- ChimeraX-users - RBVI Mailing Lists

label_seq_id in mmcif files for Chimera
by Marcin Wojdyr 07 Jul '20

07 Jul '20

Hi, I'd like to generate mmCIF files (using my own software) that can be read by Chimera. The problem is that sometimes I don't know the full sequence (SEQRES), so I don't know values for _atom_site.label_seq_id. If I skip label_seq_id entirely, the file doesn't load. ChimeraX gives warning: "Skipping atom_site category: Missing column 'label_seq_id'". If I set all label_seq_id values to null ('.') I get warning: "Unable to infer polymer connectivity due to unspecified label_seq_id for residue "ARG" near line 125" and all residues are disconnected. How should the mmCIF look like so that Chimera infers the connectivity in the same way as it does for PDB files? Cheers, Marcin

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Re: [chimerax-users] [ChimeraX] #3464: partial surface mesh
by Elaine Meng 07 Jul '20

07 Jul '20

Hi Rory, There is no "hydrophobic surface" ... maybe you mean the molecular surface shown as solid (not dot or mesh)? Chimera's presets include "hydrophobicity surface" which is perhaps misleading, simply means the molecular surface colored by hydrophobicity. What exactly are you trying to do? Show protein as mesh surface and ligand as solid surface? You can definitely do it (or any combination of mesh surface on some atoms, solid on some other atoms) by opening multiple copies of the structure, as we said in previous messages. Then in the solid-surface copy, only show the parts of the surface you want as solid. In the mesh-surface copy, show the parts you want as mesh. For example, here is an example that shows H-ras as mesh surface with its ligand GCP as solid surface (image attached below), commands: open 121p open 121p surf #1 & protein surf #2:gcp surf style #1 mesh transp #1 50 surfaces color #2 gold surfaces hide solvent This can all be done with the menu as well, but it would take a lot more typing to enter that whole procedure. I Cc'd chimerax-users(a)cgl.ucsf.edu which is the recommended address for asking ChimeraX questions (for future reference). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 6, 2020, at 10:30 AM, Gordon, Rory <rory.gordon.19(a)ucl.ac.uk> wrote: > > Hi Guys, > > Further to previous email, just tried fiddling with the transparency settings. > > I can get the protein structure to change through the transparency gradient for hydrophobic surface. > > However, for the substrate/ligands there seems to be binary system where you can either have full transparency or none at all. > > The hydrophobic surface can be coloured both for the protein and substrate/ligand. > > Cheers, > > Rory > From: Gordon, Rory <rory.gordon.19(a)ucl.ac.uk> > Sent: 06 July 2020 18:26 > To: Tom Goddard <goddard(a)sonic.net>; Elaine Meng <meng(a)cgl.ucsf.edu> > Cc: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [ChimeraX] #3464: partial surface mesh > > Hi Tom, Elaine and Eric > > I tried to establish the mesh surface with the whole protein structure selected through the GUI. I can only get the hydrophobic surface which I can colour with B-factor. > > The options of Mesh, Dot or Solid don't seem to change anything. > > Not sure how to get round this, so any help would be appreciated. > > Cheers, > > Rory > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: 02 July 2020 18:24 > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Cc: Gordon, Rory <rory.gordon.19(a)ucl.ac.uk>; Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [ChimeraX] #3464: partial surface mesh > > Another trick that makes these meshes look nicer is to make them about 50-80% transparent (command "transp #2 70"). It gives the mesh an airy look. > > Tom > > >> On Jul 2, 2020, at 10:17 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Rory, >> Here is an example image where I opened the same structure twice. I showed one copy with mesh surface and the second one with solid surface, and then simply hid parts of the solid surface. This is the way that Tom mentioned. >> Elaine >> >> <example.png> >> >> >>> On Jul 2, 2020, at 3:29 AM, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: >>> >>> #3464: partial surface mesh >>> ---------------------------------------+---------------------------- >>> Reporter: rory.gordon.19@… | Owner: Eric Pettersen >>> Type: defect | Status: closed >>> Priority: normal | Milestone: >>> Component: Surface | Version: >>> Resolution: fixed | Keywords: >>> Blocked By: | Blocking: >>> Notify when closed: | Platform: all >>> Project: ChimeraX | >>> ---------------------------------------+---------------------------- >>> >>> Comment (by rory.gordon.19@…): >>> >>> {{{ >>> Hi Eric, >>> >>> Thanks for your email. >>> >>> I had actually seen a graphic in a publication which gave me that idea. >>> >>> Thanks anyway for the pointers. >>> >>> Cheers, >>> >>> Rory >>> ________________________________ >>> From: ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> >>> Sent: 01 July 2020 18:23 >>> Cc: goddard(a)cgl.ucsf.edu <goddard(a)cgl.ucsf.edu>; meng(a)cgl.ucsf.edu >>> <meng(a)cgl.ucsf.edu>; pett(a)cgl.ucsf.edu <pett(a)cgl.ucsf.edu>; Gordon, Rory >>> <rory.gordon.19(a)ucl.ac.uk> >>> Subject: Re: [ChimeraX] #3464: partial surface mesh (was: ChimeraX bug >>> report submission) >>> >>> #3464: partial surface mesh >>> ---------------------------------------+---------------------------- >>> Reporter: rory.gordon.19@… | Owner: Eric Pettersen >>> Type: defect | Status: accepted >>> Priority: normal | Milestone: >>> Component: Unassigned | Version: >>> Resolution: | Keywords: >>> Blocked By: | Blocking: >>> Notify when closed: | Platform: all >>> Project: ChimeraX | >>> ---------------------------------------+---------------------------- >>> Changes (by Eric Pettersen): >>> >>> * status: new => accepted >>> * cc: Tom Goddard, Elaine Meng (added) >>> * project: => ChimeraX >>> * platform: => all >>> * owner: (none) => Eric Pettersen >>> >>> >>> Comment: >>> >>> Hi Rory, >>> I don't believe you can change just part of a surface into mesh, >>> it's all or nothing. You can make that part of the surface partially >>> transparent instead with Actions→Surface→Transparency. >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> ----- >>> Tom, should the command "surface style (#!4 & sel) mesh" actually do >>> nothing (with part of the surface selected)? That seems surprising. >>> Seems like it should change the whole surface into mesh. Is that a bug >>> or >>> am I misunderstanding something? >>> >>> --Eric >>> >>> -- >>> Ticket URL: >>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…> >>> ChimeraX >>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> >>> ChimeraX Issue Tracker >>> }}} >>> >>> -- >>> Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3464#comment:7> >>> ChimeraX <http://www.rbvi.ucsf.edu/chimerax/> >>> ChimeraX Issue Tracker

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artificial lines or seems on surface using soft lighting
by Steve Chou 06 Jul '20

06 Jul '20

Hi ChimeraX folks, When I used soft lighting, I saw lines/seams on the molecular surface (see the attached image). To reproduce this: ---------------------- load xxxx.pdb surface color violet lighting soft ---------------------- How to remove these artificial lines/seams? These lines also show up in the cutting plane in a section view. Many thanks in advance! Steve -- Steve Chou

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Can I only clip some models, but not all of them?
by Steve Chou 05 Jul '20

05 Jul '20

Hi ChimeraX developers and users, When a ligand is embedded in the protein, can I only clip the surface of the protein, but not the ligand (sticks)? Many thanks, Steve -- Steve Chou

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How to obtain size measures
by Andrea Dallapè 04 Jul '20

04 Jul '20

Dear UCSF Chimera and ChimeraX developers, I would like to ask you if there's a method to obtain the size measures of a protein in order to compare with the heights and lengths obtained by AFM. Could you please suggest me how could I obtain such measurements? Thank you in advance for your help and support, Andrea

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color offset and surface type for mapping Electrostatic Potential
by Steve Chou 02 Jul '20

