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I am looking for a software that is capable of converting some generic atomic format such as .xyz or POSCAR into a .stl format. Ideally it would support automatic generation of bonds so that the model would be connected rather than just being floating balls for atoms.

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  • $\begingroup$ Did you check out VESTA? It can work with xyz, cif, POSCAR, stl and several other extensions. $\endgroup$ – Xivi76 Oct 31 at 6:05
  • $\begingroup$ I need a 3D model not a 3D view. Can it open stl somebow? $\endgroup$ – Tristan Maxson Oct 31 at 13:03
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OpenBabel

This masterpiece of software can convert between a huge amount of different file formats.

The mains site can be accessed here.

In my Linux box running OpenBabel 3.0.0, the commands for reading and writing return the following:

Exporting/writing formats (obabel -L formats write):

(stl -- STL 3D-printing format is in the list)

acesin -- ACES input format
adf -- ADF cartesian input format
alc -- Alchemy format
ascii -- ASCII format
bgf -- MSI BGF format
box -- Dock 3.5 Box format
bs -- Ball and Stick format
c3d1 -- Chem3D Cartesian 1 format
c3d2 -- Chem3D Cartesian 2 format
cac -- CAChe MolStruct format
caccrt -- Cacao Cartesian format
cache -- CAChe MolStruct format
cacint -- Cacao Internal format
can -- Canonical SMILES format
cdjson -- ChemDoodle JSON
cdxml -- ChemDraw CDXML format
cht -- Chemtool format
cif -- Crystallographic Information File
ck -- ChemKin format
cml -- Chemical Markup Language
cmlr -- CML Reaction format
cof -- Culgi object file format
com -- Gaussian Input
confabreport -- Confab report format
CONFIG -- DL-POLY CONFIG
CONTCAR -- VASP format
CONTFF -- MDFF format
copy -- Copy raw text
crk2d -- Chemical Resource Kit diagram(2D)
crk3d -- Chemical Resource Kit 3D format
csr -- Accelrys/MSI Quanta CSR format
cssr -- CSD CSSR format
ct -- ChemDraw Connection Table format
cub -- Gaussian cube format
cube -- Gaussian cube format
dalmol -- DALTON input format
dmol -- DMol3 coordinates format
dx -- OpenDX cube format for APBS
ent -- Protein Data Bank format
exyz -- Extended XYZ cartesian coordinates format
fa -- FASTA format
fasta -- FASTA format
feat -- Feature format
fh -- Fenske-Hall Z-Matrix format
fhiaims -- FHIaims XYZ format
fix -- SMILES FIX format
fps -- FPS text fingerprint format (Dalke)
fpt -- Fingerprint format
fract -- Free Form Fractional format
fs -- Fastsearch format
fsa -- FASTA format
gamin -- GAMESS Input
gau -- Gaussian Input
gjc -- Gaussian Input
gjf -- Gaussian Input
gpr -- Ghemical format
gr96 -- GROMOS96 format
gro -- GRO format
gukin -- GAMESS-UK Input
gukout -- GAMESS-UK Output
gzmat -- Gaussian Z-Matrix Input
hin -- HyperChem HIN format
inchi -- InChI format
inchikey -- InChIKey
inp -- GAMESS Input
jin -- Jaguar input format
k -- Compare molecules using InChI
lmpdat -- The LAMMPS data format
lpmd -- LPMD format
mae -- Maestro format
maegz -- Maestro format
mcdl -- MCDL format
mcif -- Macromolecular Crystallographic Info
MDFF -- MDFF format
mdl -- MDL MOL format
ml2 -- Sybyl Mol2 format
mmcif -- Macromolecular Crystallographic Info
mmd -- MacroModel format
mmod -- MacroModel format
mna -- Multilevel Neighborhoods of Atoms (MNA)
mol -- MDL MOL format
mol2 -- Sybyl Mol2 format
mold -- Molden format
molden -- Molden format
molf -- Molden format
molreport -- Open Babel molecule report
mop -- MOPAC Cartesian format
mopcrt -- MOPAC Cartesian format
mopin -- MOPAC Internal
mp -- Molpro input format
mpc -- MOPAC Cartesian format
mpd -- MolPrint2D format
mpqcin -- MPQC simplified input format
mrv -- Chemical Markup Language
msms -- M.F. Sanner's MSMS input format
nul -- Outputs nothing
nw -- NWChem input format
orcainp -- ORCA input format
outmol -- DMol3 coordinates format
paint -- Painter format
pcjson -- PubChem JSON
pcm -- PCModel Format
pdb -- Protein Data Bank format
pdbqt -- AutoDock PDBQT format
png -- PNG 2D depiction
pointcloud -- Point cloud on VDW surface
POSCAR -- VASP format
POSFF -- MDFF format
pov -- POV-Ray input format
pqr -- PQR format
pqs -- Parallel Quantum Solutions format
qcin -- Q-Chem input format
report -- Open Babel report format
rinchi -- RInChI
rsmi -- Reaction SMILES format
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
smi -- SMILES format
smiles -- SMILES format
stl -- STL 3D-printing format
svg -- SVG 2D depiction
sy2 -- Sybyl Mol2 format
tdd -- Thermo format
text -- Read and write raw text
therm -- Thermo format
tmol -- TurboMole Coordinate format
txt -- Title format
txyz -- Tinker XYZ format
unixyz -- UniChem XYZ format
VASP -- VASP format
vmol -- ViewMol format
xed -- XED format
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format
zin -- ZINDO input format

