- Chimera-users - RBVI Mailing Lists

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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How to insert a nucleotide to a pdb
by Magdalena Riad 18 Nov '22

18 Nov '22

Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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Query regarding the Zone tool in UCSF chimera
by Prathvi Singh 18 Nov '22

18 Nov '22

Elaine, In UCSF Chimera, when I try to find all the atoms within 4A of a selected residue using the *Zone* tool, it selects several atoms around that residue. However, I am not able to understand which atom of the selected residue was taken as the reference point for calculating the distances. Please help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Information regarding double bonds
by Naima syed 18 Nov '22

18 Nov '22

Hello, I have one concern, before docking there is a double bond which i can check in pymol but after docking that double bond was lost. Can you please tell me how to fix this problem. Thank you

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