Hi all, I posted this last week, but it didn’t appear in the archives, so I guess it didn’t go through - if that is not the case, my apologies for the double post. I notice in the presets menu that there is the option to add custom presets, but I couldn’t find much documentation on this feature. Is it possible to save the current display options as a preset, similar to saving individual preference combinations but as a preset that can be quickly loaded? For example, displaying X-ray maps in a way that looks similar to how they are represented in Coot is a little complicated - I usually turn off “Mesh lighting”, “Cap high values at box faces”, and “Square mesh”, turn off ribbons, display all atoms and set the stick scale to 0.5, change the background to black, and alter the depth cueing - it would be very handy indeed to be able to apply all these settings at once. Also with regards to X-ray maps, I usually normalize (using vop scale #map, factor 1/SD) both the 2fo-fc and fo-fc, and then split the fo-fc into separate +ve and -ve maps, using vop threshold #map minimum 0 and vop threshold #map maximum 0. Would it be possible to assign these steps to macros or commands, and if so how would I go about doing that? Many thanks for your help, Oliver.
Hi Oliver, I didn't see another post, so no worries about that! You can't save the current display settings directly as a custom preset. You would need to create a plain text file of Chimera commands or Python code for the settings, then name it appropriately and tell Chimera where the file is located (menu Presets… Add Custom Presets). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets> Some of the main Chimera commands related to display are: color - coloring atoms, bonds, ribbons, molecular surfaces display - which atoms/bonds are shown represent - atom/bond display style ribbon - ribbon stuff surface - molecular surface stuff setattr - attributes not covered by the above (for example: setattr m stickScale 0.5) set - many global settings like background color, depth-cueing, shadows, outlines volume - density display (see meshLighting, capFaces, squareMesh options) See command documentation and also the image tips: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> A similar feature for definining macros that can be expressed as a series of commands is the alias mechanism. With the "alias" command you can define longer sets of commands as a shorter command, even including command arguments. The shorter command can be entered in the command line, and some of the aliases (those defined with "^" and without arguments) will even appear in a new Aliases menu. For details and examples see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> You can actually get quite fancy with both of these mechanisms. The main barrier is figuring out the appropriate commands or code. You can test either type of file by simply opening it in Chimera, and of course you can test individual commands by entering them in the command line. As for your normalization procedure, sounds like Python would be required to automatically insert the SD, min, and max into the other commands. Python is beyond my skill set, so others may need to respond to that part of your question. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 19, 2014, at 7:18 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all, I posted this last week, but it didn’t appear in the archives, so I guess it didn’t go through - if that is not the case, my apologies for the double post.
I notice in the presets menu that there is the option to add custom presets, but I couldn’t find much documentation on this feature.
Is it possible to save the current display options as a preset, similar to saving individual preference combinations but as a preset that can be quickly loaded?
For example, displaying X-ray maps in a way that looks similar to how they are represented in Coot is a little complicated - I usually turn off “Mesh lighting”, “Cap high values at box faces”, and “Square mesh”, turn off ribbons, display all atoms and set the stick scale to 0.5, change the background to black, and alter the depth cueing - it would be very handy indeed to be able to apply all these settings at once.
Also with regards to X-ray maps, I usually normalize (using vop scale #map, factor 1/SD) both the 2fo-fc and fo-fc, and then split the fo-fc into separate +ve and -ve maps, using vop threshold #map minimum 0 and vop threshold #map maximum 0. Would it be possible to assign these steps to macros or commands, and if so how would I go about doing that?
Many thanks for your help, Oliver.
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, I didn't see another post, so no worries about that!
You can't save the current display settings directly as a custom preset. You would need to create a plain text file of Chimera commands or Python code for the settings, then name it appropriately and tell Chimera where the file is located (menu Presets… Add Custom Presets). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets>
Some of the main Chimera commands related to display are:
color - coloring atoms, bonds, ribbons, molecular surfaces display - which atoms/bonds are shown represent - atom/bond display style ribbon - ribbon stuff surface - molecular surface stuff setattr - attributes not covered by the above (for example: setattr m stickScale 0.5) set - many global settings like background color, depth-cueing, shadows, outlines volume - density display (see meshLighting, capFaces, squareMesh options)
See command documentation and also the image tips: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
A similar feature for definining macros that can be expressed as a series of commands is the alias mechanism. With the "alias" command you can define longer sets of commands as a shorter command, even including command arguments. The shorter command can be entered in the command line, and some of the aliases (those defined with "^" and without arguments) will even appear in a new Aliases menu.
