The following sections describe the method implemented in DAMMIN, how to run
DAMMIN on the supported platforms and the required input and the generated
output files.

If you use results from DAMMIN in your publication, please cite:

The program DAMMIN implements a method to restore ab initio low
resolution shape of randomly oriented particles in solution (e.g.,
biological macromolecules) from its small angle X-ray scattering.
A search volume which encloses the particle (e.g., a sphere of
sufficiently large radius R) is filled with N densely packed spheres
of radius r, referred to as dummy atom. Given the fixed spatial
positions, the shape of the dummy atom model is completely described
by a vector X with N components which assigns each dummy atom either
to the solute phase (i.e. protein in this case) or to the solvent
phase. (In a general approach implemented in the program
MONSA, the number of phases can be
up to 4 in order to deal with protein complexes and protein-RNA
complexes.) For an adequate description of a structure the number
of dummy atoms usually reaches a few thousands. The task of shape
reconstruction from the scattering data is thus transformed to the
problem of finding a configuration X where a goal function f(X) is
minimized. The goal function takes into account the discrepancy
between the experimental data and the calculated scattering of the
dummy atom model, as well as several aspects of the model quantified
as penalties. In order to guarantee a compact and inter-connected
model, the looseness penalty and the disconnectivity penalty are
introduced. The peripheral penalty ensures that the model is close
to the center of the search volume. The contribution of the penalties
to the goal function is expected to be 10-50% for the final model.
Simulated annealing (SA) is used to perform the global minimization
of the target function. For details on the method, please refer to
the publication cited above.

The latest binary release (version 5.3) on 13 August 2007 is available
on major platforms including UNIX/Linux (32 and 64 bit), Mac OS X and all
Windows operating systems.

The program DAMMIN can be started in the batch mode when arguments are
given:

$ dammin GNOMFILE [OPTIONS]

DAMMIN accepts the following command line arguments:

Argument

Description

GNOMFILE

A relative or absolute path to a GNOM output file.

DAMMIN recognizes the following command-line options:

Option

Description

--mo <MODE>

Configuration of the annealing procedure, one of <F>AST
(bigger beads, cooling down quickly), <S>LOW (smaller beads, cooling
down slowly), or <K>eep (keeps up to 15 best models fitting the data).
Default is 'F'.

--sy <SYMMETRY>

Specify the point symmetry of the particle. Point groups
P1, ..., P19, Pn2 (n = 2, ..., 12), P23, P432 or PICO (icosahedral)
are supported. By default, no symmetry is enforced (P1).

--an <ANISOMETRY>

Particle anisometry: oblate (O), prolate (P) or unknown (default).

--dr <DIRECTION>

Direction of anisometry, applicable with P2 symmetry only: along (L), across (C) or
unknown (default).

--un <UNIT>

Angular unit of the input file, either '1' (angstrom^{-1}) or '2' (nm^{-1}); undefined by default.

Alternatively DAMMIN can be started in the interactive mode when not giving any arguments:

$ dammin

Screen Text

Default

Description

Mode: <[F]>ast, [S]low, [J]ag, [K]eep, [E]xpert

Fast

Configuration of the annealing procedure, one of Fast
(bigger beads, cooling down quickly), Slow (smaller beads, cooling
down slowly), Jag (more dummy atoms and more spherical harmonics,
annealing in repeated cycles), Expert or Keep (keeps up
to 15 best models fitting the data).

Angular units in the input file
4*pi*sin(theta)/lambda [1/angstrom] (1)
4*pi*sin(theta)/lambda [1/nm ] (2)

1

Angular units of the input file, one of [1/Angstrom] or [1/nm].
Default is [1/Angstrom].

Portion of the curve to be fitted

1.000

Percentage of the scattering curve to fit, starting at the first point.
The whole curve is used by default.

Number of knots in the curve to fit

20

Experimental data is smoothed by spline interpolation before fitting.
This defines the number of supporting points of the spline.

Constant subtraction procedure. Enter
Positive number: value to be subtracted, OR
Negative number: to skip subtraction
Zero for automatic subtraction

0.0

A constant is subtracted from the data to force the s^{-4}
decay of the intensity at higher angles. By default, an appropriate
constant is determined automatically.

