I've updated the wiki with a script doing just that: resicolor.py. The script
is available here: http://pymolwiki.org/index.php/Resicolor
You can edit the coloring scheme to your liking from within the script. I
haven't checked what the exact scheme was in sPDBv, it may be the same.
Garteiser Philippe
> Message: 3
> Date: Mon, 9 Apr 2007 13:37:11 +0200
> From: "Mirek Cygler" <mi...@bri.nrc.ca>
> Subject: [PyMOL] Color by residue type
> To: <pymol-users@lists.sourceforge.net>
> Message-ID: <000201c77a9b$6a22bed0$8657f...@pcmsg23>
> Content-Type: text/plain; charset="US-ASCII"
>
> Hi,
> I would like to color residues by their type using (more or less)
> standard colors (e.g. like in sPDBv). Could not find a command in
> Pymol that
> would do that. Did I miss it? Is there a way to avoid doing this one residue
> type at the time?
> Thanks for you help,
>
> Mirek
>
>
>
>
> ------------------------------
> ******************************
Garteiser Philippe
OMRF, Cardiovascular Biology dpt.
Doctoral candidate, OU Bioengineering
Advisors: Dr. Tim Mather, Dr M. Uli Nollert
12600 N Macarthur
Crown Pointe apt. #1423
Oklahoma City, OK 73142
home: (405) 603 7091
work: (405) 271 4924
"It does not pay to leave a live
dragon out of your calculations"
- Tolkien
----- Original Message -----
From: pymol-users-requ...@lists.sourceforge.net
Date: Tuesday, April 10, 2007 8:54 am
Subject: PyMOL-users Digest, Vol 11, Issue 5
To: pymol-users@lists.sourceforge.net
> Send PyMOL-users mailing list submissions to
> pymol-users@lists.sourceforge.net
>
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>
> or, via email, send a message with subject or body 'help' to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>
>
> Today's Topics:
>
> 1. How to make different colour on backbone cartoon and
> sidechain stick (adi di)
> 2. Re: How to make different colour on backbone cartoon and
> sidechain stick (Tsjerk Wassenaar)
> 3. Color by residue type (Mirek Cygler)
> 4. Re: Single transparent sphere (Michael Lerner)
> 5. Re: between views (Andreas Forster)
> 6. transparency cross-fading (Andreas Forster)
> 7. Re: transparency cross-fading (Harry M. Greenblatt)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 7 Apr 2007 11:50:56 -0700 (PDT)
> From: adi di <adipho...@yahoo.com>
> Subject: [PyMOL] How to make different colour on backbone cartoon and
> sidechain stick
> To: pymol-users@lists.sourceforge.net
> Message-ID: <432973.33789...@web53402.mail.re2.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dear all,
>
> I have several questions, please help me for this
>
> 1. I would like to show side chain one colour by stick
> and its backbone by cartoon another colour. So I tried
> to create to same molecules. One with normal backbone
> (no1) and the other with backbone and a sidechain
> stick (no2). And it seem fine the no1 can cover no2
> backbone so I have no problem with the unwanted
> backbone colour on the sidechain that I want but when
> I tried to ray and png them the colour was change it
> show only no2 molecule so I have backbone as the
> sidechain. Does anyone have suggestion on how can I
> let the no1 shows on no2? Or if you have easier
> suggestion please don't hesitate to tell.
>
> 2. How to show hydrogen bond and other interactions?
>
> 3. What different between normal 'aline' and
> 'optAlign'?
>
> 4. How to fix the molecule (lock or make it not move).
>
>
> 5. Does pymol have any build in procheck or
> Ramachandran plot?
>
> 6. Do you know any website for pymol beginner
> tutorial? Esp. how to create movie. I tried to read
> from pymol manual but I'm quite confuse.
>
> Thank you cery much.
> Adiphol
>
>
>
> ____________________________________________________________________________________
> Food fight? Enjoy some healthy debate
> in the Yahoo! Answers Food & Drink Q&A.