02 Jul '20

Hello everyone, I tried to map Electrostatic Potential (ESP) onto the molecular surface in ChimeraX v1.0 and PyMOL v2.1, but I found that the results were very different in these two programs. Therefore, I wrote to Elaine Meng and Tom Goddard for help. For your reference, I repost the ideals of our emails below. I first calculated the ESP with DelPhi v5.1 (a relatively old version) to get the .phi file (ESP). PyMOL commands for displaying ESP on the molecular surface are as follows: ------------------------------------------------ load 1ubq.pdb bg_color white remove resn hoh remove hydrogens hide line select heavy, name c*+o*+s*+n* show surface load 1ubq.phi, e_map ramp_new e_lvl, e_map, [-7, 0, 7] set surface_color, e_lvl, 1ubq set light_count, 1 set ambient, 0.5 set reflect, 0.2 ------------------------------------------------ ChimeraX commands for displaying ESP on the molecular surface are as follows: ------------------------------------------------ open 1ubq.pdb open 1ubq.phi hide #2 set bg white surface #1 color electrostatic #1 map #2 palette -7,red:0,white:7,blue material dull lighting simple ------------------------------------------------ In PyMOL, the colors (red/blue) are mainly on the residue (E/D, K/R) tips, while in ChimeraX, the colors are spread. Besides, the surface shapes are also slightly different in these two programs. See the image (left and middle panels) for the different colors and shapes. The color difference is caused by the color offset. The shape difference is also explained below. I changed the color offset to 0. Now the color looks similar in these two programs (left and right panels). The color offset (1.4 A) in ChimeraX gives a better idea of the possible charge interactions with other molecules. ------------------------------------------------ color electrostatic #1 map #2 palette -7,red:0,white:7,blue offset 0.0 ------------------------------------------------ The summary of the explanations from Tom: ------------------------------------------------ One idea I have for why PyMol shows redder tips is because ChimeraX is showing the potential 1.4 Angstroms away from the surface since that is about how far away a binding molecule would be. PyMol may be showing the ESP values exactly on the surface. You can try using 0 offset instead of 1.4 with the "color electrostatic" command "offset" parameter. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#map ------------------------------------------------ The summary of the explanations from Elaine: ------------------------------------------------ As Tom mentioned, the rationale for the 1.4 A projection is that Chimera and ChimeraX show the solvent-excluded surface (SES), as opposed to the solvent-accessible surface (SAS). The SAS is approximately half a probe radius outward, and the SAS represents the closest possible approach of atomic centers of waters or ligands interacting with the protein, so the result is coloring by what values of the electrostatic potential (ESP) that such ligands would "see". The diagram in this page shows the relationships among SES, SAS, and probe. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> Possible reasons for difference in Pymol, if the ESP map itself is identical: (1) coloring by offset values or not. It has been my general understanding that when programs color the SES by ESP, the default approach is to color by the values one surface-probe radius outward. (2) shape/location of the surface. Is it an SES or SAS, or neither? Pymol surfaces often look more "melty" or smoothed to me than the SES in Chimera/ChimeraX. (3) the exact color-mapping, i.e. which colors at which values. Pymol ESP coloring often uses a duller-looking blue. ------------------------------------------------ All the best, Steve -- Steve Chou

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color key
by Roberto Marabini 02 Jul '20

02 Jul '20

hi, Is there a colorkey command in chimeraX (http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…>)? If it does not exist, is there any alternative other than using chimera and photoshop? Thanks Roberto

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Is color command slower in ChimeraX than Chimera?
by Mungo Carstairs (Staff) 30 Jun '20