Maximum order of harmonics

20

The default value for the maximum order of spherical harmonics taken
in the computation of scattering intensity L=10 is usually
sufficient in most practical applications. If you wish to fit a
scattering curve over a very broad range (e.g. more than 15 >Shannon
channels) or if the particle is expected to be very anisometric,
it might be useful to compute with larger L (maximum L=20
is supported). Please note that the computational time is proportional
to L^{2}, i.e. a run with L=20 takes 4 times
more CPU than the default run.

Initial DAM: type S for sphere [default], E for ellipsoid,
C for cylinder, P for parallelepiped or start file name

S

Define a search volume, one of sphere (S), ellipsoid (E), cylinder (C),
parallelepiped (P) or user-defined pdb file.

When a spherical search volume is used, the diameter of the
sphere is by default the maximum size of the particle given
in the input file and it can be modified
when running DAMMIN in Expert mode.

When an ellipsoid is used as the search volume, the values
for the three semi-axis can be defined.

When a cylinder is used, the outer radius, the inner radius
(in the case of a hollow cylinder) and height can be defined.

The search volume can also be a parallepiped where its length,
width and height can be defined. Alternatively,

a pdb file of dummy atoms can be used as the search volume.
It is helpful, for example, in the case of refining the shape
when an averaged ab inito model is available.

Symmetry: P1...19 or Pn2 (n=1,..,12) or P23 or P432 or PICO

P1

Specify the point symmetry of the particle, one of P1...19, Pn2 (n=1,...,12),
P23, P432 or PICO (icosahedral).

Packing radius of dummy atoms

variable

The default radius of dummy atoms is determined by the maximum size of
the particle because the program packs approximately 1500 dummy atoms in
the search volume (for each asymmetric unit in case of symmetry). It is
possible to change the radius in the expert mode, which effectively
modifies the number of dummy atoms.

Expected particle shape: <P>rolate, <O>blate,
or <U>nknown

Unknown

Expected particle anisometry, either prolate, oblate or unknown.

Looseness penalty weight

variable

Looseness penalty is introduced to penalize the loosely connected
dummy atoms models in order to obtain compact models. The default
weight is of the order of 5e-3 depending on the running mode, e.g.
6e-3 in the fast mode and 2e-3 in the expert mode. It is not
recommended to change the default value. However, the looseness
penalty can be disabled by setting this weight to 0.

Disconnectivity penalty weight

variable

Disconnectivity is introduced to penalize models consisting of
isolated bodies. The default weight is of the order of 1e-3
depending on the running mode, e.g. 6e-3 in the fast mode and
2e-3 in the expert mode. It is not recommended to change the
default value. The disconnectivity penalty can be disabled
by setting this weight to 0.

Peripheral penalty weight

variable

Peripheral penalty is to ensure the model stays at the center
of the search volume. It is gradually decreasing with the
annealing temperature. It is not recommended to change the
default value.

Fixing thresholds Los and Rf

0.0, 0.0

When the shape is already well defined, some of the dummy atoms can
be fixed as particle or solvent in order to prevent unnecessary
rotations and movements of the entire model and thus to improve
the convergence. The temperature for doing so is selected using
the thresholds of "Looseness fixing" and "R-factor
fixing". It is recommended to disable this feature by accepting
the default values < 0.0, 0.0 >.

Randomize the structure

Yes

The initial structure is randomized, i.e., the spheres in the search
volume are assigned randomly to 0s (=solvent) and 1s (=particle).

Weight: 0=s^2, 1=Emphas.s->0, 2=Log

1

Choose the weighting function for the SAXS data:
0 - W(s) = s^{2} (Porod weighting)
1 - Porod weighting with emphasis of initial points (default)
2 - logarithmic scale weighting
In the case of option 0 (Porod weighting) the very low angle points
are somewhat underestimated for very anisometric (1:10) particles,
which leads to poor fits in this range.
The options 1 and 2 give better results over option 0 for very
anisometric objects.

Initial scale factor

variable

The scale factor is a factor between the computed scattering intensity
and the experimental data in the least squares fitting. The initial
scale factor has no significant effect on the modeling process because
it is calculated after each change of the model configurations.

Fix the scale factor

No

It is not recommended to fix the scale factor.

