CORMA

CORMA

Table of Contents

corma (COmplete Relaxation Matrix Analysis)

DESCRIPTION

corma (COmplete Relaxation Matrix Analysis) is a FORTRAN program for calculating the dipole-dipole relaxation matrix for a system of protons and converting that to intensities expected for a 2DNOE experiment.

Programs for structure elucidation by NMR
The mardigras and corma programs are two separate programs for structure elucidation by nmr. newhyd prepares a pdb file for input to corma.in. If the user has the coordinates in the PDB format for heavy atoms but not protons, it supplies the missing protons and their coordinates; it is a stand alone program. corma.in prepares the output pdb file from newhyd for input to mardigras or corma. mardigras uses the output pdb file from corma.in for the iterative relaxation matrix calculation.

New features
The programs mardigras, and corma have been modified to incorporate (i) an improved computation of distances when averaging due to motion or overlap of methyl groups, methylene proton pairs or symmetry-equivalent aromatic ring protons exist, (ii) internal motions as modelled by a `model-free' approach, and (iii) chemical exchange described by a kinetic matrix of exchange rates. The effect of the exchange with solvent protons and the exchange between the two amino protons are included in the complete relaxation matrix calculation of NOE intensities. If the two amino protons are unsolvable, the intensity is calculated based on r-6 averaging of the two distances.

Pseudoatom names to be used in the input and output intensity files have been changed.

The corma has also been modified to do an ensemble R factor calculation. When multiple number of PDB files (maximum 5000) of the same molecule are provided, corma calculates the NOE intensities based on the ensemble averaged relaxation rates over the number of structures.

The corma can also be used for chemical fast exchange for bound and free drug-DNA complex.

corma.in has also been modified to include internal motion parameters. and a specification for fractional occupancy of a position by a proton.

Calculation of distances for methyl, methylene or symmetryequivalent aromatic protons.
One of the most important additions to the corma/mardigras algorithm lies in the calculation of distances involving methyl groups. Methyl rotation can be modeled in one of four ways by corma/mardigras (see METHYL JUMP below under INPUT). For all models except model 0, distances are calculated iteratively to a pseudoatom at the geometric center of the three methyl protons. Geometric parameters in models 1, 2 and 3 are taken from the input model coordinates and are assumed to be correct. One should therefore have some degree of confidence in the relative orientations of methyl groups in the input model before using one of these more accurate methods of calculating distances to methyl pseudoatoms. The iterative fitting procedure, then, is simply a one-parameter (viz. distance) fit. (One could conceivably perform a multi-parameter fit over methyl orientations as well, but this would not yield a unique solution.) The advantage of this technique is that, when using corma/mardigras for structure evaluation/refinement, methyl distances can be calculated very accurately, and no additional uncertainty need be added to calculated distance bounds. For model 0, inter-residue distances to methyls (and other pseudoatoms) are calculated for the two extreme geometric cases. These extremes define the upper and lower bounds on possible distances. This will prevent unwarranted restraint on distances when the model-structure geometry is unreliable.

A similar procedure is followed for distances to pseudoatoms which represent either (1) a methylene proton pair or (2) symmetry-equivalent aromatic ring protons. These protons are chemically equivalent, or sufficiently close such that their cross-peaks are not resolvable. In both cases we assume that motion is occurring which is slow relative to the overall tumbling time (and thus does not contribute to relaxation) but fast relative to the relaxation times. Effective pseudoatom distances are obtained by r-6 averaging over the two actual distances. This approach is rigorous for aromatic ring flip but not for methylene pairs. The equivalence (often approximate) of methylene chemical shifts is not necessarily a result of their mobility, although the assumption of motion may be better for protein side-chains and other freely-rotatable methylenes. In some cases, namely for constrained methylenes in DNA and Proline, it may be a better approximation to treat them as static atoms. Note that this r-6 averaging reduces to the same interaction as the case for static methylene protons in the limit of isolated spins. All of the error is introduced in the term for transfer of magnetization between the two methylene protons. In this model, magnetization is transferred perfectly, since the two atoms are collapsed into a single pseudoatom. The result of this treatment will be an error in the calculation involving local spin-diffusion effects. The error is only in a single spin-pair, and the results of preliminary tests indicate that the the overall error introduced is minor. Consider a methylene pair near two other protons A and B. The error introduced is at its maximum when the four protons are in line and at the closest possible distance. The error is zero when the intra-methylene axis is perpendicular to the A-B axis.

