July 2020 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] label_seq_id in mmcif files for Chimera
by Greg Couch 08 Jul '20

08 Jul '20

On 7/7/2020 3:50 PM, Marcin Wojdyr wrote: > On Tue, 7 Jul 2020 at 22:38, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: >> As you know, the entity_poly_seq table says which polymeric residues are >> adjacent to each other (entity_poly_seq.num values are the >> atom_site.label_seq_id values). > Yes, it's an enhanced equivalent of the SEQRES record in the PDB > format. Files from the wwPDB always have it, but files from other > sources will often miss it. I think currently almost all the mmCIF > files in circulation originate from the wwPDB. But this is slowly > changing and people are starting to use mmCIF as a working format. The sequence information is extremely useful for eliminating ambiguities in the atom_site data. And it is frequently known by the user, even when it is missing from the mmCIF file. >> Without that information, ChimeraX >> still needs the atom_site.label_seq_id to imply the polymeric ordering. > Ok. It would be useful, though, if ChimeraX could infer the ordering > and connectivity in the same way as it does for PDB files. > > Thanks, > Marcin Adding a atom_site.label_seq_id isn't different from supplying a residue number in PDB file. When there are adjacent residues of the same type, does the PDB reader see a duplicate atom and generate a new residue? merge the residues? generate an error? I haven't tested the PDB reader, but a residue number helps it too. Learning to use mmCIF effectively will take time. Programmers should use the PDB's mmCIF Dictionary Suite to validate the mmCIF their programs output -- it won't validate completely (because it's for mmCIF files served by the PDB), but it will show where the mmCIF output can be improved. For more information about ChimeraX reading mmCIF, see https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guide…. ChimeraX's mmCIF reader tries really hard to show you the data exactly as it is specified. So if there's badly specified data, you'll be able to see it. Over time, we will improve ChimeraX's ability to handle underspecified data as developers start generating mmCIF files. But we don't plan to modify the mmCIF reader if we can help it. Adding code, to infer information that should be explicitly given in the mmCIF file, slows down the mmCIF reader for everyone. This is especially true for large structures with over a million atoms. -- Greg

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Re: [chimerax-users] [Chimera-users] Chimera X - Windows 7 home premium
by Greg Couch 08 Jul '20