Initial annealing temperature

variable

The initial annealing temperature is by default of the order of 1e-3.
In the fast mode, it is tuned automatically by the program and can
be defined in the expert mode. The annealing temperature decreases
typically to a value of the order of 1e-6. So the initial annealing
temperature can be varied between 1e-5 and 1e-4. It is not recommended
to change the default value.

Annealing schedule factor

0.95

Factor by which the temperature is decreased; 0.95 is a good value for
the annealing process. Faster cooling for smaller systems is possible by
setting the factor to 0.9.

# of independent atoms to modify

1

Number of independent dummy atoms changing the phase during one iteration.
Default is 1; it is not recommended to change this value.

Max # of iterations at each T

variable

Complete a temperature step and cool after this number of
iterations at the latest.

Max # of successes at each T

variable

Finalize temperature step and cool after at most this many
successful phase changes.

Min # of successes to continue

variable

Stop if not at least this many successful state changes within
a single temperature step can be done.

Max # of annealing steps

200

Stop if simulated annealing is not finished after this number of steps.

DAMMIN outputs a set of files, each filename starts with a customizable
prefix. If a prefix has been used before,
existing files will be overwritten without further note.

The file '-1.pdb' represents the modeled particle.
The REMARK sections of both files contain information
about the application used and about invariants of the particle,
e.g. R_{g},volume and molecular mass of the particle.

Fit of the simulated scattering curve versus a smoothed
experimental data (spline interpolation). Columns in the
output file are: 's', 'I_{exp}'
and 'I_{sim}'.

Run DAMMIN on the GNOM out file lyz.out using default
values for all parameters.

$ dammin lyz.out

Run DAMMIN on the GNOM out file lyz.out defining the
prefix to the output files as lyz00 and using default
values for all other parameters.

$ dammin lyz.out -lo lyz00

Run DAMMIN in slow mode on the GNOM out file lyz.out
defining the prefix to the output files as lyz00
and using default values for all other parameters.

$ dammin lyz.out -lo lyz00 -mo Slow

Run DAMMIN in slow mode on the GNOM out file lyz.out
defining the prefix to the output files as lyz00,
applying P2 symmetry, giving "this is a test run for
lysozyme " as project description and using default values
for all other parameters.

$ dammin lyz.out -lo lyz00 -mo Slow -sy P2 -id "this is a test run for lysozyme"

Run DAMMIN on the GNOM out file lyz.out interactively in fast mode.

