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Cannot Parse Selection Text Vmd

You'll find both, I think, but maybe there is an official vmd standard that I'm not aware of. the second step is to use the created selection to access the information about the atoms in the selections. list: Return a list of all undeleted atom selections. frame: Returns the animation frame associated with this selection. weblink

I am using vmd >> 1.9.2a26. >> Thanks, >> Eddie >> >> -- >> _________________________________________________________ >> Edward Ackad, Ph.D >> Assistant Professor of Physics >> Computational Nanophotonics >> Southern Illinois writeXXX filename: write the selected atoms to a file of type XXX; e.g., pdb, dcd. global: Moves the object into the global namespace. What molecule are you working with?

Only to find some errors are given: atom select: cannot parse selection text.... The frame number can be a non-negative integer, the word now (the current frame), the word first (for frame 0) and last (for the last frame). lmoveby offset_list: move each atom by an offset given in the list. I am not sure if there are any conventions on whether the script-writer should directly pass selections, or should only pass the text and allow the procedure to make the selection

uplevel level: Moves the object to a new level in the namespace stack. These position the water molecule > 180 degrees and +/-120 degrees with respect to the C=O bond and have the > following syntax for the 120 degree orientations: > > RESNAME-(ACC Kohlmeyer that works very well. Are you trying to do shape based, or residue based?

Any other relevant info you can provide? In the target data box, simply modify the column for the atom name > to remove the -120(a | b) portion, yielding a valid atom name. > > > Regards, > If speed is an issue, delete all representations of the molecule before setting the values. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14356.html Sincerely, Chaofu Wu, Dr. _________________________________________________________________ 上Windows Live 中国首页,下载最新版Messenger! http://www.windowslive.cn Next message: John Stone: "Re: VMD and NetCDF under Windows Vista 32bit" Previous message: Rob: "Segmentation fault on linux Fedora 11" Next

frame should be either now, last, or an integer. selection can be any valid atom selection, and can even contain other macros. On Sat, Jul 9, 2011 at 7:33 PM, Axel Kohlmeyer wrote: > On Sat, Jul 9, 2011 at 6:48 PM, Simulation Biology > wrote: > > > Hi all, When the frame is now, the atom selection will use atomic coordinates from the current frame for its associated molecule.

It is used to pick a given subset of the atom. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21283.html Is this a problem of quotation or something? I then try to >> optimize using the default (or simulated annealing as I get the same error >> for both): >> >> atomselect: cannot parse selection text: name O-120a and If no selection is given, the macro for the given name is returned.

Example: set sel [atomselect top all] set mass [$sel get mass] set xyz [$sel get {x y z}] $sel set beta 0 # all values are set to zero $sel set have a peek at these guys Charges" Reply: Prof. I was wondering how to select in my system atoms with and x-axis smaller than a number and then wrap them. It works in two steps.

setbonds: Set the bonds for the atoms in the selection; the second argument should be a list of bondlists, one bondlist for each selected atom. lmoveto position_list: move each atom to a point given by the appropriate list element. Hello, If you could provide more information, that would be very helpful in diagnosing the problem you are seeing. check over here The text cannot be changed once a selection is made.

moveby offset: move all the atoms by a given offset. In any case, when you're using a new procedure you'll need to figure out whether you should pass it just the text for the selection or the selection itself. For these 120 degree files, the parser > don't quite do this right, and the atom name gets parsed as ATOMNAME-120(a > | b).

Thanks for the help!

Then I > > read again the manual and I cannot figure out how to use the compound > > command. > > > > -compound res[id[ue]]|seg[id]|chain|fragment > > the square Only to find some errors are given: atom > select: > > > cannot parse selection text.... > > > Can this be due to the format of cgc file? Eddie: "Re: fftk Opt. The last may be closest to what you were >>> looking for. >>> >>> Best, >>> Peter >>> >>> Arneh Babakhani wrote: >>> >>>> Once I've made a selection, how do

delmacro name: Delete the macro corresponding to name. You can the AutoPSF tool from Extensions | Modeling to create a PSF file if needed. However, the optimization now crashes and says: can't read "ljPars(C3)": no such element in array can't read "ljPars(C3)": no such element in array while executing "lindex $ljPars($aType) 0" (procedure "::ForceFieldToolKit::ChargeOpt::computeIntE" line this content tab, ffTK parses the filename to pull out the atom name, which > is needed during the optimization.

This is done by a function called atomselect, which returns the name of the new atom selection. But your original suggestion works, check > it out: > > >Main< 181 % set Peptide [atomselect top "protein"] > atomselect18070 > >Main< 182 % $Peptide get name > N H I used the script posted by Justin Gullingsrud.* >> **http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-2279/fit_angle.tcl >> >> >> When I used sel_sel_angle it works fine but when I tried to use >> sel_sel_angle_frames I got error Eddie: "Re: fftk Opt.

Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA Next message: Axel Kohlmeyer: "Re: Segmentation fault on linux Fedora 11" Previous message: John Stone: "Re: Segmentation fault on linux Fedora See Tables 5.5, 5.6, and 5.8 for the recognized attribute keywords. Atom selections created within a Tcl proc that are not made global are deleted when the proc exits. The first step is to create a selection given the selection text, molecule id, and optional frame number.

Note that if a nonexistent frame is specified, the atomic coordinates will all be taken to be .