From owner-chemistry@ccl.net Thu Mar 1 11:36:00 2012 From: "Y. Yuan echemistry\a/yahoo.com" To: CCL Subject: CCL: JSDraw is Free for Academia - A Javascript Chemical/Biological Structure Editor Message-Id: <-46404-120301111641-32601-lEFU/izy0QoJeCj0x+DUcA::server.ccl.net> X-Original-From: "Y. Yuan" Content-Type: multipart/alternative; boundary="-3126525-1309629373-1330618589=:60916" Date: Thu, 1 Mar 2012 08:16:29 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Y. Yuan" [echemistry{}yahoo.com] ---3126525-1309629373-1330618589=:60916 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable We received many requests asking JSDraw academia licenses, so I think it wo= uld be good to notify everybody here.=0A=0AJSDraw, a 100% Javascript Chemic= al/Biological structure editor, is now free to all=A0academic=A0users. =A0I= f you are new to JSDraw, please feel free to take a look at it: http://www.= jsdraw.com=0A=0A=0ATony Yuan=0AScilligence=0Atyuan(*)scilligence(.)com ---3126525-1309629373-1330618589=:60916 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

We re= ceived many requests asking JSDraw academia licenses, so I think it would b= e good to notify everybody here.

JSDraw, a 100% Javascript Chemical/Biological structure editor, = is now free to all academic users. = If you are new to JSDraw, please feel free to take a look at it: http://www= .jsdraw.com

Tony Yuan

Scilligence

tyuan(*)scilligence(.)com

---3126525-1309629373-1330618589=:60916-- From owner-chemistry@ccl.net Thu Mar 1 12:40:00 2012 From: "Elaine Meng meng{}cgl.ucsf.edu" To: CCL Subject: CCL: new Chimera release Message-Id: <-46405-120301123900-18551-eFNcstYRmfpuOYgahVEmUA++server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 1 Mar 2012 12:38:58 -0500 Sent to CCL by: "Elaine Meng" [meng]^[cgl.ucsf.edu] Hello everybody, A new production release of UCSF Chimera (version 1.6) is available: http://www.cgl.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). This will be the last Chimera release supporting Mac PowerPC platforms and OS X 10.5 (Leopard). New features include a Rapid Access interface to frequently used data and tools, new ribbon spline options, improved transparency rendering, new fetch type: Uniprot protein sequence and annotations, and several options for fitting atomic structures into density maps: global search, iterative sequential fitting, symmetric fitting, etc. More details are given below; see release notes for the full list: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html Graphics, Depiction: * new spline options for ribbon closer to backbone atom positions * new initial model colors, pastel rather than saturated * improved transparency rendering (global single-layer on by default) * 3D labels drawn on top by default * fancy backgrounds: images from files, color gradients from Palette Editor * options for cleaner pocket/tunnel surface display (see "sop" command) Structure Analysis and Modeling: * AddH allows specifying less common states of Asp, Glu, Lys, Cys * FindHBond can label H-bonds with distances * Blast Protein shows more info for PDB hits (ligands, resolution, etc.) * Build Structure improvements for joining peptides, swapping substituents * tools to change chain IDs, renumber residues * minimization: - can be conjugate gradient (previously steepest descent only) - parts of structures can be ignored * distance and angle plotting for trajectories * Cage Builder tool for generating polyhedral cage models * interface to MultiFit web service (simultaneous rigid fitting of multiple structures to density, developed by the Sali Lab, UCSF) * "fitmap" command: - global search with random initial placement - iterative sequential fitting - symmetric fitting * "measure" command options: - map symmetry - surface contact area - center of mass User Interface and I/O: * Rapid Access interface to frequently used data and tools shown at startup, can be hidden/shown at any time by clicking the lightning-bolt icon * caching fetched data is turned on by default * scaling with mouse/touchpad scrolling can be turned off (Mouse prefs) * Model Panel: - group/ungroup function, such as for NMR ensembles - functions reorganized into favorites/all * new input types: SPHGEN spheres, Maestro/Glide docking output (ViewDock) * WebGL export (experimental feature) Sequence-related: * new fetch type UniProt: protein sequence and feature annotations * Multalign Viewer: - UniProt features can be mapped onto already open sequences - Region Browser improvements for handling feature annotation regions - calculation of region overall RMSD - interface to Modeller homology modeling allows including water, other HET Enjoy! On behalf of the Chimera team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Thu Mar 1 13:33:00 2012 From: "Andrew Voronkov drugdesign,,yandex.ru" To: CCL Subject: CCL: question on software for very general 3D de novo modeling Message-Id: <-46406-120301113250-22701-4kBjG/p0FA1nNy/TX2mVSw**server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 01 Mar 2012 20:32:20 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign _ yandex.ru] Dear CCL users, I need a task - to model the protein very generally. It is basically for graphic representation. I need just to get approximate shape. De novo modeling through Robetta server takes a lot of time. Can you recommend me maybe some coarse grained de novo modeling of protein structure? Something which will identify domeins, model them approiximately and will suggest different versions for their orientation. Best regards, Andrew