- Chimera-users - RBVI Mailing Lists

Solvate Tool Trouble
by Mike Bergman 25 Jul '16

25 Jul '16

Hey there. I am having trouble with the solvate tool. I am using a dimeric model (PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model TIP3PBOX), it squishes the dimer together. I tried different angstrom box sizes - 3, 5, 10, 20. Running the simulation with them overlaid wouldn't give me any useful data as I'm looking for the changes in the dimer interface. Is there a way I can stop it from doing this? Should I use a different solvate method like Shell? Thanks. Sincerely, Mikey Bergman

2 4

Threshold change
by Anindito Sen 25 Jul '16

25 Jul '16

Dear All, What will be the command (to be put in a script) for the change in the threshold of one of the displayed volumes without disturbing the others. Thanks Andy Dr. Anindito Sen (Ph.D)

2 1

Linking four proteins
by Aditya Padhi 22 Jul '16

22 Jul '16

Dear Chimera users, I have predicted a protein structure having 4 different domains (for e.g. 1-94, 95-247, 248-444 and 445-509 residues) and all are part of a single protein from 1-509 residues. They have been predicted from different web-servers. Now, I want to join them together to form a single PDB file i.e. make a single PDB file containing the entire protein from 1-509 residues from the above 4 PDB files. Afterwards, I want to run a simulation of the built structure. I searched in google for possible solution but not sure which method would be better. Is there any solution to build this one structure in Chimera? Please let me know. Thank you so much. Aditya

2 1

Color by hydrophobicity - select default scale?
by Oliver Clarke 21 Jul '16

21 Jul '16

Hi, As explained here ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html) Chimera currentlyuses the Kyte-Doolittle scale by default for coloring proteins by hydrophobicity. I wonder whether it might be worth updating this to use e.g. the scale described by Karen Fleming and co here ( http://www.pnas.org/content/108/25/10174.full)? This scale (and indeed most more recent scales in the literature, see review here: http://www.sciencedirect.com/science/article/pii/S0968000411001320) differ quite dramatically from the Kyte-Doolittle scale, which places trp and tyr as comparable to serine, which does not seem reasonable based on analysis of membrane protein structure. The Moon et al scale has the advantage that it is derived from studies of the energetics of protein folding and membrane insertion, as opposed to the energetics of isolated amino acid partitioning between ethanol and water, which as I understand it is what the K-D scale is mostly based on. Alternatively, would it be possible to allow users to select the default scale which it used for this purpose (I know it is possible to define a custom attribute for this, but this is a little cumbersome for something which sees frequent use). Cheers, Oli

2 3

Positioning changing over time
by Marvin Albert 21 Jul '16

21 Jul '16

Dear chimera users, I was wondering whether any of you could help me with this simple problem: The aim is to make a movie displaying the evolution of predefined meshes over time (see attached python script). Overall the script works and produces a movie. However the mesh gets displaced slightly between the different time points. This results in an annoying random wiggling. I checked the original .wrl files and the indicated coordinates do have consistent positions (meaning the displacements are produced by chimera). How can I get a smooth movie? Might there be something unexpected happening when I repeatedly call runCommand(“open <file1.wrl>”) and runCommand(“close all”)? Thank you so much in advance! With kind regards, Marvin

2 2

Docking Crystal Structure in to Cryo EM Structure
by Senavirathne, Gayan 20 Jul '16

20 Jul '16

Hello, I am trying to dock some crystal structures (PDB: 1KX5 and 3OS1) in to a cryo EM structure EMDB:2992. How can I do this task using the UCSF chimera software and how can I know the alignment is accurate? Thank you very much Regards, Gayan Senavirathne, PhD Postdoctoral Researcher The Ohio State University Wexner Medical Center Cancer Biology and Genetics 460 West 12th Avenue, Room 1040 Columbus, OH 43210 Phone (313) 316-6658 senavirathne.1(a)osu.edu<mailto:senavirathne.1@osu.edu>

