MarvinSpace and competitors  Astex JMol MSpace PyMol SwissPDB

General

Java/Web   yes yes yes yes yes

License  free free, open source free for academia, free when not

integratednot free, open source free

Support  no active maling list professional, 24 hours response time,

public forumannual support fee bug reports can be sent in email

Release

first known 2002 1998? 14 November, 2005 December, 1999 Unknown

latest 2005 15 April, 2006 7 June, 2006 6 February, 2006 6 June, 2003

frequency rarely 2 times a year 2 monthly 1-3 times a year Unknown

Hardware accelerated graphics   yes no yes yes yes

Features and functions

Basic molecule drawing   ball, stick, spacefill etc. ball, stick, spacefill etc. ball, stick, spacefill etc. ball, stick, spacefill etc. ball, stick, spacefill etc.

Basic molecule coloring  CPK, chain, B-factor, rainbow no B-factor coloring flexible, CPK, residue, chain, constant,

schemas; B-factor, rainbowno residue coloring 256 screen colors

Secondary structure drawing  backbone, c-alpha trace, ribbon, cartoon backbone, c-alpha trace, ribbon, cartoon pipe and plank, ribbon; cartoon;

backbone, c-alpha tracepipe and plank; ribbon; cartoon; backbone; no c-alpha trace

backbone; ribbon; c-alpha trace

Labels

types residue atom atom symbol, atom name, atom number atom, residue, seconday structure; content customizable

all types, even atomic properties can be displayed

atom types, name, charge, group

editable no no yes no no

movable no 9 wired in position yes no no

colored yes text only yes yes yes

visibility

2D/3D yes no yes no no

Measurementstypes distance, bond, torsion distance, bond, torsion distance, bond, torsion distance, bond, torsion distance, bond, torsion

live monitors no no yes no no

Surfaces

types Connolly no van der Waals, solvent accesible, Connolly; blobby

Connolly Connolly

modes solid n/a dot, mesh, solid mesh, solid, dot, mesh, solid

transparency yes n/a yes yes yes

quality wired in n/a adjusted to molecule size, configurable accuracy

4 wired in options 6 wired in modes, even the best provides low quality

triangle count reduction no n/a yes no no

Property mapping

  lipophilicity, electrostatic, local curvature, CPK, distance

n/a CPK, residue, chain, secondary, B-factor, electrostatis potential; user defined atomic/volumetric porperties

CPK, chain, seconday, B-factor CPK, chain, energy by force field, cavity, electrostatic potential, B-faactor,

3D structure build   no no integrated with MarvinSketch no no

Stereo view cross eye red+green glasses, crosseye, walleye no crosseye, walleye, hardware side-by-side; hardware

Input/ Output

File formats  Mol, PDB Mol, PDB, SDf Mol, SDF, SMILES, XYZ, PDB, Cube Mol, SDF, PDB, X-Plor, CCP4, AVS field,

DXMapPDB, CSMol, MSMS, Grasp, X-Plor, CCP4

Save image  BMP in various sizes JPEG, PNG, PPM in screen resolution,

PovRay outputBMP, JPG, PNG, Targa in arbitrary size PNG screen resolution Pov, BMP, Targa screen resolution, no

feedback

Scripting   custom language Rasmol/Chime; custom no Rasmol/Chime custom language

Usability

GUIeasy to learn

easy to use

Speed

load medium protein

load large protein

render med protein spacefill

surface generation n/a

surface rotation/zoom n/a

Quality

default settings

best settings

presentation quality

overall impression

Other comments

  handy, good performance, nice seconday structures and surfaces

fast, but lack of features, low quality images

it's a great piece of software!!! fast drawing, high quality, not too handy very low rendering quality, hard to use

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