- Chimera-users - RBVI Mailing Lists

Apple M1 chip
by 163 11 Feb '21

11 Feb '21

Hi There, Is there a version that is suitable for Apple M1 Mac? I found the old version is quite on M1 Mac. Thanks! ML

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Re: [Chimera-users] Creating new models from existing crystal structures
by Elaine Meng 08 Feb '21

08 Feb '21

You're welcome, I'm glad you figured it out! Elaine > On Feb 8, 2021, at 2:40 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > > Hi Elaine > Nevermind, I found my error. I tested the Join Model tool with 1AV1 which has four chains and I was able to correctly pick the correct C and N atoms to join residue segments from each chain. The select command that I had written originally wasn't right so it was picking the correct atoms to join. > Thanks for your help. > Best > Tiglath > > > On Feb 8, 2021, at 2:27 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > If the residue is already in a peptide bond, you can't add another peptide bond. You would have to delete the rest of the chain after 130 in one copy of the model and the rest of the chain before 131 in the other copy for it to make sense. > > > > Also, make sure that your "select" command is selecting exactly two atoms, 1 from each model. > > > > Elaine > > > >> On Feb 8, 2021, at 1:53 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > >> > >> Hi Elaine > >> > >> I've been using the biological assembly of 3R2P and I'm thinking that the reason why it's not working is because both chains are labeled A. I'm just following a paper where they're building a monomeric structure using the residue fragments but in their case the biological assembly of 3R2P is labeled as chain A and chain B. > >> From: Elaine Meng <meng(a)cgl.ucsf.edu> > >> Sent: Monday, February 8, 2021 1:01 PM > >> To: Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> > >> Cc: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > >> Subject: Re: [Chimera-users] Creating new models from existing crystal structures > >> > >> Hi Tiglath, > >> If you just opened 3r2p one time, you only have one model. Join works on bonding two separate models. Also it contains only chain A (there is no chain B in this structure) and residue 130 in chain A is already bonded to residue 131 in chain A. So I do not understand what you already did to modify the structure(s) before joining, or what you are trying to do now, sorry. > >> > >> You could send a session file if you want. > >> Elaine > >> ----- > >> Elaine C. Meng, Ph.D. > >> UCSF Chimera(X) team > >> Department of Pharmaceutical Chemistry > >> University of California, San Francisco > >> > >>> On Feb 8, 2021, at 12:35 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > >>> > >>> Hi > >>> > >>> I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process. > >>> > >>> • Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B > >>> • Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130@N#1:131@C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment) > >>> • Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate. > >>> I don't understand what the issue is. Is the command that I've written wrong? > >>> > >>> I would be very glad for your help. I can provide the pdb files of the residue segments if necessary. > >>> Thanks > >>> > >>> Tiglath > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Creating new models from existing crystal structures
by Moradkhan, Tiglath A 08 Feb '21

08 Feb '21

Hi I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process. 1. Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B 2. Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130@N#1:131@C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment) 3. Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate. I don't understand what the issue is. Is the command that I've written wrong? I would be very glad for your help. I can provide the pdb files of the residue segments if necessary. Thanks Tiglath

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Re: [Chimera-users] Video tutorials
by Tom Goddard 04 Feb '21

04 Feb '21

Hi Cynthia, Ok, I converted all the Chimera video tutorials (about 40 of them) to use standard web browser video playback. https://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html <https://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html> Thanks for pointing out that they were using the obsolete Flash plugin for movie playback. Tom > On Feb 4, 2021, at 10:29 AM, Cynthia Page wrote: > > Hi Tom, > Do you all have any plans of porting the tutorial flash videos to another player? I see there are some YouTube videos available for Chimera but I am thinking of the tutorials that are available on the website. > Maybe there is another source of video tutorial I am unaware of? > > Thanks very much, > Cynthia Page > CU Boulder > > Sent from my iPhone >

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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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APBS
by mailman-bounces＠cgl.ucsf.edu 12 Jan '21

12 Jan '21

From: benjamintam <benjamintam(a)um.edu.mo <mailto:benjamintam@um.edu.mo>> Subject: APBS Date: January 11, 2021 at 7:28:44 PM PST To: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> Dear All, I can see that we have to run the APBS locally, however, which default execute file that I need to select in the Chimera in order to run APBS? Best, Ben

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view along a crystal axis
by Michael Elbaum 11 Jan '21

11 Jan '21

Hi. I would like to view a lattice of molecules generated by "Unit Cell" along a given axis. Is there a way to set the view accordingly, say along a, b, or c axis? Other than showing the I'm showing the outline box and eye-balling, but probably there's a more precise way to do this. thanks for your help, Michael

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Identifying type of interaction
by nitya yerabandi 09 Jan '21

09 Jan '21

Hi, I'm using UCSF Chimera right now to analyze the contact residues between two proteins, Hsp70 and BAG3. I have created a distance monitor table on chimera that shows residues, atoms, and the distances between them. I am now trying to identify the type of interaction between each pair of atoms, like polar, nonpolar, hydrogen,etc. However, I am having difficulty doing this. I was wondering if you could assist me with this. Thank you, Nitya Yerabandi

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command line "vol all style surface plane z,60,8
by Dieter Blaas 08 Jan '21

08 Jan '21

Hi, I am trying to display a volume (128 px box) sliced through the middle as seen down the z axis but 8 slices thick instead of just one. I can render a single slice with "vol #0 style surface plane z,64" but I could not find out how to make it e.g. 8 slices thick. In VolumeViewer there is the parameter 'Depth' but it is not accepted as parameter in the command line! Rater, adding one more number at the end of the command starts playing a movie of one slice after the other.... Thanks a lot for hints, bw 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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Make a new pdb model from a part of pdb file
by C.J. 07 Jan '21

07 Jan '21

Hi, I have a pdb with a A chain of 1000 amino acids. How can I make a new model with a part of A chain (i.e. 500 amino acids) using command line? Thank you! Best, Jianhao

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(no subject)
by Hemapriya Kumar 07 Jan '21

07 Jan '21

While clicking on the fetch, its getting like certificate no verified as command -- With Regards Hemapriya Kumar

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RMSD after superimposition
by Subhabrata Majumder, PhD 07 Jan '21

07 Jan '21

Dear Support, I have recently started using chimera_ucsf. I was trying to look at Calpha RMSD list after superimposition two conformation of a particular protein. Do you know where should I get the list after superimposition? Thanks, Subhabrata -- Subhabrata Majumder, PhD Assistant Professor Biophysics & Structural Genomics Saha Institute of Nuclear Physics HBNI Sector 1, Block AF Saltlake Kolkata -700064 India Email subhabrata.majumder(a)saha.ac.in ; subhabrata.sinp(a)gmail.com

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Deleting lipid molecules
by Moradkhan, Tiglath A 04 Jan '21

04 Jan '21

Hi I've built a lipid particle containing 252 molecules and I'm trying to randomly delete 20 lipid molecules. Does the delete command allow this? I've tried using it but it doesn't seem to work for this case. Thanks Tiglath

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Re: [Chimera-users] betacavity web and chimera
by Elaine Meng 03 Jan '21