Nevertheless, the pseudoatom approach is the simplest reasonable model, since we have only a single experimental cross-peak and are justified in deriving only one distance. If the model geometry is correct, then we can extract the proper distances from the effective distance (using an iterative fitting procedure similar to that for methyls). If the model geometry is poor, we can at least calculate error bounds on that distance assuming extreme-case geometries. This is what is done. If methyl jump model 0 is chosen, the reported distance is the effective average distance, with upper and lower bounds adjusted accordingly. Models 1, 2 and 3 assume that the model geometry should be taken to be correct.

Model-free approach to internal motion
When the details of internal motion are not known, the model-free approach is useful. This model is now one of the options for the calculation of the relaxation matrix. The spectral density Jmodfree for the model-free model is defined in terms of the frequency C, anisotropy parameter A, order parameter S2, overall correlation times I1 and I2, and the internal correlation time Ie as

Jmodfree(C,A,S2,I1,I2,Ie)
=AS2J(I1,C)+(1-A)S2J(I2,C)+A(1-S2)J(Ip,C)+(1-A)(1-S2)J(Ipp,C)

where
J(In,C)=In/(1+(InC)2)

Ip=IeI1/(Ie+I1)

and
Ipp=IeI2/(Ie+I2)

In the program the ratio I2/I1 is used. For I2/1=1, or A=1, isotropic overall motion is obtained. If the order parameter S2 is set to 1, the internal motion is ignored. If both A and S2 are set to one, the result is isotropic overall motion with no internal motion. The `model-free' approach is same as the well-known `wobble-in-a-cone' model. (Ref.: Lipari, G. and Szabo, A. J. Am. Chem. Soc. , 104, 4546, 4559 (1982))

To use model free approach, the input PDB file has to be prepared using corma.in with model free option. The modified PDB file contains the key word and parameters that are required by model free approach. The order parameters are not included in the PDB file because they are defined for proton pairs, not for individual protons. A seperate input file with the same format as the intensity file is required for the order parameters. It is not necessary to have a complete list of order parameters in the file. The default value is 1.0 for all proton pairs. Only those order parameters which are different from 1.0 need to be included in the order parameter file.

The order parameter may be assessed via molecular dynamics calculations (Ref.: Koning, T.M.G. et al., Biochemistry, 30, 3787-3797 (1991)) or via experimental determination.(Ref.: Lane, A.N., J. Magn. Reson., 78, 425-439 (1988)) Of course, if the order parameter is less than one but identical for all proton resonances, then the relative cross-peak intensities will not be altered.

Quality factors
We added quality factors Q, Q2, Qx and Q2x to mardigras/corma output. The quality Q factor is described in J. M. Withka, J. Srinivasan and P. H. Bolton, J. Magn. Reson. 98, 611-617 (1992). The sixth root quality factors, Qx and Q2x, are obvious extrapolations from sixth root R factors.

Chemical exchange described by kinetic matrix The exchange with solvent protons and the exchange between the two amino protons are taken into account in the calculation of NOE intensity matrix. NOE intensities of exchangeable protons are weakened by the exchange with solvent protons. Neglecting of such effect produces the upper bounds of the distances. While consideration of the upper limit of the exchange rates gives the lower bounds of the distances. When the two amino protons are unsolvable, a mean distance is calculated iteratively from the relaxation rate based on r-6 averaging.

The relaxation matrix is modified by adding exchange matrices. The exchange with solvent contributes to direct relaxation, and is described by a diagonal matrix K. The element Kii equals exchange rates for exchangeable protons, and zero for nonexchangeable protons. A second exchange matrix K' is formed for proton pairs which exchange the positions. If two protons, i and j, are exchanging positions with each other with a rate k, then K'ij = K'ji = -k, and K'ii = K'jj = k. Zero is assigned to K' elements if proton pair exchange is not involved. (See, J. Jeener, B. H. Meier, P. Bachmann and R. R. Ernst, J. Chem. Phys. 71, 4546 (1979).) The modified relaxation matrix is then R' = R+K+K'.

