November 2022 - Chimera-users - RBVI Mailing Lists

Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

Hello, I have been using the Chimera interface to Modeller via a web service. This service has been down for a few days. It always stops with the following error message: Service 'opal:Modeller9v8Service' is unavailable What should I do? Please help me. Thanks, Feri

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Finding SASA for individual residues
by Prathvi Singh 29 Aug '24

29 Aug '24

Hi Elaine, Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Robbon colouring
by F.Xavier Gomis-Rüth 30 Nov '22

30 Nov '22

Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier --

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Writesel command in chimeraX
by Prathvi Singh 27 Nov '22

27 Nov '22

Hi Elaine, Is the writesel command available in chimeraX because I could not find it in the Actions menu? If not, then is any equivalent available apart from the command which saves selection as a new PDB file? Thanks once again in advance -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Visualizing negative volume as in CastP
by Neelen, Christopher 24 Nov '22

24 Nov '22

Hello everyone, I am trying to visualize cavities from a protein I am currently working on. Therefore I calculated the cavities volume using CastP. I then import the obtained files into chimera. Unfortunately CastP visualizes the cavities as a negative volume of the solvent accessible area. Chimera on the other hand only shows the surface. So is there a way to also visualize the negative volume in Chimara just like in CastP ? Thanks in advance! All the best, Chris

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Query regarding depth cueing
by Prathvi Singh 22 Nov '22

22 Nov '22

Hi Elaine, Is there a way to change the depth cueing gradually using command line in either chimera or chimeraX? If possible, then it would be a great way to emphasize on a specific part of the protein while making a chimera movie. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Alphafold
by Kornelius Zeth 20 Nov '22

20 Nov '22

Dear all - I'm using Alphafold in Chimera and I have a problem to run this properly on Colab. The people from Colab say that the error messages I get since recently are related to Alphafold developers having installed a new version. Could you please let me know what I could do to get the program running again? Thanks and have a nice day Kornelius

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Using Chimera and Autodock Vina on Catalina OS
by Rao, Mallika 18 Nov '22

18 Nov '22

Hello, I was wondering if anyone had been able to find a workaround in order to use the autodock vina add-on in Chimera for a mac that is running Catalina OS. Thanks in advance, Mallika

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Saving omega angles to file
by Prathvi Singh 18 Nov '22

18 Nov '22

Hello Elaine, Is there a way to save the omega angle of residues to a file using either chimera or chimeraX? I am able to save the phi, psi, chi angles using the *Render by attribute *tool in chimera but I could not find a way to save the omega angle. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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