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 7 Apr 2007 21:43:38 +0200
> From: "Tsjerk Wassenaar" <tsje...@gmail.com>
> Subject: Re: [PyMOL] How to make different colour on backbone cartoon
> and sidechain stick
> To: "adi di" <adipho...@yahoo.com>
> Cc: pymol-users@lists.sourceforge.net
> Message-ID:
> <8ff898150704071243k4e8f40ebk468dc38d7480a...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Adiphol,
>
> It would have been better to state "several questions" as subjcts, but
> ok...
>
> > 1. I would like to show side chain one colour by stick
> > and its backbone by cartoon another colour. So I tried
> > to create to same molecules. One with normal backbone
> > (no1) and the other with backbone and a sidechain
> > stick (no2). And it seem fine the no1 can cover no2
> > backbone so I have no problem with the unwanted
> > backbone colour on the sidechain that I want but when
> > I tried to ray and png them the colour was change it
> > show only no2 molecule so I have backbone as the
> > sidechain. Does anyone have suggestion on how can I
> > let the no1 shows on no2? Or if you have easier
> > suggestion please don't hesitate to tell.
> >
>
> What about "set cartoon_color" to control the color of the cartoon to
> show for the backbone? This is completely separated from the atom
> colors. Alternatively, you may colour everything the way you want for
> the atoms and then color the c-alpha atoms otherwise (which control
> the cartoon color). The difference with the first approach is that in
> the latter the bond with the side chain will be partially coloured as
> the backbone.
>
> > 2. How to show hydrogen bond and other interactions?
>
> You can create distance objects to show these things... have a look at
> the command "dist". Particularly useful with the selection statement
> "x within r of y".
> >
> > 3. What different between normal 'aline' and
> > 'optAlign'?
> >
>
> optAlign uses a different algorithm and I believe that it can do
> several molecules at the same time (though I'm not completely sure on
> this one; Isn't this explained on the Wiki?).
>
> > 4. How to fix the molecule (lock or make it not move).
>
> You can "disable" an object (which also hides it from view) or you can
> "mask" a selection, which makes atoms "unpickable". There's also the
> command "protect". Have a look at the help files for these.
>
> > 5. Does pymol have any build in procheck or
> > Ramachandran plot?
>
> No.
>
> >
> > 6. Do you know any website for pymol beginner
> > tutorial? Esp. how to create movie. I tried to read
> > from pymol manual but I'm quite confuse.
>
> No. There must be a "movie.py" around somewhere, written by Kristian
> Rother and edited by myself, which contains handy movie-making
> functions.
>
> >
> > Thank you cery much.
> > Adiphol
> >
>
> You're cery welcome :p
>
> Tsjerk
>
> >
> >
> > ____________________________________________________________________________________
> > Food fight? Enjoy some healthy debate
> > in the Yahoo! Answers Food & Drink Q&A.
> >
> >
> > -------------------------------------------------------------------------
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to
> share your
> > opinions on IT & business topics through brief surveys-and earn cash
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> >
> >
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 9 Apr 2007 13:37:11 +0200
> From: "Mirek Cygler" <mi...@bri.nrc.ca>
> Subject: [PyMOL] Color by residue type
> To: <pymol-users@lists.sourceforge.net>
> Message-ID: <000201c77a9b$6a22bed0$8657f...@pcmsg23>
> Content-Type: text/plain; charset="US-ASCII"
>
> Hi,
> I would like to color residues by their type using (more or less)
> standard colors (e.g. like in sPDBv). Could not find a command in
> Pymol that
> would do that. Did I miss it? Is there a way to avoid doing this one residue
> type at the time?
> Thanks for you help,
>
> Mirek
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 9 Apr 2007 09:26:19 -0400
> From: "Michael Lerner" <mgler...@gmail.com>
> Subject: Re: [PyMOL] Single transparent sphere
> To: "DeLano Scientific" <del...@delsci.info>
> Cc: jjv5 <j...@jjv5.net>, PyMOL-users@lists.sourceforge.net
> Message-ID:
> <e4c539ed0704090626t2d9d6e57ie475b040529be...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> The pseudoatom business looks very cool. I'll have to try it out.
