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
(pymol-users@lists.sourceforge.net) 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 <paul.sm...@kcl.ac.uk>
Send Time:2018 Dec 4 (Tue) 21:00
To:孙业平 <sunyep...@aliyun.com>; pymol-users <pymol-users@lists.sourceforge.net>
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 <sunyep...@aliyun.com>
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 <paul.sm...@kcl.ac.uk>
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 <sunyep...@aliyun.com>; pymol-users <pymol-users@lists.sourceforge.net>
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
Sent: 03 December 2018 03:02
To: pymol-users
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.
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