- Chimera-users - RBVI Mailing Lists

APBS mobile ion option
by Eita Sasaki 12 Aug '16

12 Aug '16

Hi, I'd like to run APBS command with mobile ions (150 mM NaCl). I tried the following command, but it did not work. apbs molecule #1 ion true _posion 1,0.15,1.16 _negion -1,0.15,1.67 If I typed just "apbs molecule #1" it works (without mobile ions). I am wondering my command was perhaps wrong but don't know the right one. I hope you could help me to solve the problem Thank you in advance. Eita

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(no subject)
by Karel W. F. de Pourcq 09 Aug '16

09 Aug '16

Dear Chimera team: I am a student of a Msc. in Bioinformatics at the Autonomous University of Barcelona. I am using Chimera to prepare visual representations of molecular events, and I write in order to ask if there is a straightforward way in which to: a) Create a sphere of a certain diameter: Yes, I found how to do it already: with the "shape" command. This is solved. b) In an orderly and distributed way, cover that sphere with a number of copies of a molecule chain, anchored over the sphere's surface by one of their ends (and the other end of the molecule protruding towards the outside). I believe I could do it manually for a small system. Is there some kind or automated and more convenient way to do this for a large sphere, linking its surface with hundreds of molecules of -for instance- dodecane? I could not find explicitly a way to do something similar to what I am trying to do. I attach an image of a 2-d representation of something similar to what I would like to represent. The difference is that I would like to cover the surface. [image: Imágenes integradas 1] I thank you a lot in advance for your time. Kind greetings from Barcelona, Spain, Karel De Pourcq

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chimera minimize script
by Bylund, Tatsiana (NIH/NIAID) [F] 09 Aug '16

09 Aug '16

Dear all, I need to minimize a lot of protein complexes and am trying to do it with a script. I have a protein complex structure without Hydrogens, but when they are added in Chimera, it outputs error Non-standard atom names: ASN HA2 (:33.K@HA2) ASN HA3 (:33.K@HA3) Total charge for #0: 32.039 Total charge for #0: 32.039 The following residues had non-integral charges: :33.K 0.039 Correct charges are unknown for 2 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log Dock prep finished Error while processing chimera_mini.py: No MMTK name for atom "HA3" in standard residue "ASN" When I delete residue K 33 (which DOES NOT have H in pub file) chimera runs minimization. Would you have any suggestions? Thank you! Kind regards, Tatsiana

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UCSF
by Amali Guruge 05 Aug '16

05 Aug '16

Dear All, What is UCSF referring to? Is it University of California San Francisco ? Thank you.

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Volume and mesh data simultaneously? Coordinate space is different
by Marvin Albert 03 Aug '16

03 Aug '16

Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap). Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh? (this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3 <http://www.filedropper.com/cube_3>) Thanks a lot in advance, Marvin

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precalculated void representation as surface
by Michalska, Karolina M. 03 Aug '16

03 Aug '16

Hi, I have a precalculated cavity represented as a grid in the pdb format, where “atoms” are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface. I appreciate your help, Karolina

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APBS webservers not working
by Ursula Schulze-Gahmen 02 Aug '16

02 Aug '16

I used to run APBS from within Chimera. But recently, the webservers that are called for the APBS calculations are not working. Do I need to go to the APBS website directly or what is the solution? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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chimera 1.11 question
by Dixon, John 01 Aug '16

01 Aug '16

Hi I was wondering if you could help When I install chimera on my main physical PC I can use function left CTRL and mouse to highlight atoms in green in the graphics interface as below. [cid:image003.jpg@01D1E728.1FE9F730] However when I install chimera on a virtual PC, this function does not work. Any ideas on how to get around this issue? thanks John Dixon Application Integration Team Client Platform Services Information Services Division, UCL Tel: 02076799163 Ext: 09163

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help for make figures
by 陈柳青 30 Jul '16

30 Jul '16

HI How to make the figures in attachment, which highlight part of a structure. Thanks very much for advise. -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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help for make figures
by 陈柳青 30 Jul '16

30 Jul '16

HI How to make the figures in attachment, which highlight part of a structure. Thanks very much for advise. -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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UI suggestions - Save map
by Oliver Clarke 29 Jul '16

29 Jul '16

Hi, minor suggestion for Chimera, related to dealing with large numbers of maps: It would be really helpful if there was a 'Save map' dialog in the 'File...' menu, with similar dropdown menus to select the map one wants to save as for the 'Save PDB' dialog. Doing so via the volume viewer is a bit clunky when there are lots (e.g. 10+) of maps loaded. Even better would be if it included a 'Save relative to map' dropdown, analogous to the 'Save relative to model' drop down in the 'Save PDB' dialog, which would resample the map to be saved on the grid of the selected target map (perhaps warning of the potential for a modest loss of quality). This would be really helpful when one aligns many different conformations of a molecule (e.g. from 3D classification) to a reference subvolume and wants to save the resulting transformed maps. Cheers, Oli.