30 Jun '20

Hi, I'm testing driving ChimeraX (or Chimera) from Jalview, in particular colouring structures using the Jalview alignment residue colouring. Ideally this should perform well at scale for large numbers of structures and/or colours (for example a graduated colouring based on some property). I've noticed that ChimeraX appears to do this slower than Chimera. Is there a reason, or something I should do to make the command faster? Here's an example like for like comparison using the Chimera/X command line (also attached as a text file): Chimera 1.15 (build 42156) > open cifID:4zho cifID:5h92 cifID:1a70 cifID:4zhp > focus > color #977b64 #0:2.A,2.B;color #e46daf #0:3.A,3.B;color #7dc891 #0:4.A,4.B;color #768daf #0:5.A,5.B;color #bb1691 #0:6.A,6.B;color #1c5355 #0:7.A,7.B;color #5b1873 #0:8.A,8.B;color #d0af91 #0:9.A,9.B;color #6cb737 #0:10.A,10.B;color #8d7c55 #0:11.A,11.B;color #844173 #0:12.A,12.B;color #1f15a0 #0:13.A,13.B;color #a27f91 #0:14.A,14.B;color #19cb64 #0:15.A,15.B;color #484537 #0:16.A,16.B;color #61be37 #0:17.A,17.B;color #84a173 #0:18.A,18.B;color #c76691 #0:19.A,19.B;color #8f31a0 #0:20.A,20.B;color #9eb9af #0:21.A,21.B;color #531564 #0:22.A,22.B;color #707046 #0:23.A,23.B;color #9b80af #0:24.A,24.B;color #ca18a0 #0:25.A,25.B;color #377382 #0:26.A,26.B;color #26a137 #0:27.A,27.B;color #d3b1a0 #0:28.A,28.B;color #e267af #0:29.A,29.B;color #c023af #0:30.A,30.B;color #b18da0 #0:31.A,31.B;color #88bb55 #0:32.A,32.B;color #1fada0 #0:33.A,33.B;color #b22773 #0:34.A,34.B;color #ad19be #0:35.A,35.B;color #6483af #0:36.A,36.B;color #c9de91 #0:37.A,37.B;color #aab2be #0:38.A,38.B;color #59d164 #0:39.A,39.B;color #6d6037 #0:40.A,40.B;color #1cd937 #0:41.A,41.B;color #b5cb82 #0:42.A,42.B;color #e28191 #0:43.A,43.B;color #9537a0 #0:44.A,44.B;color #d6b0a0 #0:45.A,45.B;color #3bcf46 #0:46.A,46.B;color #2c6737 #0:47.A,47.B;color #e586af #0:48.A,48.B;color #e22daf #0:49.A,49.B;color #e29d91 #0:50.A,50.B;color #493582 #0:51.A,51.B;color #cacca0 #0:52.A,52.B;color #7f2855 #0:53.A,53.B;color #86dd91 #0:54.A,54.B;color #b55764 #0:55.A,55.B;color #4ac155 #0:56.A,56.B;color #614a37 #0:57.A,57.B;color #9e69af #0:58.A,58.B;color #5f8855 #0:59.A,59.B;color #958fa0 #0:60.A,60.B;color #9e45af #0:61.A,61.B;color #b9beaf #0:62.A,62.B;color #4add55 #0:63.A,63.B;color #5ba273 #0:64.A,64.B;color #bedf37 #0:65.A,65.B;color #359546 #0:66.A,66.B;color #262d37 #0:67.A,67.B;color #cf5bbe #0:68.A,68.B;color #505c46 #0:69.A,69.B;color #76db37 #0:70.A,70.B;color #3d37be #0:71.A,71.B;color #a28391 #0:72.A,72.B;color #b5cf64 #0:73.A,73.B;color #88b2a0 #0:74.A,74.B;color #bb4a91 #0:75.A,75.B;color #dc8755 #0:76.A,76.B;color #d579a0 #0:77.A,77.B;color #7c9846 #0:78.A,78.B;color #b57b82 #0:79.A,79.B;color #79cd46 #0:80.A,80.B;color #aa1abe #0:81.A,81.B;color #ab4873 #0:82.A,82.B;color #c6df91 #0:83.A,83.B;color #b3b3be #0:84.A,84.B;color #802d91 #0:85.A,85.B;color #d9c4af #0:86.A,86.B;color #c64d91 #0:87.A,87.B;color #857b46 #0:88.A,88.B;color #a26d91 #0:89.A,89.B;color #c62991 #0:90.A,90.B;color #adb1a0 #0:91.A,91.B;color #584991 #0:92.A,92.B;color #93b382 #0:93.A,93.B;color #48e137 #0:94.A,94.B;color #88c56f #1:1.C;color #7b5d60 #1:2.C;color #32d660 #1:3.C;color #339b7e #1:4.C;color #702460 #1:5.C;color #6725ba #1:6.C;color #dc536f #1:7.C;color #a3db7e #1:8.C;color #a8918d #1:9.C;color #d84eba #1:10.C;color #758b7e #1:11.C;color #88d751 #1:12.C;color #75ab7e #1:13.C;color #8e527e #1:14.C;color #cf53d8 #1:15.C;color #dc636f #1:16.C;color #7d288d #1:17.C;color #707460 #1:18.C;color #6fde51 #1:19.C;color #35a960 #1:20.C;color #627d8d #1:21.C;color #bb42ab #1:22.C;color #327060 #1:23.C;color #a3357e #1:24.C;color #28bd8d #1:25.C;color #8f91ba #1:26.C;color #c856d8 #1:27.C;color #795760 #1:28.C;color #c067c9 #1:29.C;color #669b6f #1:30.C;color #adabd8 #1:31.C;color #889d51 #1:32.C;color #c18f9c #1:33.C;color #26bd51 #1:34.C;color #55cdba #1:35.C;color #7e1a60 #1:36.C;color #238451 #1:37.C;color #68678d #1:38.C;color #6da451 #1:39.C;color #a315d8 #1:40.C;color #88256f #1:41.C;color #1f17ba #1:42.C;color #4a456f #1:43.C;color #6da051 #1:44.C;color #a4bfc9 #1:45.C;color #9557ba #1:46.C;color #d6d0ba #1:47.C;color #791d60 #1:48.C;color #e2e1ab #1:49.C;color #1c616f #1:50.C;color #7fda6f #1:51.C;color #8e907e #1:52.C;color #77559c #1:53.C;color #c4bf8d #1:54.C;color #77759c #1:55.C;color #1658d8 #1:56.C;color #add1d8 #1:57.C;color #aa5aba #1:58.C;color #95d3ba #1:59.C;color #adadd8 #1:60.C;color #aa36ba #1:61.C;color #95afba #1:62.C;color #aa74d8 #1:63.C;color #731bd8 #1:64.C;color #442b6f #1:65.C;color #8f1dba #1:66.C;color #882d51 #1:67.C;color #9b2eab #1:68.C;color #764d51 #1:69.C;color #6adb51 #1:70.C;color #359160 #1:71.C;color #e283ab #1:72.C;color #ddb160 #1:73.C;color #cab2ba #1:74.C;color #5559ba #1:75.C;color #8a876f #1:76.C;color #c76aab #1:77.C;color #62a76f #1:78.C;color #793f60 #1:79.C;color #23be51 #1:80.C;color #bab09c #1:81.C;color #99397e #1:82.C;color #a42bc9 #1:83.C;color #53597e #1:84.C;color #165ad8 #1:85.C;color #9d888d #1:86.C;color #d04dab #1:87.C;color #b1d5ba #1:88.C;color #c66dab #1:89.C;color #44a151 #1:90.C;color #df5760 #1:91.C;color #66df6f #1:92.C;color #cf1dd8 #1:93.C;color #a269ab #1:94.C;color #551fba #1:95.C;color #e4a7c9 #1:96.C;color #1f5c8b #2:1.A;color #a68a40 #2:2.A;color #5f3140 #2:3.A;color #76147c #2:4.A;color #9d5140 #2:5.A;color #6c8ed6 #2:6.A;color #37804f #2:7.A;color #8edb31 #2:8.A;color #7b64e5 #2:9.A;color #ab2140 #2:10.A;color #a89a40 #2:11.A;color #b53231 #2:12.A;color #7e247c #2:13.A;color #6125d6 #2:14.A;color #a2265e #2:15.A;color #97bd7c #2:16.A;color #aa556d #2:17.A;color #a9a140 #2:18.A;color #9c3931 #2:19.A;color #9e407c #2:20.A;color #8faa6d #2:21.A;color #166f8b #2:22.A;color #9bd97c #2:23.A;color #76dad6 #2:24.A;color #cd90e5 #2:25.A;color #2628d6 #2:26.A;color #97ce31 #2:27.A;color #e2c07c #2:28.A;color #933a4f #2:29.A;color #cf328b #2:30.A;color #a27e5e #2:31.A;color #b5ca31 #2:32.A;color #946222 #2:33.A;color #8f546d #2:34.A;color #28a040 #2:35.A;color #ab4740 #2:36.A;color #8c1b6d #2:37.A;color #95946d #2:38.A;color #d63b6d #2:39.A;color #76ba5e #2:40.A;color #b5524f #2:41.A;color #8880d6 #2:42.A;color #b3ae8b #2:43.A;color #9acd31 #2:44.A;color #77924f #2:45.A;color #2cc0d6 #2:46.A;color #a9a340 #2:47.A;color #e2867c #2:48.A;color #b5b431 #2:49.A;color #498e4f #2:50.A;color #64627c #2:51.A;color #85188b #2:52.A;color #e4827c #2:53.A;color #1f1a6d #2:54.A;color #a4a27c #2:55.A;color #cdb2e5 #2:56.A;color #60a45e #2:57.A;color #7d2d40 #2:58.A;color #80c45e #2:59.A;color #444422 #2:60.A;color #7ddb40 #2:61.A;color #688240 #2:62.A;color #1fbfd6 #2:63.A;color #46c05e #2:64.A;color #71584f #2:65.A;color #2686d6 #2:66.A;color #353ce5 #2:67.A;color #c85b8b #2:68.A;color #a37a31 #2:69.A;color #3518e5 #2:70.A;color #4882d6 #2:71.A;color #b55631 #2:72.A;color #74487c #2:73.A;color #6149d6 #2:74.A;color #282c40 #2:75.A;color #211e8b #2:76.A;color #22978b #2:77.A;color #7998e5 #2:78.A;color #a66c40 #2:79.A;color #501931 #2:80.A;color #15dd7c #2:81.A;color #ca756d #2:82.A;color #3b94e5 #2:83.A;color #262cd6 #2:84.A;color #7fc322 #2:85.A;color #a88840 #2:86.A;color #2b7a8b #2:87.A;color #486cd6 #2:88.A;color #994031 #2:89.A;color #71ce31 #2:90.A;color #3a8440 #2:91.A;color #ffffff #2:92.A;color #a2c25e #2:93.A;color #cf968b #2:94.A;color #28c440 #2:95.A;color #7b3ee5 #2:96.A;color #6aa8d6 #2:97.A;color #977b82 #3:2.A;color #683191 #3:3.A;color #7dc8af #3:4.A;color #768dcd #3:5.A;color #bb16af #3:6.A;color #1c5373 #3:7.A;color #3727a0 #3:8.A;color #d0afaf #3:9.A;color #6cb755 #3:10.A;color #8d7c73 #3:11.A;color #26d755 #3:12.A;color #1f15be #3:13.A;color #7e3464 #3:14.A;color #df35be #3:15.A;color #484555 #3:16.A;color #9764cd #3:17.A;color #84a191 #3:18.A;color #c766af #3:19.A;color #6f9a55 #3:20.A;color #9eb9cd #3:21.A;color #531582 #3:22.A;color #707064 #3:23.A;color #9b80cd #3:24.A;color #d0dbaf #3:25.A;color #3773a0 #3:26.A;color #26a155 #3:27.A;color #414855 #3:28.A;color #e267cd #3:29.A;color #c023cd #3:30.A;color #b18dbe #3:31.A;color #84d991 #3:32.A;color #1fadbe #3:33.A;color #bc63cd #3:34.A;color #ad19dc #3:35.A;color #6483cd #3:36.A;color #c9deaf #3:37.A;color #aab2dc #3:38.A;color #59d182 #3:39.A;color #6d6055 #3:40.A;color #1cd955 #3:41.A;color #b5cba0 #3:42.A;color #e281af #3:43.A;color #9537be #3:44.A;color #d6b0be #3:45.A;color #3bcf64 #3:46.A;color #2c6755 #3:47.A;color #e586cd #3:48.A;color #e22dcd #3:49.A;color #e29daf #3:50.A;color #4935a0 #3:51.A;color #caccbe #3:52.A;color #d573be #3:53.A;color #e229cd #3:54.A;color #b55782 #3:55.A;color #e449cd #3:56.A;color #614a55 #3:57.A;color #9e69cd #3:58.A;color #5f8873 #3:59.A;color #958fbe #3:60.A;color #9e45cd #3:61.A;color #975564 #3:62.A;color #1cdd73 #3:63.A;color #5ba291 #3:64.A;color #bedf55 #3:65.A;color #359564 #3:66.A;color #262d55 #3:67.A;color #711fa0 #3:68.A;color #505c64 #3:69.A;color #662773 #3:70.A;color #d319be #3:71.A;color #e2a1cd #3:72.A;color #b5cf82 #3:73.A;color #88b2be #3:74.A;color #bb4aaf #3:75.A;color #dc8773 #3:76.A;color #d579be #3:77.A;color #7c9864 #3:78.A;color #9d6c91 #3:79.A;color #79cd64 #3:80.A;color #aa1adc #3:81.A;color #ab4891 #3:82.A;color #1ca373 #3:83.A;color #8b4a73 #3:84.A;color #802daf #3:85.A;color #d9c4cd #3:86.A;color #c64daf #3:87.A;color #857b64 #3:88.A;color #a26daf #3:89.A;color #c629af #3:90.A;color #adb1be #3:91.A;color #5849af #3:92.A;color #93b3a0 #3:93.A;color #48e155 #3:94.A;color #93d3a0 #3:95.A;color #dc4d73 #3:96.A;color #d53fbe #3:97.A;color #6a4f55 #3:98.A On my Macbook these color commands take about 2 seconds. ChimeraX 1.0 (2020-06-04): > open pdb:4zho pdb:5h92 pdb:1a70 pdb:4zhp > view > color #1/A:2/B:2 #977b64;color #1/A:3/B:3 #e46daf;color #1/A:4/B:4 #7dc891;color #1/A:5/B:5 #768daf;color #1/A:6/B:6 #bb1691;color #1/A:7/B:7 #1c5355;color #1/A:8/B:8 #5b1873;color #1/A:9/B:9 #d0af91;color #1/A:10/B:10 #6cb737;color #1/A:11/B:11 #8d7c55;color #1/A:12/B:12 #844173;color #1/A:13/B:13 #1f15a0;color #1/A:14/B:14 #a27f91;color #1/A:15/B:15 #19cb64;color #1/A:16/B:16 #484537;color #1/A:17/B:17 #61be37;color #1/A:18/B:18 #84a173;color #1/A:19/B:19 #c76691;color #1/A:20/B:20 #8f31a0;color #1/A:21/B:21 #9eb9af;color #1/A:22/B:22 #531564;color #1/A:23/B:23 #707046;color #1/A:24/B:24 #9b80af;color #1/A:25/B:25 #ca18a0;color #1/A:26/B:26 #377382;color #1/A:27/B:27 #26a137;color #1/A:28/B:28 #d3b1a0;color #1/A:29/B:29 #e267af;color #1/A:30/B:30 #c023af;color #1/A:31/B:31 #b18da0;color #1/A:32/B:32 #88bb55;color #1/A:33/B:33 #1fada0;color #1/A:34/B:34 #b22773;color #1/A:35/B:35 #ad19be;color #1/A:36/B:36 #6483af;color #1/A:37/B:37 #c9de91;color #1/A:38/B:38 #aab2be;color #1/A:39/B:39 #59d164;color #1/A:40/B:40 #6d6037;color #1/A:41/B:41 #1cd937;color #1/A:42/B:42 #b5cb82;color #1/A:43/B:43 #e28191;color #1/A:44/B:44 #9537a0;color #1/A:45/B:45 #d6b0a0;color #1/A:46/B:46 #3bcf46;color #1/A:47/B:47 #2c6737;color #1/A:48/B:48 #e586af;color #1/A:49/B:49 #e22daf;color #1/A:50/B:50 #e29d91;color #1/A:51/B:51 #493582;color #1/A:52/B:52 #cacca0;color #1/A:53/B:53 #7f2855;color #1/A:54/B:54 #86dd91;color #1/A:55/B:55 #b55764;color #1/A:56/B:56 #4ac155;color #1/A:57/B:57 #614a37;color #1/A:58/B:58 #9e69af;color #1/A:59/B:59 #5f8855;color #1/A:60/B:60 #958fa0;color #1/A:61/B:61 #9e45af;color #1/A:62/B:62 #b9beaf;color #1/A:63/B:63 #4add55;color #1/A:64/B:64 #5ba273;color #1/A:65/B:65 #bedf37;color #1/A:66/B:66 #359546;color #1/A:67/B:67 #262d37;color #1/A:68/B:68 #cf5bbe;color #1/A:69/B:69 #505c46;color #1/A:70/B:70 #76db37;color #1/A:71/B:71 #3d37be;color #1/A:72/B:72 #a28391;color #1/A:73/B:73 #b5cf64;color #1/A:74/B:74 #88b2a0;color #1/A:75/B:75 #bb4a91;color #1/A:76/B:76 #dc8755;color #1/A:77/B:77 #d579a0;color #1/A:78/B:78 #7c9846;color #1/A:79/B:79 #b57b82;color #1/A:80/B:80 #79cd46;color #1/A:81/B:81 #aa1abe;color #1/A:82/B:82 #ab4873;color #1/A:83/B:83 #c6df91;color #1/A:84/B:84 #b3b3be;color #1/A:85/B:85 #802d91;color #1/A:86/B:86 #d9c4af;color #1/A:87/B:87 #c64d91;color #1/A:88/B:88 #857b46;color #1/A:89/B:89 #a26d91;color #1/A:90/B:90 #c62991;color #1/A:91/B:91 #adb1a0;color #1/A:92/B:92 #584991;color #1/A:93/B:93 #93b382;color #1/A:94/B:94 #48e137;color #2/C:1 #88c56f;color #2/C:2 #7b5d60;color #2/C:3 #32d660;color #2/C:4 #339b7e;color #2/C:5 #702460;color #2/C:6 #6725ba;color #2/C:7 #dc536f;color #2/C:8 #a3db7e;color #2/C:9 #a8918d;color #2/C:10 #d84eba;color #2/C:11 #758b7e;color #2/C:12 #88d751;color #2/C:13 #75ab7e;color #2/C:14 #8e527e;color #2/C:15 #cf53d8;color #2/C:16 #dc636f;color #2/C:17 #7d288d;color #2/C:18 #707460;color #2/C:19 #6fde51;color #2/C:20 #35a960;color #2/C:21 #627d8d;color #2/C:22 #bb42ab;color #2/C:23 #327060;color #2/C:24 #a3357e;color #2/C:25 #28bd8d;color #2/C:26 #8f91ba;color #2/C:27 #c856d8;color #2/C:28 #795760;color #2/C:29 #c067c9;color #2/C:30 #669b6f;color #2/C:31 #adabd8;color #2/C:32 #889d51;color #2/C:33 #c18f9c;color #2/C:34 #26bd51;color #2/C:35 #55cdba;color #2/C:36 #7e1a60;color #2/C:37 #238451;color #2/C:38 #68678d;color #2/C:39 #6da451;color #2/C:40 #a315d8;color #2/C:41 #88256f;color #2/C:42 #1f17ba;color #2/C:43 #4a456f;color #2/C:44 #6da051;color #2/C:45 #a4bfc9;color #2/C:46 #9557ba;color #2/C:47 #d6d0ba;color #2/C:48 #791d60;color #2/C:49 #e2e1ab;color #2/C:50 #1c616f;color #2/C:51 #7fda6f;color #2/C:52 #8e907e;color #2/C:53 #77559c;color #2/C:54 #c4bf8d;color #2/C:55 #77759c;color #2/C:56 #1658d8;color #2/C:57 #add1d8;color #2/C:58 #aa5aba;color #2/C:59 #95d3ba;color #2/C:60 #adadd8;color #2/C:61 #aa36ba;color #2/C:62 #95afba;color #2/C:63 #aa74d8;color #2/C:64 #731bd8;color #2/C:65 #442b6f;color #2/C:66 #8f1dba;color #2/C:67 #882d51;color #2/C:68 #9b2eab;color #2/C:69 #764d51;color #2/C:70 #6adb51;color #2/C:71 #359160;color #2/C:72 #e283ab;color #2/C:73 #ddb160;color #2/C:74 #cab2ba;color #2/C:75 #5559ba;color #2/C:76 #8a876f;color #2/C:77 #c76aab;color #2/C:78 #62a76f;color #2/C:79 #793f60;color #2/C:80 #23be51;color #2/C:81 #bab09c;color #2/C:82 #99397e;color #2/C:83 #a42bc9;color #2/C:84 #53597e;color #2/C:85 #165ad8;color #2/C:86 #9d888d;color #2/C:87 #d04dab;color #2/C:88 #b1d5ba;color #2/C:89 #c66dab;color #2/C:90 #44a151;color #2/C:91 #df5760;color #2/C:92 #66df6f;color #2/C:93 #cf1dd8;color #2/C:94 #a269ab;color #2/C:95 #551fba;color #2/C:96 #e4a7c9;color #3/A:1 #1f5c8b;color #3/A:2 #a68a40;color #3/A:3 #5f3140;color #3/A:4 #76147c;color #3/A:5 #9d5140;color #3/A:6 #6c8ed6;color #3/A:7 #37804f;color #3/A:8 #8edb31;color #3/A:9 #7b64e5;color #3/A:10 #ab2140;color #3/A:11 #a89a40;color #3/A:12 #b53231;color #3/A:13 #7e247c;color #3/A:14 #6125d6;color #3/A:15 #a2265e;color #3/A:16 #97bd7c;color #3/A:17 #aa556d;color #3/A:18 #a9a140;color #3/A:19 #9c3931;color #3/A:20 #9e407c;color #3/A:21 #8faa6d;color #3/A:22 #166f8b;color #3/A:23 #9bd97c;color #3/A:24 #76dad6;color #3/A:25 #cd90e5;color #3/A:26 #2628d6;color #3/A:27 #97ce31;color #3/A:28 #e2c07c;color #3/A:29 #933a4f;color #3/A:30 #cf328b;color #3/A:31 #a27e5e;color #3/A:32 #b5ca31;color #3/A:33 #946222;color #3/A:34 #8f546d;color #3/A:35 #28a040;color #3/A:36 #ab4740;color #3/A:37 #8c1b6d;color #3/A:38 #95946d;color #3/A:39 #d63b6d;color #3/A:40 #76ba5e;color #3/A:41 #b5524f;color #3/A:42 #8880d6;color #3/A:43 #b3ae8b;color #3/A:44 #9acd31;color #3/A:45 #77924f;color #3/A:46 #2cc0d6;color #3/A:47 #a9a340;color #3/A:48 #e2867c;color #3/A:49 #b5b431;color #3/A:50 #498e4f;color #3/A:51 #64627c;color #3/A:52 #85188b;color #3/A:53 #e4827c;color #3/A:54 #1f1a6d;color #3/A:55 #a4a27c;color #3/A:56 #cdb2e5;color #3/A:57 #60a45e;color #3/A:58 #7d2d40;color #3/A:59 #80c45e;color #3/A:60 #444422;color #3/A:61 #7ddb40;color #3/A:62 #688240;color #3/A:63 #1fbfd6;color #3/A:64 #46c05e;color #3/A:65 #71584f;color #3/A:66 #2686d6;color #3/A:67 #353ce5;color #3/A:68 #c85b8b;color #3/A:69 #a37a31;color #3/A:70 #3518e5;color #3/A:71 #4882d6;color #3/A:72 #b55631;color #3/A:73 #74487c;color #3/A:74 #6149d6;color #3/A:75 #282c40;color #3/A:76 #211e8b;color #3/A:77 #22978b;color #3/A:78 #7998e5;color #3/A:79 #a66c40;color #3/A:80 #501931;color #3/A:81 #15dd7c;color #3/A:82 #ca756d;color #3/A:83 #3b94e5;color #3/A:84 #262cd6;color #3/A:85 #7fc322;color #3/A:86 #a88840;color #3/A:87 #2b7a8b;color #3/A:88 #486cd6;color #3/A:89 #994031;color #3/A:90 #71ce31;color #3/A:91 #3a8440;color #3/A:92 #ffffff;color #3/A:93 #a2c25e;color #3/A:94 #cf968b;color #3/A:95 #28c440;color #3/A:96 #7b3ee5;color #3/A:97 #6aa8d6;color #4/A:2 #977b82;color #4/A:3 #683191;color #4/A:4 #7dc8af;color #4/A:5 #768dcd;color #4/A:6 #bb16af;color #4/A:7 #1c5373;color #4/A:8 #3727a0;color #4/A:9 #d0afaf;color #4/A:10 #6cb755;color #4/A:11 #8d7c73;color #4/A:12 #26d755;color #4/A:13 #1f15be;color #4/A:14 #7e3464;color #4/A:15 #df35be;color #4/A:16 #484555;color #4/A:17 #9764cd;color #4/A:18 #84a191;color #4/A:19 #c766af;color #4/A:20 #6f9a55;color #4/A:21 #9eb9cd;color #4/A:22 #531582;color #4/A:23 #707064;color #4/A:24 #9b80cd;color #4/A:25 #d0dbaf;color #4/A:26 #3773a0;color #4/A:27 #26a155;color #4/A:28 #414855;color #4/A:29 #e267cd;color #4/A:30 #c023cd;color #4/A:31 #b18dbe;color #4/A:32 #84d991;color #4/A:33 #1fadbe;color #4/A:34 #bc63cd;color #4/A:35 #ad19dc;color #4/A:36 #6483cd;color #4/A:37 #c9deaf;color #4/A:38 #aab2dc;color #4/A:39 #59d182;color #4/A:40 #6d6055;color #4/A:41 #1cd955;color #4/A:42 #b5cba0;color #4/A:43 #e281af;color #4/A:44 #9537be;color #4/A:45 #d6b0be;color #4/A:46 #3bcf64;color #4/A:47 #2c6755;color #4/A:48 #e586cd;color #4/A:49 #e22dcd;color #4/A:50 #e29daf;color #4/A:51 #4935a0;color #4/A:52 #caccbe;color #4/A:53 #d573be;color #4/A:54 #e229cd;color #4/A:55 #b55782;color #4/A:56 #e449cd;color #4/A:57 #614a55;color #4/A:58 #9e69cd;color #4/A:59 #5f8873;color #4/A:60 #958fbe;color #4/A:61 #9e45cd;color #4/A:62 #975564;color #4/A:63 #1cdd73;color #4/A:64 #5ba291;color #4/A:65 #bedf55;color #4/A:66 #359564;color #4/A:67 #262d55;color #4/A:68 #711fa0;color #4/A:69 #505c64;color #4/A:70 #662773;color #4/A:71 #d319be;color #4/A:72 #e2a1cd;color #4/A:73 #b5cf82;color #4/A:74 #88b2be;color #4/A:75 #bb4aaf;color #4/A:76 #dc8773;color #4/A:77 #d579be;color #4/A:78 #7c9864;color #4/A:79 #9d6c91;color #4/A:80 #79cd64;color #4/A:81 #aa1adc;color #4/A:82 #ab4891;color #4/A:83 #1ca373;color #4/A:84 #8b4a73;color #4/A:85 #802daf;color #4/A:86 #d9c4cd;color #4/A:87 #c64daf;color #4/A:88 #857b64;color #4/A:89 #a26daf;color #4/A:90 #c629af;color #4/A:91 #adb1be;color #4/A:92 #5849af;color #4/A:93 #93b3a0;color #4/A:94 #48e155;color #4/A:95 #93d3a0;color #4/A:96 #dc4d73;color #4/A:97 #d53fbe;color #4/A:98 #6a4f55 These color commands take 15-16 seconds. Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