08 Jul '20

(This is a ChimeraX question, so sending the reply to the chimerax-users mailing too.) Looking at the image, the three gray boxes are icons for previously opened data files. To get an interactive 3D image, you would need to open an appropriate data file. If you type in the command "open 3rec" and press Enter/Return afterwards to open PDB model 3rec, does an interactive 3D image show up? If you can't get an interactive 3D image, then you probably need a newer graphics driver. I'd recommend going to the Lenovo support web site and installing a newer graphics driver. If the driver from Lenovo doesn't fix the problem, then you'll need to get one directly from Intel at https://downloadcenter.intel.com/. From the DxDiag.txt output, you have a 2nd generation i7 with HD Graphics 3000 driver version 8.15.10.2656. Lenovo has version 8.15.10.2274 from 6/9/2011 for your computer. On the Intel site, I see that version 15.28.24.4229 from 6/5/2015 is available. And you should know that we don't test ChimeraX on Windows 7, so technically you are on an unsupported platform. That said, we are unaware of anything that would prevent ChimeraX from running on Windows 7. However, with the age of your laptop, you should consider switching from Windows to Ubuntu (Linux). Intel is still supporting the Linux graphics driver for older systems. HTH, Greg On 7/8/2020 7:29 AM, MONICA MESA CADAVID wrote: > I would like to use the new Chimera X. > I installed and open the program easily. > But the images did not appear. > I attach the information of my computer because I would like to know > if I can fix the problem. > Thank you > * > * > image.png > *Monica Mesa Cadavid* > Profesor Titular > Instituto de Quimica > Facultad de Ciencias Exactas y Naturales > monica.mesa(a)udea.edu.co <http://udea.edu.co/> > Grupo Ciencia de los Materiales > Sede de Investigacion Universitaria, SIU -Torre 1, laboratorio 310 > Cra 53 # 61 - 30 > Tel. 574 - 219 6546 > > http://www.udea.edu.co/ <http://www.udea.edu.co/> > > > > *Universidad de Antioquia* > www.udea.edu.co <http://www.udea.edu.co/> > Sede Principal: Cll 67 # 53 - 108 > Medellín, Colombia > > "La información aquí contenida es para uso exclusivo de la persona o > entidad de destino. Está estrictamente prohibida su utilización, > copia, descarga, distribución, modificación y/o reproducción total o > parcial, sin el permiso expreso de Universidad de Antioquia, pues su > contenido puede ser de carácter confidencial y/o contener material > privilegiado. Si usted recibió esta información por error, por favor > contacte en forma inmediata a quien la envió y borre este material de > su computador. Universidad de Antioquia no es responsable por la > información contenida en esta comunicación, el directo responsable es > quien la firma o el autor de la misma." > > > > "La información aquí contenida es para uso exclusivo de la persona o > entidad de destino. Está estrictamente prohibida su utilización, > copia, descarga, distribución, modificación y/o reproducción total o > parcial, sin el permiso expreso de Universidad de Antioquia, pues su > contenido puede ser de carácter confidencial y/o contener material > privilegiado. Si usted recibió esta información por error, por favor > contacte en forma inmediata a quien la envió y borre este material de > su computador. Universidad de Antioquia no es responsable por la > información contenida en esta comunicación, el directo responsable es > quien la firma o el autor de la misma." > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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ChimeraX bug report submission
by Nicco 08 Jul '20

