- Chimera-users - RBVI Mailing Lists

Color surface by electrostatic potential vs color by value at atom position
by Yu Zhou 21 Feb '20

21 Feb '20

Hi there, I want to color protein surface by electrostatic potential datacalculated using APBS 1.5. I tried two methods in Chimera and got quite differentresults. The resulted images can be found in attachment. In the first attached figure (fig1_ep surface) the surface wascolored by the “Electrostatic Surface Coloring” tool, in the second attachedfigure (fig2_value atom) the surface was colored by the “Values at AtomPositions” tool. Same color palette (red: -35, white: 0, blue: +35) and potential file was used in bothcases. Thanks for your help. Yu Zhou

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Problem during Residue interaction network generation
by Aditya Padhi 20 Feb '20

20 Feb '20

Dear Chimera users, I am using the StructueViz plugin of Cytoscape to launch Chimera and then loading the MD trajectory from Gromacs, where I need to generate the residue interaction network. After this step, when I click "apply" for displaying the interaction network in Cytoscape, it often shows "Importing Residue Network from Chimera", sometimes "getting data for attribute secondarystructure" and sometimes "getting data for attribute ishelix". Even after I wait for half a day, the message continues to show and I am not able to work on Cytoscape. I have even tried to reduce the number of frames of the MD trajectory to see if that helps, but that doesn't work even. Can anyone help me to how to resolve this problem? With best regards Aditya

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Aligning a 2Fo-Fc map with the molecule in Chimera
by Miriam Gochin 20 Feb '20

20 Feb '20

The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom #0" command but got the following error: NameError: global name 'step' is not defined File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box g = volume.grid_data(subregion = 'all', step = step, mask_zone = False) Hoping to figure out how to make it work. Many thanks, --------------------------------- Miriam Gochin Touro University California / LBL miriam.gochin(a)tu.edu mgochin(a)lbl.gov 707-638-5463

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"subtract selected segment from map" from a specific map
by Dominique Gutierrez 20 Feb '20

20 Feb '20

Hello, Can I use the "subtract selected segment from map" in Segger tool to subtract the selected from a specific map and not just the map used for segmentation. In my case the segmented map is from a vop subtracted intermediate used to facilitate segmentation but I would like to quickly subtract several segments from the original map. Or is the only way to do that with vop subtract? Best, Dominique

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Hydrogen labeling scheme
by Jack Fuller 19 Feb '20

19 Feb '20

Hello, I am part of a computational chemistry research group that frequently uses chimera to add hydrogens to pdbs. My coworkers and I have noticed that chimera uses several different labeling schemes for hydrogens. We have been unable to determine how chimera chooses which scheme to use. Is there a way to specify which scheme to use or to know which scheme chimera will choose? Thank you, Jack Fuller

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Mx 230 gpu, chimera and chimerax
by Yehuda Halfon 18 Feb '20

18 Feb '20

Hi all, A friend of mine in my lab wants to buy a new laptop with mx230. Will it work fine with chimera and chimerax? The cpu is i5-10210u and 8 GB of ram. Thanks a lot, Yehuda Halfon PS I know this isn't the chimerax mailing list but I hope to get a double answer in one mail

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BLAST Database error
by Ebrahim Barzegari 18 Feb '20

18 Feb '20

I'm doing Blast protein for a single sequence. After selecting the database (pdb) and setting other params, I receive this error in Reply log: BLAST Database error: Error: Not a valid version 4 database. How can I sort out it? Thanks for help

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SplitCommand python
by Healey, Joseph 17 Feb '20

17 Feb '20

Hi Chimera Team, I’m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I’m only using it for `split`, but I’d like to first test whether a model is already split to avoid unnecessary invocation. I’m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn’t seem to be importable, as when I try: >>> from chimera import SplitMolecule Traceback (most recent call last): File "<pyshell#25>", line 2, in <module> ImportError: cannot import name SplitMolecule I’m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I’ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I’m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ‘layer’ below `chimera` itself. Can you elighten me? I’m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps. If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help. Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

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missing color option in model panel
by abhisek Mondal 15 Feb '20

15 Feb '20

Hi, Newest version of chimera does not have the color option in the model panel. Is this a bug of some sort? Please see the attached image. Regards Abhisek -- *Abhisek Mondal, Ph.D.* *Cardiovascular Research InstituteUniversity of California San Francisco555 Mission Bay Blvd. South. Rm 482Dan Minor's LabSan Francisco, CA 94158USPS address:UCSFAbhisek Mondal, Ph.D.Cardiovascular Research Institute, Box 3122555 Mission Bay Blvd., Floor 4San Francisco, CA 94143*

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Default storage folder, ChimeraX
by Martín González Buitrón 14 Feb '20

14 Feb '20

Dears all, Hope you are well. I have started to use ChimeraX in Ubuntu and I realised that one folder was created with my fetches and other things (i.e. ~/Download/ChimeraX/). How can I change this to other of my own preference? All the best, Martín

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