2 1

creating an annotated structure
by Melissa Jurica 30 Jun '20

30 Jun '20

Can you provide some guidelines for how one could create an annotated structure to share with colleagues? For example, I would like to annotate the cancer associated mutations of a protein, making it easy for someone to select and visualize the associated residue in a structure. Ideally, these annotations could be grouped and sorted. Even better, they could be linked to other resources. Thanks Melissa

2 2

Converting Chimera movie script
by Vid Sustar 26 Jun '20

26 Jun '20

The following bug report has been submitted: Platform: Linux-5.3.0-61-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hello! I have tried to adapt the cliping script from http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/scripts/clip.cmd to work in ChimeraX (because my structure is too big, to be loaded properly in earlier Chimera) I tried to convert the old commands to the ChimeraX, but I get an error in the line "clip front -0.5 120": Expected a keyword Please advise me how to change the code to work with ChimeraX to create a movie or to simply save a series of images of cliped planes Best regards, Vid Sustar Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py", line 150, in _qt_safe if data_format is None else " format " + StringArg.unparse(data_format.nicknames[0]))) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "clip2.py", line 3, in <module> ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File "clip2.py", line 3, in See log for complete Python traceback. > ui tool show Shell /usr/lib/ucsf-chimerax/lib/python3.7/site- packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn("IPython History requires SQLite, your history will not be saved") > select up Nothing selected > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py", line 150, in _qt_safe if data_format is None else " format " + StringArg.unparse(data_format.nicknames[0]))) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "clip2.py", line 3, in <module> ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File "clip2.py", line 3, in See log for complete Python traceback. > open /home/user/MASTERS/Chimera_files/PythonScripts/writeMol2.py Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py", line 150, in _qt_safe if data_format is None else " format " + StringArg.unparse(data_format.nicknames[0]))) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "writeMol2.py", line 2, in <module> ModuleNotFoundError: No module named 'chimera' ModuleNotFoundError: No module named 'chimera' File "writeMol2.py", line 2, in See log for complete Python traceback. > help help:user > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py", line 150, in _qt_safe if data_format is None else " format " + StringArg.unparse(data_format.nicknames[0]))) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 101, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2805, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 152, in provider_open name or model_name_from_path(fi.file_name)), provider_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py", line 365, in collated_open return func(*func_args, **func_kw) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core_formats/__init__.py", line 48, in open return open_python_script(session, data, file_name) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 82, in open_python_script _exec_python(session, code, argv) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/scripting.py", line 59, in _exec_python exec(code, sandbox.__dict__) File "clip2.py", line 4, in <module> ImportError: cannot import name 'runCommand' from 'chimerax' (unknown location) ImportError: cannot import name 'runCommand' from 'chimerax' (unknown location) File "clip2.py", line 4, in See log for complete Python traceback. > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 > wait wait requires a frame count argument unless motion is in progress > movie encode clip.mp4 bitrate 200 Movie encoding failed because no images were recorded. > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 120 Expected a keyword > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > windowsize 200 150 > copy file clip.jpg Unknown command: copy file clip.jpg > copy Unknown command: copy > save /home/user/Desktop/image1.png supersample 3 > movie record Already recording a movie > open /home/user/Desktop/gbpmovie.cxc No such file/path: /home/user/Desktop/gbpmovie.cxc > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 Already recording a movie > movie stop > movie record supersample 3 > movie stop > movie stop Not currently recording > close session > open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc > open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb > select :wat 157584 atoms, 157584 bonds, 1 model selected > hide sel target a > select ~sel 37869 atoms, 34860 bonds, 1 model selected > surface sel > color (#!1 & sel) white > select ::name="OQL" 2380 atoms, 2520 bonds, 1 model selected > color (#!1 & sel) red > select ::name="ONC" 4200 atoms, 3920 bonds, 1 model selected > color (#!1 & sel) blue > select ::name="NP" 2869 atoms, 1 model selected > color (#!1 & sel) yellow > lighting flat > lighting shadows false > graphics silhouettes false > movie record supersample 3 > clip front -0.5 120 ; wait 120 ; movie encode clip.mp4 bitrate 200 Expected a keyword > help help:contact.html OpenGL version: 3.3.0 NVIDIA 440.100 OpenGL renderer: GeForce RTX 2060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Micro-Star International Co., Ltd. Model: GL63 8SE OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz Cache Size: 9216 KB Memory: total used free shared buff/cache available Mem: 31G 6.1G 18G 662M 6.6G 24G Swap: 2.0G 0B 2.0G Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b] Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:126a] Kernel driver in use: i915 PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: clip2.cxc

3 2

chimerax label bug
by Lukas Kater 26 Jun '20

26 Jun '20

Hi ChimeraX developers, I have been tryinng to use 2dlabel to annotate some things in a movie. I have stumbled accross a number of problems: 1) creating 2 labels with the same name causes a crasH: 2dlab create ADP text "ADP state" color black size 26 bold true xpos 0.03 ypos 0.92 visibility false 2dlab create ADP text "ADP state" color black size 26 bold true xpos 0.03 ypos 0.92 visibility false

2 3

Local resolution legend
by Tetter Stephan 25 Jun '20

25 Jun '20

Dear ChimeraX Users and Developers, I manage to color my cryoEM maps by local resolution, but can't figure out how to display a scale bar of the color code. Any ideas? Or do I have to go back to Chimera for this? Thanks, Stephan

4 4

Morph cryoEM maps result
by Aritz Roa Eguiara 25 Jun '20

25 Jun '20

Dear ChimeraX team, This is probably a previously discussed topic but I have not managed to find it specifically anywhere. So I am trying to morph a couple of maps on ChimeraX using the volume morph command, but I do not get any slider as it happens with the atom model morphing (as far as I understand there is not option for that?) Also, once I do it I get a model that is called morph that if I run the movie is recorded but I cannot bounce or control any further, is it like a one time use command that then only leaves that model result of the last frame that cannot be used anymore? Best regards, Aritz

2 2

CIF writer renumbers residues
by Daniel Asarnow 23 Jun '20

23 Jun '20

Hi all, When I save a CIF from ChimeraX (while using ISOLDE), the warning "Not saving entity_poly_seq for non-authoritative sequences" is produced, and all the residues have been sequentially renumbered from 1. When there are missing residues, each segment has to be renumbered manually afterwards. Is there some way to avoid this with PDB or CIF inputs? Is it a bug? Best, -da

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Re: [chimerax-users] Antw: [EXT] Re: selection modes
by Elaine Meng 23 Jun '20