08 Jul '20

The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hi, I'm trying to record a movie and the movie generated stops before executing all final steps. It's like the last frames are not recorded even when I see a very high limit. I feel like movie encode starts processing before it is called. For example these commands below are not present in the movie but the movie encode is called afterwards. # Select last interaction area select /F:370,375 /E:270,309,314 show sel atoms hbonds sel select clear # Final show turn x 15 60 rock 130 turn -y 15 60 rock 130 I'm a bit puzzled of why this is happening and I don't really now how to fix it. I attach the .cxc file with the set of instructions that I use to create the movie. Please consider that my experience level is beginner so there could be something that I'm doing wrong. Thank you! Nicco 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 "/Users/niar/Dropbox (CRG > ADV)/Nicco/projects/06_Chimera/src/movies/6NQ3_Suz12_AS_event.cxc" > open 6NQ3 6nq3 title: Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex [more info...] Chain information for 6nq3 #1 --- Chain | Description A E | Histone-binding protein RBBP4 B F | Polycomb protein SUZ12 C G | PHD finger protein 19 D H | Protein Jumonji Non-standard residues in 6nq3 #1 --- ZN — zinc ion 6nq3 mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > select all 11928 atoms, 12213 bonds, 30 pseudobonds, 3 models selected > show sel cartoons > style sel stick Changed 11928 atom styles > hide sel atoms > select /A,B,C,G,D,H 6565 atoms, 6720 bonds, 15 pseudobonds, 3 models selected > hide sel cartoons > select /E 3045 atoms, 3128 bonds, 2 pseudobonds, 2 models selected > color (#!1 & sel) purple > select /F 2318 atoms, 2365 bonds, 13 pseudobonds, 3 models selected > color (#!1 & sel) cyan > select clear > set bgColor white > lighting soft > graphics silhouettes true > view > view name start > movie record supersample 1 size 720,720 limit 5000 directory > /Users/niar/Desktop/tmp_chimera pattern Frame_n* > turn z -70 > turn x 24 > turn y -40 > view name hole > wait 5 > select sequence > EEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLP 1138 atoms, 1174 bonds, 1 model selected > color sel orange > select clear > wait 10 > select sequence NHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYT 540 atoms, 552 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHQKEGYGLSWNPNLSGHLLSASDDHTICLWD 500 atoms, 516 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHTAVVEDVSWHLLHESLFGSVADDQKLMIWD 512 atoms, 526 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence AHTAEVNCLSFNPYSEFILATGSADKTVALWD 488 atoms, 500 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence SHKDEIFQVQWSPHNETILASSGTDRRLNVWD 532 atoms, 546 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHTAKISDFSWNPNEPWVICSVSEDNIMQVWQ 522 atoms, 540 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence RKTFKVDDMLSKVEKMKGEQESH 299 atoms, 299 bonds, 1 model selected > color sel red > select clear > wait 10 > turn x 20 120 rock 120 > wait > turn y 35 150 rock 150 > wait > turn y 4 90 > wait > turn y 1 50 > wait > turn x 1 35 > wait > zoom 1.5 80 > wait > move x 0.75 15 > move y -0.75 15 > wait > view name side > select /E:9-28 /E:32-39 239 atoms, 242 bonds, 1 model selected > show sel atoms > hbonds sel 51 hydrogen bonds found > select clear > wait 20 > turn x 15 60 rock 60 > wait > turn y 15 60 rock 60 > wait > ~hbonds > select /E:9-28 /E:32-39 239 atoms, 242 bonds, 1 model selected > hide sel atoms > select clear > wait 5 > move y 0.75 15 > move x -0.75 15 > wait > zoom 0.5 80 > wait > turn -x 1 35 > wait > turn -y 1 50 > wait > view hole > move x 0.75 25 > move y -0.5 25 > wait 25 > turn x 0.5 25 > zoom 3 80 > wait 80 > turn x 0.75 25 > move y 0.5 25 > wait 25 > view name zoom1 > select /F:129 /E:409 /E:346 31 atoms, 29 bonds, 1 model selected > show sel atoms > color (#!1 & sel) byelement > hbonds sel 12 hydrogen bonds found > select clear > wait 15 > turn -y 15 120 rock 120 > wait > turn x 15 60 rock 130 > wait > wait 15 > view name zoom2 > turn y -1.5 25 > move x -0.5 25 > wait 25 > turn x -1 25 > turn z 1 25 > move x 0.4 25 > wait 25 > select /F:135 /E:285,304,330 34 atoms, 30 bonds, 1 model selected > show sel atoms > color (#!1 & sel) byelement > hbonds sel 11 hydrogen bonds found > select clear > turn y -10 120 rock 180 > wait > turn x 15 120 rock 120 > wait > wait 20 > view name zoom3 > zoom 0.5 50 > turn -y 1 150 > wait > move x 0.75 15 > wait > turn x 1 20 > wait > zoom 1.5 50 > select /F:370,375 /E:270,309,314 42 atoms, 37 bonds, 1 model selected > show sel atoms > hbonds sel 8 hydrogen bonds found > select clear > turn x 15 60 rock 130 > turn -y 15 60 rock 130 > movie status \-----Movie status------------------------------ Recording 1785 frames (in 'PPM' format) saved to directory '/Users/niar/Desktop/tmp_chimera' using pattern 'Frame_n*' . Est. movie length is 74.375s. \------------------------------------------------ > movie encode /Users/niar/Desktop/Suz12_test1.mp4 format h264 quality low > wait true verbose false Movie saved to /Users/niar/Desktop/Suz12_test1.mp4 executed 6NQ3_Suz12_AS_event.cxc OpenGL version: 4.1 INTEL-14.4.23 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro12,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2,7 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 189.0.0.0.0 SMC Version (system): 2.28f7 Software: System Software Overview: System Version: macOS 10.15.3 (19D76) Kernel Version: Darwin 19.3.0 Time since boot: 1 day 20:31 Graphics/Displays: Intel Iris Graphics 6100: Chipset Model: Intel Iris Graphics 6100 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x162b Revision ID: 0x0009 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal HP LP2065: Resolution: 1600 x 1200 (UXGA - Ultra eXtended Graphics Array) UI Looks like: 1600 x 1200 @ 60 Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: CNG70302V3 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: 6NQ3_Suz12_AS_event.cxc

