March 2017 - Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] Moving icosahedron to model
by Tom Goddard 03 Mar '17

03 Mar '17

Hi David, I could not tell from the image if the surface was from a PDB or a density map. If it is from a PDB then the coordinate system is based on the crystal packing. That means the origin could be anywhere and the rotation can be arbitrary. So then getting an icosahedron outline aligned can be a real pain, although sometimes the crystal packing has a virus centered at 0,0,0 and a standard orientation like 2-fold symmetry axes along x,y,z (e.g. 2bbv). In the hard cases there are various tricks. For instance use the shape command to center the icosahedron on the atomic model (e.g. "shape icos radius 200 center #0 mesh true div 1") Tom > On Mar 3, 2017, at 11:12 AM, David Bhella wrote: > > Hi Tom > I think Kok Lian's structure is a surface from a PDB file created using multiscale models. I feel the origin and symmetry should be available from the PDB file in some way, but I too have struggled with getting icosahedral structures from PDB into a sensible orientation. > > Sent from my iPhone > >> On 3 Mar 2017, at 18:38, Tom Goddard wrote: >> >> Is your virus surface from a density map? If so it probably has the origin set in such a way that the center of the virus is not 0,0,0 while the center of your icosahedron outline is 0,0,0. To remedy that you would change the origin of the map in Volume Viewer, menu Features / Coordinates set origin index to for example 128 if the map size is 256 grid points. That is likely to put the map origin at the center of the virus particle. >> >> Tom >> >>> On Mar 3, 2017, at 1:18 AM, KL Ho wrote: >>> >>> Dear All, >>> I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. >>> >>> Best wishes, >>> KokLian >>> <image1.png>_______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Moving icosahedron to model
by KL Ho 03 Mar '17

03 Mar '17

Dear All, I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you. Best wishes, KokLian

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move icosahedron surface to a model
by Ho Kok Lian 03 Mar '17

03 Mar '17

Hi All, I am a beginner of chimera. Sorry for the simple question. May I know how to move the icosahedron surface (see attached figure) to the model according to its symmetry? Many thanks. Kok-Lian

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Segmentation fault when issuing chimera command
by Hui Shi 01 Mar '17

01 Mar '17

Hi there, Sorry for bothering you guys! I’m wondering if someone can help me to resolve the problem I have here. I’ve recently installed chimera-1.11.2 under CentOS 7 system. And I have a Nvidia GeForce TURBO-GTX1080 graphic card on my computer with NVIDIA driver Version 375.39 installed. But when I run issue the chimera command thought the terminal, an error message “Segmentation fault (core dumped)” was thrown out. I googled this problem and found in a previous message of chimera-users that this should be a problem of driver issue. Also, on the “benchmarks” link of chimera, GeForce GTX 1080 has been tested under Windows with NVIDIA 368.81 driver version. I could not find this driver version for 64-bit Linux system. Since I have already installed the newer driver version (375.39), I would think this should work. Any suggestions on how to deal with problem? Thanks a lot in advance! Hui

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Re: [Chimera-users] Error opening larger proteins
by Eric Pettersen 01 Mar '17

01 Mar '17

Hi Catherine, It turns out that the singular value decomposition function that Chimera uses to get the eigenvectors and eigenvalues for the plane computation uses a lot of memory if you use a large number of atoms to define the plane (or axis for that matter). There is a non-default setting for that svd function that I just discovered that uses much less memory and seems to produce identical results, so I have switched Chimera to using that setting. The switched version will be available as the next daily build. Look for daily builds dated March 1 or newer. Also, you may be able to get your current version to work if you simply use less atoms to compute the plane. The selection you were using — “sel :.A,.B,.C,.D” — will not only select all the protein but also all the waters, ligands, and ions. Perhaps just “sel protein” would be more appropriate (depending on what you want the plane for) and might work in your current build. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Mar 1, 2017, at 9:09 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hello, > > When I try to open large protein in Chimera, and try to define plane for the protein, It is throwing me an error saying "Memory Error". Can you please help me with this error? > > Note: Attached a snapshot of the error. > > Thanks, > Catherine > <Screenshot.png>

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Chimera-users March 2017