03 Jan '21

On Jan 2, 2021, at 10:42 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Hi Elaine, > is there a way to incorporate in chimera the option to read cavities from betacavity web (Nucleic Acids Res 2015 vol 43 W413-W418) ? Right now you do it for CASTP. > Please let me know. > THank you. > Jackie Vitali > Cleveland State University Hi Jackie, Unfortunately we don't have resources to provide visualization capability for the many useful web servers that exist. A related server with Chimera visualization capability is MOLEonline: <https://mole.upol.cz/> I hadn't heard of betacavity before. In general it would be useful to say or give examples of what outputs they do provide, to give some idea of whether it might be possible... I had to run it myself to figure that out. Looks like they just give Jmol visualization in the web browser and a script for Pymol. Maybe you could ask the authors of betacavity if they would also provide a Chimera script too, but it's probably unlikely. I also see they give lists of atoms on the right side of the results page, but not in PDB format. You could try manually showing surface for those atoms in Chimera (with a Chimera command) but it would be (1) tedious, and (2) just the molecular surface of those atoms, so there may be jagged edges and bits sticking out, not a nice enclosed blob as in their Jmol visualization. Our Castp visualization has this same issue. E.g. for 2gbp I get in the betacavity results: VOID 3 VOID-VOLUME 8.468 A^3 VOID-BNDRY-AREA 41.050 A^2 VOID-DEFINING-ATOMS 27 ATOM 131 CE1 PHE A 16 0.064 A^2 ATOM 689 CA ASN A 91 0.978 A^2 ATOM 691 O ASN A 91 3.921 A^2 ATOM 695 ND2 ASN A 91 1.857 A^2 ATOM 705 N GLU A 93 0.796 A^2 ATOM 709 CB GLU A 93 1.116 A^2 ATOM 713 OE2 GLU A 93 1.118 A^2 ATOM 829 CE2 TYR A 107 0.001 A^2 ATOM 831 OH TYR A 107 5.812 A^2 ATOM 840 CA GLY A 109 0.897 A^2 ATOM 843 N THR A 110 0.696 A^2 ATOM 846 O THR A 110 1.145 A^2 ATOM 848 OG1 THR A 110 2.830 A^2 ATOM 849 CG2 THR A 110 2.985 A^2 ATOM 863 OG SER A 112 2.918 A^2 ATOM 1174 CE1 HIS A 152 0.504 A^2 ATOM 1180 CB PRO A 153 2.424 A^2 ATOM 1182 CD PRO A 153 0.061 A^2 ATOM 1183 N ASP A 154 0.007 A^2 ATOM 1188 CG ASP A 154 1.146 A^2 ATOM 1189 OD1 ASP A 154 3.493 A^2 ATOM 1190 OD2 ASP A 154 1.781 A^2 ATOM 1944 OD1 ASN A 256 0.193 A^2 ATOM 1945 ND2 ASN A 256 0.811 A^2 ATOM 1982 OE1 GLN A 261 2.372 A^2 ATOM 2240 OH TYR A 295 0.069 A^2 ATOM 2356 O1 BGC A 310 1.045 A^2 ...and then in Chimera I could open 2gbp surf :16@ce1:91@o,nd2:93@n,cb,oe2:107@c32,oh:109@ca:110@n,o,og1,cg2:112@og:152@ce1:153@cb,cd:154@n,cg,od1,od2:256@od1,nd2:261@oe1:195@oh:310@o1 ...where the surf command is all one line although the mail program may break it up. (Or you could have multiple surf commands for subsets of those atoms.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Accession number
by Yasmeen Nasr 31 Dec '20

31 Dec '20

Hello there, This doesn’t seem very much chimera related but I hope someone could help me out. I’m trying to use phD-SNP server and SNP&GO server and they require a Swiss prot code and a uni-prot accession number respectively. Does anyone know where I retrieve such numbers for SNPs? Thank you in advance. Yasmeen Abdulhadi Sent from my iPhone

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Clustering saving PDB
by Lorena Roldán 28 Dec '20

28 Dec '20

Good afternoon, I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name) which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. However, this script is not working, and I would greatly thank any help you could provide me with. Lorena. -- <http://www.uab.cat> Lorena Roldán Martín *PhD Student in Bioinformatics* Departament de Química Unitat de Química Física Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 690799431 www.uab.cat <http://www.uab.cat> <https://orcid.org/0000-0002-6902-8285><https://www.linkedin.com/in/lorena-roldan-biomedica/>

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Density map tranformation
by Ahmad Khalifa 22 Dec '20

22 Dec '20

Hello, When I fit two maps into each other, I get the transformation matrix in the reply log, but what if the moving map doesn't converge by fitmap and require some initial manual alignment, how can I calculate the transformation matrix for that? Best regards.

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Movies and Symetries
by Stéphane DUQUERROY 21 Dec '20

21 Dec '20

Hi, I generated a set of coordinates in a single PDB file for a movie (coord flanked by MODEL / ENDMDL tags) I can read it and play it with MD movie menu The PDB File has also BIOMT matrices set for displaying the biological assembly My question is how can I play the movie with multiscale model? How Can use automatically the color zone tool to color various protomer instances for all intermediate conformations? (The only way I know for doing that is to generate and select all sym instances but they moved with each of the models!) S Duquerroy -- -------------------------------------------- Duquerroy Stéphane, PhD, Assistant Professor, Univ Paris Saclay Structural Virology Unit, Institut Pasteur 28 rue du Dr Roux, 75015 Paris - France 33 - (0) 140 613 575 --------------------------------------------

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Holiday greetings from the ChimeraX team!
by Elaine Meng 18 Dec '20

18 Dec '20

The Chimera(X) team at the UCSF RBVI wishes you a safe and happy holiday season! Our holiday card is virtual this year: =-=-=-=-=-= Atoms of Apoferritin At a miraculous 1.22 Å resolution, the electron microscopy map of mouse apoferritin (right, EMDB 11638) can be mistaken for an atomic model (left, PDB 7a4m), with each atom standing out. The map from Nakane et al. (2020 Nature 587:152-156) shows glimpses of the lightest atoms, hydrogen, directly revealing the hydrogen-bonding network. Ferritin stores iron, as many as 4500 ions (Fe3+), as crystallites within its shell of 24 proteins. Apoferritin, ferritin without its iron cargo, has rock-like stability, making it ideal for divining the limits of electron microscope resolution. The images were made with UCSF ChimeraX, using ambient-occlusion lighting, coloring to delineate trimeric subunits within the dodecahedral shell, and curved helix tubes. Best wishes for a happy and healthy 2021! Conrad, Greg, Elaine, Tristan, Tom, Scooter, Eric and Tom =-=-=-=-=-= Full-resolution image: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png>> Gallery of previous cards back to 1985: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html>>

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Create an atom object
by Yasser Almeida 15 Dec '20

15 Dec '20

Hello, How can I create an atom object, with a given xyz coordinates, via command or python? Thanks in advance, Yasser

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Volume information from segmentation data
by Juleen Dickson 14 Dec '20

14 Dec '20

Good Morning Everyone, I fear the answer to my question is probably 'no' but I wanted to ask the experts first. I have segmentation of vesicles that I did from a cryo-EM tomogram that I did in EMAN2. I can open the segmentations and view them in chimera, however, I wanted to find a way to extract volume and surface area data on the segmentations so I can do statistics on them. If I use the Volume--> Measure and color blobs, the individual blob information will show up in the log. I am not sure if this information is accurate. Is there away to do this for all of the vesicles and download the data, maybe with the volume--> Segment map? If so, how do I do it? Thanks for your help. Cheers, Juleen "Never interrupt someone doing what you said couldn't be done." *--Amelia Earhart, American aviator* "Friends... they cherish one another's hopes. They are kind to one another's dreams." *-- Henry David Thoreau* *“Life isn’t about waiting for the storm to pass. It’s about learning how to dance in the rain…” -Vivian Greene*

2 1

Can't open IMOD .mod file
by Luiza Mendonça 12 Dec '20

12 Dec '20

Good morning, Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help. Best, Luiza Mendonca Zhang Lab University of Oxford

