From: GAO F. <mc...@ya...> - 2007-01-17 17:21:46
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Hi Everyone, Could someone tell me how to perform superimposition of two or more ligands from different PDBs? Thanks in advance. Feng. pym...@li... wrote: Send PyMOL-users mailing list submissions to pym...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pym...@li... You can reach the person managing the list at pym...@li... When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. Re: Pymol cone shape? (William Scott) 2. Re: New plugin and Doubt with APBS Tools (Michael Lerner) 3. Re: Pymol cone shape? (Terry Jones) 4. Re: change the sphere size of a chosen atom ? (Tsjerk Wassenaar) 5. Re: Pymol cone shape? (Tsjerk Wassenaar) 6. Re: distance atom-protein surface (Praedor Atrebates) 7. Sequence view size (aaron bryden) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Jan 2007 12:24:46 -0800 From: William Scott Subject: Re: [PyMOL] Pymol cone shape? To: "Martin.Laurberg" Cc: pym...@li... Message-ID: <664...@ch...> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Let's ask on the pymol mailing list... On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote: > Damn, I can convert my 1969 CNS base pair restraints into what they > call > CGO drawn lines, and thereby display enforced hydrogen bonds, but I > wish > to draw cones for the base pair ladder as ribbons can do it. Oh > well, .. > > > > On Wed, 10 Jan 2007, William Scott wrote: > >> >> I think it is possible, but I don't know how. >> >> >> >> On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote: >> >>> Hi Bill, is it possible to draw a cone-shape in pymol? >>> >> ------------------------------ Message: 2 Date: Wed, 10 Jan 2007 15:49:47 -0500 From: "Michael Lerner" Subject: Re: [PyMOL] New plugin and Doubt with APBS Tools To: pym...@li... Message-ID: Content-Type: text/plain; charset=ISO-8859-1; format=flowed We discussed this a bit off-list, and it looks like this was the answer: The potentials are assigned to points in space. That's why the isosurfaces don't change, and also why the surface coloring changes when you change the shape of the surface. Hope that helps anyone else who might have this question, -michael On 1/9/07, Michael Lerner wrote: > Ra?l, > > I don't have time to look at this in detail right now, but .. what > exactly do you mean that the potentials change between frames? What > happens if you draw isosurfaces? Do they change? > > -michael > > On 1/7/07, Ra?l Mera wrote: > > Dear all, > > > > Two things. > > First, I just written a small plugin that uses the > > program "reduce" to add hydrogens to a molecule or to > > a trajectory loaded in Pymol.(since each frame of the > > trajectory is hydrogenated by reduce, I think that > > protonation states could vary between frames) This > > allow us to have a reliable protonation method in > > PyMOL, without having to save the structure as PDB and > > hydrogenate with another app, and using an open-source > > (as far as I know) and easy to install application. > > > > Since I don't have any website right now, I will try > > to make it available from the Pymol Wiki. If you want > > the plugin right now, just e-mail me. > > > > The other thing is a doubt in using the APBS Tools. > > When I use it to calculate electrostatics potentialsof > > a trajectory (but the PQR is made by PDB2PQR from a > > PDB made with PyMOL, i.e, only from the first > > snapshot) > > I get a .dx map that I think has the potentials only > > for the first frame. When I display the potential > > surface in the trajectory, the potentials seems to > > change between frames, which I wouldn't expect since I > > think that the calculation was performed only for the > > first frame. > > My doubt is: Are these changes alleatory due to a > > change > > of the structure's position changes on the grid, or > > they have some significance?, if the latter, what > > significance? (maybe the changes are produced by the > > motion of polar groups?) > > > > Thanks in advance, > > > > Raul > > > > __________________________________________________ > > Correo Yahoo! > > Espacio para todos tus mensajes, antivirus y antispam ?gratis! > > Reg?strate ya - http://correo.espanol.yahoo.com/ > > > > ------------------------------------------------------------------------- > > 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 > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > -- > Biophysics Graduate Student > Carlson Lab, University of Michigan > http://www.umich.edu/~mlerner http://lernerclan.net > -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net ------------------------------ Message: 3 Date: Wed, 10 Jan 2007 22:56:30 +0100 From: Terry Jones Subject: Re: [PyMOL] Pymol cone shape? To: William Scott Cc: "Martin.Laurberg" , pym...