Chapter 3Loading A MoleculeThe File menu is the primary means for loading molecules and other data into <strong>VMD</strong>. The built-infile readers will load molecular structures from combinations of topology files, coordinate files, andtrajectory files. Readers are also included for data such as potential maps, electron density maps,Grasp surface data, and arbitrary 3-D geometric data from Raster3D scene files. <strong>VMD</strong> can loadstructures directly from Protein Data Bank over the internet, provided that a network connectionis present. Entering the four-character PDB accession code in the molecule file broswer form willretrieve and load the structure over the network.3.1 Notes on common molecular file formats<strong>VMD</strong> natively understands several popular molecular data file formats: PDB coordinate files,CHARMM, NAMD, and X-PLOR style PSF topology files, CHARMM, NAMD, and X-PLORstyle DCD trajectory files, NAMD binary restart (coordinate) files, AMBER structure (PARM)and trajectory (CRD) files including both the old format and the new formats used by AMBER7.0, and Gromacs (e.g. GRO, G96, XTC, TRR) structure and trajectory files. These files maycontain some redundant information and can be loaded in different combinations.PDB files contains data about atoms, residues, segment names, occupancy and beta factor, andone coordinate set. PSF and PARM files contain atoms, residues, segment names, residue types,atomic mass and charge, and the bond connectivity. <strong>VMD</strong> supports four file formats used byGromacs: GRO, G96, TRR and XTC. GRO and G96 files contain structure information includingatoms, residue and segment data, and one coordinate set. CRD, DCD, TRR and XTC files containonly coordinate data (frames ). It should be noted that while PDB, GRO and G96 files weredesigned to contain only one coordinate set, multiple files can be concatenated into one larger fileto create a makeshift trajectory file which can be loaded by <strong>VMD</strong>.When <strong>VMD</strong> loads a file it requires information about atom names and coordinates and tries tofill in the rest. Since the PDB file contains all this information, it does not need to be loaded withany other data files. However, the PDB file doesn’t contain the atom types, masses, and charges,so these are guessed or assigned default values. In particular, charges will be assigned a value of0.0 if the file does not contain explicit charge information.A PSF file does not contain coordinate information so it must be loaded along with a PDB orDCD file. If a PDB and PSF are given there is no missing data and <strong>VMD</strong> makes no assumptions.If a PSF and DCD are given then only the chain identifier and occupancy and beta values aremissing so they are given a default value. A PARM file is similar to a PSF in that it too contains20
no coordinate information. It must be loaded along with a CRD trajectory file. If a PARM andCRD file are loaded together, then only the segname and chain ID for the atoms are left blank. ACRD or DCD file can be specified along with the PDB, in which case the PDB file will be readas normal, and then coordinate sets are read from the DCD or CRD until the end of the file isreached. Gromacs GRO and G96 files can be loaded on their own since they contain the necessaryatom data and coordinates. They can also be loaded along with TRR and XTC files to obtaintrajectory data. Additional coordinates from a PDB, CRD, or DCD file can be appended to thecurrent coordinate set using the Molecule File Browser form.3.2 What happens when a file is loaded?When a coordinate file is loaded by itself (i.e. just a PDB, no PSF), <strong>VMD</strong> uses heuristics to replacemissing values that would normally be provided by a structure file. If necessary, <strong>VMD</strong> does adistance-based bond search to determine connectivity. A bond is formed whenever two atoms arewithin R 1 ∗ R 2 ∗ 0.6 ofeachother,whereR 1 and R 2 are the respective radii of candidate atoms. Ifboth structure and coordinate files are loaded, no approximations or guesses are made.After the molecule is read in, new names are added to the coloring categories [§5.2.3], andassigned colors. Next, bond connectivity is established and the molecule is analyzed to identify itscomponents, i.e., to determine which residues are protein, nucleic acids, and waters, etc. A searchis then made to connect these into larger fragments of the same type, and summary information isprinted to the screen. An example output for BPTI is:Info 1) Analyzing structure ...Info 1) Atoms: 898 Bonds: 909Info 1) Backbone bonds: Protein: 231 DNA: 0Info 1) Residues: 58Info 1) Waters: 0Info 1) Segments: 1Info 1) Fragments: 1 Protein: 1 Nucleic: 0There are several types of fragments. Protein and nucleic fragments are homogeneous; eitherall proteins, or all nucleic acids. However, it is possible for a protein to be connected to a nucleicacid or some other non-protein. When this occurs, a warning message is printed, as in:Warning 1) Unusual bond between residues 1 and 2These warnings will occur with terminal amino acids, zinc fingers, myristolated residues, and poorlydefined structures.3.3 Babel interface<strong>VMD</strong> can use the program Babel, if installed, to translate a wide variety of different moleculardata files into the PDB format. Not all of these have been tested for use with <strong>VMD</strong>, so your resultsmay vary. <strong>VMD</strong> only uses Babel to read files and does not allow the use of Babel to save files toother formats. The <strong>VMD</strong>BABELBIN environment variable [§12.2] is used to specify the absolute pathto the the Babel executable (including the executable name). For more information about Babel,see http://smog.com/chem/babel/. <strong>VMD</strong> currently supports version 1.6 of Babel.21
- Page 1 and 2: VMD User’s GuideVersion 1.8.6Apri
- Page 3 and 4: 4.4.4 Molecule File Browser Form .
- Page 5 and 6: 8.3.20 molecule . . . . . . . . . .