3 3

scaling models
by Rani Wiswedel 12 Dec '20

12 Dec '20

Good day, Is there any way to ensure that the scale you are looking at is kept constant when taking images of different models? I would like to include photos of pores from my structure, but each pore is saved in a different file, so I have to re-open Chimera and adjust the view each time. I have the scale bar open and the projection set to orthographic, but I am struggling to manually adjust the view so that the scale bar looks the same length in each picture (attached below is my manual attempt (pic1)). Is there any way to set the scale each time chimera is opened so that I don't end up with pictures that have scale bars that appear to be different sizes?(example of what I would like to achieve is in the second image(pic2)) Thank you! Regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

2 1

Using UCSF Chimera inside python environment
by Jeff Saxon 10 Dec '20

10 Dec '20

Dear Chimera Users, I would like to use chimera to do some calculations on PDB filles (mainly I am interesting to cluster conformations in multi-model PDB using Ensemble cluster) Could you explain to me how I could install chimera (I am using python3 with conda) in order that I could use some of Chimera's functions directly inside of my python scripts? I have already tried install package pychimers but did not succeed conda install -c insilichem pychimera nsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0'] - pychimera -> python[version='3.4.*|3.5.*'] Your python: python=3.8 May I use chimera with my python using alternative ways of installations? Thank you in advance! J.

3 3

Chimera and All-in-One system tune up tools
by Nagy Milan 09 Dec '20

09 Dec '20

Hello, how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. Greetings Milan

2 4

Failure Running ANTECHAMER
by Eric Choi 04 Dec '20

04 Dec '20

To whom it may concern, My name is Eric Choi and I am currently a student at Ithaca College doing research about virtual ligand screening where I utilize programs like Chimera and Dock6. In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC database) by adding hydrogens (using the "steric only" method and "unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program, which predicts potential binding geometries and interactions of a molecule to a target protein. When I add hydrogens and charges to individual ligands (downloaded from the ZINC database), it works fine. However, when I downloaded different subsets of molecules (containing 100 ligands to 2000 ligands), an error message popped up saying that ANTECHAMBER failed to run (please see screenshots below). What does this mean? Is there any way that I can fix this issue? If a certain ligand is causing this problem, is there a way to see which one it is? Thank you very much for your time and help. Sincerely, Eric Choi

3 2

downtime on Monday, December 7, 2020
by Elaine Meng 03 Dec '20

03 Dec '20

Dear Chimera and ChimeraX users, We will be doing some system maintenance on Monday, December 7. During this downtime, which we expect to last one day, the Chimera and ChimeraX websites, downloads, e-mailing lists, and several web services accessed by the programs will not be available. Apologies for any inconviences this may cause, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

pythonw.exe always run new windows
by gb1995＠zju.edu.cn 03 Dec '20

03 Dec '20

After installing and opening the UCSF chimera software, pythonw.exe keeps popping up new windows, causing it to fail to work normally.I have tried to download various versions of UCSF chimera software, and found that it cannot be used when installed on the D drive and can only be installed on the C drive. But after the installation is complete, double-click to open it, and various interfaces will pop up continuously. At the same time, Microsoft Edge will pop up web pages continuously, causing the software and computer to fail to work normally.

2 3

label position
by Ruchika 02 Dec '20

02 Dec '20

Hi Elaine I selected alpha carbon of some specific residues and labeled them using label option (one letter specifier + number) in actions menu. After labeling these residues and setting these fonts, some of the labels are overlapping onto one another. I used following command (setattr m residueLabelPos 2) to place them on the alpha carbon. However, they are still overlapping. I am just wondering if there is any other way to separate the label and not overlap on each other. Please let me know. Thanks !! Regards Ruchika

2 1

(no subject)
by Prabuddha Bhattacharya 26 Nov '20

26 Nov '20

Dear Sir Can you help me with a step by step tutorial to find out the electrostatic potential map of a molecule on chimera? Thank you Best regards *Dr. Prabuddha Bhattacharya *

2 2

Error message
by Kaitlyn Merrill 22 Nov '20

22 Nov '20

Hi there, I have been using Chimera and Autodock Vina through Chimera and started getting this error message whenever I attempt to use the Autodock Vina to dock a ligand. Can you please tell me how to fix this? Thanks, Kaitlyn

2 1

Re: [Chimera-users] [chimera-dev] Problem with Matchmaker tool
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Tiglath, (1) 1av1 is not a dimer. It is a tetramer, 4 copies of the same peptide, chains A,B,C,D. See: <https://www.rcsb.org/structure/1AV1> (2) Matchmaker is working correctly, but you have to choose "Specific chain of reference structure" (not "Best-aligning") and then specify exactly which chain of 1av1 you want as the Reference. You have to use it twice, so that you can match #0 to one reference chain and #1 to a DIFFERENT reference chain. Otherwise they will both go to exactly the same place because they will match the same chain, which I guess is what happened to you before. Actually, maybe you need to use it four times with four copies of your model if you expect to get something that looks similar to 1av1. The chimera-users(a)cgl.ucsf.edu address is recommended for "how to use" questions, so I'm CC-ing it here. The chimera-dev list is more for programming questions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 20, 2020, at 5:17 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > > Hi > For some reason I'm not able to use the matchmaker tool to build a dimer model of the protein I'm studying. Here are the steps that I use: > > • I open twice the monomer model > • Then I open the dimer template, then click on the Matchmaker tool. > <image.png> > 3. In the Reference structure panel I click on the dimer template (1AV1) > 4. In the Structure(s) to match panel I click on monomer#0 (Human Monomeric Apo A-I, the protein I'm studying) then click OK > 5. Then I click on monomer #1 followed by OK > > But when I close the dimer template I get back the monomer not the dimer model of the protein. I'm not sure what I'm doing right. > Thanks > Tiglath

1 0

Question on aligning one molecule to two other molecules
by Doc Deldou 18 Nov '20

18 Nov '20

Dear Chimera team, I am trying to perform a "manual" docking of a DNA molecule in a protein structure using homology with proteins structures resolved with DNA. I know that the first part of my protein (the recognition domain) is similar to one structure and the other part (the cleavage domain) is similar to another one. So I built a dsDNA with the recognition sequence of my target protein and I first aligned it with the DNA of the similar recognition structure using the phoshore groups, then I matched aligned my protein structure to the protein part of the similar recognition structure. After that I matched aligned my protein to the similar protein cleavage domain bringing the DNA molecule with it. And now ideally I would like to align the DNA part with the DNA of the similar cleavage domain but keep the first recognition part of my DNA more or less at the same position. So I tried to align another copy of my DNA to both DNA molecules but I don't think it is possible. Do you have a trick or a command I could use to reach my goal? I'm using Chimera X. Below is what I obtained, in green my target protein, in purple the DNA I first aligned relatively to the DNA of my similar recognition structure, in "pink" the DNA strand of the similar cleavage structure with the bond to be cleaved in yellow, and the dsDNA with all the colored nucleotides is the one I am trying to position in between the two site with also the bond to be cleaved in yellow. I tried to rotate it and translate it manually to have something in between but some DNA parts are clashing with the protein part and I would like to have something the more accurate possible. [image: manualdocking.jpg] Best regards, -- Adèle Dramé-Maigné @Docdeldou Docteur en Biochimie et Instagrammeuse Blog: http://bit.ly/2zkiPWI LinkedIn: http://bit.ly/2afmtEq

2 1

Saving representives from ensemble cluster
by James Lloyd 18 Nov '20

18 Nov '20

Hi, I have a few Gromacs trajectories (just protein in solvent) which I have clustered using the ensemble cluster tool. I want to save each representive model from each cluster. However I am unsure whether these representive models need to be saved relative to another model (this option was ready ticked). Since I want to use each file separately with VinaDock, would unticking this option be wise? Thanks This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

