September 2021 - Chimera-users - RBVI Mailing Lists

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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(no subject)
by Thirumurugan Prakasam 30 Oct '21

30 Oct '21

Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png] -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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Error to run chimera remotely on a GPU computer from Mac computer
by Zongli Li 01 Oct '21

01 Oct '21

Dear listers, I ssh with "-Y" from my Mac desktop to a GPU computer and process my data there. Quite often I need to look at the 3D volumes with chimera. This had been working nicely for long time. But all suddenly it stopped working and game the error 3: X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1400 Current serial number in output stream: 1400 Did anyone encounter the same error? Any suggestions or tips to overcome this problem would be appreciated. Thanks, Zongli

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Surface exposed residue in a protein assembly
by Alessandro Strofaldi 30 Sep '21

30 Sep '21

Dear Chimera developers, I’m working on a protein complex and I’d like to analyse the SASA and hydrophobicity on the surface. I have worked with Chimera before so I know how to do those basic tasks for a monomeric protein; however, since I have five monomers interacting together I was wondering how to calculate the SASA (and later showing the hydrophobic residues of the surface) excluding the monomer-monomer interfacial regions. I would also need those values tabulated to show hydrophobicity vs primary sequence but still excluding the monomer-monomer interfaces! It seems like there is no basic tool to do that (or am I missing something?); is there any procedure I could apply? Unfortunately I can’t code in Python so I’m looking for a solution that involves using the GUI. Thank you, Best regards, Alessandro Strofaldi, PhD University of Bristol

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Select model based on its position and orientation
by Yu Zhou 29 Sep '21

29 Sep '21

Dear all, I tried global docking of two proteins and ended up with hundreds of possible poses. Is it possible to automatically select the poses based on the position and orientation of one partner, for example, the ones in which the ligand protein is close to the transmembrane region of the receptor protein and oriented with its N-terminus on the extracellular side? Thanks Yu Zhou

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questions
by ARLEY REY PAEZ 29 Sep '21

29 Sep '21

Best regard, My name is Arley, I am a postgraduate student at the federal university of Lavras, Brazil. I write this message because I have doubts about how to calculate the RMSD between two ligands after docking and redocking. My question is if Chimera works well to perform that calculation, since when for example I have two structures (ligands) that are, visually well superimposed and I calculate the value of RMSD with the use of the rmsd # 0 # 1 command, their value is high when compared With a structure that is not visually superimposed, why does that happen? Is it that chimera is not useful to carry out this task? I appreciate you can help me with that concern. Att; Arley -- Este e-mail foi enviado por um estudante da Universidade Federal de Lavras (UFLA). Caso esta mensagem possua algum conteúdo não apropriado, favor desconsiderá-la.

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Crashes during Dock Prep
by Justin Trickett 27 Sep '21

27 Sep '21

Hello, I am prepping 43 structures for docking using the "Dock Prep" feature in Chimera 1.15, and it crashes every time it gets to "Retrieving rotamers from Dunbrack library." Am I doing something wrong? Many thanks, Justin -- Justin Trickett Graduate Student College of Pharmacy, University of Rhode Island (603) 505-1061

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question on protein structure change after matchmaker (position-change) operation
by Lei Qian 27 Sep '21

27 Sep '21

Dear users, After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001). Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation? Thanks! Lei

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Running 3D-FSC script causes freeze
by Oliver Clarke 24 Sep '21

24 Sep '21

Hi, Running the chimera command file included with the example data for 3D-FSC (https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/C… <https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/C…>) causes the latest daily build of Chimera to freeze - it executes lineplot.py, but then just locks up and does not respond. This happens whether I run it as `chimera 3DFSCPlot_Chimera.cmd` or load the command file after opening the GUI. Am I doing something wrong, or has something changed in Chimera that has broken this script? Cheers Oli

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Connecting ends of a peptide
by Nicole Ostrovsky 22 Sep '21

22 Sep '21

Hello, I am trying to connect two sides of a peptide together to make it cyclic. Is there a way to do this that doesn't involve adding in another amino acid? I have been adding a glycine by individual atom using the modify structure tool but I'm wondering if I can do it a different way. Best, Nicole Ostrovsky

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Chimera-users September 2021