>
> In the meantime, I wanted to mention that you certainly can make
> transparent CGOs. Here's some code that I wrote to visualize dock
> output in our lab. The files it reads in have lines that look like
>
> <junk> x y z r <junk> temp <junk>
>
> Where x,y,z are the coordinates, r is the radius and temp is some
> index that we use to look up colors. If you save this in a file,
> you'll have a new command, sds, that will read in such a file and show
> the output as spheres. Transparency defaults to 0.4, but you can
> change it.
>
> -michael
>
> #!/usr/bin/env python
>
> """
> Use PyMOL to show DOCK spheres
> """
> from pymol import cmd,cgo
>
> colors = {'1':[.66,.66,.66],#'grey'
> '2':[1,0,0],#'red',
> '3':[.55,0,0],#'dark red',
> '4':[0.65,1,1],#'blue2',
> '5':[.25,.88,.82],#'blue7',
> '6':[0.004,.55,.55],#'blue8',
> '7':[0.004,.55,.55],#'blue8',
> '8':[0,1,1],#'blue13',
> '9':[0,1,1],#'blue13',
> '11':[0.60,.98,.60],#'pale green',
> '12':[0.56,.93,.56],#'light green',
> '13':[.20,.80,.20],#'lime green',
> '14':[.23,.70,.44],#'green8',
> '15':[.23,.70,.44],#'sea green',
> '16':[.18,.55,.34],#'sea green',
> '17':[.18,.55,.34],#'green',
> '18':[0,.5,0],#'forest green',
> '19':[0,.5,0],#'forest green',
> '20':[.13,.55,.13],#'dark green',
> '21':[.13,.55,.13],#'dark green',
> }
>
> def graph_temp_via_cgo(name,data,transparency=0):
> """
> Data should be [x,y,z,r,temp] where
> x,y,z are the coordinates,
> r is the radius
> temp is something like temperature that we
> use to look up colors.
> """
> obj = []
> for x,y,z,r,temp in data:
> #transparency = (y/200.0)
> obj.extend( [ cgo.ALPHA,1-transparency])
> obj.extend( [ cgo.COLOR] + colors[temp])
> obj.extend( [ cgo.SPHERE,x,y,z,r] )
> cmd.load_cgo(obj,name,1)
> return name
>
> def dock_file_to_data(filename):
> data = []
> f = file(filename)
> for line in f:
> if not line.strip():
> continue
> if line.startswith('#'):
> continue
> junk1,x,y,z,r,junk2,temp,junk3 = line.split()
> x,y,z,r = map(float,(x,y,z,r))
> data.append([x,y,z,r,temp])
> f.close()
> return data
> def show_dock_spheres(filename,transparency=0.40):
> """
> Reads in a DOCK sphere file and graphs the
> results as dock spheres. You can pass the
> transparency as an additional argument.
> """
> transparency = float(transparency)
> data = dock_file_to_data(filename)
> graph_temp_via_cgo('dock_spheres',data,transparency)
>
> cmd.extend('sds',show_dock_spheres)
>
>
> On 4/6/07, DeLano Scientific <del...@delsci.info> wrote:
> >
> >
> > Pre 1.0:
> >
> > fragment methane, mysph
> > remove hydro and mysph
> > alter mysph, vdw=2.0
> > as spheres, mysph
> > set sphere_transparency, 0.5, mysph
> >
> > Post 1.0:
> >
> > pseudoatom mysph, vdw=2.0
> >
> > as spheres, mysph
> >
> > set sphere_transparency, 0.5, mysph
> >
> > Cheers,
> > Warren
> >
> >
> >
> > ________________________________
> > From: pymol-users-boun...@lists.sourceforge.net
> > [ On
> > Behalf Of jjv5
> > Sent: Friday, April 06, 2007 4:55 AM
> > To: PyMOL-users@lists.sourceforge.net
> > Subject: [PyMOL] Single transparent sphere
> >
> >
> >
> > Hi,
> >
> > Does anyone know of a good way to create a single transparent sphere
> of
> > varying size? We've tried using a single atom and changing the vdw,
> but we
> > are unable to produce a surface of a single atom. CGO objects work but
> > cannot be made transparent. What we'd really like is a transparent CGO
> > sphere. Any ideas?