2 2

Re: [Chimera-users] Saving Image of row stereo
by Tom Goddard 17 Nov '20

17 Nov '20

Hi Divita, I see. If you want to depict that a molecule can be in various positions a better approach is to actually open 2 to 4 copies of it positioned slightly differently, maybe showing the copies as transparent. Another approach is to save 5 copies of the image where you move the variable molecule a bit for each, then blend the images in Photoshop or Gimp. Tom > On Nov 17, 2020, at 10:14 AM, Divita Mathur <dmathur4(a)gmu.edu> wrote: > > Thanks for your response, Tom. I guess I should tell you what I am trying to achieve. > > The row stereo image is interesting to me as it can be interpreted as a “vibrating” or “shaky” molecule (check attached). I want to represent that the green dye (and perhaps the underlying pink scaffold) is shaking and it is not constrained enough. Is there a camera setting that you can recommend? > > The screenshot has these horizontal lines which I suspect have something to do with the quality of my computer screen. > > Best, > > -- > Divita Mathur, PhD > Research Assistant Professor > George Mason University & > Center for Bio/Molecular Science and Engineering > Naval Research Laboratory > (202) 767-0687 (Office) > From: Tom Goddard <goddard(a)sonic.net> > Date: Tuesday, November 17, 2020 at 12:58 PM > To: Divita Mathur <dmathur4(a)gmu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Saving Image of row stereo > > Hi Divita, <> > > I don't think Chimera can save the row interleaved image. Such an image is not very useful since it would have to be positioned on a row interleaved stereo display (e.g. Zalman) with no scaling to appear 3d since even rows give one eye image and odd rows the other eye image. Your best bet would be to try a screen capture program. > > Tom > > > >> On Nov 16, 2020, at 6:23 PM, Divita Mathur <dmathur4(a)gmu.edu <mailto:dmathur4@gmu.edu>> wrote: >> >> Hi all, >> >> I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image? >> >> Regards, >> Divita Mathur >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://secure-web.cisco.com/1xK9pP0Vy3veE9y4SgXHuL5DpartYSf6j9ncrP3zwdNXWs…> > > <Screen Shot 2020-11-16 at 9.30.16 PM.png>

2 1

POV-Ray surface color
by Greg Williams 17 Nov '20

17 Nov '20

I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel. Where in the literature should I read to sort this out? Thanks!

4 4

Color marker and bonds
by karine.gouriet 17 Nov '20

17 Nov '20

Dear all we want to correspond the marker color with the bond color. here the bond color is the angle of the scalar product of the bond line and another vector. It is possible to change the marker color by the bond color and not the inverse ? Thanks a lot for your help. PS: I joint the file.py corresponding to the modification of rgba function we want. -- -------------------------------------- Karine GOURIET Maître de Conférences tel : 03.20.43.43.98. Unité Matériaux et Transformation CNRS UMR 8207 - Université de Lille 1 Bat C6, Bureau 213 59655 Villeneuve D'ascq http://umet.univ-lille1.fr/ --------------------------------------

2 4

Saving Image of row stereo
by Divita Mathur 17 Nov '20

17 Nov '20

Hi all, I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image? Regards, Divita Mathur

2 1

icosahedral annulus
by Pranav Shah 17 Nov '20

17 Nov '20

Hi Elaine, i was wondering if there was an "easy" way to create an icosahedral ring-mask using chimera's shape and mask commands. At the moment, I am creating two icosahedral shapes of big and small radii and them subtracting the small one from the big one, but this results in inconsistent results i.e the mask does not enclose the volume I wish to cover. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 2

Chimera morph map multiple volumes
by Ahmad Khalifa 15 Nov '20

15 Nov '20

Is there a way to morph multiple volumes into a single movie? I tried morphing two maps first with the hope that I can do another morph between the resulting morph and a third map, but it didn't work. Any suggestions or easy alternatives to join the morphs together? Thanks.

2 4

solvent exposed surface area
by Jordan Alexis Gewing-Mullins 15 Nov '20

15 Nov '20

Hi there! I hope you're doing well. I am trying to calculate the solvent exposed surface area for each amino acid in a protein, and from the tutorial it says that once I create a surface it should automatically generate a text file with the areaSAS information, but I have no clue where to find that file. Where does it get saved? Thanks, Jordan

2 2

zone & segname
by Francesco Pietra 15 Nov '20

15 Nov '20

Hello Working with charmm36, therefore with the great aid of segname for my homotrimer, when commanding sel :27.M z<3 I get also a water molecule, with O-atom Tip3 3687.W OH2 Is there any way to extend the above command in order to have the segname associated with this water residue? This is because there are eight 3687.W residues with different segnames. I tried to solve indirectly the problem with sel :3687.W@/pdbSegment=WT# where # ranges from 1 to 8 (i.e., the same residue name for segname WT1 to WT8). Contrary to my expectations, it does not work The same with sel :3687@/pdbSegment=WT# Thanks for advice francesco pietra

2 2

help
by Rayna L. DeChance 13 Nov '20

13 Nov '20

Hi, I was wondering if you knew how to cut out (clip) a part of the protein and save the remaining part as a PDB file. I attached the file I was working with that has the two proteins that are aligned together and we want only a certain part of this alignment to be clip. Thank you

2 5

distance with homotrimer
by Francesco Pietra 12 Nov '20

12 Nov '20

Hello I am trying to measure (from command line) the distance between atom NH1 in residue 27, chain M atom OG1 in residue 215, chain A command distance :27@NH1 :215@OG1 error: 6 atoms were selected. The error message is correct because the system is a homotrimer. My question: any way to specify the chains? Any of my attempts failed. Thanks for advice (getting distances from the command line would be quicker that graphically as I have a large number of disnces to measure)

2 2

I tasser models
by Sitbon, Yoel 10 Nov '20

10 Nov '20

Hello, I hope you are doing well. I obtained prediction models from I tasser and would like to visualize them on chimera. I was able to open them but i cannot open the sequence of amino acids. Do you perhaps know how to look at them? Thank you Yoel Get Outlook for Android<https://aka.ms/ghei36>

2 2

Fw: Chimera can't open files
by Cain, Cheryl A 09 Nov '20

09 Nov '20

Please see the question below. Thanks, Cheryl Cheryl Cain cheryl.cain(a)ucsf.edu Operations Coordinator, Department of Pharmaceutical Chemistry Accreditation Project Coordinator, School of Pharmacy UCSF ________________________________ From: Jie Yang <jieyang(a)scripps.edu> Sent: Monday, November 9, 2020 4:12 PM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Subject: Chimera can't open files Hi there, I have a problem that my Chimera can’t open/fetch .PDB files in my Mac(see attached). I believe the problem was because I accidentally denied access of Chimera to the Users/jieyang/Downloads. Could you let me know how should I reverse this? Thank you very much! Best Jie Yang [cid:8ef2ed16-18af-4541-aeab-3a4697900cb5]

3 2

reset all models to the same center of rotation
by C.J. 06 Nov '20

06 Nov '20

Hi Chimera community, I have several models, both maps and pdbs, aligned. But the common center for rotation is far away from the model when I use "Volume Eraser". How can I reset the center for all models in command-line way? Thank you! Jianhao

