Write At Command Station V1.0.4.rar
Baltasar Tae
If you're getting permission denied, then you're not using the correct username or something's amiss with the authentication. Most likely, it's because the sudo command only works locally, for starters, so it won't give you root on the remote box, so that's probably the problem. Make sure that the user you are logging in as on the remote server has write permissions to the location you're trying to write to.
If the problem is the destinationuser doesn't have access to that location without sudo, move the file to the destinationuser's home folder then sudo mv the file from the shell on the other server to put it in the right location.
This error occurred for me when the file already existed in the target location and the existing file had read-only permissions (preventing the file from being overwritten). In my case, I just logged in and deleted the existing file and that corrected the problem.
I was trying to copy from my local machine as username@localhost; the SSH key I was using wasn't registered to access my localhost, so I was getting permission denied. When I removed that from the source portion, it worked.
Had the same problem. I found out that the directory containing my source file did not have enough permission. So I just changed the mode recursively using:chmod -R 771 directory_path on the source machine.
If there is an identically named file owned by root on the remote host (target) the transfer will fail. This assumes you are running scp as an ordinary user on both hosts, i.e. your remote host user is not root.
ICM commands have a certain structure:
- they use command words from this list: align assign build clear compare connect convert copy compress cryptdelete display edit enumerate exit exclude filter find fix fork fprintf group gui keep learn loadmake menu minimize modify montecarlo movepause plot predict print printf quit query randomize read redo refresh rename restore rotateselect set show sort split sprintf ssearch store strip superimposetest transform translate undisplay undo unfix unselect unix wait write
alias antialias center color help history link list macro model sql web
accessibility alignment amber angle area aselection atom axisbackground ball base bar bfactor bond born boundary boxcatalog cavity cell chain charge cmyk column command comment comp_matrix conf cpk csd cursor chemical cistransdatabase distance directory disulfide dot drestraintenergy error evolution factor field filename font foreground frame functiongamess genome gradient grid grob hbond header html hydrogeniarray icmdb idb image index info input integer intensity inverse iupac json kernel key label library logical loop limitmargin material map matrix memory merit mol mol2 moldb molcart molecule movie molsarname nucleotideobject occupancy oracle origin outputpage parray pattern peptide pipe pdb plane postscript potential preference preview problem profile project property prosite protein pharmacophorerarray reaction real regression reflection residue resolution ring rgb ribbon regexp rainbowsarray segment selection selftether separator sequence session site size skin slide salt solution stack stdin stdout sticksstructure string surface symmetry system svariabletable term tether texture topology torsion trajectory transparent tree type unknown uservariable vector version view virtual volume vrestraint vselection water weight window wire xstick
add all append auto auxiliary binary bold bw cartesian clash chiral dash exact joinfast fasta flat formal format full gcg gif global graphic heavy identity italic jpeg lastleft local mmcif mmff msf mute new none nosort number off on only pca pir pmf png pseudo povreverse right similarity simple sln smiles smooth solid static stereo swiss targa tautomer underline unique wavefront xplor - the they arguments consisting of constants, named shell variables or expressions including functions, e.g. display ribbon Res(Sphere( a_H a_A 7.6 ))
- the order of arguments of different data type is arbitrary
- at the end of the command one may have a list of additional shell variables that will be redefined temporarily only for the duration of this command, e.g. montecarlo v_//x* mncalls=200 mncallsMC=20000 temperature=1000.
- several commands in one line can be separated by a semicolon
- commands can return certain shell variables, like i_out , i_2out, r_out , l_out , s_out , R_out , as_out .. with useful output
- to suppress command output redefine those shell variables: l_info=no or l_warn=no (for some commands there is also a mute option )
[ Add column Add matrix Add slide Add table ]
A family of commands adding things. Some commands use append syntax insteadIt is also used as an option equivalent to append in write command.
add one or several columns or header elements to an existing table
[ Add column function ]
Assigns residue structure to a peptide or a protein. Sometimes when you read a peptide or protein from MOL or MOL2 withno residue information present it is treated as a single residue small molecule. This command allows to restore residue layer. assign residue os1Example:build string "EACARVAAACEAAARQ"read mol Chemical( a_ exact hydrogen ) name="xxx" # read it as a single residue small moleculeassign residue a_ # restore residue structureSequence( a_1. )Sequence( a_2. )build
[ Build atom Build column Build conf Build sequence build tautomer Build model Build loop Build smiles Build string Build hydrogen Build molcart ]
clear terminal screen
clear selection clear the graphical selection as_graph Example:nice "1crn"as_graph = a_/1:5 # select five residuesclear selection # nothing again clear pattern chemarrayclear SMARTS search attributes in the input chemical array.Example:add column t Chemical("[C;D2]")clear pattern t.mol # D2 attribute will be clearedSee also: Exist pattern clear graphic [ os ] clears display properties , graphic representation memory and reset the graphic planes to the default.
