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Cannot Parse Selection Text Vmd

Some examples are: vmd> atomselect top "name CA" atomselect0 vmd> atomselect 3 "resid 25" frame last atomselect1 vmd> atomselect top "within 5 of resname LYR" frame 23 atomselect2 The newly created Charges" In reply to: Mayne, Christopher G: "Re: fftk Opt. move 4x4 matrix: Applies the given transformation matrix to the coordinates of each atom in the selection. Eddie (eackad_at_siue.edu) Date: Wed Jun 19 2013 - 13:16:20 CDT Next message: Josh Vermaas: "Re: Atom Selection & List Generation" Previous message: Mayne, Christopher G: "Re: fftk Opt. weblink

moveto position: move all the atoms to a given location. There are usually hints, for instance when the variable is named "seltext" rather than "sel" it means just the text. uplevel level: Moves the object to a new level in the namespace stack. New in VMD 1.8: writepdb requires a filename; omitting the filename no longers returns the PDB data as a string. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14363.html

See Tables 5.5, 5.6, and 5.8 for the recognized attribute keywords. 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, If VMD detects this situation, it will abort the evaluation of the atom selection. The first step is to create a selection given the selection text, molecule id, and optional frame number.

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 On 30 Mar 2009, at 01:54, Peter Jones wrote: > Dear All, > > can anyone please tell me what's wrong with this selection? > > atomselect 0 "same residue as If speed is an issue, delete all representations of the molecule before setting the values. But your original suggestion works, check > it out: > > >Main< 181 % set Peptide [atomselect top "protein"] > atomselect18070 > >Main< 182 % $Peptide get name > N H

That information is provided by the PSF file, so it definitely appears that the lack of a PSF file is your problem. 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 Assistant Professor Center for Computational and Integrative Biology (CCIB) & Department of Physics Rutgers University, Camden, NJ (856)225-6780 www.branniganlab.org Next message: hamid mosaddeghi: "CG- CNT" Previous message: Chola Regmi: "Re: Regarding http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14356.html keywords: Return a list of all recognized keywords in an atom selection text.

Kohlmeyer that works very well. Eddie On Wed, Jun 19, 2013 at 10:53 AM, Mayne, Christopher G wrote: > ffTK generates Gaussian input files for computing water interaction > energies at each interaction site Charges" Reply: Prof. lmoveby offset_list: move each atom by an offset given in the list.

Anton. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21283.html NIH Center for Macromolecular Modeling & Bioinformatics University of Illinois at Urbana-Champaign Home Research Highlights Viruses Symbiont Bacteria Molecular Motors Neurons and Synapses Bioenergetic Membranes Nanosensors Ribosome Mechanosensing Protein Folding Integrative 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 Kirby wuxiao wrote: > Hello, > Thanks a lot for your attention! > > > Date: Mon, 14 Sep 2009 14:16:24 -0500 > > From: kvandivo_at_ks.uiuc.edu > > To: xiaowu759_at_hotmail.com >

Or is the psf file needed > for running the CGTools? > Thank you for any reply to this post. http://ecoflashapps.com/cannot-parse/cannot-parse-hex-bytes.html Next: axes Up: Tcl Text Commands Previous: animate Contents Index [email protected] NIH Center for Macromolecular Modeling & Bioinformatics University of Illinois at Urbana-Champaign Home Research Highlights Viruses Symbiont Bacteria 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 floating point values are passed to integer keywords, they will be converted to integers, and vice versa.

charges part. The following line set sel [atomselect top "resid 5 and chain $names($i) and not name "[0-9]?H.*" "] gives the error: extra characters after close-quote Looking at previous e-mail from the list, If the frame is a specific integer, the selection will always use coordinates from that frame, even if the current animation frame changes. check over here For these, the optional 'frame value' is used to determine which specific frame to use.

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 Any other relevant info you can provide? delmacro name: Delete the macro corresponding to name.

Mathews Ave > > Fax : (217) 244-6078 Urbana, IL 61801, USA > > > ------------------------------------------------------------------------ > 使用新一代 Windows Live Messenger 轻松交流和共享! 立刻下载! > -- Kirby Vandivort Theoretical and Senior

writeXXX filename: write the selected atoms to a file of type XXX; e.g., pdb, dcd. Charges" Next in thread: Prof. Eddie: "Re: fftk Opt. text: Return the text used to create this selection.

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 If a macro already exists for the given name, the old selection will be replaced with the new selection. What I did is just > > try to move the water from one unit cell to another and keep the protein > in > > the original unit cell by this content If there is only one attribute, then values_lists can be either a single value or a list of values, one for each selected atom.

You are passing it the whole atom selection when you use $seltext1 and $seltext2 - i.e., you've already set them to an atom selection using atomselect. To get the PDB data as a string, first write to a file, then enter the following commands: set fd [open filename r]; set s [read $fd]; close $fd. frame: Returns the animation frame associated with this selection. Do I need >>>> brackets somewhere? >>>> Thanks, >>>> >>>> Arneh >>>> >>> >> >> Next message: Cesar Luis Avila: "Setting modstyle volumeslice options via tk console" Previous message: Peter Freddolino:

Hope this helps, Grace On Fri, Jan 11, 2013 at 11:19 PM, Chola Regmi wrote: > I am able to solve the problem by doing > sel_sel_angle_frames 0 "myfirstselection" "mysecondselection" You should ensure that your macros do not contain themselves, either directly or through a chain of other macros. The last may be closest to what you were >>> looking for. >>> >>> Best, >>> Peter >>> >>> Arneh Babakhani wrote: >>> >>>> Once I've made a selection, how do Any ideas?

Note that if a nonexistent frame is specified, the atomic coordinates will all be taken to be . Eddie wrote: > > The water Int. The text will be contained in the variable s. list: Return a list of the atom indices in the selection (BTW, this is the same as get index).

Now the optimization runs. how would I find that label and why would the water > Int. Here's what I mean: >>>> >>>> >>>>> Main< 137 % set Peptide [atomselect top "all protein"] >>>>> >>>> atomselect17053 >>>> >>>>> Main< 139 % set IndoleNitrogen [atomselect top "$Peptide and name You will have >> several labels for the oxgygen atom that are identical although the log >> files are different. >> Brian >> >> ------------------------------ >> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf

For these 120 degree files, the parser > don't quite do this right, and the atom name gets parsed as ATOMNAME-120(a > | b). If a list of attributes is given, then a list of sublists will be returned; each sublist will contain the values for the corresponding attributes. Or is the psf file needed for running the CGTools? Thanks again for the help!

Works the same as the Tcl function uplevel.