February 2022 - 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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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

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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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Chimera-users February 2022