Note that if the option ARBITRARY RATES? is specified as y then the modified relaxation matrix is R' = R+K and the exchange matrix K is read as is from the exchange file and is not modified in any manner.

Peak Integration Errors
The percentage errors in the intensities due to peak integrations may be included as an additional column in the intensity file. The format is free, but a key word ERROR% is required at the top of the column, see example1.INT.1. Note, peak integration errors in the intensity file are not used in corma. They are used in mardigras, together with the signal to noise level given in the PARM file, to determine the upper and lower distance bounds (in output file prefix.BNDS).

INPUT

corma is an interactive program and is invoked as:

unix:>corma

And the computer responds as:

CORMA 4.0 UNIX VERSION CO(mplete) R(elaxation) M(atrix) A(nalysis)

SPECTROMETER FREQUENCY IN MHz: 500.0

INCLUDE KINETIC EXCHANGE? [def=n]: y
ENTER the name of kinetic rate file: example2.exch

ARBITRARY RATES? [def=n]: n

INCLUDE FAST EXCHANGE? [def=n]: y

ENSEMBLE (MULTIPLE FAST EXCHANGE)? [def=n]: y ENTER the name of pdb filenames list file: example2.list

COMPARE WITH EXPERIMENTAL INTENSITIES? [def=n]: y

ENTER NAME OF EXPERIMENTAL INTENSITY FILE: example2.INT.1 NORMALIZE USING ONLY FIXED-DISTANCE INTENSITIES [def=f], OR USE ALL Iobs [a]? f

NAME FOR INTENSITY FILE TO BE CREATED: test1 WRITING TO FILES: test1.CRM.1 test1.INT.1

CUTOFF LEVEL FOR INTENSITIES? (ENTER 1, 2, 3, 4, or 5; 1=0.1, 2=0.01, 3=0.001, ETC.) [def=3]: 3

DISPLAY INTENSITIES IN EXTENDED PRECISION? [def=y]: y

ADD RANDOM NOISE? [def=n]: n

SELECT METHYL JUMP MODEL:

[1] 3-site for intra-residue relaxation, 18-sitefor inter-residue [2] 18-site for all methyl relaxation [3] 3-site for all methyl relaxation ENTER (1/2/3) [default=3] :3

READING PDB FILE: example2.pdb No.1 Probability: 0.5000

GENERATE POSTSCRIPT FILES FOR PLOTTING? [def=n]: n
READING PDB FILE: example2.pdb No.2 Probability: 0.5000
Total Probability1.000 Reading exchange file: example2.exch QN2 2 QN2 2 1.00000 H1 2 H1 2 1.00000
HN42 13 HN42 131.00000
HN41 13 HN42 13-1.00000 QN6 6 QN6 6 10.00000 QN6 11 QN6 11 10.00000 H3 4 H3 4 10.00000 H3 9 H3 9 10.00000 Writing the modified non-zero exchange rates H1 2 H1 2 1.00000 QN2 2 QN2 2 1.00000 H3 4 H3 4 10.00000 QN6 6 QN6 6 10.00000 H3 9 H3 9 10.00000 QN6 11 QN6 11 10.00000
HN41 13 HN41 131.00000
HN42 13 HN41 13-1.00000
HN42 13 HN42 132.00000

CALCULATING EIGENVALUES
Fixed DST:5 H5'2 2 H5'1 2 1.772
Fixed DST:65 H2'2 2 H2'1 2 1.772
Fixed DST:90 H5'2 4 H5'1 4 1.772 Fixed DST: 152 M7 4 H6 4 2.980 Fixed DST: 153 M7 4 M7 4 1.772
Fixed DST:230 H2'2 4 H2'1 4 1.772
Fixed DST:275 H5'2 6 H5'1 6 1.772 Fixed DST: 404 H2 6 H8 6 6.408
Fixed DST:495 H2'2 6 H2'1 6 1.772
Fixed DST:560 H5'2 9 H5'1 9 1.772 Fixed DST: 702 M7 9 H6 9 2.980 Fixed DST: 703 M7 9 M7 9 1.772