2 1

Re: [Chimera-users] PDB fetch broken
by Tom Goddard 05 Nov '20

05 Nov '20

Hi John, Try using the "Ignore any cached data" in the Chimera menu File / Fetch... panel. I suspect Chimera cached a bad file when the fetch was broken. If you use this ignore cached data option it will fetch a new copy of the file. Unfortunately when RCSB disabled their legacy web fetch the last couple days they made it so when you tried to fetch it returned an html page saying "PDB has discontinued this fetch" with an http "success" code (200). Since Chimera got the success code it assumed that html text was actually the PDB file and it cached it in ~/Downloads/Chimera/PDB Then when you try to open that same PDB file it is getting that cached html page instead of the cached PDB file. I asked RCSB to return an error code (404) on fetch so that does not happen, but they did even better and temporarily have reenabled the old fetch URLs to help Chimera users. They will still turn off the old fetch in a month or so. Tom > On Nov 5, 2020, at 6:26 AM, John Rose <rose(a)bcl4.bmb.uga.edu> wrote: > > Hi, > > Downloaded the Chimera 1.15 build but the problem still persists. > > Thanks, > > John Rose > > > John Rose Ph.D. > Associate Professor > SER-CAT Associate Director for Program > Rm. B204B > Department of Biochemistry and Molecular Biology > Davison Life Sciences Complex > 120 Green Street > University of Georgia > Athens, GA 30602-7229 > =============================== > Phone: 706-542-1750 > Fax: 706-542-3077 > > > > >> On Nov 4, 2020, at 1:28 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Chimera PDB fetch is broken starting November 3 and a command like "open 1a0m" produces an empty model with no error. >> >> We will be putting a new version (release candidate) of Chimera on the download page today or tomorrow that fixes this. >> >> What happened is that the RCSB has shutdown the URL Chimera uses to fetch PDB files (e.g. https://www.rcsb.org/pdb/files/1a0m.pdb <https://www.rcsb.org/pdb/files/1a0m.pdb>). Although RCSB announced this long ago the Chimera development team missed that this URL was going away. >> >> Tom >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

1 0

PDB fetch broken
by Tom Goddard 04 Nov '20

04 Nov '20

Chimera PDB fetch is broken starting November 3 and a command like "open 1a0m" produces an empty model with no error. We will be putting a new version (release candidate) of Chimera on the download page today or tomorrow that fixes this. What happened is that the RCSB has shutdown the URL Chimera uses to fetch PDB files (e.g. https://www.rcsb.org/pdb/files/1a0m.pdb <https://www.rcsb.org/pdb/files/1a0m.pdb>). Although RCSB announced this long ago the Chimera development team missed that this URL was going away. Tom

1 0

Fwd: How to setup Nvidia 3D Vision on Ubuntu
by Tom Goddard 03 Nov '20

03 Nov '20

Here's a picture from Kenneth of the DIN and USB cables needed to use the 3D Vision emitter on Linux. > Begin forwarded message: > > From: Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> > Subject: Re: [Chimera-users] How to setup Nvidia 3D Vision on Ubuntu > Date: November 3, 2020 at 11:17:18 AM PST > To: Tom Goddard <goddard(a)sonic.net> > > Actually, the pic does not have the cable in it, only the extra on-board cable that connects to the GPU and serves up the 3pin female. Here is a pic of both the din and usb cable connected to the emitter. The DIN is a must for linux. the special cable is on the left and the usb is on the right. > > kas > > > Kenneth A. Satyshur, M.S., Ph.D. > Senior Scientist, > College of Ag and Life Sciences: Department of Bacteriology; > School of Medicine and Public Health: > Departments of Biomolecular Chemistry, > Neuroscience, Oncology, and Carbone Cancer Center > (Small Molecule Screening Facility) > University of Wisconsin-Madison > Madison, Wisconsin, 53706 > 608-215-5207 >

1 0

How to setup Nvidia 3D Vision on Ubuntu
by Tom Goddard 03 Nov '20

03 Nov '20

Hi Wei, I'd suggest using Ubuntu 20.04, the latest Ubuntu, the current Chimera 1.14 or daily build will work fine on that. I am not certain that Quadro FX 4800 graphics drivers will be available for Ubuntu 20, probably they will be, but you might want to look for that online before proceeding. That graphics cards is very old, from 2008. The other thing to know is that Nvidia discontinued support for Nvidia 3D Vision stereo glasses in 2019 https://nvidia.custhelp.com/app/answers/detail/a_id/4845 meaning those glasses and emitter will no longer work using just the current Nvidia graphics driver. But they claim that there is a separate driver for the USB emitter that allows it to work. https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-dri… <https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-dri…> I have not tried it. If you get it to work I'd be interested in hearing about it since we have an old Nvidia 3D Vision system. Tom > On Oct 29, 2020, at 6:41 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: > > Hi Tom, > > Hope everything is well. > > One university's computer lab recently retired some workstations that were used for 3D visualization before. I managed to get a couple workstations with the 3D glasses and emitters. But I need to reinstall the operating system on those machines. > > The graphic card of the workstation is Nvidia Quadro FX4800. > The emitter is NVIDIA P854. > The glasses are NVIDIA-P854 and ViewSonic-PGD250. > > I plan to install Ubuntu. I am wondering which version of Ubuntu is suitable for using UCSF Chimera. Do we need to install cuda to make it work? Do we need to install an older version of Chimera? > > Sorry I just sent the message to you to follow the previous chain of conversation. Shall I email the chimera-user in the future with such questions? > > Thank you, > > Wei >

4 5

Capping in VRML
by Greg Williams 02 Nov '20

02 Nov '20

When I export a vrml file to process in my Cinema 4D application, the ends of the helices, coils and sheets are capped at the ends with a material that is different then the material I use to color the secondary structure features. In Cinema 4D, I have to change every capped end individually. Where do I change the vrml export settings so that the individual objects are capped with the right material? Thanks!

4 4

Accessible surface area calculation
by Martino Benvenuti 02 Nov '20

02 Nov '20

Good morning, I would like to know if it is possible to calculate with Chimera the accessible surface area for a selected amminoacid of a protein. May you help me to figure it out? Thank you for having developed such a great program! Have a nice day, Martino Benvenuti. -- Martino BENVENUTI Ph.D. in chemistry. <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

Screenshots for publication?
by Gustaf Olsson 02 Nov '20

02 Nov '20

Would it be acceptable to include screenshots of the Chimera GUI in publications as long as chimera is being cited as suggested? Best regards // Gustaf

2 1

Select multiple files and open in the same instance
by Ahmad Khalifa 30 Oct '20

30 Oct '20

I used to have Chimera configured to select multiple files, click open, and have them all open in the same instance. After I reinstalled it, now it opens an instance for every file, how can I change it back? Regards.

3 3

Chimera: Per-model clipping and contour level
by Selenschik, Philipp 30 Oct '20

30 Oct '20

Hello, I really enjoy working with Chimera (version 1.14), however I encounter two problems: I fitted the X-ray based crystal structure of apoferritin to my cryo-EM density map, determined the symmetry and based on that the algorithm fits 24 subunits to the map. Really nice. Now I would like to show a "sliced" image of both map and structure. I tried doing so by "Side view", enabling "clip". That works, but I would like to rotate the clipped object. Then I tried per-model-clipping. Here I can clip the map and structures separately. However, I have to choose all fitted (e.g. 12 out of 24) substructures and the clipping works only partially. What am I doing wrong? Also, I tried to figure out the best contour level setting. It seems there is no guide as to which is ideal? Based on a tutorial, I assumed 1 A³/Da for a globular protein, which turns out to be around 620*10³ A³ for my protein. The problem here is: If I slide beyond approx.. 550*10³ A³ all that remains is a square. What's wrong? I hope you can help me out :) Kind regards Philipp