For details and examples see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
You can actually get quite fancy with both of these mechanisms. The main barrier is figuring out the appropriate commands or code. You can test either type of file by simply opening it in Chimera, and of course you can test individual commands by entering them in the command line.
As for your normalization procedure, sounds like Python would be required to automatically insert the SD, min, and max into the other commands. Python is beyond my skill set, so others may need to respond to that part of your question. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 7:18 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all, I posted this last week, but it didn’t appear in the archives, so I guess it didn’t go through - if that is not the case, my apologies for the double post.
I notice in the presets menu that there is the option to add custom presets, but I couldn’t find much documentation on this feature.
Is it possible to save the current display options as a preset, similar to saving individual preference combinations but as a preset that can be quickly loaded?
For example, displaying X-ray maps in a way that looks similar to how they are represented in Coot is a little complicated - I usually turn off “Mesh lighting”, “Cap high values at box faces”, and “Square mesh”, turn off ribbons, display all atoms and set the stick scale to 0.5, change the background to black, and alter the depth cueing - it would be very handy indeed to be able to apply all these settings at once.
Also with regards to X-ray maps, I usually normalize (using vop scale #map, factor 1/SD) both the 2fo-fc and fo-fc, and then split the fo-fc into separate +ve and -ve maps, using vop threshold #map minimum 0 and vop threshold #map maximum 0. Would it be possible to assign these steps to macros or commands, and if so how would I go about doing that?
Many thanks for your help, Oliver.
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models. If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 19, 2014, at 4:18 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number. Tom On May 19, 2014, at 4:45 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Tom and Elaine, # was what I was looking for - I didn’t realize you could use that to specify all models. I will try that and see how I go. Best, Oliver. On May 19, 2014, at 8:06 PM, Tom Goddard <goddard@sonic.net> wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though. In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking. window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet # On May 19, 2014, at 8:06 PM, Tom Goddard <goddard@sonic.net> wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Oliver, Just a couple of minor notes on your script: (1) you don't need the # in the disp, ribbon, represent, modelcolor, color commands; for many commands in which the atomspec is the last part, blank atomspec (nothing) means "all applicable items" (likewise, you wouldn't need the @ in window unless you want it to use only atoms) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> (2) if # works for the volume command, that's fine, but it can also take the word "all" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> Best, Elaine On May 19, 2014, at 9:10 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
Hi Oliver, I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map. Tom On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Great, thanks Tom, I’ll look forward to trying it out! I’m guessing it’ll be in the May 21 daily build then? Really we only need sd 1 (or rms 1) - that way the threshold then corresponds to what is often thought of as the “sigma level” of the density map, and if you want it contoured at 5sd, you can just change the threshold to 5. Best, Oliver. On May 20, 2014, at 1:01 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Yes, the new vop “sd” option will be in the May 21 daily build about 20 hours from now (about 6 AM Pacific time). I agree that normalizing 1 SD to a value other than 1 would be weird. At first I tried the syntax, “vop scale #0 sdOne true”, but I abandoned that and went with “vop scale #0 sd 1” which was clearer, and since I made the option value a number it seemed reasonable to allow it to be any value and the SD of the new map would have that value. Tom On May 20, 2014, at 10:17 AM, Oliver Clarke wrote:
Great, thanks Tom, I’ll look forward to trying it out!
I’m guessing it’ll be in the May 21 daily build then?
Really we only need sd 1 (or rms 1) - that way the threshold then corresponds to what is often thought of as the “sigma level” of the density map, and if you want it contoured at 5sd, you can just change the threshold to 5.
Best, Oliver.
On May 20, 2014, at 1:01 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng wrote:
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Hi Oliver, I’m unclear about the meaning of “sigma level” in x-ray maps, and also uncertain now whether we agree on the definition of standard deviation. By standard deviation I mean sqrt(sum(v_ijk*v_ijk)), in words, the squareroot of the sum of the square of the map values. If instead, you first subtracted the mean map value then you would have the root-mean-square-deviation RMSD which will be a different value if the mean is not 0. X-ray density maps from the Uppsala electron density server don’t have mean 0, so the difference is significant. Is sigma level defined as RMSD units above the mean, or SD units above 0? Tom On May 20, 2014, at 10:01 AM, Tom Goddard wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hi Tom, Good question, and I suspect if you asked different crystallographers you may receive conflicting responses. There was a good discussion on this point on the ccp4bb some time ago, but I can’t seem to find it right now. I put sigma level in quotation marks precisely for this reason - people refer to the sigma level, but generally mean multiples of the RMSD. I know that Coot refers to rms values, and these values are often quoted as sigma levels. Would it be possible to include rmsd as a separate option for vop scale, so we can choose? Best, Oliver. On May 20, 2014, at 2:13 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
I’m unclear about the meaning of “sigma level” in x-ray maps, and also uncertain now whether we agree on the definition of standard deviation. By standard deviation I mean sqrt(sum(v_ijk*v_ijk)), in words, the squareroot of the sum of the square of the map values. If instead, you first subtracted the mean map value then you would have the root-mean-square-deviation RMSD which will be a different value if the mean is not 0. X-ray density maps from the Uppsala electron density server don’t have mean 0, so the difference is significant. Is sigma level defined as RMSD units above the mean, or SD units above 0?