Fixed DST:860 H2'2 9 H2'1 9 1.772
Fixed DST:945 H5'2 11 H5'1 11 1.772 Fixed DST: 1174 H2 11 H8 11 6.408 Fixed DST: 1325 H2'2 11 H2'1 11 1.772 Fixed DST: 1430 H5'2 13 H5'1 13 1.772 Fixed DST: 1652 H5 13 H6 13 2.460 Fixed DST: 1952 H2'2 13 H2'1 13 1.772

READING INTENSITY FILE example2.INT.1

CALCULATING INTENSITIES
WRITING INTENSITIES
SUM Iobs= 3.149E+00 SUM Icalc= 3.149E+00 Scale factor= 1.000E+00

For322 intensities, the average error= 8.453E-08 WRITING SUBMATRICES

The following is another session with corma

CORMA 4.0 UNIX VERSION CO(mplete) R(elaxation) M(atrix) A(nalysis)

SPECTROMETER FREQUENCY IN MHz: 500.0

INCLUDE KINETIC EXCHANGE? [def=n]: n

INCLUDE FAST EXCHANGE? [def=n]: y

ENSEMBLE (MULTIPLE FAST EXCHANGE)? [def=n]: n

BOUND POPULATION FRACTION [0.0 to 1.0]: .3 ENTER PDB FILE-NAME (bound): example2.pdb COORDINATE FILE example2.PDB NOT FOUND.
TRYING example2.pdb AS COORDINATE FILE.
ENTER PDB FILE-NAME (free): example2.pdb COORDINATE FILE example2.PDB NOT FOUND.
TRYING example2.pdb AS COORDINATE FILE.

COMPARE WITH EXPERIMENTAL INTENSITIES? [def=n]: y

ENTER NAME OF EXPERIMENTAL INTENSITY FILE: example2.INT.1 NORMALIZE USING ONLY FIXED-DISTANCE INTENSITIES [def=f], OR USE ALL Iobs [a]? f

NAME FOR INTENSITY FILE TO BE CREATED: test2 WRITING TO FILES: test2.CRM.1 test2.INT.1

CUTOFF LEVEL FOR INTENSITIES?
(ENTER 1, 2, 3, 4, or 5; 1=0.1, 2=0.01, 3=0.001, ETC.) [def=3]: 3

DISPLAY INTENSITIES IN EXTENDED PRECISION? [def=y]: y

ADD RANDOM NOISE? [def=n]: y

AMPLITUDE OF NOISE (IN MULTIPLES OF PRECISION: 1,2,3,4,....,10): 2

SELECT METHYL JUMP MODEL:

[1] 3-site for intra-residue relaxation, 18-sitefor inter-residue [2] 18-site for all methyl relaxation [3] 3-site for all methyl relaxation ENTER (1/2/3) [default=3] :3

READING PDB FILE: example2.pdb
Bound Probability0.3000

GENERATE POSTSCRIPT FILES FOR PLOTTING? [def=n]: y

INTENSITIES ARE PLOTTED AS HALF-TONE SQUARES. ALSO PLOT INTENSITIES WITH NUMERICAL RANK? [def=n]: y

PLOTS WILL REQUIRE 4 PAGES. USE CONDENSED MODE (100X100 PER PAGE)? [def=n]: n

Scanning intensity file example2.INT.1 for dummy atoms

pseudoatom representing methylene: QN22 pseudoatom representing methylene: QN6 11
pseudoatom representing methylene: QN66 example2.INT.1 : total of 3 dummy atoms found
Updated number of unique spins:63

OK -- END OF INPUT
READING PDB FILE: example2.pdb
Free Probability 0.7000

Scanning intensity file example2.INT.1 for dummy atoms

pseudoatom representing methylene: QN22 pseudoatom representing methylene: QN6 11
pseudoatom representing methylene: QN66 example2.INT.1 : total of 3 dummy atoms found
Updated number of unique spins:63

