- Chimera-users - RBVI Mailing Lists

determine angle of rotation among two states
by Sen, Anindito 18 Apr '23

18 Apr '23

Dear All, How can I determine the angle of rotation between 2 states of an atomic model, with one state being somewhat skewed from the other. Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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Doubt regarding the analysis of covalent bonds between the ligand and protein
by Krishna Priya K R 17 Apr '23

17 Apr '23

I am a MSC student working on docking . By using UCSF chimera 1.14 I tried to analyse the H bonds and covalent bonds. Even after following every step for H bond analysis it shows 0 bond and i am not able to find the option to analyse the covalent bond between the protein and ligand. Hope you will help me to rectify my problem. My contact details : 8848890240 Email id : krishnapriyaifs1999(a)gmail.com

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Issues with Chimera
by Bella Carnahan 17 Apr '23

17 Apr '23

Hi! My name is Bella Carnahan and I am a graduate student at the University of Delaware. I am trying to model a small peptide in Chimera 1.17 and keep getting an error message telling me I have a missing file. I have redownloaded the software twice now and have not been able to fix the problem. I have attached a screenshot of the error/any relevant windows. -Bella Carnahan

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Chimera 1.17 release
by Eric Pettersen 14 Apr '23

14 Apr '23

Hello everybody, A new production release of UCSF Chimera (version 1.17) is available: https://www.rbvi.ucsf.edu/chimera/download.html <https://www.rbvi.ucsf.edu/chimera/download.html> Updating to 1.17 is required to continue to use the following tools: BLAST protein, Modeller comparative and loop modeling, and multiple sequence alignment with Clustal Omega and MUSCLE. Due to imminent changes in web services, these tools will soon stop working in older versions of Chimera. Version 1.17 can also fetch UniProt sequences (previously broken by UniProt website changes). Alternatively or in addition, you may want to consider switching to UCSF ChimeraX instead, as it also has tools to run these web services, as well as many new features and enhancements. https://www.rbvi.ucsf.edu/chimerax/index.html <https://www.rbvi.ucsf.edu/chimerax/index.html> Note that Chimera 1.17 includes an export-to-ChimeraX feature, as detailed in the release notes: https://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.17.html <https://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.17.html> Enjoy!

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Chimera cannot read multi-molecules .xyz files in
by Francois Berenger 09 Apr '23

09 Apr '23

Dear list, I can read one molecule fine in .xyz format using chimera. However, if my .xyz file has several molecules (like a MD trajectory), chimera fails to read it in. Is there planned support for MD trajectories given as .xyz file? I have chimera-1.16. I shall test with ChimeraX very soon. Regards, F.

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Aligning homdimers
by James Nettles 04 Apr '23

04 Apr '23

I’m asking a question that has been asked and answered before in 2009 - but not with exact solution that I would like. I have a relatively small homo dimer( <200 residue) and would like to fit with a homo dimer of the almost same sequence but slightly different conformations. I would like to fit the dimers as a pair (A/B to A/B) rather than A to A and B to B separately. In other word, I’m wanting to spread the deviation across both monomer units of the dimer in a single step rather than fitting separately and then recombining. I know Chimera isn’t formally supported any more, but I’m running this on an old machine with an old OS , so ChimeraX isn’t an option here. Thanks so much in advance - this group has always bee fabulous over the years. Best regards, Jim

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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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