From: Frieda R. <fr...@ns...> - 2007-02-28 17:57:21
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Hi, I am loading multiple pdb files into the applet, for example, load "fileset" "file1.pdb" "file2.pdb" "file3.pdb" I am having trouble understanding the correct uses use of the commands file and display. The documentation has not cleared it up completely for me. So, for example, with this script: restrict none select file=2 or file=3 trace 0.2 select [fe] and file=2 spacefill display file=2 or file=3 the traces appear, but the spacefilled [fe] does not appear. Why does the rest of the structure in file2.pdb appear (in trace), and not the iron atom (in spacefill) ? If I add the command file 2 at the top of the script, the spacefilled [fe] does appear. I do not understand the rationale for this- I guess I find it hard to understand the interaction of the commands "display" and "file". Can someone please explain how these command are working? Thanks, Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Bob H. <ha...@st...> - 2007-02-28 19:22:58
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Frieda Reichsman wrote: > Hi, > > I am loading multiple pdb files into the applet, for example, > load "fileset" "file1.pdb" "file2.pdb" "file3.pdb" > > I am having trouble understanding the correct uses use of the commands > file and display. The documentation has not cleared it up completely > for me. > > So, for example, with this script: > > restrict none > select file=2 or file=3 > trace 0.2 > > select [fe] and file=2 > spacefill > > display file=2 or file=3 > > the traces appear, but the spacefilled [fe] does not appear. Why does > the rest of the structure in file2.pdb appear (in trace), and not the > iron atom (in spacefill) ? > Be sure you issue first model 0 Otherwise you can only see the first model in the first file. Now when you select file=2 or file=3 trace 0.2 you will see all file data. What I think you are missing is that we might have three files and multiple models: -------File1---------|-----File2----------|----File3------------ --model--|---model---|------model---------|---model--|--model--- 1.1 1.2 2.1 3.1 3.2 When Jmol starts, the default is only to show the first model, numbered 1.1. The default is: select * model 1.1 display * Now, that select refers to ALL atoms in ALL models in ALL files, but only the first model is "displayable" and only its atoms are displayed. So whenever you need to display more than one model at the same time, you issue: model 0 # make all models displayable display 1.2 or 2.1 or display file=1 or file=2 or display file < 3 etc. What you are missing is the "model 0", or the equivalent in a context of animations, "frame 0". Those two commands are 100% synonymous. By the way, the reason [Fe] works here is that "Fe" is the PDB group. That's not a general method of showing iron, and if there were "Fe1" instead, it would not show it. I recommend instead: select _Fe That works for any file type, including PDB. Bob |
From: Frieda R. <fr...@ns...> - 2007-02-28 20:06:29
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Further discussion below: On Feb 28, 2007, at 2:22 PM, Bob Hanson wrote: > Frieda Reichsman wrote: > >> Hi, >> >> I am loading multiple pdb files into the applet, for example, >> load "fileset" "file1.pdb" "file2.pdb" "file3.pdb" >> >> I am having trouble understanding the correct uses use of the >> commands file and display. The documentation has not cleared it up >> completely for me. >> >> So, for example, with this script: >> >> restrict none >> select file=2 or file=3 >> trace 0.2 >> >> select [fe] and file=2 >> spacefill >> >> display file=2 or file=3 >> >> the traces appear, but the spacefilled [fe] does not appear. Why >> does the rest of the structure in file2.pdb appear (in trace), and >> not the iron atom (in spacefill) ? >> > Be sure you issue first > > model 0 OK, good- this almost works - however in some instances with this set- up, I want to NOT show the first file first, and instead only the second two. When I say file 0 restrict none prior to displaying files 2 and 3, the representation of file 1 appears briefly in the applet, then disappears, then the desired 2nd and 3rd appear. If I use restrict none file 0 the file 1 structure is mostly NOT displayed- except for an existing monitor line, which appears briefly. If a monitor does this then I assume a halo will do it, etc., that is, objects not covered by 'restrict'. So, if I use restrict none file 0 select * script all_off.spt # this turns of monitors, halos, echos, etc. before displaying files 2 and 3, now I get a pretty clean switch between views, with nobody appearing and disappearing. Is there a simpler way to do this? <snip> > What I think you are missing is that we might have three files and > multiple models: > > -------File1---------|-----File2----------|----File3------------ > --model--|---model---|------model---------|---model--|--model--- > > 1.1 1.2 2.1 3.1 3.2 > This is useful to know - but I do not have multiple models... > When Jmol starts, the default is only to show the first model, > numbered 1.1. > > The