- Page 7 and 8: List of Figures2.1 Sample VMD sessi
- Page 9 and 10: Chapter 1IntroductionVMD is a molec
- Page 11 and 12: 1.4 AcknowledgmentsThe authors woul
- Page 13 and 14: • TachyonThe Tachyon multiprocess
- Page 15 and 16: Figure 2.1: Sample VMD session disp
- Page 17 and 18: 2.5 An Introduction to Atom Selecti
- Page 19: selection: protein and (name CA or
- Page 23 and 24: Chapter 4User Interface ComponentsV
- Page 25 and 26: • Center (hot key ’c’)This mo
- Page 27 and 28: Hot Key Command Purposer, R mouse m
- Page 29 and 30: Hot Key Command Purpose+,f,F animat
- Page 31 and 32: information. Atoms shows the number
- Page 33 and 34: Animation SpeedThe rate of playback
- Page 35 and 36: can change the view of the scene, e
- Page 37 and 38: • Perspective - The view of the s
- Page 39 and 40: 4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
- Page 41 and 42: Hiding a rep. To hide a rep, double
- Page 43 and 44: Periodic TabThe Periodic tab contro
- Page 45 and 46: • Name - the name of the atom as
- Page 47 and 48: Figure 4.10: The Material Formslide
- Page 49 and 50: force-feedback (haptic) devices suc
- Page 51 and 52: the simulated spring is connected t
- Page 53 and 54: Figure 4.13: The Sequence formmolec
- Page 55 and 56: • Selections by chain: When there
- Page 57 and 58: Chapter 5Molecular Drawing MethodsE
- Page 59 and 60: When three or more bonds join at on
- Page 61 and 62: segment pieces are colored accordin
- Page 63 and 64: • Representation Method - The sur
- Page 65 and 66: 5.1.19 BeadsA bounding sphere is dr
- Page 67 and 68: those names to color the atoms. Mol
- Page 69 and 70: Figure 5.1: RGB color scale: the th
- Page 71 and 72:
esname ALA to CYS TYRselects atoms
- Page 73 and 74:
esname ’A 1’More importantly, r
- Page 75 and 76:
the numeric sense) or greater than
- Page 77 and 78:
Keyword Arg Descriptionall bool eve
- Page 79 and 80:
FunctionDescriptionsqr(x) square of
- Page 81 and 82:
Chapter 6Viewing ModesThere are man
- Page 83 and 84:
sci-fi and horror movie showings. T
- Page 85 and 86:
Name Description Default Render Com
- Page 87 and 88:
• Dotted spheres are not drawn wi
- Page 89 and 90:
Chapter 8Tcl Text InterfaceThe Tcl
- Page 91 and 92:
• speed n: Set animation speed to
- Page 93 and 94:
last frame. If the frame is a speci
- Page 95 and 96:
- BWG - Blue to white to green.- Bl
- Page 97 and 98:
• antialias < on | off >: Turn an
- Page 99 and 100:
• cylinder {x1 y1 z1} {x2 y2 z2}
- Page 101 and 102:
• kill: Disconnect from the simul
- Page 103 and 104:
- ambient- specular- diffuse- shini
- Page 105 and 106:
the area contributions are coming f
- Page 107 and 108:
8.3.19 molLoad, modify, or delete a
- Page 109 and 110:
• modselect rep number molecule n
- Page 111 and 112:
• index n: Returns the id of the
- Page 113 and 114:
8.3.26 rockRotate the current scene
- Page 115 and 116:
8.3.33 vmdinfo(Tcl) Returns informa
- Page 117 and 118:
• -minmax {{ x min y min z min }
- Page 119 and 120:
In the VMD script library at http:/
- Page 121 and 122:
Sourceraster3dmsmsfaqbiocoretachyon
- Page 123 and 124:
Table 8.4: Description of Tcl callb
- Page 125 and 126:
version (2.2). Thus if you have Pyt
- Page 127 and 128:
• align(ref=None, move=None, fram
- Page 129 and 130:
esid5.frame()50>>> resid5.frame(22)
- Page 131 and 132:
ef=AtomSel(’backbone’,frame=0)f
- Page 133 and 134:
functions (e.g., listall()) overlap
- Page 135 and 136:
• update ui():• update on():Upd
- Page 137 and 138:
9.5.7 labelPython operations availa
- Page 139 and 140:
• add volumetric(molid, name, ori
- Page 141 and 142:
• set colorupdate(molid, rep, ono
- Page 143 and 144:
9.6 High-level Python InterfaceVMD
- Page 145 and 146:
9.6.2 MoleculeRepThe MoleculeRep cl
- Page 147 and 148:
Chapter 10Vectors and MatricesTcl d
- Page 149 and 150:
• veccross v1 v2 - Returns the ve
- Page 151 and 152:
• transaxis amount [deg|rad|pi]
- Page 153 and 154:
-axiszamount [rad|deg|pi] - Adds a
- Page 155 and 156:
Chapter 11Molecular Analysis11.1 Us
- Page 157 and 158:
vmd> set sel [atomselect top "water
- Page 159 and 160:
The decimal in ”1.0” is importa
- Page 161 and 162:
# get the sidechain atoms (CB and o
- Page 163 and 164:
Applying this to the alanin.pdb coo
- Page 165 and 166:
have the same number of atoms, then
- Page 167 and 168:
set transformation_matrix [measure
- Page 169 and 170:
}display update offfor {set i 0} {$
- Page 171 and 172:
Chapter 12Customizing VMD SessionsT
- Page 173 and 174:
• -nt : Do not display the VMD ti
- Page 175 and 176:
• VMDIMMERSADESKFLIP : Enable a s
- Page 177 and 178:
axes location lowerleftstage locati
- Page 179 and 180:
Index.mailcap, 177.vmdrc, 26, 89, 1
- Page 181 and 182:
VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 1
- Page 183 and 184:
move, 35atom, 35fragment, 35highlig
- Page 185 and 186:
short circuit logic, 72, 75sleepcom