2 4

Help with something really simple
by M. Elizabeth Stroupe 29 Oct '20

29 Oct '20

Hi ChimeraX team, I need to measure a simple angle between three atoms, two within one model and the third in another model to describe a domain motion. In Chimera I could do this from the Structure Analysis tab but now it seems you can only measure distances. I tried the following command(s) and they both gave me an error. I also tried including commas between the angles. What am I doing wrong? angle #1/A:602@C7m,:222@CB,#17/A:602@C7M measure angle #1/A:602@C7m #1/A:222@CB #17/A:602@C7M Thank you! Beth

2 1

MD Simulation on Chimera
by Samiha I Amer 27 Oct '20

27 Oct '20

Please may I know the ideal system specification to run a successful molecular Dynamics simulation on Chimera? Thank you Sent from Yahoo Mail on Android

2 1

REGARDING CHIMERA SESSION FILE
by ASIF JAHAN SHUVRO 26 Oct '20

26 Oct '20

Dear concern, this is Asif from BRAC University, Biotechnology program. I hope you're in good health. I need a little help from you. Recently, I have joined two peptide fragments by forming a peptide bond between them using your standalone UCSF Chimera software. The file has been saved as a Chimera session fle. However, I'm not finding any clue on how to convert it into an entire pdb file. I'm not being able to do any other modification to it since a pdb file is required for this purpose. Could you please help me out on this regard? kindly let me know how can I generate a pdb file from that session file format. I wish to hear your reply. Thanks in advance! Regards, Asif Jahan Shuvro Biotechnology Program Department of Mathematics & Natural Sciences BRAC University

2 2

Morphing PDB
by Reza Khayat 26 Oct '20

26 Oct '20

Hi, Is it possible to morph multiple chains serially? I have a trimer in two different conformations, I would like to morph Chain A in conformation 1 to Chain A in conformation 2. Then, I'd like to do this with chain B and finally chain C. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

Running Chimera on X server
by Ahmad Khalifa 26 Oct '20

26 Oct '20

The refresh rate of Chimera running on a linux server is very slow. I'm connected to the server with an ssh client with X server. I wonder if it's because Chimera is not configured properly or possibly the X server. I also tried to make some movies but they are always blank (black screen). Any suggestions?

2 1

Query on selecting one water molecule
by Izzati Mokthar 26 Oct '20

26 Oct '20

Hi, I am Izzati. I would like to ask how to select only one water molecule in chimera? Thank you

2 2

(no subject)
by Yasser Almeida 22 Oct '20

22 Oct '20

Dear Anabel, As others pointed out, you can just represent the beads as balls, points, or wire, and remove all the pseudbonds. On the other hand, how did you obtained your pdb? If you used GNOM in the ATSAS package (GUI version), it writes pdbs with a bigger bead size, which Chimera fails to represent by default. But if you use GNOM in the command line, it writes pdbs with a smaller bead size, which are more compact, smoother, and better for representation in Chimera, and others. Best, Yasser Dear Chimera team, > I am a user from your software and I would like to have a > superimposition of some crystallographic structures in a recent saxs > pdb model I obtained. However, I cannot visualize the saxs pdb file > with Chimera. Would you have any tips or inputs how can I do this? > Thank you very much in advance for all your help, > Kind regards, > Anabel

1 0

Broken links, system requirements
by Calvin Dodge 21 Oct '20

21 Oct '20

Hello, I have been trying to find out what the hardware requirements are for Chimera. For example, how can it be run in a cluster environment with CUDA cards, but no Nvidia graphics cards? My search for information has been hampered by an apparent failure or reorganization of the main site -https://www.cgl.ucsf.edu/chimera/ Every internal link from that page (like to Downloads) is broken. Will the broken links be fixed? Is another page the preferred one for Chimera? Do I need the OSMesa version to run without graphics cards? Thanks, Calvin Dodge Calvin Dodge Systems Analyst Office: 832-271-7148 Email : cdodge(a)x-iss.com<mailto:ellorente@x-iss.com> http://www.x-iss.com<https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> [cid:image001.png@01D5DB72.2E9C2F40]<http://www.x-iss.com/> Smart Management and Analytics for Clusters

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Re: [Chimera-users] Broken links, system requirements
by Greg Couch 21 Oct '20

21 Oct '20

Your university might want the regular version of Chimera to remotely display data. In that case, you should set up VirtualGL as well. And a RDP solution, like x2go. It doesn't perform as well as Chimera running locally on the desktop, but it might be sufficient. -- Greg On 10/21/2020 11:21 AM, Calvin Dodge wrote: > > Greg, > > Thanks for your reply _/I/_ don’t want to run Chimera in a cluster > environment, but the university I’m doing the install for does. I’ll > install the headless version. > > Sincerely, > > Calvin Dodge > > */Calvin Dodge/*/ > Systems Analyst/ > > /Office: 832-271-7148/ > > / > /Email : cdodge(a)x-iss.com <mailto:ellorente@x-iss.com> > > http://www.x-iss.com > <https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> > > <http://www.x-iss.com/> > > Smart Management and Analytics for Clusters > > *From: *Greg Couch <mailto:gregc@cgl.ucsf.edu> > *Sent: *Wednesday, October 21, 2020 12:24 PM > *To: *Calvin Dodge <mailto:cdodge@x-iss.com>; > chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > *Subject: *Re: [Chimera-users] Broken links, system requirements > > (We're working on the web site issues.) > > So the real question is why do you want to run Chimera in a cluster > environment? > > Chimera is not designed to run in a cluster environment, it is > designed to run a user's desktop computer using 3D graphics. Chimera > does not use CUDA. That said, there is a headless version for Linux > that uses a software implementation of OpenGL to create images that > you could use in a cluster, so no graphics card is needed. > > ChimeraX, our successor to Chimera, can take advantage of CUDA in some > circumstances, but it is not required. ChimeraX also only works > headless on Linux, with a software implementation of OpenGL. The > headless operation is included in every Linux version. So no graphics > card is needed there either. We are investigating ways to take > advantage of the graphic card's performance when running headless, but > we're not there yet. > > HTH, > > Greg > > On 10/21/2020 9:24 AM, Calvin Dodge wrote: > > Hello, > > I have been trying to find out what the hardware requirements are > for Chimera. For example, how can it be run in a cluster > environment with CUDA cards, but no Nvidia graphics cards? > > My search for information has been hampered by an apparent failure > or reorganization of the main site -https://www.cgl.ucsf.edu/chimera/ > > Every internal link from that page (like to Downloads) is broken. > > Will the broken links be fixed? Is another page the preferred one > for Chimera? Do I need the OSMesa version to run without graphics > cards? > > Thanks, > > Calvin Dodge > > */Calvin Dodge/*/ > Systems Analyst/ > > /Office: 832-271-7148/ > > / > /Email : cdodge(a)x-iss.com <mailto:ellorente@x-iss.com> > > http://www.x-iss.com > <https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> > > <http://www.x-iss.com/> > > Smart Management and Analytics for Clusters > > > > _______________________________________________ > > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

issues with visualization of saxs models in chimera
by Anabel Pacios Michelena 20 Oct '20

20 Oct '20

Dear Chimera team, I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this? Thank you very much in advance for all your help, Kind regards, Anabel

3 2

Writing residues coordinates and COMs
by Yasser Almeida 20 Oct '20

20 Oct '20

Hello, I am writing a python script to iterate through all the residues of my model and write the residue coordinates and its correspondent center of mass. I tried with 'runCommand' with the command 'write' but it only accepts a model to be written, not a specific residue. Any thoughts? Thanks in advance. Yasser

2 2

Query about energy minimisation
by Izzati Mokthar 19 Oct '20

19 Oct '20

Hi, I am Izzati. I have a few queries on UCSF Chimera. I need your guide to use the tools. I have two questions. Below are the questions: 1.I would like to do energy minimisation for protein structure with PDB ID: 2J9F. I click Structure editing > Minimize Structure. To be honest, I don't know how to set the settings. I used the default setting and a warning pops up as the attached picture. Do you have any suggestion of reference that I can refer to, to do the energy minimisation? [image: 5.png] 2. I need to also do molecular dynamics for my research. May I know whether I can use chimera to run molecular dynamics as well. If yes, where can I refer to the tutorials? Thank you in advance for your response. Regards, Izzati.