CALCULATING EIGENVALUES
Fixed DST:5 H5'2 2 H5'1 2 1.772
Fixed DST:65 H2'2 2 H2'1 2 1.772
Fixed DST:90 H5'2 4 H5'1 4 1.772 Fixed DST: 152 M7 4 H6 4 2.980 Fixed DST: 153 M7 4 M7 4 1.772
Fixed DST:230 H2'2 4 H2'1 4 1.772
Fixed DST:275 H5'2 6 H5'1 6 1.772 Fixed DST: 404 H2 6 H8 6 6.408
Fixed DST:495 H2'2 6 H2'1 6 1.772
Fixed DST:560 H5'2 9 H5'1 9 1.772 Fixed DST: 702 M7 9 H6 9 2.980

Fixed DST: 703 M7 9 M7 9 1.772
Fixed DST:860 H2'2 9 H2'1 9 1.772
Fixed DST:945 H5'2 11 H5'1 11 1.772 Fixed DST: 1174 H2 11 H8 11 6.408 Fixed DST: 1325 H2'2 11 H2'1 11 1.772 Fixed DST: 1430 H5'2 13 H5'1 13 1.772 Fixed DST: 1652 H5 13 H6 13 2.460 Fixed DST: 1952 H2'2 13 H2'1 13 1.772

READING INTENSITY FILE example2.INT.1

CALCULATING INTENSITIES
WRITING INTENSITIES
SUM Iobs= 3.149E+00 SUM Icalc= 3.160E+00 Scale factor= 1.003E+00

For322 intensities, the average error= 1.455E-04 WRITING SUBMATRICES

WRITING PLOT FILE test2.PLT.1

WRITING RANK FILE test2.RNK.1

As shown above the program prompts for the required information. Follwing is additional information:

For the ensemble calulations the filenames list file has free format, with the first column being the pdb filenames and the second column being the population of the structures. The two columns are separated by at least one space (tab is not valid). The total population must sum to 1.0.

The pdb file names: The string that is entered is truncated after the first (if any) "." and appended with "PDB" or "pdb" by the program. If neither of these names is successful in the file name search, then the string that was entered is tried. So, if the desired coordinate file is "myfile.PDB", entering any of: myfile myfile.PDB myfile.pdb myfile.junk will retrieve the file "myfile.PDB". If your directory has both "myfile.PDB" and "myfile.pdb", you must change one of their names in order to access "myfile.pdb".

The format for the exchange rate file (no restriction on the name) is

(a4,i3,x,a4,i3,x,f10.4)

The exchange rates are in [1/sec].

Description of the file may be given at the beginning of the file starting with HEADER or REMARK.

The intensity file: Like the coordinate file, the string entered here is truncated and appended with "INT.n" (UNIX) or "INT;n" (VMS) and the directory is searched for any files with n = 0, ..., 9. This naming convention is rigid. All intensity file names must have the format name.INT.n (or name.INT;n VMS).

The program creates files prefix.CRM prefix.INT and prefix.PLT (and prefix.RNK) using the prefix of the string typedin by the user. Only the first characters before a "." or space are used for the prefix.

prefix.INT is a formatted file similar to file.INT with the inclusion of distances and a ranking of intensities.

prefix.PLT and prefix.RNK are files containing POSTSCRIPT instructions that can be sent to the laserwriter.

If the files already exist the user is asked if they can be overwritten. If not the prefixes are incremented until a unique name is found.

While a cutoff level of .001 may be appropriate, it may be desirable to display the intensities with more significant digits. The extended precision will display up to 5 digits (10.00001).

The random number generator used is that supplied by the UNIX or VMS compilers. The "seed" for the random number sequence is set according to the system clock time at the time of the run. This makes it highly unlikely that exactly the same random number sequence will be assigned to the intensities generated by different runs of corma.

Methyl jump models are calculated according to the equations described in J. Tropp, J. Chem. Phys., 72, 6035-6043 (1980). The 3-site jump model is the most physically realistic model. Methyl-methyl relaxation is modeled with an nsquared-site jump model. For a discussion of the jump models and their applications, see the mardigras man pages.

