- Chimera-users - RBVI Mailing Lists

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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