- Chimera-users - RBVI Mailing Lists

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

2 1

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

2 1

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

2 1

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

2 6

change aminoacid in sequence alignment
by Jacqueline Vitali 27 Feb '22

27 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

2 2

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

2 1

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

2 2

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

3 5

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

2 1

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

2 1