March 2012 - Chimera-users - RBVI Mailing Lists

how to show backbone carbonyl oxygen
by james09 pruza 03 Mar '12

03 Mar '12

Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James

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How to show the electron density of just selected residues? Thanks
by Pingyang Liu 02 Mar '12

02 Mar '12

Hi, How to show the electron density of just selected residues? Thanks I followed the Chimera tutorial, but still the electron density of the whole protein was displayed. Another question: what does the convexity of a protein structure tell? I did not find much information about convexity online. Thanks a lot. Best, Andy --

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segmentation fault
by nauton lionel 02 Mar '12

02 Mar '12

Hello I send this Email, because I can't used chimera-1.6 for linux 64 bits ( 2-29-2012 version) it crash with this comment "segmentation fault", everytime I tried to load pdb or mol2 files. and I don't have this problem with chimera-1.6rc for linux-32 bits or chimera-1.6( 2-29-2012 version) and chimera-1.5.3 for linux 64bits works well on the same PC I used fedora 16... regards

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Chimera 1.6 officially released
by Eric Pettersen 02 Mar '12

02 Mar '12

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 <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebu… > * 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 <http://www.cgl.ucsf.edu/chimera/1.6/docs/UsersGuide/rapid.html> * 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, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] reading SMILES description into Chimera
by Elaine Meng 01 Mar '12

01 Mar '12

Hi Boaz, You can just use the command line, for example: open smiles:CC1=CC=C(C=C1)S(=O)(=O)[O-] I'm thinking it may be a mistake that SMILES shows up as a file type in the "Open File" dialog. The only other place I can think of is in Build Structure (under Tools... Structure Editing), where the Start Structure section includes a SMILES option. In that case you would just type or paste in the SMILES string in the indicated field. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 1, 2012, at 7:08 AM, Boaz Shaanan wrote: > Hi, > > I'm trying to read a small molecule for which I have a SMILES description into Chimera. I selected 'smiles' from the input options but it's not clear to me how to proceed. Do I have to generate a text file with the smiles description in it? do I paste the smiles description in the file name line? or what? > > Thanks for your help. > > Boaz > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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