pymol-users Mailing List for PyMOL Molecular Graphics System

For anyone who has found this thread, I've taken some time and put together
an alignment + RMSD script for Pymol (using BioPython). You can find it on
GitHub, here <" rel="nofollow">https://github.com/nclement/cvc-scripts/tree/master/alignment>
.
It's a bit overkill, and only handles single chain proteins, but it's quite
robust if it fits your needs.

On Wed, Jul 4, 2018 at 3:05 PM Thomas Holder <tho...@sc...>
wrote:

> Hi Nathan,
>
> I have some insights for this issue. Basically the long gaps between the
> selected parts become too expensive in the alignment scoring. Changing e.g.
> the gap extension penalty leads to the expected result:
>
> # default is extend=-0.7, lowering to -0.6
> super gold & contact_all, test, cycles=0, object=super, extend=-0.6
>
> I think PyMOL's handling of selection gaps during the alignment could be
> improved, they should be handled different from regular alignment gaps.
>
> Cheers,
>   Thomas
>
> > On Jun 28, 2018, at 2:14 PM, Thomas Holder <
> tho...@sc...> wrote:
> >
> > Hi Nathan,
> >
> > Thank you very much for the files and instructions. I can reproduce the
> problem. I haven't seen this before and don't know yet what's going wrong,
> we will investigate.
> >
> > Cheers,
> >  Thomas
> >
> >> On Jun 28, 2018, at 10:50 AM, ncl...@cs... wrote:
> >>
> >> The alignment in this example is nearly perfect. Even the residues left
> >> out of the fitting have perfect matches at the sequence level (as can be
> >> seen by saving the super object and turning on the sequence alignment
> and
> >> contact_all).
> >>
> >> PyMOL>load 1AY7_u.pdb, test
> >> CmdLoad: "1AY7_u.pdb" loaded as "test".
> >> PyMOL>load 1AY7_b.pdb, gold
> >> CmdLoad: "1AY7_b.pdb" loaded as "gold".
> >> PyMOL>select contact_rec, gold & chain R & (all within 10 of gold &
> chain
> >> L) & n. ca
> >> Selector: selection "contact_rec" defined with 33 atoms.
> >> PyMOL>select contact_lig, gold & chain L & (all within 10 of gold &
> chain
> >> R) & n. ca
> >> Selector: selection "contact_lig" defined with 33 atoms.
> >> PyMOL>select contact_all, contact_rec + contact_lig
> >> Selector: selection "contact_all" defined with 66 atoms.
> >> PyMOL>super gold & contact_all, test, cycles=0
> >> MatchAlign: aligning residues (66 vs 185)...
> >> MatchAlign: score 143.882
> >> ExecutiveAlign: 58 atoms aligned.
> >> Executive: RMS =    0.524 (58 to 58 atoms)
> >>
> >> <1AY7_u.pdb><1AY7_b.pdb>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Michel,

By chance can you attach an example image?

Thanks,
Jarrett J.

On Mon, Dec 17, 2018 at 11:52 AM Michel Rickhaus <mic...@gm...>
wrote:

> Hi all
>
> Did anyone else note that rendering sticks on high resolution with
> ray_trace_mode, 1 yields black lines down the middle of the sticks in some
> instances? I guess its where the cylinder meets up.
> Any idea how to prevent this? It's quite annoying to remove the manually
> in an image editor after
>
> Cheers
> Michel
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

Hi all

Did anyone else note that rendering sticks on high resolution with
ray_trace_mode, 1 yields black lines down the middle of the sticks in some
instances? I guess its where the cylinder meets up.
Any idea how to prevent this? It's quite annoying to remove the manually in
an image editor after

Cheers
Michel

Hi Michel,

Some operations should be compatible with the "color" command, in particular all BEGIN/END operations, as long as there is no COLOR operation. Only those which have the color as part of the operation arguments (like CYLINDER and TRIANGLE) won't be recolorable.

Example:

from pymol import cgo, cmd
obj = [
   cgo.BEGIN, cgo.TRIANGLES,
   cgo.VERTEX, 0.0, 0.0, 0.0,
   cgo.VERTEX, 1.0, 0.0, 0.0,
   cgo.VERTEX, 0.0, 1.0, 0.0,
   cgo.END
   ]
cmd.load_cgo(obj, 'foo')
cmd.color('blue', 'foo') 

Cheers,
  Thomas

> On Dec 17, 2018, at 3:06 PM, Michel Rickhaus <mic...@gm...> wrote:
> 
> Hi all
> 
> I was wondering whether it is possible to change the appearance of a CGO Object after creation. I typically set the attributes of each CGO (plane for instance) using 
> 
> dict = {'ALPHA':1.0, 'COLOR':[0.99, 0.87, 0.67], 'INVERT':False} 
> 
> before the creating of the CGO and calling dict. Sometimes I'd like to change these after creation. The typical PyMol commands (color..) do not seem to work. If I dont set transparency using dict, i can use set cgo_transparency later. The same does not work for color (there is no set cgo_color or related...)
> It seems to have been asked in part before (https://www.mail-archive.com/pym...@li.../msg08330.html)
> 
> 
> Any help is appreciated
> 
> Michel

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi all

I was wondering whether it is possible to change the appearance of a CGO
Object after creation. I typically set the attributes of each CGO (plane
for instance) using

dict = {'ALPHA':1.0, 'COLOR':[0.99, 0.87, 0.67], 'INVERT':False}

before the creating of the CGO and calling dict. Sometimes I'd like to
change these after creation. The typical PyMol commands (color..) do not
seem to work. If I dont set transparency using dict, i can use set
cgo_transparency later. The same does not work for color (there is no set
cgo_color or related...)
It seems to have been asked in part before (
https://www.mail-archive.com/pym...@li.../msg08330.html
)


Any help is appreciated

Michel

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  
>  

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...) 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
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.