$ dammin
*** Ab inito shape determination by simulated ***
*** annealing using a single phase dummy atoms model ***
*** Win 9x/NT, UNIX/Linux/Mac release version 5.3 ***
*** Last modified --- 13/02/07 18:00 ***
*** Please reference: D.Svergun (1999). Biophys. J. ***
*** 76, 2879-2886. ***
*** Copyright (c) ATSAS Team ***
*** EMBL, Hamburg Outstation, 1999 - 2007 ***
Type dammin /help for batch mode use
====== DAMMIN started on 18-Aug-2009 09:34:18
Mode: <[F]>ast, [S]low, [J]ag, [K]eep, [E]xpert < Fast >:
Log file name .......................... < log >: t01
Input data, GNOM output file name ...... < .out >: lyz
Project identificator .................................. : t01
Enter project description .............. :
Random sequence initialized from ....................... : 93435
** Information read from the GNOM file **
Data set title: Lysozyme, high angles (>.22) 46 mg/ml, small angles (<.22 mg/
Raw data file name: Lyzexp.dat
Maximum diameter of the particle ....................... : 50.00
Solution at Alpha = 0.107E+01 Rg : 0.154E+02 I(0) : 0.657E+01
Radius of gyration read ................................ : 15.40
Number of GNOM data points ............................. : 213
Angular units in the input file:
4*pi*sin(theta)/lambda [1/angstrom] (1)
4*pi*sin(theta)/lambda [1/nm ] (2) < 1 >: 2
Angular units multiplied by ............................ : 0.1000
Dmax and Rg divided by ................................. : 0.1000
Maximum s value [1/angstrom] ........................... : 4.960e-2
Number of Shannon channels ............................. : 7.894
Portion of the curve to be fitted ...... < 1.000 >:
Number of knots in the curve to fit .................... : 20
*** Warning: constant reduced to avoid oversubtraction
A constant was subtracted .............................. : 3.454e-2
Maximum order of harmonics ............................. : 10
Initial DAM: type S for sphere [default],
E for ellipsoid, C for cylinder, P for parallelepiped
or start file name .................... < pdb >: S
Symmetry: P1...19 or Pn2 (n=1,..,12)
or P23 or P432 or PICO ................. < P1 >:
Sphere diameter [Angstrom] ............................ : 500.0
Packing radius of dummy atoms .......................... : 17.90
Radius of the sphere generated ......................... : 250.0
Number of dummy atoms .................................. : 1974
Number of equivalent positions ......................... : 1
Expected particle shape: <P>rolate, <O>blate,
or <U>nknown .......................... < Unknown >:
Excluded volume per atom ............................... : 3.247e+4
Radius of 1st coordination sphere ...................... : 50.48
Minimum number of contacts ............................. : 5
Maximum number of contacts ............................. : 12
Looseness penalty weight ............................... : 6.000e-3
No of non-solvent atoms ................................ : 1974
Initial DAM looseness .................................. : 6.949e-3
Disconnectivity penalty weight ......................... : 6.000e-3
Initial DAM # of graphs ................................ : 1
Discontiguity value .................................. : 0.0
Center of the initial DAM: 0.0000 0.0000 0.0000
Peripheral penalty weight .............................. : 0.3000
Peripheral penalty value ............................... : 0.5944
Looseness fixing threshold ............................. : 5.000e-2
R-factor fixing threshold ............................. : 1.500e-2
No of non-solvent atoms ................................ : 981
Randomized DAM looseness ............................... : 0.1054
Randomized DAM # of graphs ............................. : 5
Discontiguity value .................................. : 5.110e-3
Randomized peripheral penalty value .................... : 0.5960
Initial DAM shape anisometry ........................... : 1.973e-2
Initial DAM non-prolateness ............................ : 0.0
Initial DAM non-oblateness ............................. : 7.403e-3
Weight: 0=s^2, 1=Emphas.s->0, 2=Log .................... : 1
*** Porod weight with emphasis at low s ***
Initial scale factor ................................... : 9.224e-15
Initial R^2 factor ..................................... : 0.2739
Initial R factor ..................................... : 0.5234
Initial penalty ........................................ : 0.1795
Initial fVal ........................................... : 0.4534
Tuning the annealing parameters. Please wait...
Variation of the target function ....................... : 3.594e-4
CPU per function call, seconds ......................... : 4.063e-4
Initial annealing temperature .......................... : 1.078e-3
Annealing schedule factor .............................. : 0.9000
# of independent atoms to modify ....................... : 1
Max # of iterations at each T .......................... : 138180
Max # of successes at each T ........................... : 13818
Min # of successes to continue ......................... : 46
Max # of annealing steps ............................... : 100
==== Simulated annealing procedure started ====
j: 1 T: 0.108E-02 Suc: 13818 Eva: 16326 CPU: 0.642E+01 SqF: 0.6070
Rf: 0.45421 Los:0.1120 Dis:0.0228 Per: 0.5380 Sca: 0.981E-14

Run DAMMIN on the GNOM out file lyz.out interactively in
expert mode where all parameters can be tuned.