@li... Message-ID: <17829.24846.423655.550648@terry-jones-computer.local> Content-Type: text/plain; charset=us-ascii Hi William You can do it, or something that's as close to a cone as you could wish for, by using a triangle fan. The apex of the fan is the top of the cone and then you just add points around the base of the cone at whatever granularity you like. That would take some programming though, but it's not too difficult if you know some Python, as the CGO interface is very simple. I wrote a pymol plugin to do something similar: it takes an input specification file, parses it, and draws many CGO objects as a result. It works just fine. Making the resulting cones smoothly colored or transparent would be more, and harder, work though. Without doing that, your cones may not play nicely with the rest of the stuff drawn by pymol (which in my case is nothing at all :-)). Terry | Let's ask on the pymol mailing list... | | On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote: | | > Damn, I can convert my 1969 CNS base pair restraints into what they call | > CGO drawn lines, and thereby display enforced hydrogen bonds, but I wish | > to draw cones for the base pair ladder as ribbons can do it. Oh well, .. | > | > On Wed, 10 Jan 2007, William Scott wrote: | >> | >> I think it is possible, but I don't know how. | >> | >> On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote: | >>> Hi Bill, is it possible to draw a cone-shape in pymol? ------------------------------ Message: 4 Date: Thu, 11 Jan 2007 09:16:23 +0100 From: "Tsjerk Wassenaar" Subject: Re: [PyMOL] change the sphere size of a chosen atom ? To: mc...@ya..., fen...@ma... Cc: pym...@li... Message-ID: <8ff...@ma...> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Ni Hao Feng, First of all, please do not include an complete daily digest in a question (or reply) on this or any user list. If required, cut out only that part which connects to your question or reply. Then, in addition to Bobs comments, you can also use the terminal or a script, using the command: set sphere_scale, 0.3 (or another value) This will do what it says and scale your atoms sphere radius with the factor given. Another possibility is to assign a different atomic radius to your atom: alter e. s, vdw=newradius_float_argument maybe like: alter e. s, vdw=vdw*0.9 Note that you may have to "rebuild" your scene, if you were already using a sphere representation. Best, Tsjerk -- 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: 5 Date: Thu, 11 Jan 2007 09:24:05 +0100 From: "Tsjerk Wassenaar" Subject: Re: [PyMOL] Pymol cone shape? To: "William Scott" Cc: "Martin.Laurberg" , pym...@li... Message-ID: <8ff...@ma...> Content-Type: text/plain; charset="iso-8859-1" Hi William, Maybe the attached python script will be of some use. It contains a function (and some helper functions) to draw a CGO arrow in PyMOL. It contains code for drawing a cone for the head of the arrow. Hope it helps, Tsjerk On 1/10/07, William Scott wrote: > Let's ask on the pymol mailing list... > > On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote: > > > Damn, I can convert my 1969 CNS base pair restraints into what they > > call > > CGO drawn lines, and thereby display enforced hydrogen bonds, but I > > wish > > to draw cones for the base pair ladder as ribbons can do it. Oh > > well, .. > > > > > > > > On Wed, 10 Jan 2007, William Scott wrote: > > > >> > >> I think it is possible, but I don't know how. > >> > >> > >> > >> On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote: > >> > >>> Hi Bill, is it possible to draw a cone-shape in pymol? > >>> > >> > > > ------------------------------------------------------------------------- > 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 > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- 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 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: arrow.py Url: http://sourceforge.net/mailarchive/forum.php?forum=pymol-users/attachments/20070111/9f700702/attachment.pl ------------------------------ Message: 6 Date: Thu, 11 Jan 2007 08:36:04 -0500 From: Praedor Atrebates Subject: Re: [PyMOL] distance atom-protein surface To: pym...@li... Message-ID: <200...@ya...> Content-Type: text/plain; charset="iso-8859-1" I needed to have a measurement of the "actual" physical long dimension of a protein model to compare with x-ray scattering data. I activated the surface mesh feature and at the extreme ends of the longest axis, right at the surface boundary, created a carbon atom at each position, then simply used the distance measurement wizard to measure the distance between the too points. praedor On Wednesday 10 January 2007 11:29, Andreas Henschel wrote: > Hi Giacomo, > > you can either create an atom at that position > (see eg. http://www.rubor.de/bioinf/tips_python.html#chempy) and than > use the distance command (or wizard). [...] > Giacomo Bastianelli wrote: > >Dear Pymol users, > > > >I would like to measure the distance between an atom and > >a specific point (not another atom) in the surface of the protein. > >Is it possible with pymol? > >do I need additional scripts? > > > >Thanks in advance, -- Reichstag fire is to Hitler as 9/11 is to Bush ------------------------------ Message: 7 Date: Thu, 11 Jan 2007 13:02:45 -0600 From: "aaron bryden" Subject: [PyMOL] Sequence view size To: pym...@li... Message-ID: <977...@ma...> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Is their any way to get the size in pixels of the sequence view like their is of the internal gui, or the size in pixels of the space actually used for drawing? I know that glGetDouble(GL_VIEWPORT) but this doesn't take into account the internal gui or the sequence view. I can find a way to get the size of the internal gui but not the sequence view. thanks, Aaron ------------------------------ ------------------------------------------------------------------------- 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 http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ------------------------------ _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest, Vol 8, Issue 5 ***************************************** --------------------------------- Don't pick lemons. See all the new 2007 cars at Yahoo! Autos. |