2 2

new release of UCSF Chimera
by Elaine Meng 18 Jul '16

18 Jul '16

Hello everybody, A new production release of UCSF Chimera (version 1.11) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac OS X, Linux. 64-bit builds are recommended for all capable platforms; this will be the last release to support 32-bit builds. New since version 1.10: Molecular Dynamics Simulation tool, more Add Ions types, residue interaction networks (RINs) from trajectories shown in Cytoscape, protein contact/distance map data export, Segment Map updated to new version of Segger, volume contour levels can be specified in RMSDs from zero or SDs from mean, "flat ribbon" publication preset, Ribbon Styles tutorial, "set showCofR" to show crosshairs at center of rotation. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.11.html General I/O, Display: * standard shortcuts for File menu (Ctrl/Cmd-q for Quit, etc.) * "wall-eye stereo pair" option in Save Image dialog * PubChem fetch uses PubChem3D instead of Pub3D * "set showCofR" command to show "+" at center of rotation * "pipes" command-line implementation of PipesAndPlanks * reduced triangles in STL output for atoms/bonds Structure Analysis and Modeling: * Molecular Dynamics Simulation tool (thanks to V Munoz Robles and JD Marechal, Universitat Autonoma de Barcelona) * many more ion types in Add Ions tool * axes can be defined normal to previously defined planes * RR Distance Maps can show distance differences for a pair of structures (means, std devs already available), export data * MD Movie calculation of trajectory RINs, display in Cytoscape * PDB2PQR updated to use new web service URL Volume Data (density maps, electrostatic potential): * new input map format: IMAGIC density * Segment Map updated to new version of Segger * "volume" command options "rmsLevel" and "sdLevel" to specify thresholds in units of RMSD from zero and SD from the mean * "vop" options to sharpen map, create new zero-valued map 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

1 0

using scipy with Chimera
by Xiao-Bo Li 16 Jul '16

16 Jul '16

Hi, I need to use scipy with Chimera. I like to copy over the scipy folder from my ubuntu's "/usr/lib/python2.7/dist-packages/scipy" directory. This is what I have done in the past, and it works fine. However, when i installed the .bin file for Chimera from Chimera's website (I tried versions 1.11 and 1.8.1), I find that the numpy versions there are 1.7.0b2. The numpy version on my ubuntu computer is 1.11.0. Since my ubuntu python's numpy, and Chimera's numpy are different versions, I can no longer using the scipy folder for Chimera. Can you please update Chimera's numpy version to 1.11.0? XBL

2 2

Re: [Chimera-users] A question about colouring a resmap output file in Chimera.
by Elaine Meng 15 Jul '16

15 Jul '16

Hi Thanos, I’ve never used Resmap myself (it is a separate program from Chimera), but as I understand it, the output file contains the local resolution values calculated from the input map. You would have both that original map and the resmap output map open in Chimera, show an isosurface of the original map, and color it by the values in the resmap map. It is best to send Chimera-related questions to the list CC’d here (chimera-users(a)cgl.ucsf.edu) because often other people know more about something than I do. >From this earlier post to the list, I thought Resmap also output a Chimera script that you could run to perform the coloring: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011679.html> However, even if you didn’t run such a script you could do the coloring using the Surface Color tool or the “scolor” command in Chimera. Finally, there must be more information about how to use Resmap with Chimera, and how it calculates the values, in the Resmap manual and the Resmap paper in Nature Methods, see: <http://resmap.sourceforge.net/#manual> 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 Jul 15, 2016, at 4:47 PM, T-I <ignatiou(a)gmail.com> wrote: > Hello Elaine. > My question today is: > > I have run Resmap on my em-density map (.mrc) to calculate the local resolution > > When i open both the original .mrc file and the _resmap.mrc file in chimera i don't understand how to then colour the map with the values found in the resmap calculation. > > what do i do exactly? > > also i don't understand where the resmap values are?? > many thanks > Thanos >

1 0

Troubleshooting Residue Errors
by Mike Bergman 15 Jul '16

15 Jul '16

Good Morning. I am trying to Dock Prep the kappa1 dimer (PDB ID: 2Q20) in order to run Molecular Dynamics simulation. I keep getting an error that I'm not sure how to solve. I cleared the reply log and tried again so I could attach the reply log to this email. I have not modified the structure at all prior to the dock prep. When I looked at the residues, they seemed fine to me, but maybe you can help me figure out what's wrong. Any help would be appreciated. Thank you very much. Sincerely, Mikey Bergman

2 1