- Chimera-users - RBVI Mailing Lists

Video issues
by Mark Warren 14 Feb '18

14 Feb '18

Hi, Running win10 and using Chimera 1.12. Upon startup I'm getting the splash logo, then the rapid access screen. All OK so far. However I load any protein and the dialog along the bottom status bar confirms its loaded but the screen still shows the rapid access screen. I can toggle the lightning button in the bottom right as much as I like but it remains on the rapid access screen. Any ideas what to check? Thanks The Medicines Discovery Catapult is one of a network of elite technology and innovation centres established by Innovate UK as a long-term investment in the UK's economic capability. Applying business-led research, Catapults help businesses transform great ideas into valuable products and services to compete in the global markets of tomorrow. Medicines Discovery Catapult is a company limited by guarantee, registered in England and Wales with company number 09928547. Our registered office is at Medicines Discovery Catapult, Mereside, Alderley Park, Alderley Edge, Cheshire, SK10 4TG. This email and any attachments may contain confidential information and is intended solely for the addressee. If you have received it in error, please send it back to us and immediately and permanently destroy all copies. Do not use, copy or disclose the information contained in this message or in any attachment.

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Feature to remove default bond between hydrogen atoms of water while loading MD trajectory
by NARINDER Kaur Harika 13 Feb '18

13 Feb '18

Dear Sir/Ma'am, I hope you are doing good. I am interested in making MD movie from AMBER trajectory in chimera 1.12 version. Unfortunately when I load prmtop and mdcrd files in MD movie, it shows default bond between hydrogens of water molecule. I dont want to show this bond while presenting my research at meetings so I would be really grateful if I can get any help regarding removing this unwanted bond in water molecules. For further clarity I have attached avi movie file of small section of my trajectory. Thank you very much for your help and support. With Regards, Narinder Kaur Harika Georgia state university

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TM tendency hydrophobicity scale
by Shyam Saladi 13 Feb '18

13 Feb '18

Hi all -- I have put together a Chimera attribute definitions to color residues according to the TM tendency hydrophobicity scale: Zhao and London, Protein Sci 15:8 (2006), doi: 10.1110/ps.062286306 An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity In case it's helpful to others, it's attached to this message. Perhaps the Chimera team would also be interested in including it with the other scales <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> online as well. Thanks, Shyam -- Shyam Saladi <http://shyam.saladi.org> NSF Graduate Research Fellow Biochemistry and Molecular Biophysics California Institute of Technology

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Errno 13
by Dustin Park 13 Feb '18

13 Feb '18

Hello, After using docking preparation and run, I set the executable location to vina and clicked ok. However, the result is that there is a chimera error ([errno 13] Permission denied. Can you explain to me how to get past the docking preparation step and why this error is coming up? Not sure how else to do this step. Thank you.

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Pipes command deletes the previous pipes model
by vamsee 12 Feb '18

12 Feb '18

Hello Elaine, I'm trying to create pipes models with different edge colors for 2 models. I use the following command for the first model (model # - 0.11). *pipes #0.11 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue* Then I try to create the second pipes model using the same command with the model number changed (model number #0.12) *pipes #0.12 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor red* Basically the difference between the two pipes models is the edge color. But, when I run the second command, it deletes the first pipes model (#0.11). I'm not sure what is going on. I'm attaching the whole code here. Please advise. *open 0 4G80.pdb* *split* *delete #0.1-10* *focus* *color white,r #* *pipes #0.11 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue* *pipes #0.12 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue* Thank you, Vamsee

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"Save Image..." with higher pixel than my screen comes out blank
by Jun Ha Song 12 Feb '18

12 Feb '18

Hello, I have been fan of "Save Image..." when I am making figures. I have been using the function for some time, and last time I used it was Friday (Feb 9th, 2018). I would take images of 5000x3750 with supersample of 4x4 all the time. However, today, I noticed that the function was not working. When I specify pixel that is above the screen resolution (1920x1080), it would just be blank black image with specified image size. However, if I do not change the Chimera resolution and keep it default (ex. 1024x768), it is properly imaged. I have not had any system change in my computer. The only change is that I am currently using my laptop's screen, whereas before I have been using monitor connected to my laptop via HDMI cable. What could be the reason for this sudden malfunction? Best, Junha.

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Error while using minimize
by Andres Benitez 12 Feb '18

12 Feb '18

Hello, I am trying to use minimize to resolve side chain positions which were mutated using pymol. The file is saved as a pdb, but I am getting errors when I try to use the minimize function. I am wondering if the error is because the structure has some loops removed, or if there is something else going on. I've attached the chimera session file and a text file with the errors I am getting. Thanks, Andres Benitez

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Download specific chain only
by Healey, Joe 12 Feb '18

12 Feb '18

Hi again Chimera team, I need to download a chain from an enormous macromolecular complex as it's so large it actually crashes Chimera! Is it possible to do this directly in chimera somehow (downloading just that specific chain or chains? The fetch dialogue doesn't seem to like the typical underscore notation (e.g. 5IV5_BB ) Thanks Joe Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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Surface/Cap colouring
by Healey, Joe 11 Feb '18

11 Feb '18

Hi chimera team, Is there an easy way to control the transparency of a surface and its clipping cap separately? I managed to do this in one session where the caps are solid, but the rest of the surface is transparent (e.g. see this link: https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=… ) [https://lh5.googleusercontent.com/QS16L041E4BqEh_EynLj2msR0gbNQVXbSZ7QexXke…]<https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=…> 3J9Q_wholetier_sliced_colcap.tif<https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=…> drive.google.com However in a different session I'm struggling to figure out how I achieved this. If I alter the surface colour in the Inspect dialog, it sets the surface and cap transparency to be the same. If I change the suface cap colour in the Effects > Side View dialogue, it gives the desired differential transparency, but colours ALL the surface endcaps identically which isn't what I want. Help me unpick what I did! Many thanks Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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Hydrogen bonds for specific residues
by Seera Suryanarayana 10 Feb '18

10 Feb '18

Dear users, I have done simulations for 100ns and I generated clusters. I want know the hydrogen bonding during simulations for specific residues. Kindly let me know how do we select particular residues for hydrogen bonding in chimera. Thanks in advance, Surya Graduate student India.

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