2 4

atom ID
by Francesco Pietra 18 Oct '20

18 Oct '20

Dear all Which is the quickest way to identify the atom ID? As visualized in the context of a multimer, where three identical subunits, distinct by chain name, bind the same peptide, also distinct by chain name. Atom IDs are needed to build a QM-MM simulation. thanks francesco pietra

2 2

PyChimera addCharge
by Matas Tiskus 16 Oct '20

16 Oct '20

Hello, I was looking for ways to add charges to protein structures in a python script and write a .mol2 file. I believe it is possible to do with importing pychimera into the script, but i can't seem to make it work. How would the code for this purpose look like? Matas

2 3

Re: [Chimera-users] [chimera-dev] Building a dimeric protein model
by Elaine Meng 15 Oct '20

15 Oct '20

On Oct 15, 2020, at 1:41 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > Hi > I've built a monomeric model using Chimera's MODELLER interface. I was wondering whether it's possible to use this model in Chimera to create a dimer. The dimer of the protein that I'm studying is composed of two antiparallel symmetric monomers. > Thank you > Tiglath > Hi Tiglath, Sure, but you would need to know the proper positioning of the two monomers in the dimer. There is nothing in Chimera to figure that out automatically. If there is a known dimer structure of a related protein and you think your modeled protein forms a similar dimer, you can simply (1) save your new monomer model as a PDB file (2) start a new Chimera, open that new PDB file two times so that you have two copies open (3) open the known dimer structure of the related protein, let's say it has chains A and B (4) superimpose one copy of your monomer model onto chain A of the known dimer structure, and superimpose the other copy of your monomer model onto chain B of the known dimer structure. Different methods of superimposing structures are discussed in the link below. Probably the easiest is to use the Matchmaker tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (4) close the known dimer structure, and what you have left is the approximate dimer with two copies of your model, which can be saved as a session, or combined into a single model (see "combine" command) and then saved as a PDB file. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Alternatively if you have a dimeric template structure you can use Modeller to make a dimeric comparative model directly, but to do that you would have to use the Modeller interface in our newer program ChimeraX. The one in Chimera only allows modeling monomers. Modeller interface in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> This chimera-dev e-mail address is mostly for programming questions. For general user questions like this (for future reference) a better address to use is chimera-users(a)cgl.ucsf.edu CC'd here, and there is also a similar address for ChimeraX: chimerax-users(a)cgl.ucsf.edu I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

kill graphics windows after crash
by Dieter Blaas 15 Oct '20

15 Oct '20

Hi, please forgive me when this question is not directly related to Chimera: Sometimes Chimera becomes unresponsive because of a slow network connection. When I then try exiting it or killing it with <ctrl> c from the terminal I used to start it or killing the chimera-related process as shown with ps -ealf|grep UCSF or grep chimera the chimera windows remain and I cannot remove them. Any way of doing so? Thanks for hints, best, Dieter ----------------------------------------------------------------------- Dieter Blaas, Max Perutz Labortories 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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how to get specific view
by Shuo 15 Oct '20

15 Oct '20

Dear sir or madam, I wonder how to get specific view parameter in Chimera, just like command get_view in Pymol. So that next time I can easily adjust the view in Chimera. Best Shuo

2 1

Modelling missing residues in a protein
by Edmund Marinelli 14 Oct '20

14 Oct '20

Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD

4 4

MOLE 2.5 plugin
by Reza Khayat 13 Oct '20

13 Oct '20

Hi, I'm receiving the following error when launching the MOLE 2.5 plugin from Chimera. The plugin was installed as suggested by the developers: Favorites -> Preferences -> Add -> Select directory The plugin's icon appears in my tool bar. However, launching it generates the following error in the Reply Log. Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1rc\share\chimera\toolbar.py", line 26, in _guard func() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 954, in <lambda> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 76, in display dialog = find(name, create=1) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 61, in find return d() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' Error in toolbar callback: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: See reply log for Python traceback.? Any help is appreciated. Best wishes, Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

Help on using Modeller interface
by Moradkhan, Tiglath A 09 Oct '20

09 Oct '20

Hi I'm currently trying to use the Modeller interface but I'm having difficulties. I am trying to model a monomeric protein but one of the templates is a homotetramer containing chains A, B, C and D. I only need to use chain A to model the protein but I'm not sure how to do it. Whenever I use the Modeller interface, it uses all of the chains which is not what I want. Unfortunately, this is the only template that I can use since the others are either structures that have since been refuted or don't really correspond to the protein I'm studying. I would be very grateful for your help. Thanks Tiglath

2 3

Help for Chimera please
by EMILIE MONTELLIER 09 Oct '20

09 Oct '20

Hello, I have just downloaded your Chimera software. It looks great! I would like to map a list a specific amino acid on p53 protein and I struggle to find a way to do it. I have downloaded the PDB file of 1TUP TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA (at [ https://www.rcsb.org/ | https://www.rcsb.org ] ). For exemple what would be the command to hightlight amino acid 175 + 248 + 273 + 282 on p53 protein? Thanks by advance for your help, Regards, Emilie Emilie Montellier, PhD Postdoctoral Researcher Institute for Advanced Biosciences Team Tumor Molecular Pathology & Biomarkers Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

2 1

Latest nightly broken on Mac (10.15.7)
by Oliver Clarke 09 Oct '20

09 Oct '20

Hi, In the notes for the latest nightly Chimera build, it states "Many user-interface problems on Mac fixed by upgrading the Tk windowing toolkit to version 8.6.10" - this sounds great, but it seems to have broken basic functionality, at least on my system. See screen recording here: https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0 <https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0> Many UI elements are not responsive any more (including the "Report a Bug" dialog, hence why I am reporting here). This is using Mac OS X 10.15.7 on a macbook pro 16", using the trackpad. Cheers Oli

3 4

AutoDOCK plugin for UCSF Chimera
by James Starlight 08 Oct '20

08 Oct '20

Dear Chimera users! Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb

3 2

matchmaker and MSA
by arrafzaher＠campus.technion.ac.il 06 Oct '20

06 Oct '20

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

2 14

Volume eraser accelerator not working properly
by Ahmad Khalifa 01 Oct '20

01 Oct '20

As I keep clicking "es", the shadows / lighting keep changing, but after clicking 10 times or so, it finally erases. Is this something I'm doing? How can I change to a more easier accelerator?

2 1

bound ligand's are exposed to solvent. Current calculations do not protect surface of ligand embedded in protein
by Anne-Frances Miller 01 Oct '20

01 Oct '20

Dear Chimera, I see on-line advice on calculating areaSAS and areaSES, however Chimera is calculating these for my bound flavin as if the protein were not there. I would like to assess the area exposed outside the protein, not total area (on an atom-by-atom basis). Indeed, the show surface command produces two surfaces, one for the FAD and a different one for the protein, even though both are chain A. Can I edit the pdb file to cause Chimera to create a single surface for both chains including both bound FADs, so that SASA calculated will represent the extent to which the FAD protrudes from the protein? (My protein is a heterodimer with two bound FADs, my Chimera version is 1.13.1 running on Mac OS 10.15.6) Thank you, Anne-Frances Novel Meritorious Research (and teaching) —————————————— A.-F. Miller, Ph. D. Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin Chair, Div. of Biological Chemistry, American Chemical Society

2 2

Undo for volume eraser
by Ahmad Khalifa 30 Sep '20

30 Sep '20

Is there a way to undo a recent erasing that I did? Also, are there ways to use custom shapes, or other surfaces to erase density?