The gray-scale plots generated by corma are POSTSCRIPT code and can be large. If the user is not interested in looking at the plots, they can be suppressed, saving disk space and run time. The PLT and RNK files can be previewed by using the pageview command on a Sun workstation running the NeWS environment. In any event, they can be sent to a POSTSCRIPT printer to obtain a hard copy.
The ranks of the intensities can be displayed on a logarithmic scale ranging from 0-9, 0 corresponds to the input level of precision and 9 corresponds to the most intense cross-peak. This option results in generation of prefix.RNK file.

The plots are set to display the cross peaks with no more than 50x50 on a page. For very large molecules it may be best to display more on each page. This results in smaller squares and a decrease in the ability to distinguish their relative intensities. But the overall picture may be all that is needed.

There is currently no way to resize the display without running corma again.

In some cases, additional input may be requested if an error is detected.

OUTPUT

On output, the program creates three (or four) files:

(1) prefix.CRM which displays the calculated intensities by residue submatrices for all submatrices which contain any elements larger than the level of precision defined above. In prefix.CRM the display is limited to three significant figures. (Berkeley 4.3BSD UNIX f77 compiler: calculated intensities below the PRECISION level defined during input will be displayed as " 0. " in these submatrices for clarity.)

(2) prefix.INT.n contains the intensities (and distances and relaxation rate) in columnar format.
In the case where unresolved intensities were added to the end of the input intensity file, corma will print out the sum of the peaks contributing to the unresolved peak, followed by the individual cross-peak elements:

UNRESOLVEDsumIcalc kIobs H1' 2 H2" 2 H1' 2 H2' 2 0.12357 0.12197 H1' 2 H2" 2 2.287 -1.57649 0.07582 H1' 2 H2' 2 2.982 -0.32115 0.04774

(3) prefix.PLT.n contains the POSTSCRIPT plotting instructions for the laserwriter. (Optional output)

(4) prefix.RNK contains the POSTSCRIPT file for plotting ranks. (Optional output)

INPUT FILE FORMATS

The following formatted data files are necessary for running corma. file.pdb is a modified PDB (Protein Data Bank) coordinate file and is prepared by using corma.in. (See corma.in man pages.) A HEADER card can go in line 1 to describe the source of the coordinates. This file must also contain the keyword ISOTROPIC, LOCAL or MODELFREE on line two (2) in the format:

REMARK CORRELATION TIME: ISOTROPIC

ISOTROPIC assumes a single effective isotropic correlation time for all interactions. (NOTE if the ratio for methyl TAUc is not 1, then the correlation times involving methyl protons will still be reduced.)

LOCAL assumes that each interaction can be assigned an effective isotropic correlation time that is a function of the local motion or diffusion time (TDIFF) of each of the protons (see below for TDIFF).

MODELFREE assumes the modelfree approach. (See the section on the modelfree approach and mardigras and corma.in man pages.)

The atomic coordinates are entered in PDB format beginning on line 3. There is no need to eliminate non-hydrogen atoms from the PDB file, the program can handle stripped or full coordinate sets.

NOTE: ALL PROTONS MUST BEGIN WITH THE LETTER "H". So, a set of coordinates obtained from the Protein Data Bank which contains proton coordinates MUST BE EDITED to ensure that the PROTONS ARE APPROPRIATELY LABELED.
See notes on the program newhyd.

All METHYL PROTONS are labeled in sequence Hx1, Hx2, Hx3, or Hxy1, Hxy2, Hxy3. IF MORE THAN ONE METHYL GROUP APPEARS IN A RESIDUE, THEIR NAMES MUST BE DISTINCT.

corma maintains a database of the amino and nucleic acids and recognizes methyl protons from these as long as they follow the name of the atom to which they are bonded.

The OCCUPANCY factor, the first field after the coordinates, is used to turn protons "on" or "off" for the case of deuteration or alternate conformations (enter a value of 1.00 or 0.00). To specify fractional occupancy, use a number between 0.0 and 1.0. This may be appropriate, for example, in the case of partial amide exchange for a deuteron.

