

spcsym¹⁵ identify chains related by non-crystallographic symmetry

symop¹⁵ rotation and translation of a non-crystallographic symmetry

symwgt¹⁵ set non-crystallographic symmetry restraint weighting specs

1 Group 1 input lines set up standard groups dictionary.

2 Note that, if at this point all the lines from restrm through ellres are left out the values will be taken from the prores file. This is the default file of idealized groups. A prores file is supplied with the Xtal system which contains all the usual groups encountered in protein structures.

3 Group 2 input lines set up ideal coordinates of residues.

4 Group 3 input lines set up distance restraints.

5 Group 4 input lines set up plane restraints.

6 Group 5 input lines set up chiral centre restraints.

7 Group 6 input lines set up contact restraints.

8 Group 7 input lines set up torsion angle restraints.

9 Group 8 input lines set up anisotropic thermal restraints.

10 Note that the following lines are optional. All references to chain identities and user residue numbers are in terms of the names and numbers supplied through the PROATM program. These names and numbers are translated to pointers for use in the calculations. Some error messages may display these pointers. In this case the chain pointers will be 1, 2, ... In order of chain identification encountered in the atom or proat lines loaded in PROATM. The residue pointers will be the sequence number for the residue in order of loading by PROATM.

11 Group 9 input lines set up special distances restraints.

12 Group 10 input lines set up special plane restraints.

13 Group 11 input lines set up contact exclusion restraints.

14 Group 12 input lines set up backbone torsion angle restraints.

15 Group 13 input lines set up non-crystallographic symmetry restraints.

PROTIN Option Code

print atom coordinates atl no

neutron data neu no

number of unit cells used in search cel n 3

number of main chains in a plane nap n 5

limit for van der Waals distances vdw d 5

expect hydrogen atoms hat no

expect individual aniso t.f. ani no

atl

dataset number dset n 1

disulb 1 chain identifier of CYS residue on one side of the S-S bridge

2 residue sequence number on that side

3 chain identifier of CYS residue on other side of the S-S bridge

4 residue sequence number on the other side

firstp 1 name of the first atom, in the notation of PROATM on loading, to have the population parameter refined. This atom and all atoms to the end of the atoms loaded will have their population parameters refined in the subsequent PROLSQ run

spcpep 1 chain identifier symbol e.g. A2

2 number of cis peptide bonds in chain

3 residue sequence number of cis peptide

altchn 1 primary chain identifier for mothers of alternate chains

2 secondary chain identifier for mothers of alternate chains

p s

if there is 1 chain and 1 alternate chain: 1 0

if there is 1 chain and 2 alternate chains: 1 1

if there are 2 chains and each has 1 alternate chain: 1 2

if there are 2 chains and only chain 1 has 1 alternate chain: 1 0

if there are 2 chains and only chain 2 has 1 alternate chain: 2 0

Alternate conformations of discretely disordered residues are assigned during atom loading a different chain number from the mother chain for a given residue. Only the atoms which are modelled in different positions should be included among the input atoms.

restrm 1 group name for residue e.g. NAMINO ; ASP ; HIS

2 name of atom in the group e.g. CA for α carbon

3 x Cartesian coordinate in Å relative to Cα as origin in each group

4 y Cartesian coordinate

5 z cartesian coordinate

6 order number of atom within the group, e.g. 1 for N, 2 for Cα, etc. For all standard groups, save glycine, this number starts at 5 because the coordinates of restrm main are automatically taken for the first four atoms of every group. This number may also be negative in reslnk lines to designate atoms belonging to a previous residue

7 single letter code which is to be used as a synonym for the group name e.g. G for GLY. Used only for standard groups

reslnk fields as for restrm

residu fields as for restrm

reside fields as for restrm

distrm 1 group name as defined in res*** input lines e.g. NAMINO

2 order number of origin atom for corresponding distance

3 order number of terminus atom for corresponding distance

4 code to define weight that is to be used to restrain distance

1 bonded pair 2 angle pair

3 planar 1-4 distance 4 XH bond distance

5 Y-X-H angle distance 6 H-X-H angle distance

5 code to define weight that is to be used to restrain B values

0 any distance for which B restraint is not required

1 bond distance between two main chain atoms

2 angle distance between two main chain atoms

3 bond distance involving at least one side chain atom

4 angle distance involving at least one side chain atom

5 bond distance involving a hydrogen

6 angle distance involving a hydrogen

Fields 6-9, 10-13, etc. are as for fields 2-5. Note that lines may be continued by placing a "c" as the last field on a line. The next line must then have the same ID for both line type and group name. Fields continue in groups of four to complete the required restraints.

dislnk fields as for distrm

disres fields as for distrm

plares 1 group name

2- the order number of the atoms of the group which are to be restrained to planarity. If a group has no planes fields 2- are left blank

plapro fields as for plares

platrm fields as for plares

plalnk fields as for plares

plalnl 1- codes specifing all the possible "restraining pairs" among the atoms specified in the reslnk input lines

Note that only the number of atoms specified to be in planes and given in the PROTIN line under directive nap will be considered to restrain the plane.

chiral 1 group name

2 descriptor code for how the chirality of the group is defined

1 for groups intrinsically chiral

0 for chirality related to nomenclature, e.g. LEU VAL

vdwdis 1 name of atom species e.g. HYDROGEN (limit 12 characters)

