May 2014 - Chimera-users - RBVI Mailing Lists

Chimera License
by Chamila Jayasinghe 16 May '14

16 May '14

Hi, I am computer technician from University of Calgary, Department of Biological Sciences. We are hoping to Chimera for one of our Biochemistry tutorials for about 20 students. Is this consider as non-commercial use. Do we need to purchase license for the installation. Many thanks! Chamila Jayasinghe Faculty of Science (IT)

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re Registration
by Anna Lohning 15 May '14

15 May '14

Hi I am using Chimera and tried to register but came up with an error. Are you please able to do so manually? My details are: Dr Anna E. Lohning Asst Professor - Biochemistry Faculty of Health Sciences & Medicine Bond University 4229 QLD Australia alohning(a)Bond.edu.au I intend to use it for Research. Thanks very much. Its a great program. Kind regards Anna Dr Anna Elizabeth Lohning Assistant Professor - Biochemistry Faculty of Health Science & Medicine Bond University ROBINA 4229 (07) 5595 4779 alohning(a)bond.edu.au

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Re: [Chimera-users] Ionisation state of ligand and protein residues processed with chimera
by Elaine Meng 15 May '14

15 May '14

Dear Tao, Chimera AddH does not have the option to predict protonation state for different pH values, but you can do it using a different tool in Chimera to add hydrogens: menu Tools… Structure Editing… PDB2PQR, or command "pdb2pqr". In the graphical interface opened from the menu, click the triangle next to "Options" to show the options: Use PROPKA to predict protonation states: change to "true" pH value to use with PROPKA: default 7, you can change to the pH you want See documentation for more information: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html> Then Apply or OK will run the calculation using a web service at the NBCR. One thing that might be confusing is that the result is opened as a new model in Chimera (i.e. original could be model 0, results will be model 1 so that there are two copies of the structure open in Chimera). PDB2PQR also assigns charges but the choices are different from Chimera's Add Charge (except for PDB2PQR AMBER and Add Charge AMBER ff99SB, AMBER ff99bsc0 all give the same charges). Depending on which charges you want, you could try running Dock Prep before or after PDB2PQR. If you run Dock Prep after, make sure to do it on the PDB2PQR results (model 1 in my example) and turn off the "add hydrogens" option because you want only the hydrogens from PDB2PQR. There might be errors, however, because PDB2PQR sometimes generates hydrogen names that are not recognized by the Add Charge step of Dock Prep… you may have to re-name some N-terminal -NH3+ hydrogen(s) from H to H1 to get it to run without error. Or, you could do the pKa prediction outside of Chimera using some other program, for example: H++ web server (this also adds the hydrogens) http://biophysics.cs.vt.edu/ PROPKA web server (this just predicts the pKa of each ionizable sidechain, and then you would use this information in combination with your desired pH to add hydrogens with Chimera or some other program): http://propka.ki.ku.dk/ That PROPKA program is the same one that the PDB2PQR server uses. 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 May 14, 2014, at 6:27 PM, 崔涛 <cuitao(a)mail.hzau.edu.cn> wrote: > Dear Elaine > Thanks very much for your quick reply which helped me a lot. > The documentation mentions “AddH aims to generate protonation states reasonable at physiological pH”. Now I have a new question. Is there a way and how to generate protonation states reasonable at other pH (such as 6.0 or 8.0) with chimera? I have found options to specify different tautomers in chimera. However, I didn’t find options for changing pH. > Best regards, > Tao

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Transition from PyMol
by R Michael Sivley 14 May '14

14 May '14

I'm attempting to transition from Chimera to PyMol and I'm struggling to reproduce the results of a visualization script. The script maps numeric values onto certain residues in a protein structure. Those residues are marked by spheres, and those spheres are colored by spectrum according to the residue value. In PyMol I overwrite the atom bfactors, and then display the CA of annotated residues as a sphere, colored by spectrum. The PyMol code (post-bfactor overwrite): cmd.show(selection="name CA and br. b >%f"%min_score-0.0001,representation="spheres") cmd.spectrum("b","blue_red",selection=include,minimum=min_score,maximum=max_score) In Chimera I've generated an attribute file, and used defattr to assign values to residues. I get the spheres by creating spheres centered on the CA atom of the annotated residues: rc("open %(struct_loc)s"%params) rc("defattr %(tempf)s"%params) rc("ribcolor dark grey") # temporary for resi in params['resis']: rc("shape sphere center %s@CA radius 1 color grey"%resi[0]) rc("rangecolor %(anno)s %(minval)s blue %(maxval)s red"%params) At this point, I can color the residues themselves using their attribute values, but I can't color the spheres, because they don't contain the information necessary to color them. I've uploaded the PyMol and Chimera generated images to imgur here: PyMol: http://imgur.com/a/GVfWi#0 Chimera: http://imgur.com/a/GVfWi#1 <http://imgur.com/a/n1PNl#1>Any help in reproducing the PyMol image in Chimera would be much appreciated. I haven't begun working on orientation (PyMol's `orient` equivalent), but any quick tips there would certainly be helpful as well. Thanks! Mike

