VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Apr 02 2016 - 21:20:57 CDT

Hi,
  At present, there are no special flags that have any specific effect on the
export of VMD molecular scenes to the various scene file formats, and that's
why you didn't find anything in the User's Guide.

Essentially VMD attempts to provide as close to WYSIWYG output as
possible, within the limits of what each of the file formats is
capable of supporting. You haven't said much about what you're
trying to accomplish by exporting the scenes in one of the formats you
listed, so it's hard to give specific guidance. In general, the
resolution parameters for the graphical representations will have the
greatest impact on the geometry that you get in scene file formats like
OBJ or STL that only support triangle meshes. VMD will use actual
spheres and cylinders when exporting to file formats such as
like X3D or VRML which support such primitives. What do you plan to
do with the exported scene files after export?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Apr 02, 2016 at 05:09:00PM -0400, James Kress wrote:
> I have read the "VMD Images and Movies Tutorial" but it gives no
> information on what parameters can be specified in the File Render
> Controls for obj, x3d, stl, VRML 2.0 and other files for use in other 3D
> representation systems.\001 It also does not provide, nor does the VMD
> documentation, the default settings used to create these other 3D file
> representations.
>
>
>
> Where can I get this information and how do I modify the renderer command
> to provide higher resolution, higher-antialiasing, and better materials
> and material properties for these output formats?
>
>
>
> Thanks.
>
>
>
> Jim Kress
>
>
>
> James Kress Ph.D., President
>
> The KressWorks(R) Foundation
>
> An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
>
> "Engineering The Cure" (c)
>
> (248) 605-8770
>
>
>
> Learn More and Donate At:
>
> Website: [1]http://www.kressworks.org
>
> Facebook: [2]https://www.facebook.com/KressWorks.Foundation/
>
> Twitter: @KressWorksFnd
>
>
>
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> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of MannyEful E
> Sent: Saturday, April 02, 2016 1:28 PM
> To: John Stone <johns_at_ks.uiuc.edu>; MannyEful E <mannyeful_at_gmail.com>;
> vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Residence Time Script (v2.)
>
>
>
> Thank you John and Norman!
>
>
>
> On Thu, Mar 31, 2016 at 4:38 PM, John Stone <[3]johns_at_ks.uiuc.edu> wrote:
>
> Don't use the variable name "list" because "list" is a Tcl command.
> You could rename that to "lst" or something more indicative of what
> it actually contains and the problem might go away.
> In general you should avoid using Tcl command names as variables, as
> they can cause confusing syntax errors and the like.
> That seems to be a likely source of your problem.
>
> Cheers,
> John
>
> On Thu, Mar 31, 2016 at 01:51:48AM +0100, MannyEful E wrote:
> > Hello Everyone,A
> > I have seen a few requests for the average residence time of water
> > molecules around the protein and am currently working on such a
> script. I
> > get a few errors which I believe are the result of the incorrect
> syntax.
> > Could someone please point me in the right direction?
> > The script is attached below and the two lines responsible for the
> errors
> > are highlighted with arrows. (<-----------)
> > The error message:
> > A invalid character "." in expression "...st +])/[llength $list]."A
> > In sum, the script does the following:
> > 1. For each water molecules it counts the number of separate
> occasions
> > that it approaches the polymer, including the times that it leaves
> but
> > returns (A).A
> > 2. It also records how long they stay (B).
> > 3. An array of A/B is produced (C).
> > 4. Finally, the average and stdev of C is obtained and printed. A
> (The
> > errors crop up here when I try to output my results in double
> precision,
> > whilst using a proc function.)