$ dammin
*** Ab inito shape determination by simulated ***
*** annealing using a single phase dummy atoms model ***
*** Win 9x/NT, UNIX/Linux/Mac release version 5.3 ***
*** Last modified --- 13/02/07 18:00 ***
*** Please reference: D.Svergun (1999). Biophys. J. ***
*** 76, 2879-2886. ***
*** Copyright (c) ATSAS Team ***
*** EMBL, Hamburg Outstation, 1999 - 2007 ***
Type dammin /help for batch mode use
======
DAMMIN started on 18-Aug-2009 12:07:24
Mode: <[F]>ast, [S]low, [J]ag, [K]eep, [E]xpert < Fast >: E
Log file name .......................... < .log >: t01
Input data, GNOM output file name ...... < .out >: lyz
Project identificator .................................. : t01
Enter project description .............. : This is a test run for lysozyme
Random sequence initialized from ....................... : 120818
** Information read from the GNOM file **
Data set title: Lysozyme, high angles (>.22) 46 mg/ml, small angles (<.22) 15 mg/
Raw data file name: Lyzexp.dat
Maximum diameter of the particle ....................... : 50.00
Solution at Alpha = 0.107E+01 Rg : 0.154E+02 I(0) : 0.657E+01
Radius of gyration read ................................ : 15.40
Number of GNOM data points ............................. : 213
Angular units in the input file:
4*pi*sin(theta)/lambda [1/angstrom] (1)
4*pi*sin(theta)/lambda [1/nm ] (2) < 1 >: 2
Angular units multiplied by ............................ : 0.1000
Dmax and Rg divided by ................................. : 0.1000
Maximum s value [1/angstrom] ........................... : 4.960e-2
Number of Shannon channels ............................. : 7.894
Portion of the curve to be fitted ...... < 1.000 >:
Number of knots in the curve to fit .... < 20 >:
Constant subtraction procedure. Enter
Positive number: value to be subtracted, OR
Negative number: to skip subtraction , OR
Zero for automatic subtraction ......... < 0.0 >:
*** Warning: constant reduced to avoid oversubtraction
A constant was subtracted .............................. : 3.454e-2
Maximum order of harmonics ............. < 20 >: 15
Initial DAM: type S for sphere [default],
E for ellipsoid, C for cylinder, P for parallelepiped
or start file name .................... < .pdb >: S
Symmetry: P1...19 or Pn2 (n=1,..,12)
or P23 or P432 or PICO ................. < P1 >: P1
Sphere diameter [Angstrom] ............ < 500.0 >:
Packing radius of dummy atoms .......... < 10.90 >: 10
Radius of the sphere generated ......................... : 250.2
Number of dummy atoms .................................. : 11590
Number of equivalent positions ......................... : 1
Expected particle shape: <P>rolate, <O>blate,
or <U>nknown .......................... < Unknown >:
Excluded volume per atom ............................... : 5661.
Radius of 1st coordination sphere ...... < 28.20 >:
Minimum number of contacts ............................. : 5
Maximum number of contacts ............................. : 12
Looseness penalty weight ............... < 2.000e-3 >: 2.0E-2
No of non-solvent atoms ................................ : 11590
Initial DAM looseness .................................. : 3.635e-3
Disconnectivity penalty weight ......... < 2.000e-2 >:
Initial DAM # of graphs ................................ : 1
Discontiguity value .................................. : 0.0
Center of the initial DAM: 0.0000 0.0000 0.0000
Peripheral penalty weight .............. < 0.3000 >: 0.5
Peripheral penalty value ............................... : 0.5997
Fixing thresholds Los and Rf < 0.0, 0.0 >: 0,0
Randomize the structure [ Y / N ] ...... < Yes >:
No of non-solvent atoms ................................ : 5749
Randomized DAM looseness ............................... : 9.166e-2
Randomized DAM # of graphs ............................. : 14
Discontiguity value .................................. : 2.787e-3
Randomized peripheral penalty value .................... : 0.5953
Initial DAM shape anisometry ........................... : 4.752e-3
Initial DAM non-prolateness ............................ : 4.005e-3
Initial DAM non-oblateness ............................. : 0.0
Weight: 0=s^2, 1=Emphas.s->0, 2=Log .... < 1 >:
*** Porod weight with emphasis at low s ***
Initial scale factor ................... < 8.809e-15 >:
Fix the scale factor [ Y / N ] ......... < No >:
Initial R^2 factor ..................................... : 0.2918
Initial R factor ..................................... : 0.5402
Initial penalty ........................................ : 0.2995
Initial fVal ........................................... : 0.5913
Tuning the annealing parameters. Please wait...
Variation of the target function ....................... : 6.450e-5
CPU per function call, seconds ......................... : 2.250e-3
Initial annealing temperature .......... < 1.000e-3 >:
Annealing schedule factor .............. < 0.9500 >:
# of independent atoms to modify ....... < 1 >:
Max # of iterations at each T .......... < 811300 >:
Max # of successes at each T ........... < 81130 >:
Min # of successes to continue ......... < 270 >:
Max # of annealing steps ............... < 200 >:
==== Simulated annealing procedure started ====
j: 1 T: 0.100E-02 Suc: 81130 Eva: 83447 CPU: 0.191E+03 SqF: 0.7583
Rf: 0.52963 Los:0.0913 Dis:0.0021 Per: 0.5852 Sca: 0.868E-14