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search for the conserved domain alignment algorithm
by ce 13 May '14

13 May '14

Hi, Does Chimera constain an algorithm that can generateconserved domain alignment in the exact way as Entrez CDD alignment works ? Yours sincerelly, XY

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x,y coordinates of the Chimera screen
by Jan Kosinski 13 May '14

13 May '14

Hi, When I load a model in Chimera I can move the model on the plane of the screenwith the move command along the x,y axes. Is it possible to get the current range of the coordinates of the x and y axes of the screen, so I could automatically (without setting positions with savepos) move my models to particular points on the screen? For example, move to left upper corner in a movie... Or move the model outside the screen and create nice fly-in effect in movies. Thanks, Jan

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1.9 production release
by Eric Pettersen 13 May '14

13 May '14

Hello everybody, A new production release of UCSF Chimera (version 1.9) is available: http://www.rbvi.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). New features include multiple sequence alignment using Clustal Omega or MUSCLE web services, building double-helical nucleic acids, "colorkey" command, "struts" command to reinforce structures for 3D printing, "vseries" volume series playback and processing options, more efficient save/restore of coordinates in sessions, Dynameomics amino acid rotamer library, WMV2 movie output, COLLADA export. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.9.html Display, Interface: * icon for menu selection mode: Append, Intersect, Replace, Subtract * distance monitor line style and color can be saved as preferences * silhouette outlines can be controlled per-model * Axes/Planes/Centroids objects can be recolored with Actions menu * "colorkey" command implementation of Color Key tool Structure Analysis and Modeling: * new Align Chain Sequences tool for multiple sequence alignment of structure chains using a Clustal Omega or MUSCLE web service (these can also be called to realign the sequences in an existing Multalign Viewer window) * "mda" command to Blast-search and retrieve structures similar to a query sequence, lay them out left->right by N->C along the query * APBS interface omits explicit solvent by default * "coulombic" command allows specifying atoms/charges to use for ESP calculation independent of the surface to color * Build Structure tool allows generating nucleic acid double helices, specifying phi angle when joining peptides * "adjust" command to change bond angle or length * MD Movie session support for partly loaded trajectories * Morph Conformations pairs chains by ID if the sets of IDs are same * "ramachandran" command can assign probabilities as attributes * Rotamers/swapaa include Dynameomics rotamer library (Daggett group) Volume Data (density maps, ESP maps): * "vop" volume operations to take pointwise maximum or multiply maps * "vseries" command options to open and close volume time series, jump playback to a specific frame, perform various processing such as alignment, normalization, cropping, compressing, save to file * new volume input format VTK structured points (ASCII) General, I/O: * some Preferences reorganization, new categories: Labels, Selection * more efficient save/restore of coordinates in sessions * new output movie format WMV2 * new export formats COLLADA, VTK * "struts" command to add strengthening bonds for 3D printing * "leap" command for using Chimera with a Leap Motion Controller Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to get translation and rotation vectors for move and turn commands
by Jan Kosinski 13 May '14

13 May '14

Hi, I have the same model loaded in Chimera twice. One model has been moved to a different position and rotated manually using mouse. How can I get x,y,z coordinates for the centers of the to models to calculate x,y,z axis definition compatible with the move command? And how to get rotation information for turn command? I tried with cofr command but it seems to give coordinates in different reference frame. I would like to avoid using savepos/reset/fly commands in this case. Python solution would be fine. Thanks in advance for your help, Jan

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EM density map rescaling issue???
by Christian Geiss 13 May '14

13 May '14

Dear Chimera User list, I have a fundamental problem when loading pdb structures and EM density maps as *.em. The scale doesn't fit at all, with other words my pdb structure is tremendously bigger than the EM structure. One work-around is to resample the EM structure from current 64 px boxsize with 8.6 A pixelsize to 1 A pixelsize, giving ~ a 500 pixel volume, but then the volume gets quite big und my chimera gets really slow in handling those structures (pdb and big EM map at once)...is there any other way to solve this issue like scaling the EM structure on the fly in not such a memory consuming way...I also wonder if there is any information about the pixelsize in the EM header, because then the scaling should be done usually automatically??? Thanks in advance, Chris P.S. I couldn't find anything related to this in the chimera archive... -- *Christian Geiss, M.sc.* Universitaet Frankfurt BMLS Frangakis Group Max-von-Laue-Strasse 15 D - 60438 Frankfurt am Main Phone: +49-(0)69-79842597 Fax: +49-(0)69-79846467 geiss(a)biophysik.org

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threshold level problem
by 李智海 13 May '14

13 May '14

Hello, I am a freshman for Chimera, sorry for a possibly stupid question but i seem to be confused by the difference between threshold level in volume view and the sigma value that is used to contour the density map in some articles. please help me out! Thank you very much! Zhihai Li

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