- Chimera-users - RBVI Mailing Lists

how to solve the problem of topology
by Kenji MATSUI 17 Feb '22

17 Feb '22

Dear Chimera Thank you very much for your kind answers. Sorry, I have a question about the issue of ligand topology for the docking study. The topology did not match when I used this ligand for the docking study. Could you tell me how to solve this problem? The thing I tried 1. I tried to add hydrogen atoms on UCSF Chimera by following the URL below, but it did not work Reference: https://www.swissparam.ch/SwissParam_gromacs_tutorial.html 2. Compare with the contents of the Mol2 file for cholesterol that was correctly docked. 25-hydroxycho_only_0216 → original file 25-hydroxycho_only_0216_Chimera →after adding H using UCSF Chimera --------------------------------------------------------------------------- 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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(no subject)
by Cathy 15 Feb '22

15 Feb '22

I am supposed to pull up the picture of VIG which is one of the amino acides in the GABA T Complex. Can someone please tell me how to do this? Thank you. --

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Adding charges to insulin receptor
by Saousen Diaf 15 Feb '22

15 Feb '22

Hello Elaine, I want to energy minimize a model of insulin receptor using chimera, but it is asking me to specify the net charges of some residues, which most of them are glycans that I added using CHARMM GUI, would you please help me with that? Thank you in advance for your help. Best Saousen

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multiple small molecule overlay
by Tyler St Denis 15 Feb '22

15 Feb '22

Hello, I have had success overlaying two small molecules in chimera by using the following process and using the "match sel" command in the command line. Each molecule I want to compare has 3 similar nitrogens http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-August/010205.html Though this process works for overlaying two small molecules, it does not work for a third. The first error I received indicates "an odd number of atoms has been selected." Clearly the 'match sel' command works by comparing pairs of homologous atoms -- is there a way to expand this 'pair' to a larger set (e.g. triplets) to multiple small molecules? Thanks! Tyler _______________________ Tyler G. Saint-Denis, Ph.D. Postdoctoral Fellow T. Don Tilley, Ph.D. Laboratory College of Chemistry University of California, Berkeley tstdenis(a)berkeley.edu 914-462-1954 [05537c13-eec7-4b35-bc2c-f774f520f544]

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Visualizing gaussian output files in UCSF chimera
by Prathvi Singh 15 Feb '22

15 Feb '22

Hello again Elaine, I have one more question. Is there a way to open & visualize a gaussian output file (it has extension of *.log*) in UCSF chimera? I found that if you convert the *.log *file to *.mol *file using gaussian's software GAUSSVIEW, you can visualize the *.mol *file in chimera. However, the identity of the residues is lost; all the residues are shown as UNK. Is there a better way to do this? Thanks again & always -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Regarding ramachandran plot
by Prathvi Singh 15 Feb '22

15 Feb '22

Hi Elaine, Is there a way to see the phi and psi values of two different proteins on the same ramachandran plot? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [Chimera-users] Chimera-users Digest, Vol 226, Issue 6
by Martti Tolvanen 12 Feb '22

12 Feb '22

Hi Kaina and Elaine, If the goal is just to demonstrate the similarities of the two domains in your proteins, you could also consider breaking the model in two and superimposing each domain separately. Another feasible but tedious approach for rotating bonds (which I do not recommend because it means altering the structure from what was observed) would be to measure torsion angles in the protein backbone of the "linker" region of one model and then set the torsion angles into the same values in the other model, using the command line or a script. Best, -Martti -- Martti Tolvanen Lecturer in bioinformatics U of Turku, Finland -----Original Message----- From: chimera-users-request(a)cgl.ucsf.edu [mailto:chimera-users-request@cgl.ucsf.edu] Sent: 11. helmikuutata 2022 23:31 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 226, Issue 6 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."

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superimposing structures with Chimera
by Elaine Meng 11 Feb '22

11 Feb '22

> On Feb 10, 2022, at 1:42 PM, Kaina Quintero Chavez <kaina.quintero(a)uabc.edu.mx> wrote: > > Hi, My name is Kaina. I am a current college student in UABC. I am currently doing my thesis in biology and came upon using UCSF chimera and am in a stuck position on how to use the superimpose feature. I was hoping you can guide me or reference me to a workshop/ course? anything really to get the job done. > Thanks, hope to here from you. > -- > Kaina Hi Kaina, We usually recommend the chimera-users(a)cgl.ucsf.edu address for asking questions -- I CC'd it here, hope that's OK. Also it would be helpful to include more information when you send a question, like what you are trying to superimpose, what you tried already, what problem(s) caused you to be stuck, etc... but I will try to answer below. There are lots of different ways to superimpose structures in Chimera and it depends on your situation as to which one you would use. There is a discussion of the different ways here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> If you have atomic structures of proteins or nucleic acid chains, probably the easiest approach is to try using the Matchmaker tool, menu: Tools... Structure Comparison... Matchmaker. You would choose one structure as the reference and the other one as the one to match, and then just click "Apply" to see if the default settings work. Here is the help for Matchmaker <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/match…> ...and this tutorial includes examples of using it <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html> There is also a "matchmaker" command that does the same thing, and the help includes some example commands: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> However, maybe your situation is different and you would need to use one of the other methods discussed in the first link above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Animation utility question
by Zhang, Bixia 11 Feb '22

11 Feb '22

Dear developers, I have a question about using the animation tool in chimera. I made a pdb files with three chains, they are different protein domains. I am trying to make animation showing chain B moves (rotate and translate) in relative to A and C. For all the desired positions of B, I added to the scenes and dragged to the timeline. But when I hit play, I noticed that the relative position of B was maintained same as the last scene. Does that mean I failed to save the position of previously scenes? I also noticed that if I don’t move the chain, and I just rotate the whole thing and the animation works. Is there a special command to save the relative position? I tried savepos but it doesn’t seem to help. I would appreciate it if you could help me with this issue. Thank you! Best, Bixia

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Chimera
by Kaina Quintero Chavez 10 Feb '22

10 Feb '22

Hello, I was wondering if the university or program had a course of using the superimpose feature, I would like to conduct an experiment and would need assistance in the usage and also permission of the images -- Kaina

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