Menu
▾
▴
Re: [PyMOL] how to make selected residues blurry?
|
From: Jared S. <jar...@co...> - 2018-12-09 20:47:02
|
Hi Yeping -
The `set_view` command sets the view matrix for the camera in PyMOL. Once you have the view you want set up in the viewport, you can copy the matrix to the system clipboard using the “Get View” button in the top GUI window and paste it into your .pml script, or print it to the console by using the `get_view` command.
Hope that helps.
Cheers,
Jared
On December 9, 2018 at 10:40:52 AM, sunyeping (sun...@al...(mailto:sun...@al...)) wrote:
> Hi Jared,
>
> Your solution is very clever and helpful, but I don't know how to use the set_view command. I think it is vey important here because after this setting the scene becomes very close to the original figure in the paper. Could you explain how do you set the 18 float numbers?
> Thank you very much and best regards.
>
> Yeping
> > ------------------------------------------------------------------
> > From:Jared Sampson <jar...@co...>
> > Send Time:2018 Dec 6 (Thu) 12:09
> > To:孙业平 <sun...@al...>
> > Cc:pymol-users <pym...@li...>; "Smith, Paul" <pau...@kc...>
> > Subject:Re: [PyMOL] how to make selected residues blurry?
> >
> > Hi Yeping -
> >
> > I had replied to your first email (on 11/30) with a similar suggestion to Paul's of using the `cartoon_transparency` setting, but now after looking at the original figure you're trying to replicate more closely, I realize that there isn't actually any transparency in that figure at all!
> >
> > The authors achieved this effect simply by using lighter and darker shades of ("palecyan" and "deepteal") for the hemagglutinin chain. The following script reproduces the original figure you shared almost exactly.
> >
> > bg_color white
> > fetch 4gms, async=0
> >
> >
> > # hemagglutinin selections
> > select ha, chain A
> >
> > select l130, ha and resi 133-138
> >
> > select l150, ha and resi 155-163
> >
> > select h190, ha and resi 187-196
> >
> > select l220, ha and resi 225-228
> >
> > select loops, l130 or l150 or h190 or l220
> >
> >
> > # antibody selection
> > select h2, chain H and resi 51-59
> >
> > deselect
> >
> >
> > # basic view
> > hide everything
> >
> > as cartoon, ha
> >
> > as cartoon, h2
> >
> > cartoon tube
> >
> >
> > # colors
> > color orange, h2
> >
> > color palecyan, ha
> >
> > color deepteal, loops
> >
> >
> > set_view (\
> > -0.718157351, 0.514449000, -0.468602538,\
> >
> > -0.667115033, -0.317360103, 0.673974276,\
> >
> > 0.198008969, 0.796632588, 0.571111977,\
> >
> > 0.000045628, -0.000060942, -75.169761658,\
> >
> > 20.388980865, -23.567779541, 38.543788910,\
> >
> > 52.026283264, 98.326217651, -20.000000000 )
> >
> >
> > set ray_opaque_background, 1
> > ray 800, 800
> >
> >
> > I've uploaded the resulting image (with the script in the description) to PyMOL wiki: https://pymolwiki.org/index.php/File:4gms_colors.png
> >
> > Hope that helps.
> >
> > Cheers,
> > Jared
> >
> >
> > On December 5, 2018 at 3:33:35 AM, sunyeping via PyMOL-users (pym...@li...(mailto:pym...@li...)) wrote:
> >
> > Hi Paul,
> >
> > Now I get closer to the final anwer!
> > After following your steps, I get the effect I want. However, afer I "ray" the structure, a small part of the structure which I don't mean to set transparent become blur. Please see the image in the red circle in fig-3 (https://drive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing).
> > How does that happen and how to fix it?
> >
> > Thank you again and best regards.
> > Yeping
> > ------------------------------------------------------------------
> > From:Smith, Paul <pau...@kc...>
> > Send Time:2018 Dec 4 (Tue) 21:00
> > To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
> > Subject:RE: [PyMOL] how to make selected residues blurry?
> >
> >
> > Hi Yeping,
> >
> >
> >
> >
> >
> > To avoid this ‘breaking’ of your protein you will first need to create a copy of the entire molecule, set the transparency of the copy to your desired value, then hide the residues you want to make transparent on your original object.
> >
> >
> >
> >
> >
> > So, you will do something like this:
> >
> >
> >
> >
> >
> > # create a copy of your original object:
> >
> >
> > create new_obj, <original_object>
> >
> >
> >
> >
> >
> > # set all residues on the copy to be transparent:
> >
> >
> > set cartoon_transparency, <value>, new_obj
> >
> >
> >
> >
> >
> > # hide the residues you wish to be transparent on your original object:
> >
> >
> > select hide, <your_selection>
> >
> >
> > cartoon_skip, hide and <original_object>
> >
> >
> >
> >
> >
> > This should prevent the your molecule from appearing to be broken.
> >
> >
> >
> >
> >
> > Cheers,
> >
> >
> > Paul
> >
> >
> >
> >
> >
> > From: sunyeping <sun...@al...>
> > Sent: Tuesday, December 4, 2018 3:23:00 AM
> > To: pymol-users; Smith, Paul
> > Subject: Re: [PyMOL] how to make selected residues blurry?
> >
> >
> > Hi, Paul,
> >
> > Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract":
> > extract new_obj, sele
> > I find the new object is broken from the rest part of the structure. And then I use the commend:
> > set cartoon_transparency, 0.7, new_obj
> > The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
> > Could you help me with the "breaking" problem?
> >
> > Best regards,
> >
> > Yeping
> >
> >
> >
> > ------------------------------------------------------------------
> > From:Smith, Paul <pau...@kc...>
> > Send Time:2018 Dec 3 (Mon) 20:38
> > To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
> > Subject:RE: [PyMOL] how to make selected residues blurry?
> >
> >
> > Hi,
> >
> >
> >
> >
> >
> > The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.
> >
> >
> >
> >
> >
> > Cheers,
> >
> >
> > Paul
> >
> >
> >
> >
> >
> >
> >
> >
> > From: sunyeping via PyMOL-users(mailto:pym...@li...)
> > Sent: 03 December 2018 03:02
> > To: pymol-users(mailto:pym...@li...)
> > Subject: [PyMOL] how to make selected residues blurry?
> >
> >
> >
> >
> >
> >
> > Dear all,
> >
> >
> >
> >
> >
> >
> >
> >
> > Could you please check this figure at the following link?
> >
> >
> >
> > https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are: residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry.
> >
> >
> >
> >
> >
> >
> >
> > I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
> >
> >
> >
> > set transparency, 0.8, sele
> >
> >
> >
> > but it doesn't work.
> >
> >
> >
> >
> >
> >
> >
> > Could anyone help me figure it out？ With sincere thanks.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
|