> >
> > Thanks,
> > Jim
> >
> > -------------------------------------------------------------------------
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to
> share your
> > opinions on IT & business topics through brief surveys-and earn cash
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> >
> >
> >
>
>
> --
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 10 Apr 2007 12:49:51 +0200
> From: "Andreas Forster" <docandr...@gmail.com>
> Subject: Re: [PyMOL] between views
> To: "Dirk Kostrewa" <dirk.kostr...@psi.ch>, a.perra...@nki.nl
> Cc: PYMOLBB <pymol-users@lists.sourceforge.net>
> Message-ID:
> <77fa84b50704100349h761e8ef7te35da7280ea33...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Tassos, Dirk,
>
> sorry for the very late reply, but I've just now finished going
> through a
> few hundred list mails that had accumulated.
>
> For converting scenes to movies, Joel Bard's slerpy is really shweet.
> Check
> it out at
>
> What I do is the following - after putting slerpy's two scripts into the
> current directory and opening pymol:
> - load session.pse
> - import slerpy
> - F1 (or wherever your first scene resides)
> - sscene (makes slerpy understand scene 1)
> - F2
> - sscene (makes slerpy understand scene 2)
> - swrite arbitraryName (saves parameters for interpolation)
> - srecord (does the interpolation)
> - set ray_trace_frames, 1 (makes sure your images are ray-traced
> before they
> are saved)
> - mpng anotherName (writes out 50 images covering the interpolation from
> scene 1 to scene 2)
> - go have a coffee
> - make movie from images in ImageReady
>
> I was amazed. This worked exactly as I had expected. The most taxing
> part
> was walking to the coffee machine. Thanks, Joel!
>
>
> Andreas
>
>
> On 3/30/07, Dirk Kostrewa <dirk.kostr...@psi.ch> wrote:
> >
> > Hi Tassos,
> >
> > I found the following article, but haven't tried it on my own:
> >
> >
> >
> > I hope this helps!
> >
> > Best regards,
> >
> > Dirk.
> >
> > Anastassis Perrakis wrote:
> > > Dear pymolers -
> > >
> > > One can store 'Scenes' and then switch between them; the algorithm
> > > that goes from one scene to each other is very nice.
> > >
> > > Can one ask Pymol to write frames going from one scene to another
> to
> > > png files to make a movie ?
> > >
> > > or does anyone have python code that can render the transitions
> > > between views/scenes in a different way ?
> > >
> > > best - tassos
> > >
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 6
> Date: Tue, 10 Apr 2007 13:12:04 +0200
> From: "Andreas Forster" <docandr...@gmail.com>
> Subject: [PyMOL] transparency cross-fading
> To: pymol-users@lists.sourceforge.net
> Message-ID:
> <77fa84b50704100412k1ea1d0ceg8a66be0ef6bfd...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hey all,
>
> I've run into the following problem while making some movies with MacPyMOL
> 0.99rc6.
>
> I have a protein in surface representation that I start with
> transparency =
> 0 and a cavity (voidoo-created map) as surface with transparency = 1.
> In
> other words, the protein surface is visible, the cavity is not. When
> I
> cross-fade the transparencies, like so:
>
> for i in range (1, 41):
> cmd.set ("transparency", i*0.025, "protein")
> cmd.set ("transparency", 1-(0.016*i), "cavity")
> cmd.ray
> cmd.png ("fadeOut_%02d" %i)
>
> the protein disappears and the cavity appears gracefully. However, those
> parts of the cavity hidden behind a wall of protein don't fade in as the
> protein surface disappears. They only appear when the protein surface
> transparency has reached 1, and there is a sudden jerk between the
> second-to-last and the last image created by above script as the cavity
> becomes fully visible. I remember that this issue has come up before
> but
> don't remember if there is a solution. Could someone enlighten me please?
