- Chimera-users - RBVI Mailing Lists

Model placement side by side
by George Tzotzos 07 Jan '22

07 Jan '22

Hi, Having superimposed 4 structures using MatchMaker, is there a way to view the aligned structures in a window grid? Moving them manually after superimposition is not optimal. Thanks in advance for any suggestions and best wishes for 2022

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Introduce a-helices into protein structure ab initio
by Chara Spanou 06 Jan '22

06 Jan '22

Hello chimera-users, I would like to introduce a-helices into my protein structure ab initio. Is it possible to do this with chimera? Another option that I have is to take a-helical pieces of sequence from a different model and introduce these into the desired model. Would that be more feasible? There is a chance I also need to introduce loops and turns ab initio to best localize the introduced a-helices within my protein structure. Can you please indicate how can a chimera user build all this ab initio? Thank you in advance for your time and help, Chara SpanouPhD studentUniversity of Cologne

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report rotate and shift value in MatchMaker
by Yanhe Zhao 06 Jan '22

06 Jan '22

Greeting there, Happy New Year! How can find the rotate and shift value after I done the 'MatchMaker' in Chimera? Thanks and regards, Yanhe

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Question: PDB file creation
by Kenji MATSUI 05 Jan '22

05 Jan '22

Dear Chimera company Thank you for allowing me to use your software. I am Japanese, so I hope you will understand that there are some inappropriate expressions. I would like to ask you one question. I would like to know how to overlay the docked protein (osh4)-ligand (cholesterol) complex (the gray one in the figure) and the complex on the PDB. [image: image.png] Aim I would like to know how well the docked data matches the data in the PDB. Methods I have tried I did it based on the following link from Chimera. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matcha… Thank you for your cooperation. --------------------------------------------------------------------------- 松井健治東京農工大学大学院工学府産業技術専攻修士〒184-8588 東京都小金井市中町2-24-16 Mail: s214903z(a)st.go.tuat.ac.jp Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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report rotate and shift in MatchMaker
by Yanhe Zhao 04 Jan '22

04 Jan '22

Greeting there, How can find the rotate and shift value after I done the 'MatchMaker' in Chimera? Thanks and regards, Yanhe

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Opening .py files
by Henry Shook 04 Jan '22

04 Jan '22

Chimera User Support, I'm working on dockprepping the sars-2 main protease and whenever I try and save it as a .py file, I can't open it from sources other than the saved session I wrote. Whenever I try and open it from a dropbox or my finder, I get the message: Error while processing /Users/8642165/Desktop/Research/DC AP Research /[7l0d]DOCKPREPPEDFINAL.py: File "[7l0d]DOCKPREPPEDFINAL.py", line 1 @<TRIPOS>MOLECULE ^ SyntaxError: invalid syntax File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1325, in _openPython loadFunc(sandboxName, fileName, f) See reply log for Python traceback. Is there any way that I can fix this problem? Thanks, Henry Shook

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Helix Display Artefact
by Sebastian Guettler 28 Dec '21

28 Dec '21

Dear Chimera users, I have a problem with what I think is some sort of a helix display artefact is UCSF Chimera (including the latest release, 1.16). I attach an image. In cartoon display, the helix appears turned inside out for the last turn. It is displayed normally in ChimeraX and PyMol, and the display problem is independent of the secondary structure assignment algorithm (dssp, ksdssp, Stride). Any suggestions on how to solve this issue are welcome. Thank you, Sebastian --------------------------------------------- Sebastian Guettler, PhD Team Leader The Institute of Cancer Research (ICR) Divisions of Structural Biology and Cancer Biology London, UK --------------------------------------------- [cid:image001.jpg@01D7FC0A.1ED3ABA0] The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Blank screen after MD simulations
by Sri Oruganty 28 Dec '21

28 Dec '21

Hello, I am a senior in high school, and I was interested in learning about proteins and mutations. I download Chimera to run MD simulations on a specific protein, but not all the frames are loading. After the frame number gets to a certain point (i.e. 14) every subsequent frame is completely blank. Why is this happening? Best regards, Srigouri Oruganty Pronouns: She, her, hers sri.oruganty(a)gmail.com (610)-207-6325

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Problem related to the "Near" atom in the "Adjust Torsions" tool of UCSF chimera
by Prathvi Singh 26 Dec '21

26 Dec '21

Hi Elaine, I have one more query. I have a residue (its ID is #0:140.a) in a protein model. I want to change the torsion angle between its backbone N, backbone C-alpha, sidechain C-beta & sidechain C-gamma. In order to do that, I execute the following command: rotation 1 :140.a@CA,140.a@CB The execution activates the torsion & lists it in the "Adjust Torsions" tool. However, I have noticed that the "near" atom in the "Adjust Torsions" tool is sometimes assigned to backbone N & other times is assigned to backbone C. This is messing up my calculations. Is there a way to fix the "near" atom to backbone N so that it does not change to backbone C? Thanks again -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Move models around independent of each other in Chimera X
by Prathvi Singh 24 Dec '21

24 Dec '21

Hi, First of all, thank a million to the chimera X development team for incorporating the drag & drop feature in chimera X. I really missed it in chimera. However, after opening two models in the same window, I am unable to find a way to move/rotate model-1 in such a way that it does not move/rotate model-2. I could do this in chimera by unchecking the box for model-2 but when I do the same in chimera-X, it doesn't seem to work. Also, I am unable to find a way to disable depth cueing in chimera X. Please help. Thank you -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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