Importing/reading formats (obabel -L formats reads):

abinit -- ABINIT Output Format
acesout -- ACES output format
acr -- ACR format
adfband -- ADF Band output format
adfdftb -- ADF DFTB output format
adfout -- ADF output format
alc -- Alchemy format
aoforce -- Turbomole AOFORCE output format
arc -- Accelrys/MSI Biosym/Insight II CAR format
axsf -- XCrySDen Structure Format
bgf -- MSI BGF format
box -- Dock 3.5 Box format
bs -- Ball and Stick format
c09out -- Crystal 09 output format
c3d1 -- Chem3D Cartesian 1 format
c3d2 -- Chem3D Cartesian 2 format
caccrt -- Cacao Cartesian format
can -- Canonical SMILES format
car -- Accelrys/MSI Biosym/Insight II CAR format
castep -- CASTEP format
ccc -- CCC format
cdjson -- ChemDoodle JSON
cdx -- ChemDraw binary format
cdxml -- ChemDraw CDXML format
cif -- Crystallographic Information File
ck -- ChemKin format
cml -- Chemical Markup Language
cmlr -- CML Reaction format
cof -- Culgi object file format
CONFIG -- DL-POLY CONFIG
CONTCAR -- VASP format
CONTFF -- MDFF format
crk2d -- Chemical Resource Kit diagram(2D)
crk3d -- Chemical Resource Kit 3D format
ct -- ChemDraw Connection Table format
cub -- Gaussian cube format
cube -- Gaussian cube format
dallog -- DALTON output format
dalmol -- DALTON input format
dat -- Generic Output file format
dmol -- DMol3 coordinates format
dx -- OpenDX cube format for APBS
ent -- Protein Data Bank format
exyz -- Extended XYZ cartesian coordinates format
fa -- FASTA format
fasta -- FASTA format
fch -- Gaussian formatted checkpoint file format
fchk -- Gaussian formatted checkpoint file format
fck -- Gaussian formatted checkpoint file format
feat -- Feature format
fhiaims -- FHIaims XYZ format
fract -- Free Form Fractional format
fs -- Fastsearch format
fsa -- FASTA format
g03 -- Gaussian Output
g09 -- Gaussian Output
g16 -- Gaussian Output
g92 -- Gaussian Output
g94 -- Gaussian Output
g98 -- Gaussian Output
gal -- Gaussian Output
gam -- GAMESS Output
gamess -- GAMESS Output
gamin -- GAMESS Input
gamout -- GAMESS Output
got -- GULP format
gpr -- Ghemical format
gro -- GRO format
gukin -- GAMESS-UK Input
gukout -- GAMESS-UK Output
gzmat -- Gaussian Z-Matrix Input
hin -- HyperChem HIN format
HISTORY -- DL-POLY HISTORY
inchi -- InChI format
inp -- GAMESS Input
ins -- ShelX format
jin -- Jaguar input format
jout -- Jaguar output format
log -- Generic Output file format
lpmd -- LPMD format
mae -- Maestro format
maegz -- Maestro format
mcdl -- MCDL format
mcif -- Macromolecular Crystallographic Info
MDFF -- MDFF format
mdl -- MDL MOL format
ml2 -- Sybyl Mol2 format
mmcif -- Macromolecular Crystallographic Info
mmd -- MacroModel format
mmod -- MacroModel format
mol -- MDL MOL format
mol2 -- Sybyl Mol2 format
mold -- Molden format
molden -- Molden format
molf -- Molden format
moo -- MOPAC Output format
mop -- MOPAC Cartesian format
mopcrt -- MOPAC Cartesian format
mopin -- MOPAC Internal
mopout -- MOPAC Output format
mpc -- MOPAC Cartesian format
mpo -- Molpro output format
mpqc -- MPQC output format
mrv -- Chemical Markup Language
msi -- Accelrys/MSI Cerius II MSI format
nwo -- NWChem output format
orca -- ORCA output format
out -- Generic Output file format
outmol -- DMol3 coordinates format
output -- Generic Output file format
pc -- PubChem format
pcjson -- PubChem JSON
pcm -- PCModel Format
pdb -- Protein Data Bank format
pdbqt -- AutoDock PDBQT format
png -- PNG 2D depiction
pos -- POS cartesian coordinates format
POSCAR -- VASP format
POSFF -- MDFF format
pqr -- PQR format
pqs -- Parallel Quantum Solutions format
prep -- Amber Prep format
pwscf -- PWscf format
qcout -- Q-Chem output format
res -- ShelX format
rsmi -- Reaction SMILES format
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
siesta -- SIESTA format
smi -- SMILES format
smiles -- SMILES format
smy -- SMILES format using Smiley parser
sy2 -- Sybyl Mol2 format
t41 -- ADF TAPE41 format
tdd -- Thermo format
text -- Read and write raw text
therm -- Thermo format
tmol -- TurboMole Coordinate format
txt -- Title format
txyz -- Tinker XYZ format
unixyz -- UniChem XYZ format
VASP -- VASP format
vmol -- ViewMol format
xml -- General XML format
xsf -- XCrySDen Structure Format
xtc -- XTC format
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format
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  • 1
    $\begingroup$ This is a pretty fully featured answer that doesn't require going through intermediate formats (what I feared). $\endgroup$ – Tristan Maxson Oct 31 at 17:50
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If you have access to CrystalMaker, you can output .stl (and other 3D formats) with bonds retained. You can then pop it into Blender or PowerPoint or any other program to view the 3D structure. Mercury also has some 3D file output formats. For some examples, you can see my post here. SAMSON now has an option to output 3D .obj files.

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  • 1
    $\begingroup$ A good blender plugin would be a godsend to this community. I think the last I looked the most popular one is difficult to use and very not functional. $\endgroup$ – Tristan Maxson Oct 31 at 22:54
  • $\begingroup$ Totally agree with you there! Would be awesome! $\endgroup$ – Andrew Rosen Nov 1 at 2:55

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