Tom
On May 20, 2014, at 10:01 AM, Tom Goddard wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke wrote:
Hi Elaine, Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? Best, Oliver. On May 19, 2014, at 1:00 PM, Elaine Meng wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Here is the discussion to which I alluded. The general consensus seems to be that referring to RMS levels is more appropriate - my apologies for any confusion. https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02559.html Best, Oliver. On May 20, 2014, at 2:32 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Tom,
Good question, and I suspect if you asked different crystallographers you may receive conflicting responses. There was a good discussion on this point on the ccp4bb some time ago, but I can’t seem to find it right now.
I put sigma level in quotation marks precisely for this reason - people refer to the sigma level, but generally mean multiples of the RMSD. I know that Coot refers to rms values, and these values are often quoted as sigma levels.
Would it be possible to include rmsd as a separate option for vop scale, so we can choose?
Best, Oliver.
On May 20, 2014, at 2:13 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
I’m unclear about the meaning of “sigma level” in x-ray maps, and also uncertain now whether we agree on the definition of standard deviation. By standard deviation I mean sqrt(sum(v_ijk*v_ijk)), in words, the squareroot of the sum of the square of the map values. If instead, you first subtracted the mean map value then you would have the root-mean-square-deviation RMSD which will be a different value if the mean is not 0. X-ray density maps from the Uppsala electron density server don’t have mean 0, so the difference is significant. Is sigma level defined as RMSD units above the mean, or SD units above 0?
Tom
On May 20, 2014, at 10:01 AM, Tom Goddard wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke wrote:
> Hi Elaine, > Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? > Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? > Best, > Oliver. > On May 19, 2014, at 1:00 PM, Elaine Meng wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hi Oliver, Ok, if I add a vop scale “rmsd" option it seems sensible that it should both shift the map to have mean 0 and scale so RMSD is 1. Or should I not do the shift? The reason I think the shift to make mean 0 is probably best is that without the shift you could not easily set a threshold at 2 sigma (2*RMSD above the mean) because you wouldn’t know the mean value. But I’m uncertain about this since I don’t understand what the 0 value of the x-ray map represents in cases where it is not 0. I could additionally have an option “mean 0” that would shift the map values to make the mean 0, if that is useful. Tom On May 20, 2014, at 11:32 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Tom,
Good question, and I suspect if you asked different crystallographers you may receive conflicting responses. There was a good discussion on this point on the ccp4bb some time ago, but I can’t seem to find it right now.
I put sigma level in quotation marks precisely for this reason - people refer to the sigma level, but generally mean multiples of the RMSD. I know that Coot refers to rms values, and these values are often quoted as sigma levels.
Would it be possible to include rmsd as a separate option for vop scale, so we can choose?
Best, Oliver.
On May 20, 2014, at 2:13 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
I’m unclear about the meaning of “sigma level” in x-ray maps, and also uncertain now whether we agree on the definition of standard deviation. By standard deviation I mean sqrt(sum(v_ijk*v_ijk)), in words, the squareroot of the sum of the square of the map values. If instead, you first subtracted the mean map value then you would have the root-mean-square-deviation RMSD which will be a different value if the mean is not 0. X-ray density maps from the Uppsala electron density server don’t have mean 0, so the difference is significant. Is sigma level defined as RMSD units above the mean, or SD units above 0?
Tom
On May 20, 2014, at 10:01 AM, Tom Goddard wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng wrote:
Hi Oliver, You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models.