The file is also modified by the substitution of "atomic diffusion times" (TDIFF; in nanoseconds) in the last field which usually contains the crystallographic B factors in a

PDB file. These values are used in the calculation of the correlation times TAUc for the H-H vectors:

1/TAUc=1/TDIFF(i)+1/TDIFF(j)

For the ISOTROPIC calculation only one TDIFF value need be entered (for the first H atom enter a value that is twice the correlation time). This value must be repeated for each H atom in the file. This allows one to specify different overall correlation times for different parts of the molecule it is felt to be appropriate. It has been suggested, for example, that base-moiety protons in DNA have a different effective correlation time than sugar protons. (See the model-free approach also)

For LOCAL, the first H atom in each residue should have a TDIFF value that will be used in calculating the correlation times involving all the protons in that residue.

The program corma.in will read a PDB file that contains temperature factors and calculate an appropriate TDIFF value for each of the protons. See the man page on corma.in.

NOTE: TDIFF values are in nanoseconds.

For MODELFREE, for each H atom the last six items are B, tau1, tau2/tau1, A, Ssq, taue. See the section on the modelfree approach for definitions. (See mardigras and corma.in man pages also.)

The following are examples for the input pdb file as prepared by corma.in:

line#a9------
1HEADER COMMENT GOES HERE This is for an ISOTROPIC calculation.
2REMARK CORRELATION TIME: ISOTROPIC a4--8x------a4--xa3-2xi4--4x--f8.3----f8.3----f8.3----f5.1-xf6.3-3 ATOM H1 GUA 1 0.123 0.456 0.789 1.0 2.000 (etc.)

or
1HEADER This is for a LOCAL calculation.
2REMARK CORRELATION TIME: LOCAL a4--8x------a4--xa3-2xi4--4x--f8.3----f8.3----f8.3----f5.1-xf6.3-3 ATOM H1 GUA 1 0.123 0.456 0.789 1.0 1.000 4 ATOM H2 GUA 1 1.123 2.456 3.789 1.0 1.000 (etc.) n ATOM H2 THY 2 4.123 5.456 6.789 1.0 2.000 (etc.) m ATOM H9 CYT 2 7.123 8.456 9.789 1.0 3.000 (etc.)

or
1HEADER This is for a MODELFREE calculation.
2REMARK CORRELATION TIME: MODELFREE a4--8x------a4--xa3-2xi4--4x--f8.3----f8.3----f8.3------6f4.1-3 ATOM 1 H HB 1 -0.792 -9.630 -2.257 0.8 2.0 0.9 0.5 0.7 0.6 (etc.)

file.INT is an experimental intensity file in the format:

line #
1 HEADER Whatever you like can go here. 2 REMARK Whatever you like can go here. 3 MIXING TIME: 0.275 (Tm in seconds, f5.3) 4 ATOM1 ATOM2
5 HB2 11 HG1 32 0.020
(atomiii atomjjj intensity; iii, and jjj are residue numbers in format: (a4,i3,x,a4,i3,x,f10.0)
4 (etc.)

The format of the output .INT file is different than the format of the input file. This is recognized, and in fact corma can read an input file with the format described above, or a .INT file that was generated by corma (the program reads the second line and looks for the string `DISTAN' to decide how the file will be read).

NOTE: The format of the .INT file has changed with version 2.0 onwards to allow more than 99 residues. The program senses this by noting the position of the second occurrence of the string `H'. Old .INT files created for earlier versions of corma should be read correctly.
Unresolved peaks may be entered in the experimental intensity file, but they must be assigned to a pair or a group of crosspeak intensities. This can be done in two ways: 1) For methyl, methylene and symmetry-equivalent aromatic ring protons, the unresolved peaks may be entered simply by referring to the group by a general name. The general names are as follows (Note that the naming conventions have been changed from earlier versions of corma):

For methyls, use the character "M": HD11, HD12, HD13 of LEU ----> MD1 of LEU For methylenes, use the character "Q": HB1, HB2 of LYS ----> QB of LYS

For amino proton pairs, also use the character "Q": HN21, HN22 of GUA ----> QN2 of GUA

For ring protons, use the character "R": HD1, HD2 of PHE ----> RD of PHE

Note, for methyls in residues other than `standard amino-acid' and THY, the nomenclature of methyl protons in .pdb file has to start with "HM" instead of "H". For the two unresolved geminal protons, for example, HB1 and HB2, the order of 1,2 can not be reversed.