_______________________________________________ 
PyMOL-users mailing list 
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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...) 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
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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Archives: http://www.mail-archive.com/pym...@li...  
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Hello all,

Pymol svn 4190 could not find some font it was looking for. Pymol 1.9.0.0 ran fine without this problem.  How would I go about fixing this, maybe tell it to use another font?

Best,
Quyen

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
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.

Hello,  After optimizing the Iron-sulfur clusters existing in the photosystem I, the coordinates transforms to another frame, what I need to do is to transfer back to the original coordinates by getting the transformation matrix.

here what I did ..using pymola1- I loaded post and pre-processing object2- I aligned them together3- I tried to get the transformation matrix with this commandprint cmd.get_object_matrix("pre-processing object")and this step returns a 4*4 matrices (-0.017042629420757294, 0.6273888349533081, -0.7785196304321289, -27.565351122804373, 0.15071848034858704, 0.7713475823402405, 0.6183096766471863, -142.13367787636093, 0.9884297847747803, -0.1067996621131897, -0.10770488530397415, -81.02178268868633, 0.0, 0.0, 0.0, 1.0)finally,  I used this command to apply the matrix ...cmd.transform_object( "post_processing object", [-0.017042625695466995, 0.15071852505207062, 0.9884297847747803, 101.03673254990264, 0.6273888349533081, 0.7713475823402405, -0.10679969936609268, 118.27556096672724, -0.7785196304321289, 0.6183096766471863, -0.10770490765571594, 57.69601938212094, 0.0, 0.0, 0.0, 1.0])am I doing it in a correct way ??and I need to find the transformed structure, how I could do it ?
Thank you,  Fedaa Ali 

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’ )." rel="nofollow">(https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpymolwiki.org%2Findex.php%2FCartoon%23Various_Transparency_Levels&data=01%7C01%7Cpaul.smith%40kcl.ac.uk%7Ccf93cb90e1834838588a08d65997dd36%7C8370cf1416f34c16b83c724071654356%7C0&sdata=h82rBhFhb%2FU7sha1Gt5FGpOe%2BZ0oAJ8tA7KxC4Zl%2FT8%3D&reserved=0>). 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?
" rel="nofollow">https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0%2Fview%3Fusp%3Dsharing&data=01%7C01%7Cpaul.smith%40kcl.ac.uk%7Ccf93cb90e1834838588a08d65997dd36%7C8370cf1416f34c16b83c724071654356%7C0&sdata=4g1hw5KnhhRjRDo0d2DVc1hSrJJTSbmwlCgsGFP1Lw0%3D&reserved=0>


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.

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
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.

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?
" rel="nofollow">https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0%2Fview%3Fusp%3Dsharing&data=01%7C01%7Cpaul.smith%40kcl.ac.uk%7C2bf336b34d554aedf37e08d658cbb9c8%7C8370cf1416f34c16b83c724071654356%7C0&sdata=tgPlIectw3pV9ppkv9IeX6YsqnRepi%2Bmb75aB0UzGPk%3D&reserved=0>


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.

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.

 here what I did ..
using pymol1- I loaded post and pre-processing object2- I aligned them together3- I tried to get the transformation matrix with this commandprint cmd.get_object_matrix("pre-processing object")and this step returns a 4*4 matrices(-0.017042629420757294, 0.6273888349533081, -0.7785196304321289, -27.565351122804373, 0.15071848034858704, 0.7713475823402405, 0.6183096766471863, -142.13367787636093, 0.9884297847747803, -0.1067996621131897, -0.10770488530397415, -81.02178268868633, 0.0, 0.0, 0.0, 1.0)I am not sure if this is the right way or not?and if it is right what should I do in order to apply it to the post-processing object ? should I apply it as it is or the inverse of it?
Thank you, Fedaa Ali 
    On Saturday, December 1, 2018, 5:59:37 PM GMT+2, Fedaa Nada via PyMOL-users <pym...@li...> wrote:  
 
 After optimizing the structure the coordinates transforms to another frame, what I need to do is to transfer back to the original coordinates by getting the transformation matrix when I tried to get this matrix using pymol, I got an error and I can't figure out the problem because I am new to pymol.
please, could anyone help me how to get the transformation matrix? 

Thank you Fedaa Ali   _______________________________________________
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Archives: http://www.mail-archive.com/pym...@li...
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After optimizing the structure the coordinates transforms to another frame, what I need to do is to transfer back to the original coordinates by getting the transformation matrix when I tried to get this matrix using pymol, I got an error and I can't figure out the problem because I am new to pymol.
please, could anyone help me how to get the transformation matrix? 

Thank you Fedaa Ali