If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2014, at 4:18 PM, Oliver Clarke wrote:
> Hi Elaine, > Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? > Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? > Best, > Oliver. > On May 19, 2014, at 1:00 PM, Elaine Meng wrote:
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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It seems sensible to do the shift. I think Coot does the same think actually (although you’d need to check with Paul Emsley to be certain) - the map statistics output by Coot for every map that I’ve looked at, both from the EDS and elsewhere, have means that are arbitrarily close to zero (the highest I could find was 1e-6, and most are closer to 1e-11, too small to make any difference to the normalization). Oliver. On May 20, 2014, at 2:54 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
Ok, if I add a vop scale “rmsd" option it seems sensible that it should both shift the map to have mean 0 and scale so RMSD is 1. Or should I not do the shift? The reason I think the shift to make mean 0 is probably best is that without the shift you could not easily set a threshold at 2 sigma (2*RMSD above the mean) because you wouldn’t know the mean value. But I’m uncertain about this since I don’t understand what the 0 value of the x-ray map represents in cases where it is not 0. I could additionally have an option “mean 0” that would shift the map values to make the mean 0, if that is useful.
Tom
On May 20, 2014, at 11:32 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Tom,
Good question, and I suspect if you asked different crystallographers you may receive conflicting responses. There was a good discussion on this point on the ccp4bb some time ago, but I can’t seem to find it right now.
I put sigma level in quotation marks precisely for this reason - people refer to the sigma level, but generally mean multiples of the RMSD. I know that Coot refers to rms values, and these values are often quoted as sigma levels.
Would it be possible to include rmsd as a separate option for vop scale, so we can choose?
Best, Oliver.
On May 20, 2014, at 2:13 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
I’m unclear about the meaning of “sigma level” in x-ray maps, and also uncertain now whether we agree on the definition of standard deviation. By standard deviation I mean sqrt(sum(v_ijk*v_ijk)), in words, the squareroot of the sum of the square of the map values. If instead, you first subtracted the mean map value then you would have the root-mean-square-deviation RMSD which will be a different value if the mean is not 0. X-ray density maps from the Uppsala electron density server don’t have mean 0, so the difference is significant. Is sigma level defined as RMSD units above the mean, or SD units above 0?
Tom
On May 20, 2014, at 10:01 AM, Tom Goddard wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number.
Tom
On May 19, 2014, at 4:45 PM, Elaine Meng wrote:
> Hi Oliver, > You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models. > > If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> > > One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> > > You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On May 19, 2014, at 4:18 PM, Oliver Clarke wrote: > >> Hi Elaine, >> Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? >> Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? >> Best, >> Oliver. >> On May 19, 2014, at 1:00 PM, Elaine Meng wrote: > > > _______________________________________________ > Chimera-users mailing list > Chimera-users@cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Oliver, Ok, in tonight’s daily build there will be two new options to “vop scale”. One “rms” scales the map so that sqrt(sum(v*v)/N) is 1 (“vop scale #0 rms 1”), and the other “sd” shifts the map so that the new map has mean 0 and then scales to make sqrt(sum(v*v)/N) equal to 1 (“vop scale #0 sd 1”). In my earlier email I incorrectly said the standard deviation value did not subtract the mean before squaring. The standard deviation (SD) does subtract the mean before squaring. The RMS (root mean square) value does not subtract the mean. Also the terminology is RMS, not RMSD. The term root mean square deviation (RMSD) is used for a comparison between two data sets and is not applicable to this map scaling discussion. Oddly, I find Uppsala electron density server maps have mean values different from 0. This is probably because Chimera fetches the O format map (.omap) which has only one byte per value. For instance Chimera reports 4pfd.omap (2fo-fc) to have mean -0.01 and SD 0.33, so the mean is off from 0 by about 3% of the SD. The deviations from 0 are small and probably do not make a significant difference. But that is where my idea came from that the mean was not 0. Tom On May 20, 2014, at 12:06 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
It seems sensible to do the shift.
I think Coot does the same think actually (although you’d need to check with Paul Emsley to be certain) - the map statistics output by Coot for every map that I’ve looked at, both from the EDS and elsewhere, have means that are arbitrarily close to zero (the highest I could find was 1e-6, and most are closer to 1e-11, too small to make any difference to the normalization).
Oliver.
On May 20, 2014, at 2:54 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
Ok, if I add a vop scale “rmsd" option it seems sensible that it should both shift the map to have mean 0 and scale so RMSD is 1. Or should I not do the shift? The reason I think the shift to make mean 0 is probably best is that without the shift you could not easily set a threshold at 2 sigma (2*RMSD above the mean) because you wouldn’t know the mean value. But I’m uncertain about this since I don’t understand what the 0 value of the x-ray map represents in cases where it is not 0. I could additionally have an option “mean 0” that would shift the map values to make the mean 0, if that is useful.
