[Chimera-users] Custom presets

[Tom Goddard]

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 at 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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>>>>> 
>>>> 
>>> 
>>> 
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>> 
> 
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