default is: > > select * > model 1.1 > display * > > Now, that select refers to ALL atoms in ALL models in ALL files, but > only the first model is "displayable" and only its atoms are > displayed. > > So whenever you need to display more than one model at the same > time, you > issue: > > model 0 # make all models displayable > > display 1.2 or 2.1 > > or > > display file=1 or file=2 > > or > > display file < 3 > > etc. > > > What you are missing is the "model 0", or the equivalent in a > context of animations, "frame 0". Those two commands are 100% > synonymous. > > By the way, the reason [Fe] works here is that "Fe" is the PDB > group. That's not a general method of showing iron, and if there > were "Fe1" instead, it would not show it. I recommend instead: > > select _Fe I have noticed the underscore before an element name is some previous posts but not really known how to use it. Would _c be carbon, and _ca, calcium? Is this documented (yet)? Finally, I have made no progress in being able to load jvxl data and have it appear - see previous post - help is needed... I used to be able to do this, cannot find my error. Using isosurface mysurface "abcd.jvxl" or isosurface "abcd.jvxl" or isosurface file "abcd.jvxl" ... no surface appears... can anyone confirm? Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Frieda R. <fr...@ns...> - 2007-02-28 21:49:48
|
Further discussion below: On Feb 28, 2007, at 2:22 PM, Bob Hanson wrote: > Frieda Reichsman wrote: > >> Hi, >> >> I am loading multiple pdb files into the applet, for example, >> load "fileset" "file1.pdb" "file2.pdb" "file3.pdb" >> >> I am having trouble understanding the correct uses use of the >> commands file and display. The documentation has not cleared it up >> completely for me. >> >> So, for example, with this script: >> >> restrict none >> select file=2 or file=3 >> trace 0.2 >> >> select [fe] and file=2 >> spacefill >> >> display file=2 or file=3 >> >> the traces appear, but the spacefilled [fe] does not appear. Why >> does the rest of the structure in file2.pdb appear (in trace), and >> not the iron atom (in spacefill) ? >> > Be sure you issue first > > model 0 OK, good- this almost works - however in some instances with this set- up, I want to NOT show the first file first, and instead only the second two. When I say file 0 restrict none prior to displaying files 2 and 3, the representation of file 1 appears briefly in the applet, then disappears, then the desired 2nd and 3rd appear. If I use restrict none file 0 the file 1 structure is mostly NOT displayed- except for an existing monitor line, which appears briefly. If a monitor does this then I assume a halo will do it, etc., that is, objects not covered by 'restrict'. So, if I use restrict none file 0 select * script all_off.spt # this turns of monitors, halos, echos, etc. before displaying files 2 and 3, now I get a pretty clean switch between views, with nobody appearing and disappearing. Is there a simpler way to do this? <snip> > What I think you are missing is that we might have three files and > multiple models: > > -------File1---------|-----File2----------|----File3------------ > --model--|---model---|------model---------|---model--|--model--- > > 1.1 1.2 2.1 3.1 3.2 > This is useful to know - but I do not have multiple models... > When Jmol starts, the default is only to show the first model, > numbered 1.1. > > The default is: > > select * > model 1.1 > display * > > Now, that select refers to ALL atoms in ALL models in ALL files, but > only the first model is "displayable" and only its atoms are > displayed. > > So whenever you need to display more than one model at the same > time, you > issue: > > model 0 # make all models displayable > > display 1.2 or 2.1 > > or > > display file=1 or file=2 > > or > > display file < 3 > > etc. > > > What you are missing is the "model 0", or the equivalent in a > context of animations, "frame 0". Those two commands are 100% > synonymous. > > By the way, the reason [Fe] works here is that "Fe" is the PDB > group. That's not a general method of showing iron, and if there > were "Fe1" instead, it would not show it. I recommend instead: > > select _Fe I have noticed the underscore before an element name is some previous posts but not really known how to use it. Would _c be carbon, and _ca, calcium? Is this documented (yet)? Finally, I have made no progress in being able to load jvxl data and have it appear - see previous post - help is needed... I used to be able to do this, cannot find my error. Using isosurface mysurface "abcd.jvxl" or isosurface "abcd.jvxl" or isosurface file "abcd.jvxl" ... no surface appears... can anyone confirm? Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Angel H. <ang...@ua...> - 2007-02-28 23:12:49
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Frieda Reichsman wrote: > I have noticed the underscore before an element name is some previous > posts but not really known how to use it. Would _c be carbon, and _ca, > calcium? Is this documented (yet)? http://wiki.jmol.org:81/index.php/AtomSets Valid for any element symbol, including D and T. |