Tom
On May 20, 2014, at 11:32 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Tom,
Good question, and I suspect if you asked different crystallographers you may receive conflicting responses. There was a good discussion on this point on the ccp4bb some time ago, but I can’t seem to find it right now.
I put sigma level in quotation marks precisely for this reason - people refer to the sigma level, but generally mean multiples of the RMSD. I know that Coot refers to rms values, and these values are often quoted as sigma levels.
Would it be possible to include rmsd as a separate option for vop scale, so we can choose?
Best, Oliver.
On May 20, 2014, at 2:13 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
I’m unclear about the meaning of “sigma level” in x-ray maps, and also uncertain now whether we agree on the definition of standard deviation. By standard deviation I mean sqrt(sum(v_ijk*v_ijk)), in words, the squareroot of the sum of the square of the map values. If instead, you first subtracted the mean map value then you would have the root-mean-square-deviation RMSD which will be a different value if the mean is not 0. X-ray density maps from the Uppsala electron density server don’t have mean 0, so the difference is significant. Is sigma level defined as RMSD units above the mean, or SD units above 0?
Tom
On May 20, 2014, at 10:01 AM, Tom Goddard wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though.
In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking.
window @ set dcstart 0.4 set dcend 1.0 sop cap off vop zone ~@ @ 5 volume # style mesh volume # squaremesh false volume # linethickness 1.5 volume # meshlighting false volume # capfaces false background solid black scolor # color blue disp # ~ribbon # represent stick # modelcolor gold # color byhet #
On May 19, 2014, at 8:06 PM, Tom Goddard wrote:
> For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number. > > Tom > > > On May 19, 2014, at 4:45 PM, Elaine Meng wrote: > >> Hi Oliver, >> You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models. >> >> If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> >> >> One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> >> >> You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> >> >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On May 19, 2014, at 4:18 PM, Oliver Clarke wrote: >> >>> Hi Elaine, >>> Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? >>> Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? >>> Best, >>> Oliver. >>> On May 19, 2014, at 1:00 PM, Elaine Meng wrote: >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users@cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Great, thanks Tom. You’re absolutely right, it should be RMS not RMSD, I misspoke. I’ll look forward to trying these options out, they should be very handy for dealing with X-ray data. Best, Oliver. On May 20, 2014, at 3:59 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
Ok, in tonight’s daily build there will be two new options to “vop scale”. One “rms” scales the map so that sqrt(sum(v*v)/N) is 1 (“vop scale #0 rms 1”), and the other “sd” shifts the map so that the new map has mean 0 and then scales to make sqrt(sum(v*v)/N) equal to 1 (“vop scale #0 sd 1”).
In my earlier email I incorrectly said the standard deviation value did not subtract the mean before squaring. The standard deviation (SD) does subtract the mean before squaring. The RMS (root mean square) value does not subtract the mean. Also the terminology is RMS, not RMSD. The term root mean square deviation (RMSD) is used for a comparison between two data sets and is not applicable to this map scaling discussion.
Oddly, I find Uppsala electron density server maps have mean values different from 0. This is probably because Chimera fetches the O format map (.omap) which has only one byte per value. For instance Chimera reports 4pfd.omap (2fo-fc) to have mean -0.01 and SD 0.33, so the mean is off from 0 by about 3% of the SD. The deviations from 0 are small and probably do not make a significant difference. But that is where my idea came from that the mean was not 0.
Tom
On May 20, 2014, at 12:06 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
It seems sensible to do the shift.
I think Coot does the same think actually (although you’d need to check with Paul Emsley to be certain) - the map statistics output by Coot for every map that I’ve looked at, both from the EDS and elsewhere, have means that are arbitrarily close to zero (the highest I could find was 1e-6, and most are closer to 1e-11, too small to make any difference to the normalization).
Oliver.
On May 20, 2014, at 2:54 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
Ok, if I add a vop scale “rmsd" option it seems sensible that it should both shift the map to have mean 0 and scale so RMSD is 1. Or should I not do the shift? The reason I think the shift to make mean 0 is probably best is that without the shift you could not easily set a threshold at 2 sigma (2*RMSD above the mean) because you wouldn’t know the mean value. But I’m uncertain about this since I don’t understand what the 0 value of the x-ray map represents in cases where it is not 0. I could additionally have an option “mean 0” that would shift the map values to make the mean 0, if that is useful.