clear error clears all error and warning bits previously set by ICM. See also Error ( i_code )
color
[ Color specification Color object ]
color accessibility g_mesh [ r_maxShade ]modify the color of each surface element of a grob to create perception of depth.The procedure calculates for each surface element (triangle) the extent it is occluded from ambient light by other parts of the molecule, and makes the elements darker proportionally to occlusion. Thus, concave regions such as pockets become dark since the surrounding bulk of the protein blocks the light from most directions, while protrusions remain bright since they are well exposed.Repeated application of thecommand or using a larger r_maxShade (the default is 0.8) generates a more dramaticshading of the shape.Example:color accessibility g_electro 0.7color accessibility g_electro 0.7 # do it two times for a more dramatic effectTo be able to come back to the initial coloring you may need to do this: clrs = Color(g_electro) # change grob color, e.g. with color accessibility color grob clrs
Uniquely coloring by object, molecule, residue or atom
color graphic_representation [ as_molecules ] [objectmoleculeresidueatom]
a special command to color the displayed and selected molecules differently. The graphic representation field can be either empty, or one of those: wire xstick cpk surface skin ribbon, residue label, atom label, site label, variable label .E.g. select graphically some atoms and do this:color xstick as_graph & a_*.//c* molecule color ribbon as_graph objectcolor cpk as_graph moleculecolor residue label as_graph residue
color background
color background color_specsets the background to the specified color color_spec in one of the supported formats .Examples:color background blue color background lightyellowcolor background rgb=255,255,255 # white. integers in 0..255 rangecolor background rgb=0.,1.,0. # green. reals in 0.. rangeTo change it permanently, go to preferences or change the value of the COLOR.bg string (e.g. COLOR.bg = "grey" ) See also: COLOR.bg , rgb, color background example .
color by alignment
color as [wirecpkskinribbonxstickballsticksurface..] alignment
colors specified graphics representations of the selected residues by the colors of an alignment as you see it in the alignment window of the Graphics User Interface. The color of a residue is controlled by the following factors:
- residue type
- consensus character at the residue position in the alignment
- colors as provided by the CONSENSUSCOLOR.tabtable.
Example: read sequence s_icmhome+"sh3" nice "1fyn" make sequence a_1 # extract 1st sequence group sequence sh3 align sh3 color a_1 ribbon alignment display skin white a_1 molecule color a_1 alignment # colors all representations including skin
color grob
[ Color grob unique Color grob matrix Color grob by atom selection Color grob map Color grob potential ]
sets a metric for calculating a distance between different conformations in a stack .
The goal of the two following compare commands is to provide a desired setting before the montecarlo command and stack operations. This command defines a filter which is used to decide how many and what conformations from the stochastic optimization trajectory are kept as low energy representatives of a certain area in conformational space. This metric is also used for the subsequent stack manipulations, e.g. compress stack.
The compare command defines the distance measure between molecular conformations which is used to form a set of different low energy conformers in the course of the stochastic global optimization procedure. The defined distance is compared with the vicinity parameter and determines whether two conformations should be considered different or similar (i.e. belonging to the same slot in the conformational stack). The compare command determines the spectrum of conformations that will be retained in the stack, accumulated during a montecarlo procedure. The default comparison set is a set of all free torsion variables (see compare vs_ ). Other methods compare atom RMSD with and without superposition, using chemical superposition, andcompare only the atoms in the interface with a molecule ( compare surface ). Please note that the compare command can change the compareMethod preference.Example: montecarlo v_//2 compareMethod ="chemical static" # suitable for docking See also montecarlo, compareMethod
Unrelated array comparison tools:
- Index( compare)
- Distance
Compare by deviations of cartesian coordinates with or without superposition
compare [ static ] as
The command needs to be run when Cartesian root-mean-square deviation for positions of selected atoms ( as_ ) as a distance measure between stack conformations. Set the vicinity parameter to about 2.0 Angstrom if you want to consider conformations deviating by more than 2 A as different conformational families.
By default the selected atoms in different conformations will be optimally superimposed before the coordinate RMSD is calculated. The static option suppresses superposition and measures absolute deviation of the coordinates between conformations. The static option is relevant for ligand atoms in docking simulations to a static receptor.
The result of this procedure is that an internal flag is set to perform cartesian RMSD calculations during montecarlo run, and a set of selected atoms is marked for comparison.
Compare by deviations of internal coordinates/torsions.
compare vs
use angular root-mean-square deviation for selected internal variables (usually torsion angles) as distance (set vicinity to at least 30.0 degrees accordingly)
Examples: compare v_//phi,psi # compare ONLY the backbone angles vicinity=30.0 # consider two conformations # with phi-psi RMSD < 30. as similar compare a_2//ca static # compare Cartesian deviations # of the second molecule's alpha-carbon atoms # without prior optimal superposition vicinity=3.0 # consider two conformations with second # molecule deviation < 3 A as similar
Compare by coordinate deviations of the surface patches only
Compare by surface patch rmsd: dynamically selecting comparison atoms compare surface as_currentObjSelection as_staticReferenceObject.
Similarly to compare static as_ it will look at absolute deviations of coordinates, but the comparison will be applied dynamically only to a patch sub-selection of the atoms in the current object in the selectSphereRadius (default 5. A) proximity to the non-current-object atoms of the as_ selection. The selection typically would look like this: a_activeIcmObject.//ca a_staticPdbReceptorObject.//ca
Example: compare a_runObj.//ca a_recName.//ca surface
Note that this command dynamically calculates a subset of as_currentObjSelection near as_staticReferenceObject . This distance (static RMSD) is used inside montecarlo command or in compress stack .
The surface mode is useful for protein-protein docking simulations when you want to measure the sRmsd distance between the current conformation and the stack conformations ONLY for the interface residues of the moving molecule. The interface residues are dynamically determined as those which are close to the static receptor specified in the second part of the selection. This static receptor should reside in a separate object.
The vicinity size is determined by the selectSphereRadius parameter
An example in which we sRmsd-compare only those carbons of barstar which are next to the barnase surface. read pdb "1bgs" # a complex read pdb "1a19.a/" # the protein ligand only convert ... # make maps and other actions to prepare protein-protein docking compare a_//c* a_1.1 surface # will use only selectSphereRadius = 7. ... montecarlo
compress
[ Compress alignment Compress grob Compress stack Compress binary ] b1e95dc632