- Chimera-users - RBVI Mailing Lists

Smoothing and binning volume data
by Tom Goddard 16 Mar '17

16 Mar '17

Not sure what you are asking. You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool. To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors. Tom > On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote: > > Dear Tom, > > How are you? > I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering. > > Could you please send me some information on where I could look for this information? > > Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above) a certain threshold value? > > I hope that I am not asking anything too strange. > Especially the first thing would help me greatly. > > Thank you, > Andrea > > -- > Andrea Fera, PhD – [Senior Research Scientist] > Advanced Molecular Imaging ; DUNS 824-XXX-XXX > Unit for Cytoskeletal Dynamics , NICHD, National Institute of Health >

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VPAT (Voluntary Product Accessibility Template)
by Ashdale, Martin 16 Mar '17

16 Mar '17

Good Morning, I am looking into using your product with my AP Biology classes and I need to get approval to download your software. The IT Department would like the VPAT (Voluntary Product Accessibility Template) so that I can submit it for approval. If you have it available could you please send it to me. I appreciate your time and look forward to teaching with your product. Thanks, Martin Ashdale Biology Teacher Harford Technical High School 200 Thomas Run Road Bel Air, MD 21015 (410) 638-3804

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Selecting certain atoms with exception
by Kelvin Lau 14 Mar '17

14 Mar '17

Dear Chimera users, I'm trying to do the following: -select all the atoms of a single residue (trp) -except for one (residue number 285) I am not sure how to use a negation command to leave out only 285. Any ideas? Cheers Kelvin -- Kelvin Lau Structural Plant Biology Laboratory Department of Botany and Plant Biology Science III University of Geneva 30 Quai E. Ansermet 1211 Geneva Switzerland Email: kelvin.lau(a)unige.ch Phone: +41 22 379 3026

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possible Chimera bug - saving bonds in MOL2 format
by Marek Maly 13 Mar '17

13 Mar '17

Hello, it seems that Chimera (1.11.2) has problem to save some bonds in MOL2 format. If you open attached file "source.mol2" , Chimera reads/show perfectly all the bonds including those where is "Ru" atom present, but when you save it in MOL2 format in Chimera (see attached file "Chimera_MOL2.mol2"), then all the "Ru-x" bonds are omitted and naturally if you open this "Chimera MOL2" file in Chimera no "Ru-x" bonds are shown. Interestingly, if the original MOL2 file "source.mol2" is opened in Chimera and then saved in PDB format ("Chimera_PDB.pdb"), all bonds are written and so if this PDB file is opened in Chimera all bonds are visualized. Would be nice if the perfect bond preservation which works in MOL2->PDB case worked also in MOL2->MOL2 case. Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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chimera 1.11.2 interlaced stereo
by Jean-Marie WURTZ 13 Mar '17

13 Mar '17

Hi, I am a long time user of chimera and had never such a problem. I would like to use the interlaced stereo with a zalman monitor but I get the following error : Unable to turn on stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I must say that VMD stereo is working. But I understood also that both programs work differently with regard to steero. My configuration: Dell M4500 precision Windows 10 Quadro FX 1800M driver 342.01 What can I do to get it working? Thanks for your help. Best regards -- Jean-Marie Wurtz Professeur de Bioinformatique Tél : +33 (0)3 69 48 51 04 Fax : +33 (0)3 88 65 32 76 jm.wurtz(a)unistra.fr<mailto:jm.wurtz@unistra.fr> wurtz(a)igbmc.fr<mailto:wurtz@igbmc.fr> IGBMC-CEBGS Département de Biologie et de Génomique Structurales Equipe de Biologie Structurales de Cibles Epigénétiques Parc d'Innovation, 1 rue Laurent Fries BP 10142 F - 67404 ILLKIRCH CEDEX http://archive.igbmc.fr/recherche/Prog_ISB/Eq_JCava/index.html [UniversitÃ© de Strasbourg]<http://www.unistra.fr>