> > #################### A The Residence Script: A A
> #####################
> > puts "Bash usage: vmd -dispdev text -gro file.gro -xtc file.xtc -e
> > residence_times_v2.tcl"
> > puts "Next, type: residence nth unit pol"
> > puts "e.g.: residence 1st 500 pvc "
> > #################################################################
> > # process used to calculate the average of values in an array
> > proc lavg list {
> > expr {double([join $list +])/[llength $list].}
> > }
> > A
> > A # process used to calculate the stdev of values in an array
> > proc stddev list {
> > A set m [lavg $list]
> > A expr {sqrt([mean2 $list]-$m*$m)}
> > A }
> > A
> > #################################################################
> > A
> > #proc residence {nth pol unit} {
> > # Variables for Atomselection
> > set nth 1st; # which repeat is it
> > set unit 5; # how many units is the polymer
> > set pol pva; # what is the polymer name
> > set min1 0.0; A A # lower limit for the hydration shell1 in
> angstroms
> > set max1 10.5;A # higher limit of the hydration shell1 in
> angstroms
> > set fp1 [open "residence_times_tracker.xvg" w]; # tracks the
> calculation
> > outputs
> > set fp2 [open "residence_times_output.xvg" w]; # tracks the output
> > section
> > set atom_ref ${pol}${unit};A # VMD residue name of the reference
> atom
> > set sel [atomselect top all];A # select all the atomsA
> > set all [$sel num];A # count the number of atoms
> > set fn [molinfo top get numframes]; # count the number of frames
> > set stepsize 40.00;
> > #################################################################
> > # set all the histograms to zero
> > for {set i 0} {$i < $all} {incr i} {
> > set hist1($i) 0; A # counter: If it is within region
> > set hist2($i) 0;A A # note: If it left
> > set hist3($i) 0; A # counter: Sum of those that leftA
> > set hist4($i) 0; # counter
> > }
> > #################################################################
> > # loop through all the frames
> > for {set i 0} {$i < $fn} {incr i} {
> > # do the following for all the frames except the last one
> > if {$i < [expr $fn - 1]} {
> > # go to the next frame
> > animate goto $i;
> > # outputs frame we are on
> > puts $fp1 "Frame $i of $fn: [expr {double(($i * $stepsize)/1000)}]
> ns ";A
> > # make selections in frame and in next frame
> > set sel1 [atomselect top "(name OW and same resid as (resname SOL
> and
> > (within $max1 of resname $atom_ref))) and not (name OW and same
> resid as
> > (resname SOL and (within $min1 of resname $atom_ref)))" frame $i];A
> > set sel2 [atomselect top "(name OW and same resid as (resname SOL
> and
> > (within $max1 of resname $atom_ref))) and not (name OW and same
> resid as
> > (resname SOL and (within $min1 of resname $atom_ref)))" frame [expr
> $i +
> > 1]];A
> > A A A $sel1 update; # updates dynamic water selection1 for this
> frame
> > A A A $sel2 update; # updates dynamic water selection2 for this
> frame
> > puts $fp1 "Both selections made";
> > # creates a list of atoms indices from the next frame
> > set list2 [$sel2 get index];
> > puts $fp1 "List of future atom indices made: \n $list2";
> > # for every water oxygen atom that is near the polymer
> > # get the atoms index
> > foreach present [$sel1 get index] {
> > puts $fp1 "ID: $present";
> > # check: Is it near the polymer (Always true in this loop)
> > incr hist1([expr $present - 1]);A # add 1 if present near the
> area of
> > interest
> > puts $fp1 "HIST1: $hist1([expr $present - 1])";
> > # check: Is it coming back?
> > if { $hist2([expr $present - 1]) == 1 } A {
> > incr hist3([expr $present - 1]);A # add 1 if previous hist2 was 1
> > because it left and came back.A
> > puts $fp1 "HIST3: $hist3([expr $present - 1])";
> > }A
> > # check: Will it leave?
> > # compare the atom indices to the list of selection2
> > # and if it is present, it will return a value greater than 1
> > # so add one to our approaches counter
> > # if it has left it returns a -1
> > if { [lsearch -exact $list2 $present] >= 0} {
> > set hist2([expr $present - 1]) 1;
> > incr hist4([expr $present - 1]);
> > puts $fp1 "It will stay in the next frame";A
> > } else {
> > set hist2([expr $present - 1]) 0;
> > puts $fp1 "It will leave in the next frame";
> > }
> > }
> > } else {
> > # go to the next frame
> > animate goto $i;
> > # outputs frame we are on
> > puts $fp1 "Frame $i of $fn: [expr {double(($i * $stepsize)/1000)}]
> ns ";A
> > # make selections in frame and in next frame
> > set sel1 [atomselect top "(name OW and same resid as (resname SOL
> and
> > (within $max1 of resname $atom_ref))) and not (name OW and same
> resid as
> > (resname SOL and (within $min1 of resname $atom_ref)))" frame $i];A
> > foreach present [$sel1 get index] {
> > puts $fp1 "ID: $present";
> > #Any present? Always in this loop
> > incr hist1([expr $present - 1]); # add 1 because it is present
> near area
> > of interest
> > # check: Is it coming back?
