March 2023 - 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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Chimera when saving as ray
by Shona Hepworth (CHE - Postgraduate Researcher) 30 Mar '23

30 Mar '23

Hello, When I try to save my image by ray tracing it has the following in the reply log. Is this an issue? It is also taking a very long time - I assume this is because I have set surface transparency to 90% but is there anything I can do to speed up the saving as a ray? I tried saving as chimera but the image quality isn't as good. [cid:3D248385-806F-44B1-9B22-478D459DFF1C] Thanks in advance, Shona

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Energy minimization
by Nedra Rached 27 Mar '23

27 Mar '23

Hello; I attempted to do energy minimization on my protein but i get this error message when i try to run it: AttributeError: '_molecule.Atom' object has no attribute 'gaffType' So, could you please help me to resolve this issue Best regards

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Select close residues by name
by Marco Sette 23 Mar '23

23 Mar '23

Dear all, I have a series of pdb files and I would select particular regions that contain specific residues, for example KAYFPG, of which I do not know the exact position in the sequence. Actually I open the sequence window and search for the sequence but this is time consuming if you have multiple pdb. Is there a command to shorten this search? Using the select command seems not possible as I can select all residues of a particular amino acid and not neighbour residues by name. Thanks for your help, Best Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette

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Restoring the original numbering of the amino acids of a chain after a Loop Modeling
by svle＠tiscali.it 20 Mar '23

20 Mar '23

Hi, after a modeling a missing loop in a chain of a protein the amino acid numbering has been shifted by -1 due , I guess , to the "no corresponding structure residue" that I read in the status bar of the panel for Tool --> Sequence --> Sequence in the first position. The catalytic triad of interest now has positions X-1 , Y-1 and Z-1 instead of X,Y and Z. It is possible to restore the original numbering? Thanks. Saverio VOUCHER CONNETTIVITÀ per P.IVA e PMI: internet a canone 0 per 48 mesi. ATTIVA ORA https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

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ligand
by José Manuel González Hernández 19 Mar '23

19 Mar '23

Hello, Is there a way to change features such as width and height of a ligand instead of the ribbons? Thanks, José

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Re: [Chimera-users] Delete pseudobonds
by Justin Prado 17 Mar '23

17 Mar '23

Good evening, I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you. Thank you Justin Prado

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Chimera Deployment to several MacOS Computers
by Sonny Mei 15 Mar '23

15 Mar '23

Hello, I hope all is well! I am trying to deploy Chimera into several computers and do not want to manually do this. I decided to write a script and was wondering if there is a direct download link? The link I found on your site requires users to accept the license before the dmg file is installed. Thank you, Sonny Mei -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

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Creating discs
by Prathvi Singh 14 Mar '23

14 Mar '23

Hi Elaine, Is it possible in chimera or chimeraX to create such planes for membrane proteins which show the plasma membrane boundaries as shown in: https://www.cgl.ucsf.edu/chimera/ImageGallery/framedD3R.html If yes, then kindly tell me how to do it. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Query colors?
by Esser, Lothar (NIH/NCI) [E] 13 Mar '23

13 Mar '23

Hi, in my current project I am reading about 50 pdb files. Chimera does a good job at assigning pleasant colors automatically and I would like to get access to the chosen colors to write 2dlabels with the same color. How do I get access to the molecular (ribbon color) ? It's probably trivial but well, I somehow could not figure this out. Thanks, Lothar Dr. Lothar Esser National Institutes of Health 37 Convent Dr. Rm2122B Bethesda, MD 20892

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Chimera-users March 2023