2 atomic number of species or atomic scattering factor pointer (carbonyl is arbitrarily set to 3)

3 van der Waals diameter of the species or distance between centres of two non-bonded atoms of the species

vdwtrm 1 group name

2 number of non-bonded contacts for group

vdwres fields as for vdwtrm

vdwlnk 1 group name

2 number of non-bonded contacts for group

3 number of non-bonded contacts specified for prolyl link

vdwcon 1 group name

2 order number of origin atom corresponding to a possible non-bonded contact

3 order number of terminus atom for corresponding possible non-bonded contact

4 non-bonded distance restraint class:

1 relative position of the given atoms is determined by only one torsion angle

2 relative position of the given atoms is determined by two or more torsion angles

These lines follow their corresponding vdwres, vdwtrm, or vdwlnk lines. Fields 5-7, 8-10, etc. are as fields 3-4, continuing onto additional lines as required to satisfy the counts given in the preceding vdwres, vdwtrm, or vdwlnk lines.

tortrm 1 group

2 atom order number for C(i-1)

3 atom order number for N(i)

4 atom order number for Cα(i)

5 atom order number for C(i)

6 atom order number for N(i+1)

7 atom order number for Cα(i+1)

Fields after 7 are ignored in tortrm lines

8 atom order number for Cβ(i)

9 atom order number for Cγ(i)

10 atom order number for Cδ(i)

11 atom order number for C∊(i)

12 atom order number for Cζ(i)

13 atom order number for N(i)

C(i-1)-N(i)-Cα(i)-C(i) specifies φ

N(i)-Cα(i)-C(i)-N(i+1) specifies ψ

Cα(i)-C(i)-N(i+1)-Cα(i+1) specifies ω

N(i)-Cα(i)-Cβ(i)-Cγ(i) specifies χ(1)

Cα(i)-Cβ(i)-Cγ(i)-Cδ(i) specifies χ(2)

torres fields as for tortrm

neighb 1 group

2- neighbour identification codes

-1 for atoms from residue i-1

0 for atoms from residue i

1 for atoms from residue i+1

5 for atoms from terminal groups e.g. OT of carboxyl terminus

chidis 1 group

2 distance identification codes (as specified in field 4 of the distrm line)

chiwgt 1 group

2- weighting code for side chain chi angles

0 for no specifications

2 for planar e.g. χ(5) of ARG

3 for staggered e.g. aliphatics

4 for orthonormal e.g. χ(2) of aromatics

secstr 1 name for element of structure up to 20 characters maximum

2 code for secondary structure element

1 α helix

2 3(10) helix

3 π helix

4 collagen type helix

5 parallel β sheet

6 anti-parallel β sheet

7 classic β bulge position 1

8 classic β bulge position 2

9 β bend [or turn] type I position 2

10 β bend [or turn] type I position 3

11 β bend [or turn] type II position 2

12 β bend [or turn] type II position 3

13 γ turn position 1

14 γ turn position 2

15 γ turn position 3

3 characteristic φ value

4 characteristic ψ value

5 literature reference of up to 40 characters

elltrm 1 group name

2 order number for atom for which ellipsoid is being specified

3 order number for atom p(0)

4 order number for atom p(1)

5 order number for atom s(0)

6 order number for atom s(1)

Note that negative numbers are used to point to atoms in preceding residues.

Fields 7-11, 12-16, etc. for additional ellipsoid atoms; new lines to continue.

ellres fields as for elltrm

intrad 1 origin chain identifier

interd 1 origin chain identifier

2 target chain identifier

Note: There must be spcdis lines following each intrad or interd line supplied. The number required will depend upon the number of special inter-group distances for this chain block to be restrained. e.g. Sγ - Sγ from two different CYS groups that form a bridge; distance from solvent to protein; etc. One line per pair of atoms for which distance is to be restrained.

spcdis 1 residue sequence number of group to which origin atom belongs

2 order number of origin atom within group

3 residue sequence number of group to which target atom belongs

4 order number of target atom

5 restrain atoms to this distance (in Å)

6 code to determine weight that should be used to restrain distances. Same as those shown for disres lines

7 code to determine weight that should be used to restrain temperature factors. Same as those shown for disres lines

spcpla 1 chain identifier of first atom in special plane

2 residue sequence number of first atom in special plane

3 order number of first atom in special plane

4-6 the same quantities as in 1-3 for the second,

7-9 third, ... atoms which define the special plane

etc

excon 1 chain identifier of first atom for which contacts are to be excluded

2 residue sequence number of first atom

3 order number of first atom

4-6 same as in 1-3 for the second atom which defines the contact exclusion

secsel 1 chain identity; all chains of this type will be set

2 residue sequence number of the initial group for this region of structure

3 residue sequence number of the final group for this region of structure

4 code for structure type

-1 restrain φ & ψ values to those of initial structure

0 no restraints on φ & ψ

n restrain φ & ψ values specified in secstr line for this n

spcsym 1-n chain identities in this special non-crystallographic symmetry group

Each spcsym line must be followed by one or more symop lines.

symop 1-12

symwgt 1 initial residue sequence number to which the symop applies

2 final residue sequence number to which the symop applies

3 weighting code

implication for

Code main chain side chain

1 1 1

2 1 2

3 1 3

4 2 2

5 2 3

6 3 3

where 1=tight; 2=medium; 3=loose

4-6 as in 1-3 for all group spans specified. etc