- Chimera-users - RBVI Mailing Lists

change the protonation states
by 孙钦超 24 Mar '22

24 Mar '22

I would like to make the Glu and Asp protonated, and the Lys and Arg uncharged. While I was trying to do it by addH function with chosing the protonation sates option -> Asp, or chose His. The resulting protonation states of Glu and Arg were the same, as Glu deprotonated and Arg protonated. How could I reach the right protonatation states as I expected? Thanks Qchao

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tile function
by Hansen, Bryan (NIH/NIAID) [E] 23 Mar '22

23 Mar '22

Hi, Is there an option with the tile command in ChimeraX to get the volumes to rotate in place like it did with Chimera or maybe a different command now that I haven't found yet? Right now when I use Tile the maps rotate together round a single axis, but I liked it a lot in chimera with the tile were the maps rotated on their own axis. Thanks I'm sure it's most likely a command option that I missed in the documentation or a new command I haven't found yet. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Visualizing
by Prathvi Singh 23 Mar '22

23 Mar '22

Hi Elaine, I was wondering whether it is possible to show the axis guides at the bottom left or bottom right side of the screen just like in VMD? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Mac Studio
by Greg Williams 21 Mar '22

21 Mar '22

I just bought a Mac Studio running OS 12.3. I downloaded Chimera 1.16. None of my old .py files will open. The app tells me the files are open, but there’s no content. I can Fetch new files from the pdb, and they work fine. Is this an incompatibility with the new hardware? I know you encourage people to use Chimera X, but I need the vrml export function, so 1.16 is what I have to use. Thank you. Greg Williams

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reading output files (pdbqt) from an external vina dock run back into chimera
by Joern Werner 20 Mar '22

20 Mar '22

Hello is there a way of reading a series of pdbqt files of docked ligands using vina dock externally back into chimera for inspection and analysis? It looks like Viewdock, should do this but I have a directory full of individual ligand files and I don't know how to prepare them so that Listview reads them into an ordered set i.e. ligand1 ligand2 etc. I can read individual ligands fine. Many thanks Joern

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Place Objects output to mrc
by Pranav Shah 17 Mar '22

17 Mar '22

Hi Elaine, Is it possible to convert object instances generated by the Place Objects plugin developed by the Briggs group into mrc maps? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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question on cyclization of peptide
by JESSE JAYNES 15 Mar '22

15 Mar '22

Hi Folks, I have greatly appreciated the access to Chimera, thank you. I need to generate a pdb of a cyclized version of linear 10mer peptide. Is that possible to do in Chimera? Thank you,Jesse

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Re: [Chimera-users] Chimera Help Needed- Wring output of status line to file
by Elaine Meng 10 Mar '22

10 Mar '22

Hello, CCing chimera-users(a)cgl.ucsf.edu (recommended address for questions to ensure it doesn't fall through the cracks... and also because often other people know the answer when I do not)... <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> I guess you are talking about method "b" in that post? I believe the values would also go to the Reply Log in addition to the status line. You can save the Reply Log contents using a bit of python. That is beyond my expertise personally, but fortunately is described at the bottom of this page on basic scripting: <https://www.rbvi.ucsf.edu/chimera/current/docs/ProgrammersGuide/basicPrimer…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 10, 2022, at 5:46 PM, Morais Brown <moraisbrown(a)outlook.com> wrote: > > Hello, > > I followed your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007160.htmla… created a script that get the rmsd values of my residues of interest using a reference structure. How do I record these RMSD values to a file so that I can plot them? I only see them fluctuating in the status line when I play my trajectory. > > Best, > Morais

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Help for USCF chimera
by cindy g 10 Mar '22

10 Mar '22

Good morning, By Uscf chimera I have a complex with an antibody and an antigen. After determining the predicted paratopes and highlighting only their side chains, I would like to identify the side chains of the amino acids of the antigen which are in a zone <5A from the side chains of the predicted paratopes. I don't know how to do it with command lines or anything. Thank you in advance for your help Cordially

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Fwd: Download UCSF Chimera question
by Elaine Meng 10 Mar '22

10 Mar '22

> From: "zhacj(a)163.com" <zhacj(a)163.com> > Subject: Download UCSF Chimera question > Date: March 8, 2022 at 7:03:22 PM PST > To: meng <meng(a)cgl.ucsf.edu> > > Hello, > Dr. Elaine Meng, > This is West China Sceond hospital in Chengdu, China, we need to use Chimera to our scientific research，but now we encounter a difficulty to need your help: > > After we download Chimera from https://www.cgl.ucsf.edu/chimera/download.html <https://www.cgl.ucsf.edu/chimera/download.html>， we cant install and run this software, we Not sure if this downloaded installation package is available, could you please tell me Where to download the correct installation package, or could you please send the correct installation package to me, thats very thank you! > And our system environment is Linux, connda, CentOS. > Looking forward your reply, Thanks again. > Charles Zha > Project Director > zhacj(a)163.com <mailto:zhacj@163.com> > Tel: +86-28-84457808 Mob:+86-13008108764 Hello, All of the download packages and download instructions are already on that page -- make sure you get the one for Linux. I don't know what you mean by "can't install" -- you would need to say more about exactly what steps you tried and what happened. <https://www.rbvi.ucsf.edu/chimera/download.html <https://www.rbvi.ucsf.edu/chimera/download.html>> Forewarding to the chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> address , in case anybody else has helpful comments. Also you have more details to provide about your problem, please send your question to that address. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Information Regarding Accessibility of Chimera
by Scott Heck 09 Mar '22