23 Jun '20

> From: "Philipp Milkereit" <Philipp.Milkereit(a)vkl.uni-regensburg.de> > Subject: Antw: Re: [chimerax-users] Antw: [EXT] Re: selection modes > Date: June 18, 2020 at 9:06:02 AM PDT > To: <meng(a)cgl.ucsf.edu> > > Hi Elaine > just a follow-up question on the Select Menu_Mode:Add, do you think it could make sense to apply this mode also to user-defined names listed in the Basic Actions window? That seems at the moment neither in ChimeraX 0.93 nor in 1.0 the case, but could be an easy way to add fast a bunch of named selections to the current selection. Also for the subtract/intersect modes that might be an interesting option? > > best wishes, > > Philipp > >>> Elaine Meng <meng(a)cgl.ucsf.edu> 18.06.2020 17:33 >>> > Hi Philipp, > I don't think there is an ISOLDE for 1.0 yet. If I look at the toolshed it says ISOLDE 1.05b "works with 0.93" > > <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde>> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jun 18, 2020, at 1:18 AM, Philipp Milkereit <Philipp.Milkereit(a)vkl.uni-regensburg.de> wrote: > > > > Dear Elaine, > > > > thanks for your help! > > Your example does not work for me on ChimeraX 0.93 (2020-04-03) both on a Windows and a Linux sytem. But after installing the new production version 1.0 the selection mode works indeed there on user defined selectors as expected, which is great! > > Apparently there should be also now versions of the Isolde plugin (1.0b5 ?) which are compatible with ChimeraX 1.0, so no reason anymore to stay with 0.93.. > > > > Best, > > > > Philipp > > >>> Elaine Meng <meng(a)cgl.ucsf.edu> 18.06.2020 01:15 >>> > > Hi Philipp, > > This works fine for me using the menu. For example, start ChimeraX, then: > > > > open 2gbp > > menu: Select... Structure... Secondary Structure... Strand > > menu: Select... Define Selector... (I gave it the name "mystrands") > > menu: Select... Clear > > menu: Select... Structure... Ligand > > menu: Select... Menu Mode... Add > > menu: Select... User-Defined Selectors... mystrands > > > > Now both the ligand and strands are selected. Also works if I use commands for any of those steps. When you use the menu, the corresponding commands are echoed in the Log, and it actually works by running the commands, so it doesn't make sense that commands would work and the menu wouldn't. > > > > Tested in version 1.0. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > > > On Jun 17, 2020, at 1:11 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> wrote: > > > > > > Dear all, > > > > > > is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the „append“ selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line „select add“ command. > > > > > > Many thanks for your help, > > > > > > Philipp Milkereit

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Re: [chimerax-users] [Chimera-users] convert .mod to .mrc
by Elaine Meng 23 Jun '20

23 Jun '20

Dear Emmanuel Moebel, I can't think of a simple way to make an index map from IMOD meshes, only a multistep process for each mesh object. At first I misread the question and thought you said "ChimeraX" so below are steps for both Chimera and ChimeraX in case anybody might be interested. I have not tried the entire process, however. I hope this helps, Elaine =-=-= The following instructions are for Chimera: Each IMOD mesh object from the file is a surface piece. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod…> You can specify that surface piece in a "mask" command as "sel" (after selecting it with the mouse) and specifying input map as "ones" to create a map that has values of 1 inside, 0 outside. Then you can scale the map by using "vop scale" to multiply values by a constant (e.g. for values of 2 or 3 instead): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale> Maybe if you did this for multiple mesh objects you could combine the results into one map with "vop add"; not sure how well this would work. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add> Then you can save your index map as MRC using the Volume Viewer File menu or command "volume" <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu…> =-=-= The following instructions are for ChimeraX. Each IMOD mesh object from the file is a surface model in ChimeraX. <http://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html> You can specify that surface model in a "volume onesmask" command to create a map that has values of 1 inside, 0 outside, then multiply values by a constant (e.g. for values of 2 or 3 instead) using "volume scale": <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#scale> Maybe if you did this for multiple mesh objects you could combine the results into one map with "volume add"; not sure how well this would work. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add> Then you can use "save" to write your index map as MRC: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 23, 2020, at 7:00 AM, Emmanuel Moebel <emmanuel.moebel(a)inria.fr> wrote: > > Dear Chimera community, > > I am visualising a tomogram segmentation with Chimera, the format of the file is .mod and has been obtained with the IMOD software. I would like to get a voxel map from it : a volume with integer values, for ex. '0' for background, '1' for membrane, '2' for filament. Output file format needs to be .mrc or .em. Is this possible to achieve with Chimera? > > Thanks in advance, > Emmanuel Moebel, PhD

1 0

select model Z-translate
by 张佳星 23 Jun '20

23 Jun '20

Dear all， How can i do select model Z-translate use mouse? like command move z distance models when i click toolbar- Right Mouse-Move model,selected one model,scroll the mouse +right mouse ,all model will zoom Many thanks for your help, Jiaxing Zhang

2 1

Re: [chimerax-users] [Chimera-users] Structure Minimization and Molecule Movement (ChimeraX-1.0)?
by Elaine Meng 20 Jun '20

20 Jun '20

Dear Ammar, For future reference, for ChimeraX questions it is better to use the chimerax-users(a)cgl.ucsf.edu mailing list instead of this one. We announced ChimeraX on both "announce" lists, however, because we thought Chimera users would want to know about it. (1) Moving only a subset of atoms. In ChimeraX, the way to move only a subset of the models or the atoms with the mouse is to assign the mouse to move only the selected models or atoms, then select the atoms of interest, and then move them with the mouse. For example, all of the icons in the "Right Mouse" tab of the toolbar represent different modes, and clicking an icon assigns that function to the right mouse button ( = trackpad + Alt on Windows, trackpad + command key on a Mac). Click the icon that looks like a blue sphere with arrows around it to assign the right mouse button to "move selected atoms." Then dragging with the right mouse button (or trackpad equivalent) will translate the selected atoms and additionally pressing Shift will rotate the selected atoms. Right Mouse icons and what they mean: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> Similar between Chimera and ChimeraX: there are multiple possible ways to select the ligand, e.g. choosing its residue name from menu: Select... Residue... [residue name], or Ctrl-clicking on one of its atoms and then pressing the keyboard up arrow key to promote the selection to the whole residue. <http://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html> Although the Right Mouse icons only assign functions to the right mouse button, with the "mousemode" command, you can assign any of these functions to any mouse button alone or in combination with modifier keys. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> (2) There is no minimize structure tool in ChimeraX currently. There are limited local "jiggling" calculations with the "tug" and "minimize" mouse modes but only for structures with only standard biopolymer residues and water, not ligands in general: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> .... and more extensive molecular dynamics capabilities with the ISOLDE plugin for refinement/modeling into density maps: <https://isolde.cimr.cam.ac.uk/what-isolde/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 20, 2020, at 6:18 PM, Ammar Jastaniah <ajasta2(a)uic.edu> wrote: > > Hi, > I am not able to find the minimize feature function in ChimeraX-1.0. Is there an equivalent to the regular Chimera version, which is to be found under Tools ==> Structure Editing ===> Minimize Structure? > > Also. Are you able to move a PDB file ligand molecule around while keeping the other receptor PDB structure stationary/in its place in ChimeraX-1.0? Once again, this is achievable in Chimera by clicking on Tools ==> Movement ===> Movement Mouse Mode. > Thank you. > Ammar

1 0

ViewDock script
by Moustafa, Ibrahim M. 19 Jun '20

19 Jun '20

Dear All, I'm trying to run ViewDock from a script using the following command in a loop: runCommand("viewdock " + filename + " AutoDock") It works fine. However, the ViewDock window remains opened after reading each file. For large number of files it is not practical to close them manually. Is there a command to close the opened ViewDock windows to add to the script? Thank you for your help. Ibrahim

3 4

RMSD command in ChimeraX
by Hrvoje Rimac 19 Jun '20

19 Jun '20

Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms. P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454 Best regards, Hrvoje Rimac Hrvoje Rimac, PhD. Postdoctoral Fellow Department of Medicinal Chemistry Faculty of Pharmacy and Biochemistry University of Zagreb A.Kovačića 1, 10000 Zagreb Croatia http://www.pharma.unizg.hr/