> > if { $hist2([expr $present - 1]) == 1 } A {
> > incr hist3([expr $present - 1]);A # add 1 if previous hist2 was 1
> > because it left and came back.A
> > puts $fp1 "HIST3: $hist3([expr $present - 1])";
> > }A
> > # in order to account for those occasions where the water molecule
> > remained at the last frame
> > # artificially set all atoms present in the area of interest to
> leave in
> > the last frameA
> > set hist2([expr $present - 1]) 1;
> > incr hist4([expr $present - 1]);
> > puts $fp1 "It will stay in the next frame";A
> > }
> > }
> > $sel1 delete; array unset sel1; # unset the selection1A
> > $sel2 delete; array unset sel2; # unset the selection2A
> > }
> > #################################################################
> > # set new constants to zero
> > set hist_final {};A
> > set counter 0;
> > set comebacks 0;
> > # loop through all atoms (non-oxygens as well)
> > for {set i 0} {$i < [llength $hist1([expr $all - 1])]} {incr i} {
> > puts $fp2 "Atom ${i} : [lindex $hist1([expr $all - 1]) $i]";
> > # find the atoms that have residence times (ie if the hist1 counter
> is
> > greater than zero, a residence time is available)A
> > if {[lindex $hist1([expr $all - 1]) $i] > 0} {
> > # count the number of atoms with residences recorded
> > incr $counter;
> > puts $fp2 "Number of atoms with residences: $counter Counter";
> > # calculate the individual residence times for each oxygen atom
> that was
> > near the molecule
> > puts $fp2 " [lindex $hist1([expr $all - 1]) $i] / [lindex
> $hist4([expr
> > $all - 1]) $i] = [expr [lindex $hist1([expr $all - 1]) $i] /
> [lindex
> > $hist4([expr $all - 1]) $i]]";
> > # populate the array hist_final
> > lappend hist_final [expr {double([lindex $hist1([expr $all - 1])
> $i]) /
> > double([lindex $hist4([expr $all - 1]) $i])}];
> > # identify how many times the water molecules returned after
> leaving
> > set comebacks [expr $comebacks + [lindex $hist3([expr $all - 1])
> $i]];
> > } else {
> > puts $fp2 "No residence times to record ${i} - number [lindex
> $hist1([expr
> > $all - 1]) ${i}]";
> > }
> > }
> > puts $fp2 "$counter : Number of oxygen atoms with residences within
> $max1
> > of the polymer over $fn frames";
> > puts $fp2 "$comebacks : Number of times any of the $counter water
> > molecules";
> > puts $fp2 "[expr {[lavg (double($hist_final))] * $stepsize}] ps :
> Average
> > residence time "; A <--------------
> > puts $fp2 "[expr {[stddev (double($hist_final))] * $stepsize}] ps :
> Stdev
> > "; A <-----------
> > close $fp1;
> > close $fp2;
> > #################################################################
> > # unset all the selections for faster execution
> > array unset nth;
> > array unset unit;
> > array unset pol;
> > array unset min1;A
> > array unset max1;A
> > array unset fp1;
> > array unset fp2;
> > array unset atom_ref;A
> > array unset fn;A
> > array unset stepsize;
> > $sel delete; array unset sel;
> > array unset list2;A
> > array unset present;
> > for {set i 0} {$i < $all} {incr i} {
> > array unset hist1($i); A
> > array unset hist2($i);A A
> > array unset hist3($i); A A
> > array unset hist4($i);
> > }
> > array unset all;A
> > array unset hist_final;A
>
> > array unset counter;
> > array unset comebacks;
> > #################################################################
> > #}
> > END
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [4]http://www.ks.uiuc.edu/~johns/ Phone: [5]217-244-3349
> [6]http://www.ks.uiuc.edu/Research/vmd/
>
>
>
> References
>
> Visible links
> 1. http://www.kressworks.org/
> 2. https://www.facebook.com/KressWorks.Foundation/
> 3. mailto:johns_at_ks.uiuc.edu
> 4. http://www.ks.uiuc.edu/~johns/
> 5. tel:217-244-3349
> 6. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/