Sentence examples for atoms excluding from inspiring English sources

Using one TLS group per protein molecule or domain, we iteratively fitted TLS parameters (Schomaker and Trueblood, 1968; Winn et al., 2001) to the atomic B-factors of the protein atoms excluding atoms with large deviations in B-factor from the TLS-derived B-factor (the parameter p TLS described the percentage of atoms included in TLS-fitting; see 'Materials and methods').

The number of heavy atoms (excluding hydrogen atoms) contained within a MF ranges varies mainly from 10to9090 atoms.

Ligand atoms (excluding hydrogen atoms) are defined to be hydrophobic if they were not hydrogen-bond donors or acceptors or directly bonded to a ligand's donor or acceptor atoms.

The RMSDs of all backbone and heavy atoms excluding the N terminal tail (S26 to K135) were 0.40 and 1.10 Å, respectively.

RMSD was calculated for all substrate heavy atoms excluding the phosphate.

Overlaying the ground-state and metastable-state structures and comparing the difference in positions of all non-hydrogen atoms excluding the nitro/nitrito groups showed there was no major rearrangement of the structures; the average positional change (RMS) was 0.109 Å.

Indeed, removing non-active atoms excludes the possibility of further having active components in the neighborhood of already suppressed atoms.

In the case of vdW interactions, Cα-based radial distribution function (a reflection of local order) (Leach AR, 2001) constructed from the statistical dataset with 'bonded' atoms excluded was used to derive the PMF.

All relaxation for PG and PtG sheets in the present and absence of HF and SO3 molecules were done using B3LYP density functional with split basis set (for all atom excluding Pt the basis set was 6-31G (d,p), for Pt atom the basis set was lanl2dz) as implemented in Gaussian 09 suite of program [33].

For example, the all-atom (excluding hydrogens) RMSD to the starting conformation is 1.4±0.1 Å (average and standard deviation over the full 59 ns), with no trend of an increasing RMSD during the simulation.

In these calculations we defined neighbouring structures as those that had an all-atom (excluding hydrogens) RMSD less than 1.75 Å, but validated that the conclusions below are the same using other definitions of neighbours (not shown).