Re: [PyMOL] shadows commands

[harold steinberg]

Thank you Annemarie!


> On Apr 6, 2016, at 1:33 AM, Honegger Annemarie  wrote:
> 
> Hi Adam:
> 
> The commands for shadow rendering are: 
> 
> util.ray_shadows('black')
> util.ray_shadows('heavy')
> util.ray_shadows('medium')
> util.ray_shadows('light')
> util.ray_shadows('none')
> 
> How to find out what commands a menu item corresponds to:
> Set a log file (Pull-down Menu File:Log…). As you select different commands 
> from the graphical user interface, 
> the commands activated by the menu items get written to the log file. You can 
> now open the log file in a text editor 
> and copy-paste the command to your .pml script.
> 
> best regards
> 
> Annemarie
> ___
> 
> Dr. Annemarie Honegger PhD
> Department 
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
> 
> e-Mail: honeg...@bioc.uzh.ch 
> 
> websites
> http://www.bioc.uzh.ch/plueckthun 
> http://www.bioc.uzh.ch/plueckthun/antibody 
> 
> http://www.bioc.uzh.ch/plueckthun/nanowelt 
> 
> 
> 
> 
>> On 06 Apr 2016, at 05:57, pymol-users-requ...@lists.sourceforge.net 
>>  wrote:
>> 
>> Message: 5
>> Date: Tue, 5 Apr 2016 16:28:06 -0500
>> From: harold steinberg > >
>> Subject: [PyMOL] shadows commands
>> To: pymol-users > >
>> Message-ID: > >
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hi All,
>> 
>> I?m trying to write scripts that include shadow options.
>> 
>> In the menus at the top of the program users can choose: 
>> Setting/Rendering/Shadows and then they can pick: None, light, medium, 
>> heavy, black, matte, soft, occlusion 1, and occlusion 2.
>> 
>> How do I put those shadows into a script? (I reached the web and the wiki to 
>> no avail).
>> 
>> and where are they in the settings? I?d like to modify them.
>> 
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] pymolrc location

[Sampson, Jared M.]

It should be a plain text file with no filename extension (i.e. no ".txt") in 
your home directory, with the full path:

/Users/yourusername/.pymolrc

You can do this with any text editor (including TextEdit--press Cmd-Shift-T to 
make it plain text), or, alternatively, the shell command:

echo "set auto_show_classified" >> ~/.pymolrc

which appends the quoted text to a new line in .pymolrc, creating the file if 
it doesn't exist.

Cheers,
Jared

On Apr 8, 2016, at 11:42 AM, harold steinberg 
> wrote:

Sorry to be inept… I've never had the opportunity to learn beyond the basics of 
Unix.

create a txt file or create a pml file?
Place it on the hard drive next to the library and system folder?
Or place it in the User folder next to the library folder?


On Apr 8, 2016, at 9:47 AM, David Hall 
> wrote:

Make a file at ~/.pymolrc

-David

On Apr 8, 2016, at 10:35 AM, harold steinberg 
> wrote:

where in OS X is pymolrc located?

On Apr 7, 2016, at 2:39 PM, Thomas Holder 
> wrote:

pymolrc

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] pymolrc location

[harold steinberg]

Thank you Jared!


> On Apr 8, 2016, at 11:34 AM, Sampson, Jared M.  
> wrote:
> 
> It should be a plain text file with no filename extension (i.e. no ".txt") in 
> your home directory, with the full path: 
> 
> /Users/yourusername/.pymolrc
> 
> You can do this with any text editor (including TextEdit--press Cmd-Shift-T 
> to make it plain text), or, alternatively, the shell command:
> 
> echo "set auto_show_classified" >> ~/.pymolrc
> 
> which appends the quoted text to a new line in .pymolrc, creating the file if 
> it doesn't exist.
> 
> Cheers,
> Jared
> 
>> On Apr 8, 2016, at 11:42 AM, harold steinberg > > wrote:
>> 
>> Sorry to be inept… I've never had the opportunity to learn beyond the basics 
>> of Unix.
>> 
>> create a txt file or create a pml file?
>> Place it on the hard drive next to the library and system folder?
>> Or place it in the User folder next to the library folder?
>> 
>> 
>>> On Apr 8, 2016, at 9:47 AM, David Hall >> > wrote:
>>> 
>>> Make a file at ~/.pymolrc
>>> 
>>> -David
>>> 
 On Apr 8, 2016, at 10:35 AM, harold steinberg > wrote:
 
 where in OS X is pymolrc located?
 
> On Apr 7, 2016, at 2:39 PM, Thomas Holder  > wrote:
> 
> pymolrc
 
 H. Adam Steinberg
 7904 Bowman Rd
 Lodi, WI 53555
 608/592-2366
 
 
 --
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net 
 )
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users 
 
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 
 
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>> 
>> 
>> --
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>> )
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>> 
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 
>> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] pymolrc location

[harold steinberg]

where in OS X is pymolrc located?

> On Apr 7, 2016, at 2:39 PM, Thomas Holder  
> wrote:
> 
> pymolrc

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] pymolrc location

[David Hall]

Make a file at ~/.pymolrc

-David

> On Apr 8, 2016, at 10:35 AM, harold steinberg  
> wrote:
> 
> where in OS X is pymolrc located?
> 
>> On Apr 7, 2016, at 2:39 PM, Thomas Holder  
>> wrote:
>> 
>> pymolrc
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
> 
> 
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Re: [PyMOL] pymolrc location

[harold steinberg]

Sorry to be inept… I've never had the opportunity to learn beyond the basics of 
Unix.

create a txt file or create a pml file?
Place it on the hard drive next to the library and system folder?
Or place it in the User folder next to the library folder?


