- Chimera-users - RBVI Mailing Lists

MD simulation in Chimera : 10 ns simulation is equivalent to 1 million of production steps 10 fs each?
by Giovanni Roviello 29 Jan '21

29 Jan '21

Dear Sirs, I would like to perform a MD simulation by UCSF Chimera. Should I wish to perform a 10 ns simulation (for example) how could I set the parameters related to time? For example in production a number of phase steps of 1000000 and a time step of 10 fs is OK? Does the relaxation time Nosé thermostat has effect on the overall simulation time? In simpler words if I set 1000000 steps, 10 fs time step, and I leave selected Nosè thermostat with 0.2 ps (but leave unselected the barostat option) will it correspond to a 10 ns MD simulation? Of course if I will publish using Chimera I will cite the program and the reference as indicated in https://www.cgl.ucsf.edu/chimera/docs/credits.html Thank you in advance for your kind help. Kind regards, Giovanni _______________________________________________________ Dr. Giovanni N. Roviello, Ph.D. Researcher at Istituto di Biostrutture e Bioimmagini IBB - CNR; Via Mezzocannone 16; I-80134 Naples; Italy giroviel(a)unina.it giovanni.roviello(a)cnr.it http://www.ibb.cnr.it/?command=viewu&id=387&lang=en https://orcid.org/0000-0001-6065-2367

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less color depth possible?
by Cheng, Tat 27 Jan '21

27 Jan '21

Hi all, We are trying to set up cryoEM data processing in the university HPC. We use X2go for remote accessing the HPC, but it doesn't have enough color depth, so Chimera (24-bit) doesn't start. One workaround is to download the volume from HPC to local machine, but it is less convenient. But I wonder is there a way to use Chimera in less color? Thanks a lot. Best, Tat

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how to color an model by an attribute in chimerax
by sunyeping 27 Jan '21

27 Jan '21

Dear all, I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: attribute: entropy match mode: 1-to-1 recipient: residues :1 0.0 :2 0.0014948 :3 0.0090952 :4 0.0004805 :5 0.1102497 :6 0.0095258 :7 0.0008226 :8 0.0042205 :9 0.0037255 :10 0.0006678 :11 0.0027988 :12 0.0193925 :13 0.0153925 :14 0.0052115 :15 0.0020136 .......... However, when I input the command "color byattr attr.txt", I get the following error information: "No known/Registered attribute attr.txt" Could anyone tell me what is the correct way to do this? With many thanks. Best regards

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coloring the volume series
by Arto Pulk 26 Jan '21

26 Jan '21

Dear all, I would like to make a movie using volume series. I have 10 maps (from Relion) that I upload to volume series. Now I would like to color the moving parts of the map. One can use zone coloring, but it does not do the precise job to color specific volumes of the map as it is radius specific. Then there is "surface coloring" by "volume data value". I can make a mask and color the mask region, but it makes the color gradient and I do not have control of the region outside of the mask at it will be mixture of colors. The best way to color is to use "segment map" and then go to "Regions" and "color density map". It does good job to color specific map volumes but the colors are not permanent. If you Play the Volme Series then colors vanish. So, is there any good way to color Volume Series? Regards, Arto Institute of Technology University of Tartu Nooruse 1 50411, Tartu Estonia Dr. Arto Pulk email: arto.pulk(a)ut.ee phone: 58244846

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Chimera RMSD
by Elaine Meng 25 Jan '21

25 Jan '21

> From: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Subject: Chimera RMSD > Date: January 23, 2021 at 11:27:17 AM PST > > Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started. > > Sincerely, > Sharyn Hi Sharyn, You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified. We have a command-line "atom specification" syntax for that kind of thing. There is a longish page with lots of examples here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues. E.g. something like rmsd #0:12.A,57-63.A #1:14.A,59-65.A ... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A. Or to use CA-only or backbone only: rmsd #0:12.A,57-63.A@ca #1:14.A,59-65.A@ca rmsd #0:12.A,57-63.A@n,ca,c,o #1:14.A,59-65.A@n,ca,c,o Of course the numbers could be the same in the two models, I just was trying to give a more general example. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. the chimera-users(a)cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions

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adding chimera-trimmings alias
by Dmitry A. Semchonok 25 Jan '21

25 Jan '21

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command line > vol all surface level 0.1 colour gradient
by Dieter Blaas 20 Jan '21

20 Jan '21

Dear Elaine, please forgive me for asking again, I cannot find your previous mail and my notes: How can I, in command line, do the following, i.e. what is the correct syntax? vol all style surface level 0.1 colour by gradient colours 5 palette rainbow set I have a number of volumes loaded and want to colour their surfaces, at level 0.1 by 'volume data gradient norm' with 5 rainbow colours setting them to the full range Thanks a lot, best Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Coloring peptide bonds in Chimera
by Tynan A. Becker 19 Jan '21

19 Jan '21

Good afternoon, I have been trying to figure out how to color just a single peptide bond between 2 residues in a protein. What I have figured out so far is to show chain trace under actions|atoms/bonds. Then invert the selection (whole protein). This shows the bonds. I can select a residue and color the bond on both sides. But I want to color the bond between 2 residues. If I pick the bond by manual selection, the action|color|choice doesn't work. The manual tantalizingly suggests using the "halfbond" setting or "bondcolor" for the command line. The problem that I encounter is that I can't figure out how to tell the program which bond I want. I've read the "atom specifications" page of the manual and tried every logical combination I can figure to tell the program which bond I want to color. But each time, I get the "mangled atom specifier" error. I was told today that there is a way to do this, but I'm stuck. Any input is welcome. Thank you, Tynan

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Problem with electron density
by Elaine Meng 14 Jan '21

14 Jan '21

Dear Francesco, Probably you just need to use "vop cover" as described in these previous posts: <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html>> <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html>> Details on the "vop cover" command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>> For future: the recommended address for questions is chimera-users(a)cgl.ucsf.edu (CC'd on this message) ... since I'm not the expert in everything (or might be sick or away from work), it's helpful if more people see the question! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Francesco Papi <Francesco.Papi(a)iit.it> > Subject: Chimera: Problem with electron density > Date: January 14, 2021 at 3:03:55 AM PST > To: "meng(a)cgl.ucsf.edu" <meng(a)cgl.ucsf.edu> > > Dear Elaine, > I am using Chimera to get a picture of a small molecule (cif file) in an electron density map (xplor file). My issue deals with the position of some atoms of the molecule in an adjacent unit cell (see attached image) which prevents me to see some atoms within the map. I thought to simply expand the map beyond the cell boundaries and eventually crop the map, but it didn’t work. I have checked different tutorials and the chimera mailing list for troubleshooting but I haven’t found a solution to this problem. Is there something you can think of? > Thank you. > Regards, > Francesco Papi > > Francesco Papi, PhD > PostDoc > Center for Nanotechnology Innovation@NEST > Istituto Italiano di Tecnologia > Piazza San Silvestro, 12 > 56127 Pisa, Italy > Phone: +39 050 509 495 > E-mail: francesco.papi(a)iit.it <mailto:francesco.papi@iit.it> > Skype: francesco.papi.89 >

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Can't open large .bild files
by Hannah Bridges 13 Jan '21

13 Jan '21

Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

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