RasMol protocols

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RasMol specifications


Unique identifier OMICS_05076
Name RasMol
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Herbert J. Bernstein <>

Publication for RasMol

RasMol in pipeline

PMCID: 3123238
PMID: 21605466
DOI: 10.1186/1471-2105-12-195

[…] server with programs written in fortran 90. matlab (v.7.5) was used to analyze geometry. networks were visually analyzed using cytoscape [] (v.2.6.2) and related crystal structures were surveyed in rasmol [] (v. and pymol [] (v.1.3). the threading program was written in fortran 90 and energy-minimization was carried out using charmm []. structural alignments were performed using dali […]

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RasMol in publications

PMCID: 5840701
PMID: 29510698
DOI: 10.1186/s12917-018-1391-6

[…] genscan software., the positions of amino acid substitutions on the ha molecule were analyzed on the 3-dimensional structure obtained from the protein databank (pdb accession number, 1jsd) with the rasmol 2.7.3 program., for studying the viral replication and pathogenicity in chicken, groups of six 4-week-old spf chickens were oral, intranasally, or intratracheally inoculated with 0.2 ml of 106 […]

PMCID: 5811516
PMID: 29479304
DOI: 10.3389/fnins.2018.00061

[…] l7543, sigma) and anti-actin (1:2,000, a2066, sigma) as primary antibodies (lopez-gallardo et al., )., the three-dimensional structure of the bovine p.mt-nd5 (pdb 5lnk) was obtained with the rasmol 2.6 program (http://www.rasmol.org)., the statistical package statview 6.0 was used to perform all the statistics. data for mean and standard deviation are presented. the unpaired two-tailed […]

PMCID: 5774166
PMID: 29347906
DOI: 10.1186/s12870-018-1236-2

[…] proteins []. figure  showed the predicted 3-dimensional structures of the csdir16 protein. structures of the csdir16 protein were modeled using cphmodels 3.2 to generate atomic coordinates, using rasmol windows software output csdir16 to visualize the 3-dimensional protein structure. analysis of the predicted 3-dimensional structure showed that csdir16 has a 14 β-fold (yellow) and 1 β-turn […]

PMCID: 5785718
PMID: 29417095
DOI: 10.21956/wellcomeopenres.13423.r28075

[…] and lamc3 amino acid sequences for human ( homo sapiens), mouse ( mus musculus), and zebrafish ( danio rerio) were aligned using muscle. full length alignments were represented as a barcode with rasmol colouring using geneious software ( ). for phylogenetic trees, the lamc1-like protein from nematostella vectensis was included as an out-group for the bilaterians and lamc2 sequences […]

PMCID: 5663110
PMID: 29084541
DOI: 10.1186/s12934-017-0795-5

[…] no. 3itj) was adopted as the structure template. similarly, the 3d structure template of kmtrx gene was also from the homologous sctrx2 from s. cerevisiae (pdb accession no. 2hsy.1.a). software rasmol was used to view and analyze the predicted 3d structure of kmtrxr, as was shown in fig. ., expression pattern analysis of differentially expressed genes related to oxidative stress […]

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RasMol institution(s)
Glaxo Wellcome Medicines Research Centre, Stevenage, Herts, UK

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