- Chimera-users - RBVI Mailing Lists

Four letter residue names
by Francesco Pietra 21 Apr '21

21 Apr '21

Hi all A pdb file deriving from a mmCIF file (with chimerax) and comprising both nucleotides and proteins, shows the protein residue names with four characters (i.e., using also column 21), such as ALAM in one subunit, or GLNm in another subunit. I read on passing somewhere (and I am unable to trace that back) that chimera accepts such four character names but was unable to find a description from chimera help. I also got lost in deciphering the intricacies of mmCIF files. What is the scope of the column 21 character? Could that simply be ignored, or deleted, for use with the CHARMM FF? Thanks for advice francesco pietra

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Chimera Errors
by Henry Shook 18 Apr '21

18 Apr '21

Chimera Team, I have been using Chimera to test several Sialic Acid isomers on the Sars-CoV-2 spike protein over the past couple of months and a couple of days ago, I have been getting this error telling me that there was an "application stderr" and "application stdout". Previously to a couple of days ago, anytime I tried to run it during the day, this message would show up, however, I was able to run the docks from 9-12 pm at night without any problem, so I just worked on the docking during that time. Now, no matter what time I run the docks at, this message shows up. I have not changed any procedures from when I started until now. Is there a way I can fix this problem? I attached a screen recording of my procedures and how I arrived at the problem. Here is a link <https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=…> if the video does not load. Thanks! Henry Shook Screen Recording 2021-04-18 at 11.19.06 AM.mov <https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=…>

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ADP EM Chimera plugin
by Eric Pettersen 15 Apr '21

15 Apr '21

Hi Vilde, Since ADP EM is a third-party plugin, I don't know that I know that much more than you about how it works. Hopefully the plugin developers will get back to you. Nonetheless, I can offer some generic advice about seeing/finding the fitted structure. First, check the Model Panel (Favorites→Model Panel) to ensure that the structure model is shown (the "Shown" column for the structure model is checked). Second, type the 'window' command (Favorites→Command Line) to ensure the view is large enough to show the position of the structure. Third, click on the color well in the Volume Viewer panel (the square next to "Color") and adjust the 'A' component of the color (A = alpha, or opacity) so the the contour surface is semi-transparent, in case the structure is completely within a contour. --Eric Eric Pettersen UCSF Computer Graphics Lab > Hello, > > I’m trying to use the ADP EM molecular fitting tool (Chimera Plugin) to fit my PDB-models into a low resolution map. The plugin works as it should, but I’m having trouble visualizing the solutions. Once the fitting is finished (the table with all the coordinates is produced) and I chose for example solution 1, the PDB structure disappears in the Chimera Window. The EM map is still showing. If I click on the “Back to initial”-button, the PDB structure comes back, but in the initial position, of course. I have tried to save the solutions, but they are still not showing (the solutions are selected as “show” as a cartoon in the model panel). According to the description of the plugin developers, the solutions/fits should be visualized just by selecting one, no extra steps needed. > I’m doing something wrong in Chimera or is there a bug? > I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result. > > Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far. > > Best regards, > Vilde Leipart > PhD-student, > > Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences > Høgskoleveien 12, 1430 Ås, Norway > > Honey Bee Research Lab, Arizona Sate University > 427 East Tyler Mall, Tempe, AZ 85287

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Pixel size/box size and map display
by Cynthia Lee Page 14 Apr '21

14 Apr '21

Hi, I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. Can someone set me straight on this? Many thanks, Cynthia

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Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 14 Apr '21

14 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made. 1. Connection to 13.107.4.52 on tcp/80 (www.msftconnecttest.com) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 13 Apr '21

13 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made. 1. Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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combine models
by Francesco Pietra 11 Apr '21

11 Apr '21

Hi (1) I am faced by the coordinates for a nucleics/protein assembly being given in several bundle.pdb, while I need a sequential, continuous pdb file that comprises all nucleotides and proteins, not made of models (2) If I load all the bundles to chimera, I see all expected ligands around the small molecule. (3) With all models selected, copy/combine (adopting default first model as reference and allowing renaming chains) generates a new model. The new model laks some proteins that should lie near the ligand, as described at (2). I feel that I am missing something. Thanks for advice francesco pietra

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greeting and acknowledgement
by kajihara 09 Apr '21

09 Apr '21

Dear Prof. Ferrin, Dear stuff of Chimera, I am prof Yasuhiro Kajihara, Department of chemistry, Osaka University. Last April, Corona pandemic suddenly attack us, and our university closed in-person style classes. I needed to do online class of biochemistry. I recommended students to download UCSF Chimera for understanding protein structure and behavior. The Chimera soft wear was great help for us under the terrible Corona Pandemic and all students enjoy to deal with Chimera. They got unbelievable knowledge through the Chimera. I could not find a suitable word to express my thank. I thank you again for your great support and kindness to deliver it as free. Within a week 80 students will start download chimera. So, I need to send greeting e-mail to give my thanks. Sincerely Yasuhiro Kajihara, Ph. D. Department of Chemistry Osaka University Machikaneyama, 1-1, Toyonaka, 560-0043 Japan kajihara(a)chem.sci.osaka-u.ac.jp

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Where does Chimera copy command save images?
by Martti Tolvanen 09 Apr '21

09 Apr '21

I have tried to use the command copy on command line to save images, with a goal to do that in a script. The messages of rendering a high-res image and image saved come up, but the file is nowhere to be found. My guess is that the default save location is in the Chimera program folder, which would not be permitted, but Chimera just doesn't see it as a failed attempt. I do have a workaround of including the full path in a filename, but I'm just curious where the file would be going by default, and whether there is some command to change the working folder by a command. FYI it's Chimera 1.15 in Windows 10. Martti Tolvanen University Lecturer in Bioinformatics U of Turku, Finland

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Query about adding charge to ligand
by Nirban Dey 19MSM0098 08 Apr '21

08 Apr '21

Hello, I am a Masters student of VIT University India. I am using chimera to prepare my ligand. In the add charge option I noticed that if my ligand has negative or positive charge and I try to add AM1-BCC it gives error but I can add Gasteiger charge. Even if I set charge to +0 for the ligands that have charge like -1 or +1 and try to add AM1-BCC it gives error. I want to know what is the reason that Gasteiger charge can be added but AM1-BCC cannot be added..Kindly help me in this regard. Thanking You Nirban

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