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Re: [Chimera-users] [chimera-dev] B factor
by Elaine Meng 27 Jul '16

27 Jul '16

On Jul 26, 2016, at 5:12 PM, Bashayer Althufairi <althufairib(a)mymail.vcu.edu> wrote: > Hello > As you know many crystallographers need to determine the ave. B factor of selected amino acids or sometimes they wanna know B factor of N-termius Vs. C-terminus of a protein. I'm working on a protein where I need to predict B factor of certain amino acids sequence as well as difference between the values for analysis. Is this possible by Chimera? If yes, I'd like to know Please the way step be step, If no, I wish you could recommend a simple way to do it by educational simple software like PyMol. > Thank You in Advance > -- > Bashayer Althufairi > Medicinal Chemistry department > Virginia Commonwealth University Hello Bashayer Althufairi, This is really a Chimera user question so I’m CCing the chimera-users mailing list. The chimera-dev list is for Chimera programming questions. Chimera doesn’t predict any B-factors, but you can see the B-factors from the PDB file for a structure, e.g. in a histogram in the Render by Attribute (in menu under Tools… Structure Analysis). This tool can color the structure to show the B-factor values. It also automatically calculates the average B-factor per residue (over the atoms in each individual residue so that each residue can have one number). It can also save the values to a file (see File menu of that tool) although of course the PDB file already contains the per-atom B-factor values. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> See also the tutorial for coloring by B-factor: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> But maybe you mean that you want to select several residues and then calculate a single average B-factor for them. You can do that with Attribute Calculator (in menu under Tools… Structure Analysis) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcul…> For example, you could select several residues and open Attribute Calculator, turn on the options to “Restrict formula domain to current selection” and “Show calculation results in Reply Log”, calculate a new attribute named whatever you want for “molecules” with formula: average(atom.bfactor). Click Apply to calculate a single average over all selected atoms, value reported in Reply Log. If you have predicted B-factor values you can also read them into Chimera as a custom attribute (see file format for doing that <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defi…> … it is the same format as used for the saving mentioned above). When you read in those values they are also available for use in Render by Attribute and in Attribute Calculator, and with the latter you could calculate the differences between the bfactor attribute from the PDB file and your custom attribute (the predicted values). The differences would then be another attribute also available for coloring using Render by Attribute. See also the attributes tutorial for examples of using Attribute Calculator and Render by Attribute: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html> I don’t use other programs so I don’t have any advice about using them for this purpose. 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

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Help with Autodock Vina
by Jonathan Y Wang 27 Jul '16

27 Jul '16

To whom it may concern, Hi, I was trying to dock a ligand into my receptor and all of the other ligands so far have worked and outputted a value, but this one compound never outputs a .pdbqt file. The other files such as the .conf and .pdb files have been created, the bottom of the screen no longer says "execution in progress", and the green box remains. I've looked at the tutorial for AutodockVina online and tried fidgeting around with it, but I seem to be extremely lost. I was wondering if you had any pointers, tips, or anything at all that could help me. All the best, Jonathan Wang

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Auto start and nogui option causing segmentation fault?
by Daniel P Farrell 26 Jul '16

26 Jul '16

Hello, I don't know if maybe i'm doing something wrong, or if there's a problem, but I'm on a mac el capitan 10.11.6 and I'm getting these weird errors when I try to start chimera in nogui mode. I usually set various tools to auto-start once I start chimera, but recently I was messing around and added a few, and now I'm getting these errors when i start chimera via --nogui. Problem is, I don't know which one is causing the seg fault, but I feel like it shouldn't be calling these gui options with the nogui options on anyway. Once I started getting these errors I went to Favorites->add to favorites/toolbar->reset & save, and now I don't get the segfault. I do get a few other errors if I adda few back to the auto start / on toolbar options. chimera production version 1.11 (build 41179) 2016-07-15 05:43:21 UTC with many auto-start options on """ >chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' [1] 1045 segmentation fault ~/Desktop/Chimera.app/Contents/MacOS/chimera --nogui """ after removing most auto-start options """ >chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' Starting extension 'Model Panel' failed Starting extension 'Keyboard Shortcuts' failed Starting extension 'IDLE' failed > """ should I be adding a different flag or something when I start chimera via nogui? Thanks, Dan

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Saving Attribute settings and Worm Radius Consistency
by Nicole Persky 26 Jul '16

26 Jul '16

Hi All, I've started using Chimera to map two different datasets onto structures. For one, we use color, and for the other we use worm radius. I've encountered two problems while trying to make figures for publications: 1- when I save my session the image is saved but when I go to "render by attribute" to tweak the settings a little, the threshholds under colors and worm radius have been reset. How to I get them not to reset, but to keep the thresholds? 2- I am trying to compare three different images with the same worm radius thresholds. For one of the images the lowest number of my attribute is LARGER than the lowest number I want to define on my threshhold (I would like to set the lower worm radius to 1 for a value of 1 however for this dataset my lowest value is 2. I cannot just set the value starting at 2 because there is a gradient to the largest value that gets thrown off). Yet, I cannot set the threshold lower than the lowest value of my attribute. Does anyone know a way around this? thanks so much, Sincerely, Nicky

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saving multiple models in Chimera
by Kamil Kuder 26 Jul '16

26 Jul '16

Dear Sirs/Madamme I have multiple PDB'a (ca.40) in the model panel. While trying to save each model in single file using option "Save multiple models in multiple files" I got this message: You must provide a file name that contains either $name or $number. I set the name to eg. A1_01 and/or A1_$01 but none of this works. How shall I manage that? Many thanks Kind regards Kamil J. Kuder, PhD Jagiellonian University Medical College Faculty of Pharmacy Department of Technology and Biotechnology of Drugs Medyczna 9 30-600 Krakow POLAND tel.: +48 12 602 55 86

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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

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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)

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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

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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

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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

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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>

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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

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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

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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 >

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