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ChimeraX: mmcif connectivity lost in some chains; OK in Coot
by Anderson, Jacob 18 Jun '20

18 Jun '20

Dear ChimeraX team, Thank you very much for your work on this great software. We use it daily, and without which it would be extremely difficult to articulate our science. I am touching base with a problem I am having after migrating from a pdb --> mmcif format.For context, I am running ChimeraX on Ubuntu 20.04 using a fresh deb install this morning: chimerax --version UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. To be explicit, my problem is entirely reproducible. Specifically, I have a file (attached) that when opened in ccpem's Coot v0.9-pre, has all the connectivity present. However, when I switch to ChimeraX, the connectivity of some chains are lost. A good example of this contrast on chain connectivity fidelity is chain LA and LB. (photo attached). I tried reading through the ChimeraX documentation on this CIF format,<https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guide…> but it remained not totally clear to me what is going awry in some chains but not in others. If you might have any insight on how to overcome this problem in chimerax, and allow all the chains to remain their connectivity, I would very much appreciate your thoughts/wisdom on the topic. ~Jacob [cid:0f6782e1-eb79-43db-93e8-0f8f44417fb3]

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Antw: [EXT] Re: selection modes
by Philipp Milkereit 18 Jun '20

18 Jun '20

Dear Elaine, thanks for your help! Your example does not work for me on ChimeraX 0.93 (2020-04-03) both on a Windows and a Linux sytem. But after installing the new production version 1.0 the selection mode works indeed there on user defined selectors as expected, which is great! Apparently there should be also now versions of the Isolde plugin (1.0b5 ?) which are compatible with ChimeraX 1.0, so no reason anymore to stay with 0.93.. Best, Philipp >>> Elaine Meng <meng(a)cgl.ucsf.edu> 18.06.2020 01:15 >>> Hi Philipp, This works fine for me using the menu. For example, start ChimeraX, then: open 2gbp menu: Select... Structure... Secondary Structure... Strand menu: Select... Define Selector... (I gave it the name "mystrands") menu: Select... Clear menu: Select... Structure... Ligand menu: Select... Menu Mode... Add menu: Select... User-Defined Selectors... mystrands Now both the ligand and strands are selected. Also works if I use commands for any of those steps. When you use the menu, the corresponding commands are echoed in the Log, and it actually works by running the commands, so it doesn't make sense that commands would work and the menu wouldn't. Tested in version 1.0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 17, 2020, at 1:11 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> wrote: > > Dear all, > > is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the „append“ selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line „select add“ command. > > Many thanks for your help, > > Philipp Milkereit >

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selection modes
by Philipp Milkereit 17 Jun '20

17 Jun '20

Dear all, is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the "append" selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line "select add" command. Many thanks for your help, Philipp Milkereit

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Re: [chimerax-users] ChimeraX troubleshooting
by Tom Goddard 17 Jun '20

17 Jun '20

Hi Joseph, Ok, it is complaining about a ChimeraX preference file C:\Users\Joseph\AppData\Local\UCSF\ChimeraX\ui-1 that saves your last ChimeraX window size (which is used when you start ChimeraX the next time), and saves any tools you added to the Favorites menu. It is supposed to be a text file but yours somehow contains all binary 0. Could you send us that ui-1 file, then delete it, and hopefully ChimeraX will start if there are no other problems. I will open a bug report and we will look at how this happened and probably put in some code so that if a preference file is unreadable ChimeraX will still start and just warn you about the corrupted file. You will get an email about that bug report and it would help if you could reply to that email with the ui-1 file as an attachment to help us debug the problem. Tom > On Jun 17, 2020, at 2:03 PM, Joseph Chamieh <joseph.chamieh(a)umontpellier.fr> wrote: > > Dear Tom > Thank you for your answer, this is the result of what you asked for: > > C:\>"C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug > C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses > import imp, sys, os > Traceback (most recent call last): > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193, in _run_module_as_main > "__main__", mod_spec) > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85, in _run_code > exec(code, run_globals) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895, in <module> > exit_code = init(sys.argv) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 502, in init > sess.ui = ui_class(sess) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 110, in __init__ > self.settings = UI_Settings(session, "ui") > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\settings.py", line 165, in __init__ > ConfigFile.__init__(self, session, tool_name, version=version) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\configfile.py", line 289, in __init__ > self._config.read(self._filename, encoding='utf-8') > File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 696, in read > self._read(fp, filename) > File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 1079, in _read > raise MissingSectionHeaderError(fpname, lineno, line) > configparser.MissingSectionHeaderError: File contains no section headers. > file: 'C:\\Users\\Joseph\\AppData\\Local\\UCSF\\ChimeraX\\ui-1', line: 1 > '\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00' > > I remain at your disposal for any further information > Best regards > Joseph > > > _____________________________________________________________________ > Joseph Chamieh, PhD, HDR > Institut des Biomolécules Max Mousseron, UMR CNRS 5247, > Université de Montpellier, > Place Eugène Bataillon, case courrier 1706, > F-34095 Montpellier Cedex 5, France > Phone: +33 4 67 14 39 20 > Fax: +33 4 67 63 10 46 > http://www.dsbc.univ-montp2.fr/recherche_en.html <http://www.dsbc.univ-montp2.fr/recherche_en.html> > http://orcid.org/0000-0003-4209-1337 <http://orcid.org/0000-0003-4209-1337> > ______________________________________________________________________ > > De : Tom Goddard [mailto:goddard@sonic.net] > Envoyé : Wednesday, June 17, 2020 7:01 PM > À : Joseph Chamieh <joseph.chamieh(a)umontpellier.fr> > Cc : chimerax-users(a)cgl.ucsf.edu > Objet : Re: [chimerax-users] ChimeraX troubleshooting > > Hi Joseph, > > To see why ChimeraX is failing to start on Windows, run it from a Windows Command Prompt as follows (two dashes in --debug) > > "C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug > > and send us the error message this gives. > > Tom > > > >> On Jun 17, 2020, at 1:51 AM, Joseph Chamieh <joseph.chamieh(a)umontpellier.fr <mailto:joseph.chamieh@umontpellier.fr>> wrote: >> >> Dear ChimeraX developers, >> First I would like to thank you for your wonderful job. I was looking for a software able to modelize my peptide in 3D and do all the calculations on it and I found ChimeraX yesterday, I downloaded and installed the software and directly found it as the best answer for my “problems”, however it worked in the morning and after a restarting of my laptop on midday, I was not able to start the software, so I uninstalled/reinstalled, I restarted again but since then I could not find the solution, I use an HP laptop Win 10 64 bit, I attached the dxdiag summary. >> I would appreciate it if you could help me find the solution. >> Best regards >> Joseph >> >> _____________________________________________________________________ >> Joseph Chamieh, PhD, HDR >> Institut des Biomolécules Max Mousseron, UMR CNRS 5247, >> Université de Montpellier, >> Place Eugène Bataillon, case courrier 1706, >> F-34095 Montpellier Cedex 5, France >> Phone: +33 4 67 14 39 20 >> Fax: +33 4 67 63 10 46 >> http://www.dsbc.univ-montp2.fr/recherche_en.html <http://www.dsbc.univ-montp2.fr/recherche_en.html> >> http://orcid.org/0000-0003-4209-1337 <http://orcid.org/0000-0003-4209-1337> >> ______________________________________________________________________ >> >> <DxDiag.txt>_______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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maximized on startup
by Anthony James Schaefer 17 Jun '20

17 Jun '20

Hello, Would it be possible to add an option for the ChimeraX app to be maximized on startup? I've got the window size set to 'last used' and I almost always maximize ChimeraX. With this combo, ChimeraX starts out the size of my screen, but not maximized. Thanks, Tony

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