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Re: [Chimera-users] [chimerax-users] animations
by Elaine Meng 12 Mar '17

12 Mar '17

Hi Giorgio, You would still have to use the “export” command that exports one file at a time, but it can be run at every frame by combining it with the “perframe” command. For example, in Chimera the following (should be all one line even though the Mail app may break it up): perframe "export ~/temp/$1.x3d" zero 2; play wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 50; wait 50; ~perframe …where ~/temp is a directory that already exists, will make files 01.x3d …. 50.x3d in that directory. In ChimeraX, there is a “perframe” command and “save” to export X3D, but no “play wiggle” command. <http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> 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 9, 2017, at 11:44 AM, Giorgio Luciano <giorgio.luciano(a)gmail.com> wrote: > > Thanks for the info and sorry for my late reply. I generally export using x3d what I was thinking about is, how can someone export the single model for an animation ? As an example if I make wiggle a molecule play (wiggle #0 24-67,68-119,123-244,267-286,290-355,356-387 200 ) may I export in batch the molecules for the single frame ? > Any help will be greatly appreciated :) >

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Re: [Chimera-users] question on MAV
by Elaine Meng 10 Mar '17

10 Mar '17

> On Mar 10, 2017, at 12:59 AM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > I would appreciate it if you could let me know how to make specific residues bold in MAV. Not all of them but only specific residues. > Thank you so much for your help. > Jackie Vitali Hi Jackie, Sorry, MAV (Multalign Viewer) does not have the option to use different fonts for different residues… as you probably saw, the Preferences… Appearance options only change the font of all the residues. To highlight specific residues in MAV, you could draw a box around them to make a region, and then using the Region Browser, change region background color and/or outline color, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> ...or you could create a custom header to put a symbol above the column. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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replay morph created with vop morph?
by Oliver Clarke 09 Mar '17

09 Mar '17

Hi all, Is there any way to replay a morph created using vop morph? Or to change the representation of the map prior to playing? I have a sequential morph of multiple different conformations (which I can’t make with the morph map GUI tool), but I would like to change the display of the map before creating a movie (which vop morph does not seem to allow). Example command: vop morph #1,2,3,4,5 interpolateColors false constantVolume true Cheers Oli

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Can you delete a residue attribute?
by Mungo Carstairs (Staff) 08 Mar '17

08 Mar '17

Hi, I would like to be able to set and remove residue attributes (using Chimera commands over the REST service). Setting is fine, but removing seems to be limited to changing the value to either an empty string or None. https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html Is there any way to actually remove attributes after they have been set on residues? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

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running DockPrep and Vina from python
by Lee A.G. 06 Mar '17

06 Mar '17

Hello I have been trying to run DockPrep and Vina from a python script to generate a pdbqt file to be used in subsequent Vina docking studies (with a config file). What I have at present is the following (I have edited DockPrep\_init_.py to make nogui=True ; the receptor has been loaded as model #0, and the ligand as model #1) from DockPrep import prep model=Midas.open('4iaq.pdb') prep(model) modelname='4iaq.mol2' from WriteMol2 import writeMol2 writeMol2(model, modelname) #VinaRun OutFileName='C:/Autodock/5HT/4iaq/Test2/4iaq' rc("vina docking receptor #0 ligand #1 output " + OutFileName + " prep true wait true") The generated 4iaq.receptor.pdb file contains the protein as modified by DockPrep, without the charges etc, and with the original PDB residue numbering. The 4iaq.receptor.pdbqt file contains the unmodified protein with charges etc, and with the original PDB residue numbering. The 4iaq.mol2 file contains the modified protein, with charges etc, but with residue numbering modified to start at 1. What I hoped to produce was a 4iaq.receptor.pdbqt file containing the modified protein with charges etc, and with the original PDB residue numbering, and this is just about the only thing I don't have. Any help would be very gratefully received. Anthony

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