Re: [PyMOL] Caver 3.0 pugin
This issue have been solved. Caver works fine. Does anyone tried to include path information obtained by caver to the NAMD steered md simulation? I'm looking for the protocol for guiding namd forces along the direction obtaned from CAVER. James 2013/11/15 James Starlight > Dear Pymol Users! > > > In the latest 3.0 releases of the CAVER plugin lack the source path for > the caver.jar launch file. Could you tell me how I could define this path > manually from pymol shell? I've try to make calculations with thus plugin > having Caver 3.0 dir in the work folder but obtained error that > /where/caver3 not found > > > Thanks for help > > James > -- DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Drawing chain to visualize backbone
Hi Simon - I don't think you need to do any deleting of atoms at all--there are a few settings that will be helpful here. Here's how I would do what I think you're asking for: # load and set basic representation load structure.pdb as cartoon # create the smooth version create smooth, structure cartoon tube, smooth set cartoon_tube_radius, 1.5 set cartoon_smooth_loops, on, smooth set cartoon_transparency, 0.5, smooth # give everything a "loop" secondary structure for the smooth version alter smooth, ss="L" rebuild Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Nov 14, 2013, at 8:41 AM, Simon Schweizer wrote: > Dear all, > > I have a complex protein (with a knot in the polypeptide chain) > and want to show the rough course of the chain, so everyone can > easily see that there is a knot inside. > > I don't know how to draw such a complex 3D object in a drawing > program, so I want to do that in PyMol (or another similar program). > > What I did is copying a part of the protein sequence and transformed > it in a new object. I want to superimpose the new object drawed > in ribbons with the whole protein in cartoon representation. I made > the ribbons big. How can I make it transparent, too, by the way? > > For showing the rough course of the polypeptide chain, the ribbon > should not follow every alpha-helix, loops and so on. What I want to > do is like box filtering the chain. > I tried to delete atoms, but then the ribbon is broken. How can > I connect these atoms, must the c-alpha carbons be connected > by peptide bonds so the ribbon is drawed? But I want to delete > atoms, so the connections between the remaining atoms that > form the ribbon will have larger distances than normal bonds. > Is that possible to do that at all in PyMol? > > Another option would be: taking some c-alpha carbons that > show the rough course of the chain, and building a povray > file that draws it like a ribbon or flexible tube, and input that > povray code into the povray-file of the rendered protein. > > Any help is greatly apprechiated! > Thanks! > Simon > > -- > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access > Free app hosting. Or install the open source package on any LAMP server. > Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! > http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] movie, ~1700 residues, out of memory
Hi Christian,
set defer_builds_mode to 3, this will prevent caching the geometry for all
states.
http://pymolwiki.org/index.php/Defer_builds_mode
Cheers,
Thomas
On 09 Nov 2013, at 13:58, Christian Becke wrote:
> Dear pymol users,
>
> I'm trying to create a movie, using lsqman and pymol, of a molecule of
> ~1700 residues (HETATMs deleted, no hydrogens, alternative conformations
> removed). I created 60 pdb files with lsqman and loaded them (as
> different states of the molecule) into pymol. In the default "lines"
> representation, pymol plays all right through all 60 frames. However, as
> soon as I try a more fancy representation ("sticks" or "cartoon"), pymol
> runs out of memory, recommending to "reduce the quality, size, or
> complexity of the scene" (this is on Linux, pymol svn revision 4037, on
> a Core2 Duo, NVIDIA Quadro, 4 GB RAM). From what I read, people created
> movies of the ribosome using pymol, so ~1700 residues should not be a
> problem, right?
> I tried reducing the viewport to stamp size (120 x 240), to no avail.
> Which other settings should I check in order to "reduce quality, size,
> or complexity"?
> I would be grateful for any hints on how to get this going.
>
>
> Thanks in advance,
>
> Christian
--
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[PyMOL] Caver 3.0 pugin
Dear Pymol Users! In the latest 3.0 releases of the CAVER plugin lack the source path for the caver.jar launch file. Could you tell me how I could define this path manually from pymol shell? I've try to make calculations with thus plugin having Caver 3.0 dir in the work folder but obtained error that /where/caver3 not found Thanks for help James -- DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
