- Chimera-users - RBVI Mailing Lists

desinstallation
by Isabelle Fourré 18 Jul '18

18 Jul '18

Dear Chimera users, How to desinstall correctly Chimera? I forgot to install it as "root" so the executable file has not been copied in my /usr/local/bin directory, and I would like to restart all the process. I did not find any README file... Thanks a lot -- Isabelle FOURRÉ Maître de conférences (Assistant professor) Laboratoire de Chimie Théorique Sorbonne Université (campus Pierre et Marie Curie) 4 place Jussieu | Tour 12-13 4e étage Boite courrier 137 | Pièce 418 75252 PARIS Cedex 05 Tél : 01 44 27 96 59 --

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Movie question
by Yanhe Zhao 17 Jul '18

17 Jul '18

To whom may concern, This is Yanhe Zhao, from ut southwestern medical center. I am making a movie with Chimera, i know how to make it by saving different positions. Now I add 2d label in special position and make it again, no label in movie. Do we have way to copuling the position with our label or another different way? e.g. by saving scenes? The final movie version should have labels fade in and out at different time point. I really appreciate if someone can do me the favor. Best, Yanhe

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Include position from multiple frames in one image
by David Sáez 16 Jul '18

16 Jul '18

Hi, I have a molecular dynamics simulation created using Amber, and I visualize the result in Chimera using MD Movie. I would like to show the wandering of a small molecule inside the active site, but in just one picture. Is it possible to include all the positions sampled by some selected atoms in the exported image? Thanks for your help.

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turning kdssp off
by Mateusz Sikora 16 Jul '18

16 Jul '18

Dear Chimera users, is there any way to turn the secondary structure assignment (kdssp) off? I am transforming a set of coordinates from a MD trajectory into electron density. I collapsed many frames of the trajectory into a single file, meaning there are many unphysical overlaps (I only care about the density). Problem is, that the PDB file I am opening is rather large (couple of millions of atoms) and kdssp gets absolutely stuck on it. I would appreciate some help. Best regards, Matt

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MD movie error
by ChuHui Fu 16 Jul '18

16 Jul '18

Hi all, When I was trying to use MD Movie option on the attached pdb trajectory file, chimera kept telling me that there were missing residues. "Chimera Error Residue 3864.het not in first model on line 126754 of /homes/cfu/model1_sep_475.B_md_traj_system.pdb" But I checked that the number of atoms in each one of the pdb files and there didn't seem to be any missing. Then I separated the trajectory files and use vimdiff to compare the models pairwise, but doesn't seem like there are different residues, (unless I missed them). Can anyone suggest what I might have done wrong? model1_sep_475.B_md_traj_system.pdb <https://drive.google.com/a/haverford.edu/file/d/1w82K6a2FfLDzphcn6Jj2VwCjok…> Thanks!! -- ChuHui Fu B.S.Candidate in Chemistry Haverford College, Class of 2019 cfu(a)haverford.edu

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Coordset and reset bug
by Cristina Paulino 13 Jul '18

13 Jul '18

Dear Chimera team, I just stumbled on a bug that wasn’t present before (not sure from which version on). Chimera gets stuck if you try to make a movie were a specific set of frames of a morph is recalled and at the same time the camera position is reset to save position. Here the specific example that doesn’t work anymore, but did initially: coordset #3 1,61,1 reset morph2 90 wait 90 Now I had to change, so that both movements happen independent. coordset #3 1,61,1 wait 61 reset morph2 90 wait 90 Any change this bug could be fixed? It is a nice feature to be able to keep the morph going while it moves to another saved-position. Best, Cristina ____________________________________________________________________________________ Dr. Cristina Paulino Assistant Professor at the Department of Structural Biology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Faculty of Science and Engineering , University of Groningen Nijenborgh 7, 9747 AG Groningen, The Netherlands Room 5171-0054 Phone: +31 50 363 34 02 Email: c.paulino(a)rug.n <mailto:c.paulino@rug.nl>l https://www.rug.nl/research/electron-microscopy <https://www.rug.nl/research/electron-microscopy> http://www.membraneenzymology.com <http://www.membraneenzymology.com/> ____________________________________________________________________________________

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Delete pseudobonds
by Javier Marchena 12 Jul '18

12 Jul '18

Hi, A pseudobond has been automatically created in one of my structures, because of "missing segments". I want to delete the pseudobond in order to create a real covalent bond between those two atoms. But I have problems with deleting the pseudobond, I have not found a way to do it. Could you help me out? Thanks in advance. PS: I send you the molecule in pdb format just for you to see the pseudobond.

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Output chain sequences
by Healey, Joe 11 Jul '18

11 Jul '18

Hi Chimera Team, I've been experiencing issues with the "Align Chains" tools that connect to Clustal and Muscle - I think ostensibly this might be because the servers are no longer available or something. I'm happy to make the alignments myself, but to do this I'd like to try and simply export the sequences of all open models to a fasta file or similar. I know this can be done manually sequence-by-sequence thtrough the GUI. Could you tell me what the python (or chimera syntax) would be to do this if it's possible? I'm envisaging something to the effect of this, but I can't quite get what I need back in terms of the sequence (it returns a `bound object'?): ``` from chimera import openModels all_mods = chimera.openModels.list(modelTypes=[chimera.Molecule]) with open('output.fasta', 'w') as ofh: for mod in all_mods: ofh.write('>%s\n%s' % (mod.name, mod.sequence) ``` Thanks, Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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Use of sym command
by Lee A.G. 11 Jul '18

11 Jul '18

Hi Elaine I am trying to use the sym command to generate BIOMT-described copies of a protein. As a test I have used 2oli, as in your contribution of 12 Jan 2009. Having loaded 2oli and entered the command sym #0 #0 I get the error message "No symmetric molecule copies". Any help gratefully received Anthony Lee

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3D environment
by Heymann, Bernard (NIH/NIAMS) [E] 11 Jul '18

11 Jul '18

Hi I'm interested in acquiring a PC with capabilities to use ChimeraX for 3D VR visualization of large volumes (2k cube). What is the best configuration (CPU, GPU, VR hardware) for around a $5-10k budget? Bernard

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