>
> Thanks.
>
>
> Andreas
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 7
> Date: Tue, 10 Apr 2007 16:52:50 +0300
> From: "Harry M. Greenblatt" <harry.greenbl...@weizmann.ac.il>
> Subject: Re: [PyMOL] transparency cross-fading
> To: pymol-users@lists.sourceforge.net
> Message-ID: <f8584f2c-37ab-4f9c-8d98-b44080caf...@weizmann.ac.il>
> Content-Type: text/plain; charset="us-ascii"
>
> BS"D
>
> Dear Andreas
>
> I ran into a similar problem more than two years ago when I wanted
>
> to fade one surface and bring in another one. *But*, I thought the
> problem did not appear when you ray trace the image; are you implying
>
> the problem exists even in the ray traced image? Below is the query I
>
> sent, and Warren's answer to me:
>
> > I wanted to slowly fade in one surface while fading out
> > another. In other words, make one progressively less
> > transparent, while the other is made more transparent. It
> > turns out, unfortunately, that during the transition, the two
> > transparent surfaces affect each other adversely, and one
> > essentially blocks the other, even though they should be
> > transparent. This is shown on the second picture. The gray
> > surface is 20% transparent, and the salmon surface is 80%
> > transparent. The gray surface is fine by itself, but seems
> > "covered" in certain regions when the (mostly transparent)
> > salmon surface is present. In ray tracing, this seems not to
> > be a problem (see first picture...).
>
>
> > Harry,
> >
> > You've hit a limitation with PyMOL's OpenGL renderer: it can't
> > currently do
> > a global Z-sort of all transparent triangles in a scene...just
> > within a
> > single object. This will be addressed eventually, but not soon.
> >
> > Ray tracing with transparency_mode=1 is the only way to get proper
> > intersections of transparent surfaces.
> >
> > Sorry!
> >
> > Warren
> >
>
> On Apr 10, 2007, at 2:12 PM, Andreas Forster wrote:
>
> > Hey all,
> >
> > I've run into the following problem while making some movies with
> > MacPyMOL 0.99rc6.
> >
> > I have a protein in surface representation that I start with
> > transparency = 0 and a cavity (voidoo-created map) as surface with
>
> > transparency = 1. In other words, the protein surface is visible,
>
> > the cavity is not. When I cross-fade the transparencies, like so:
> >
> > for i in range (1, 41):
> > cmd.set ("transparency", i*0.025, "protein")
> > cmd.set ("transparency", 1-(0.016*i), "cavity")
> > cmd.ray
> > cmd.png ("fadeOut_%02d" %i)
> >
> > the protein disappears and the cavity appears gracefully. However,
>
> > those parts of the cavity hidden behind a wall of protein don't
> > fade in as the protein surface disappears. They only appear when
> > the protein surface transparency has reached 1, and there is a
> > sudden jerk between the second-to-last and the last image created
> > by above script as the cavity becomes fully visible. I remember
> > that this issue has come up before but don't remember if there is a
>
> > solution. Could someone enlighten me please?
> >
> > Thanks.
> >
> >
> > Andreas
> >
> ----------------------------------------------------------------------
>
> > ---
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to
> > share your
> > opinions on IT & business topics through brief surveys-and earn cash
> >
> >
> page=join.php&p=sourceforge&CID=DEVDEV________________________________
>
> > _______________
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> >
>
> ------------------------------------------------------------------------
>
> -
> Harry M. Greenblatt
> Staff Scientist
> Dept of Structural Biology harry.greenbl...@weizmann.ac.il
> Weizmann Institute of Science Phone: 972-8-934-3625
> Rehovot, 76100 Facsimile: 972-8-934-4159
> Israel
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to
> share your
> opinions on IT & business topics through brief surveys-and earn cash
>
>
> ------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
>
>
>
> End of PyMOL-users Digest, Vol 11, Issue 5
> ******************************************