Tom
On May 20, 2014, at 11:32 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Tom,
Good question, and I suspect if you asked different crystallographers you may receive conflicting responses. There was a good discussion on this point on the ccp4bb some time ago, but I can’t seem to find it right now.
I put sigma level in quotation marks precisely for this reason - people refer to the sigma level, but generally mean multiples of the RMSD. I know that Coot refers to rms values, and these values are often quoted as sigma levels.
Would it be possible to include rmsd as a separate option for vop scale, so we can choose?
Best, Oliver.
On May 20, 2014, at 2:13 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
I’m unclear about the meaning of “sigma level” in x-ray maps, and also uncertain now whether we agree on the definition of standard deviation. By standard deviation I mean sqrt(sum(v_ijk*v_ijk)), in words, the squareroot of the sum of the square of the map values. If instead, you first subtracted the mean map value then you would have the root-mean-square-deviation RMSD which will be a different value if the mean is not 0. X-ray density maps from the Uppsala electron density server don’t have mean 0, so the difference is significant. Is sigma level defined as RMSD units above the mean, or SD units above 0?
Tom
On May 20, 2014, at 10:01 AM, Tom Goddard wrote:
Hi Oliver,
I added to tonight’s Chimera daily build a vop option to scale by one over the standard deviation: “vop scale #0 sd 1” If you want the new map to have standard deviation 5 you could instead use “vop scale #0 sd 5”. So the sd option value specifies the standard deviation of the new map.
Tom
On May 19, 2014, at 9:10 PM, Oliver Clarke wrote:
> Using # doesn’t seem to work with vop if there are any non-volume models, as it complains that they are not surfaces. Using the selection ~@ (everything that isn’t an atom) seems to work fine though. > > In case it is of use to anyone else, here are the presets I came up with for X-ray maps. Seems to work okay as a starting point to then tweak by adjusting clipping, using vop zone on an atom selection, etc. Would like to normalize to RMS automatically but that will require a little more thinking. > > window @ > set dcstart 0.4 > set dcend 1.0 > sop cap off > vop zone ~@ @ 5 > volume # style mesh > volume # squaremesh false > volume # linethickness 1.5 > volume # meshlighting false > volume # capfaces false > background solid black > scolor # color blue > disp # > ~ribbon # > represent stick # > modelcolor gold # > color byhet # > > On May 19, 2014, at 8:06 PM, Tom Goddard wrote: > >> For commands that want a specifier, I think you can always specify “all models” using “#” — just the # sign without a number. >> >> Tom >> >> >> On May 19, 2014, at 4:45 PM, Elaine Meng wrote: >> >>> Hi Oliver, >>> You could "hard-code" a model number or list of model numbers into a preset by simply including them in the commands in the preset definition file (e.g., one line in the file could be something like: color red,r #0). Choosing the preset is the same as executing all the commands in the file. For many commands, if you don't include a command-line atom specification, they will apply to all applicable items (e.g.: color red). Similarly, the volume command takes specific model numbers or the word "all" to mean all currently open volume models. >>> >>> If you mean you want to specify model number on the fly at the time of invoking a macro, that can only be done with aliases. See the "alias" documentation for how to specify arguments to your macro: >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> >>> >>> One semi-exception to the above is that you could use the word "sel" in many commands to mean the currently selected models or atoms. Then, you can interactively select only the parts of interest to be subsequently acted upon by the commands in your alias or preset that have "sel" as the atom/model specification. See the individual command man pages for how atoms/models are specified, as sometimes the specification needs to be preceded by a keyword. >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> >>> >>> You can test your commands in the command line and then save them to a file using the command history, and/or test Chimera command files (*.com,*.cmd) and Python files (*.py) by simply opening them with File… Open. >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/history.html> >>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> >>> >>> I hope this helps, >>> Elaine >>> ---------- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> On May 19, 2014, at 4:18 PM, Oliver Clarke wrote: >>> >>>> Hi Elaine, >>>> Thanks for the info! How do I specify the model or map number in the preset command? Is there a wildcard I can use? >>>> Usually I would be specifying the model or map number explicitly in any commands that I use, but presets seem to be applied to all open models or maps - how do I do that? >>>> Best, >>>> Oliver. >>>> On May 19, 2014, at 1:00 PM, Elaine Meng wrote: >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users@cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > > _______________________________________________ > Chimera-users mailing list > Chimera-users@cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >
participants (3)
-
Elaine Meng -
Oliver Clarke -
Tom Goddard