> On Apr 8, 2016, at 9:47 AM, David Hall  wrote:
> 
> Make a file at ~/.pymolrc
> 
> -David
> 
>> On Apr 8, 2016, at 10:35 AM, harold steinberg  
>> wrote:
>> 
>> where in OS X is pymolrc located?
>> 
>>> On Apr 7, 2016, at 2:39 PM, Thomas Holder  
>>> wrote:
>>> 
>>> pymolrc
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>> 
>> 
>> --
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] Cryo Maps - gaussian isosurface

[harold steinberg]

Thank you Thomas, that certainly works, but it’s not as smooth as Chimera. I 
took a bit of a crash course in Chimera and figured out how to gaussian the map 
and then export it as a .mrc file. I could then open that in PyMOL and proceed!


> On Apr 8, 2016, at 2:56 PM, Thomas Holder  
> wrote:
> 
> Hi Adam,
> 
> As I understand, you want to do some low-pass smoothing on the map, correct? 
> I'm not aware that this functionality would be available in PyMOL. However, 
> PyMOL can downsample the map, which averages 8 voxels into 1 and thus also 
> provides some level of smoothing. Try this:
> 
> fetch emd_6413, map, async=0
> map_halve map
> map_halve map
> isomesh mesh, map
> 
> Hope that helps.
> 
> Cheers,
>  Thomas
> 
> On 05 Apr 2016, at 15:24, harold steinberg  wrote:
> 
>> Hi All,
>> 
>> I’m trying to make an isomesh of EMD-6413 (a cryo map) in Pymol. It’s a 
>> large map with a lot of extra, not very clean. In Chimera I can just 
>> gaussian the map with a new map to the level I want with a slider and it 
>> looks good, but I’d much rather work in PyMOL!
>> 
>> PyMOL can gaussian maps, I do it all the time, but on maps that I create in 
>> PyMOL. How do I get an isomesh on EMD-6413 that I can gaussian?
>> 
>> Normally I would use:
>> alter all, q=1
>> set gaussian_resolution, 5
>> map_new mapA, gaussian, 1, pdb code, 6
>> isosurface surfA, mapA
>> 
>> But in in this case I don’t want to use a pdb, just the cryo map.
>> 
>> I can isosurface the cryo map with the following:
>> isosurface mapname, EMD-6413, 4 (any number between 1-6)
>> 
>> but that doesn’t allow me to apply the gaussian to the map…
>> 
>> How do I create an isosurface with a gaussian?
>> 
>> Thanks for any help,
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] How to add multiline labels

[Thomas Holder]

Hi Amin,

Multi-line labels are supported in Incentive PyMOL 1.7.0 and later. Simply use 
a linefeed character ("\n") to break a line.

Examples:
label all, "Hello\nWorld"
label guide, resn + "\n" + resi

See also the related label_multiline_* settings:
http://pymol.org/d/setting:label

Cheers,
  Thomas

On 07 Apr 2016, at 01:12, a...@imtech.res.in wrote:

> Hi everyone. I am having what seems like a trivial problem. I am not able to 
> figure out how to add mutiline lables i.e. how do I specify the point at 
> which I would like the text to go to the next line? Any suggestions would be 
> highly appreciated.
> 
> Regards,
> 
> Amin.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Cryo Maps - gaussian isosurface

[Thomas Holder]

Hi Adam,

As I understand, you want to do some low-pass smoothing on the map, correct? 
I'm not aware that this functionality would be available in PyMOL. However, 
PyMOL can downsample the map, which averages 8 voxels into 1 and thus also 
provides some level of smoothing. Try this:

fetch emd_6413, map, async=0
map_halve map
map_halve map
isomesh mesh, map

Hope that helps.

Cheers,
  Thomas

On 05 Apr 2016, at 15:24, harold steinberg  wrote:

> Hi All,
> 
> I’m trying to make an isomesh of EMD-6413 (a cryo map) in Pymol. It’s a large 
> map with a lot of extra, not very clean. In Chimera I can just gaussian the 
> map with a new map to the level I want with a slider and it looks good, but 
> I’d much rather work in PyMOL!
> 
> PyMOL can gaussian maps, I do it all the time, but on maps that I create in 
> PyMOL. How do I get an isomesh on EMD-6413 that I can gaussian?
> 
> Normally I would use:
> alter all, q=1
> set gaussian_resolution, 5
> map_new mapA, gaussian, 1, pdb code, 6
> isosurface surfA, mapA
> 
> But in in this case I don’t want to use a pdb, just the cryo map.
> 
> I can isosurface the cryo map with the following:
> isosurface mapname, EMD-6413, 4 (any number between 1-6)
> 
> but that doesn’t allow me to apply the gaussian to the map…
> 
> How do I create an isosurface with a gaussian?
> 
> Thanks for any help,
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] selecting faces and vertices in CGOs

[Thomas Holder]

Hi Albert,

This is currently not possible and adding this would be a very major project.

Cheers,
  Thomas

On 30 Mar 2016, at 10:40, Albert Solernou  wrote:

> Dear All,
> I was wondering if there is a way to select faces, vertices and/or edges
> from a CGO either using the mouse or the command line. How difficult
> would be to add this, and how would you do that?
> 
> It would be very useful for us if we could get that working.
> 
> Thanks,
> Albert
> 
> -- 
> -
>  Dr Albert Solernou
>  EPSRC Research Fellow,
>  Department of Physics and Astronomy,
>  University of Leeds
>  Tel: +44 (0)1133 431451

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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