2 1

scipy
by Hernando J Sosa 29 Sep '20

29 Sep '20

Is scipy installed with Chimera? If not how can it be installed? Thanks Hernando >From Chimera idle: >>> import chimera >>> import scipy Traceback (most recent call last): File "<pyshell#1>", line 2, in <module> ImportError: No module named scipy ___________________________________

2 1

Re: [Chimera-users] Troubleshooting request for help
by Cain, Cheryl A 29 Sep '20

29 Sep '20

Hi Tanuja, I've added chimera-users(a)cgl.ucsf.edu to this email as they should be able to help you there. Thanks, Cheryl Cheryl Cain cheryl.cain(a)ucsf.edu Operations Coordinator, Department of Pharmaceutical Chemistry Accreditation Project Coordinator, School of Pharmacy UCSF ________________________________ From: Saswat, Tanuja (NIH/NCI) [F] <tanuja.saswat(a)nih.gov> Sent: Friday, September 25, 2020 9:56 AM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Cc: Goins, Jerquan (NIH/NCI) [C] <jerquan.goins(a)nih.gov> Subject: Troubleshooting request for help Hi, I am a researcher at the NIH who uses this software to complete analysis. But as of recently some of the features that I usually use have not been able to access them. Can you guys assist me in finding a resolution. I’ve CC’s my IT support in case there was something above my cresds level. Regards -- Tanuja Saswat, Ph.D. Postdoctoral Research Fellow Laboratory of Dr. Laurie T. Krug HIV and AIDS Malignancy Branch (HAMB) Center for Cancer Research National Cancer Institute tanuja.saswat(a)nih.gov<mailto:tanuja.saswat@nih.gov> Building 10, Room 4A08 Ph:240-858-3201 NCI Website<https://urldefense.proofpoint.com/v2/url?u=https-3A__ccr.cancer.gov_HIV-2Da…>

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vop subtract removing too much of my map
by Ahmad Khalifa 29 Sep '20

29 Sep '20

I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1! how can I get precise subtraction?

3 7

clustering models of a single pdb
by Subhrangshu Das 29 Sep '20

29 Sep '20

Dear sir, I have 100 pdb files. named as output.1.pdb to output.100.pdb what i do manually for clustering is as follows 1. select 100 pdbs -> open in chimera -> golto *File *-> *save PDB.. *-> *Save Multiple Models as PDB File *(renamed as all.pdb) 2. open chimera -> goto *Tools *->* MD/Ensemble Analysis *->* MD Movie* 3. in *Get Ensemble Info *dialogue box set -> *Trajectory format :* *PDB* *PDB frames contained in:* *single file* * Browse *to select File <all.pdb> *Use frames **first **through * *last* 4. on click *OK,* a dialogue box pops out, *MD Movie: PDB trajectory from all.pdb*, in which, goto *Analysis -> Cluster...*5.. on click* Cluster,* a dialogue box pops out,* Get Clustering Parameters,* in which I set *Cluster trajectory *as: *Starting frame: * *1* *step size: **1* *Ending frame:* * 100* *Cluster based on current selection, if any: * *true* *Ignore solvent and non metal ions: true* *Ignore hydrogens: * *true* *Ignore metal ions: * *alkali* 6. on click *OK, *after some RMSD calculation, i get the *Clustering* result, which I save to a text file <cluster> Now, as I need to do this for multiple times, I want to automate these steps by a python script. Can you please help with a scipt or some command help for the aforesaid tasks. Any help will be helpful in these regard. -- Thanks & Regards, Subhrangshu Das Junior Research Fellow, CSIR-IICB Department of Structural Biology & Bioinformatics Contact - IICB TRUE Campus, CN-6, Salt lake, Sector V, Kolkata-700091 *+919804938813*

3 3

tile from command line
by Dieter Blaas 28 Sep '20

28 Sep '20

Hi, I am trying to use the command line command TILE as given here: Usage <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/usageconvent…>: *tile* /models/ [ columns /N/ ] [ spacingFactor /f/ ] [ independentRotation true|false ] [ viewAll true|false ] [ label true|false ] I tried (following the syntax of e.g. "vol all level 0.02": "tile vol all columns 3" or "tile all columns 3" or "tile models all columns 3" or "tile #0, #1, #2, #4, #5, #6 columns 3" but none works can you please give me an example! Thanks, 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 ------------------------------------------------------------------------

2 1

Is RTX support planned?
by Gokhan Tolun 25 Sep '20

25 Sep '20

Hi Tom, Are there any plans to implement RTX (real-time ray tracing) support to ChimeraX (and even better, allow the use of physically modelled materials and textures)? Thanks, Gökhan Gökhan Tolun<https://scholars.uow.edu.au/display/gokhan_tolun>, M.S., Ph.D. Senior Lecturer School of Chemistry and Molecular Bioscience<https://www.uow.edu.au/science-medicine-health/schools-entities/school-of-c…> | Faculty of Science, Medicine and Health (SMAH)<https://smah.uow.edu.au/index.html> | Room 125 / Building 18 Molecular Horizons Research Institute<https://www.uow.edu.au/molecular-horizons/index.html> Illawarra Health and Medical Research Institute<https://www.ihmri.org.au/researchers/gokhan-tolun/> University of Wollongong NSW 2522 Australia T +61 2 4221 3365 uow.edu.au<http://uow.edu.au/> | Facebook<https://www.facebook.com/UOW> | Twitter<https://twitter.com/uow> | Instagram<https://www.instagram.com/uow/> | LinkedIn<http://www.linkedin.com/edu/school?id=10255> NOTICE: This email is intended for the addressee name and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Please consider the environment before printing this email.

2 1

X-PLOR format, finding a maximum
by Gustaf Olsson 25 Sep '20

25 Sep '20

Hello Chimera users This might be a somewhat “of-topic” question though I thought that this would be a good place to start. When loading density maps (particularly the X-PLOR format density maps) into Chimera the 'volume viewer’ window provides a maximum number of gridpoints for the map. My question has to do with the format of the XPLOR files. The documentation regarding this format is rather sparse and my I have not been keeping my knowledge regarding matrices up to date. Is there a way to identify this maximum value by just inspecting the content of these files? I have a lot of these files and as I en up presenting results only for ligands with grids visible above a specific cut-off, I though it would save me a lot of time and headache if I could just load the density maps with maximum densities above the cutoff. My though was to just parse the files through AWK or similar to find files with a x > a and then only load these. Sadly, I keep looking at the content of these files and I am not able to make much sense of what I am looking at. Any solutions, suggestions or suggested reading to be able to find a way to create a solution would be greatly appreciated. Best regards // Gustaf

2 1

Error reading multiple models
by Francesco Pietra 25 Sep '20

25 Sep '20

In my hands CHIMERA can't read multiple models as in .trj.xyz provided by ORCA software in QM calculations Error reading 5-sulf-min_trj.xyz: Coordinate line of XYZ file '/home/francesco/work_AGAs/VITTORIO/5-sulf-min_PBE0_OPT_FREQ_SMD/ 5-sulf-min_trj.xyz' is not element,x,y,z: '36' That is no problem for Jmol, however I would be interested in opening the models with also CHIMERA (which can open these models as a single-model-file. thanks for advice francesco pietra

2 1