For other unresolved peaks, the line `UNRESOLVED' must follow all of the resolvable intensities (including unresolved methyl and methylene groups). After this line, unresolved peaks are entered by listing the cross-peaks that contribute to the unresolved peak, and the intensity of that peak.

H5' 10 M 10 0.006 H6 10 H6 10 0.271 H6 10 M 10 0.060 M 10 M 10 2.299 UNRESOLVED H1' 2 H2" 2 H1' 2 H2' 2 0.124 H2" 2 M 2 H2" 2 H1' 4 H2" 2 H2" 4 H2" 2 H2' 4 H2" 2 H3' 4 H2" 2 H4' 4 H2" 2 H5" 4 H2" 2 H5' 4 0.115 --a7--x--a7---3x--a7--x--a7---3x--a7--x--a7---3x---f10---

Up to 99 cross-peaks may be assigned to a given unresolved peak (this number may be changed with the parameter mxpu in PARMS.INC). If there are more than three cross-peaks, additional ones may be entered on subsequent lines by leaving the intensity field blank (i.e. the blank is interpreted as a continuation sign).

Other problems can arise if a methyl is expected by the built-in naming rules and only one or two protons are actually found in the pdb file, e.g. the structure is a high pH structure and side-chain amines are not protonated. This will result in unpredictable results: floating point errors, or just erroneous results that are hard to detect. If an input intensity (.INT) file is provided, you may find that perfectly normal proton labels are being flagged as unknown.

ACKNOWLEDGEMENTS

corma is distantly related to a program (NOEFT100) written by Greg Young (now of Wright State University) and still contains relics of the original code from that program.

BUGS

There probably are some. This program was developed at UCSF on Sun SPARC stations with SunOS Release 4.1.3 UNIX operating system. It has not been fully tested on any other system and may therefore experience machine- or implementationdependent problems.

AUTHORS:

Brandan A. Borgias
Paul D. Thomas
He Liu
Anil Kumar

REFERENCES

The general calculations are described in: J. W. Keepers and T. L. James, J. Magn. Reson. 57 404-426 (1984); B.A. Borgias and T.L. James, J. Magn. Reson. 79 493-512 (1988); The mardigras algorithm is described in B. A. Borgias and T. L. James, J. Magn. Reson. 87 (1990) 475-487 and B. A. Borgias and T. L. James, Meth. Enzymol. 176 (1989) with features described in B.A. Borgias, M. Gochin, D.J. Kerwood, and T.L. James, In Progress in Nuclear Magnetic Resonance Spectroscopy, J.W. Emsley, J. Feeney, and L.H. Sutcliffe (Eds), Oxford: Pergamon Press, 22, 83-100 (1990), T. L. James, Curr. Opin. Struct. Biol., 1, 1042-1053, (1991). The R factor and the sixth root R factor are considered in P.D. Thomas, V.J. Basus and T.L. James. Proc. Nat. Acad. Sci. USA, 88, 1237-1241 (1991). The description for averaging of pseudoproton relaxation rates and distances can be found in H. Liu, P. D. Thomas and T. L. James, J. Magn. Reson. 98, 163-175 (1992). Effect of internal motion on the interproton distances is considered in A. Kumar, T. L. James, and G. C. Levy, Israel J. Chem. 32, 257-261 (1992). Application to the chemical exchange problems is described in H. Liu, A. Kumar, K. Weisz, U. Schmitz, K. D. Bishop, and T. L. James, J. Am. Chem. Soc., 115, 1590 (1993). An application of the ensemble averaging is given in U. Scmitz, A. Kumar, and T. L. James, J. Am. Chem. Soc., 114, 10654 (1992).

CONTACT

For more information about CORMA software, please contact:
Thomas James
Department of Pharmaceutical Chemistry
University of California
San Francisco, CA 94143-0446
fax: 415.476.8780

email: james@picasso.uscf.edu

SEE ALSO

mardigras


Table of Contents