09 Mar '22

Good morning, I am a member of the IT staff for the Biotechnology department at NCSU, and we are wanting to install and use Chimera for one of our instructors to use in their classes. Prior to student use, I will need to have the software approved by the university, and they require proof of the software being accessible to all students. They specifically ask this in the form of VPAT, WCAG 2.0 Standards or other accessibility documentation. Any assistance you can provide would be greatly appreciated. Best regards, Scott -- *Scott Heck | Pronouns: **They/Them <https://www.mypronouns.org/>* IT Implementation Specialist 1 P: 919.513.1021 Office Hours: M-Th 6am-5pm CALS IT Service Portal <https://ncsu.service-now.com/calsit/> NC State University Campus Box 7572 330 Patterson Hall Raleigh, NC 27695

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Changing distance between two atoms
by Prathvi Singh 04 Mar '22

04 Mar '22

Hi Elaine, I have a PDB file which has two serine residues: SER10.A and SER20.A. The distance between their sidechain O-atoms (OG atoms) is 8.925Å. I want to bring the sidechain O-atom of SER10.A closer to the sidechain O-atom of SER20.A along an imaginary line which passes through the coordinates of these two atoms such that the distance between them gets reduced to 4Å. If I am thinking right, this would also require shifting the rest of the atoms of SER10.A towards SER 20.A in a similar manner. Is it possible to achieve this in chimera? I am attaching a screenshot just for reference. Thanks anyways and regards -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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change aminoacid in sequence alignment
by Jacqueline Vitali 26 Feb '22

26 Feb '22

I have a "residue" KCX (PDB records are Hetatm). In the sequence alignment it comes as X. Is there a way to change it to K without making a PDB file and changing it to K there? Thank you,. Jackie Vitali Cleveland State University

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Average distance between two non-bonded atoms
by Francesco Pietra 24 Feb '22

24 Feb '22

Hi all Is it any command to measure the average distance between two non bonded atoms all over a molecular dynamics trajectory? Ideally linked to examining the trajectory with Tools ... MD/Ensemble Analysis ... MDmovie (I am using psf/dcd) I.e., doing the average of the distance from all frames. Thanks francesco pietra

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Depth-cued view
by Thirumurugan Prakasam 24 Feb '22

24 Feb '22

Hi, I need to make some stacked COF with stacked view with descending order transparency as shown below within the same molecule [image: image.png] from a stacked view [image: image.png] Please let me know how I can select each 2D layer and decrease the transparency while going down. Please help me to make some nice images. Looking forward to hearing from you, Many thanks, Thiru -- 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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Saving segmented regions from EM map not working
by Shruthi Viswanath 23 Feb '22

23 Feb '22

Hello Chimera team, We have a problem with saving segmented regions from EMD 2329 using Segger. When we segment one of the 9 spokes from this EM map and try to do File -> save selected regions to .mrc from the Segger window it displays a box around the selected region (see screenshot) and the saved .mrc file just shows a small blob and does not look like the original selected region. Could it be because of the lower than usual density range of this particular map? Thanks very much Shruthi -- Shruthi Viswanath Reader F (Assistant Professor), National Center for Biological Sciences (NCBS) GKVK, Bellary Road, Bangalore, India 560065 Tel: +91 80 6717-6152 Email: shruthiv(a)ncbs.res.in Web: https://www.ncbs.res.in/faculty/shruthi

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Molecular dynamics simulation plugin
by Enrico Martinez 21 Feb '22

21 Feb '22

Dear Chimera Users, I have a question related to the molecular dynamics simulation plugin integrated into the Chimera. As I understand it correctly, Chimera uses Amber integrated into the GUI. Here are my questions: 1) What are the limitations of this version of MD engine compared to the Amber software, which we may use to run molecular dynamics in terminal? 2)May I increase the integration step to 2 fs (assuming that there are constraints on the hydrogen atoms) during the production phase? 3) how the ligands may be parametrized ? What is the difference between two methods that are used for charges ? 4) Is it really slower compared to Amber ? May I use multi-cpu stations for the run ? I've just made it on my iMAC with 6 available CPUs but would like to try on the 96 CPUs linux station. Yours with thanks Enrico

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Regarding command line
by Aradhya Tripathi 20 Feb '22

20 Feb '22

Hello Sir, I am Aradhya Tripathi, currently working as a Ph.D scholar. I have installed the Chimera 1.15 version but the command line is not working in my workstation. Please give suggestions to solve this issue. I look forward to your valuable suggestions. With regards! Aradhya Tripathi CSIR-CDRI India

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error code -1073741819
by Gregor Schmidberger 18 Feb '22

18 Feb '22

Dear chimera support, I cannot start chimera 1.16 anymore. I attached the error code as png. Do you know how to solve this problem? Thanks a lot! Best regards, Gregor Schmidberger

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how to solve the problem of topology
by Kenji MATSUI 18 Feb '22

18 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 16 Feb '22

16 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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