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Re: [chimerax-users] [Chimera-users] Difference in alignment of cofactor between Chimera and ChimeraX
by Elaine Meng 07 Jul '20

07 Jul '20

Hello Derek, You're welcome! Thought I should also mention that in matchmaker you can specify more than one pair of chains, i.e. use multiple pairs of chains for the fit. Which way is better depends on what you are trying to achieve: overall superposition of whole complex, or best fit of a single pair of chains. This multichain fit can be done in either Chimera or ChimeraX with a matchmaker command option. I'll use ChimeraX commands to illustrate: open 3u7q open 5n6y hide ribbon The ChimeraX log shows that 3u7q has four chains, two alpha (A,C) and two beta (B,D) whereas 5n6y has 6 chains, two alpha (A,D), two beta (B,E) and two delta (C,F). So perhaps you want to use all of the alpha and beta chains from the structures for the fit instead of only A with A. Now the trick is to figure out which alpha goes with which alpha and which beta with which beta. I might be lazy and first just try ABCD in 3u7q as pairing with ABDE in 5n6y and see if that looks right. I might also use coloring by polymer (figures out a color based on chain sequence) to make it clearer what's what. color bypolymer mm #2/A,B,D,E to #1/A,B,C,D pair ss <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> .... which actually looks right. The alphas and betas are colored the same within a given PDB structure but different between the structures, probably because of small sequence differences (something like one structure has a couple more residues on one end or the other; I didn't investigate, but it's expected). The Log reports: RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) ...now to check the placement of cofactors: show ligand ~ribbon You can see a more symmetrical fit, with similar displacements on both sides. I hope this helps, Elaine > On Jul 7, 2020, at 9:39 AM, Derek Harris <derek.harris(a)aggiemail.usu.edu> wrote: > > Hello Elaine, > > Thank you very much for the rapid response. Following your commands, and seeing all the ligands, I now see what's happening. Just as you said; the proteins are each composed of two identical catalytic halves. In one half there is a nice alignment of the cofactors, but in the other half there is not. I was isolating, and only viewing, the chain where there isn't good alignment. > > Thanks again! > > Derek Harris > Postdoctoral Fellow > Seefeldt Lab > Department of Chemistry and Biochemistry > Utah State University > > > On Tue, Jul 7, 2020 at 9:35 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Derek, > It does not make sense for the cofactor alignment to be different if the protein alignment is the same, because the cofactors are just moved rigidly along with their proteins. Also the results should be identical between Chimera and ChimeraX, assuming you are using the same options. > > I get exactly the same alignment between these two proteins in the Chimera vs. ChimeraX. > > Chimera commands (including display ligand only): > open 3u7q > open 5n6y > mm #0 #1 > ~ribbon > show ligand > > ChimeraX commands: > open 3u7q > open 5n6y > mm #2 to #1 > ~ribbon > hide > show ligand > > In both programs, I get the same RMSD message to the Log: > > RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > > In both programs, matchmaker ends up choosing to align chain A to chain A. Thus the cofactors in chains A are better superimposed than the ones in the other chains. > > 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 6:47 PM, Derek Harris <derek.harris(a)aggiemail.usu.edu> wrote: > > > > Hello, > > > > I am trying to reproduce an alignment I had previously done in Chimera in ChimeraX with matchmaker command. > > > > The protein alignment between the two programs is the same, but in ChimeraX the active-site cofactor of the matchstruct isn't aligning appropriately to the refstruct cofactor and is unreasonably placed in relation to even its own protein. In Chimera the two cofactors align nicely. > > > > The two structures I am trying to align are 3U7Q and 5N6Y. > > > > Thanks in advance for any assistance you can offer! > > > > Derek Harris > > Postdoctoral Fellow > > Seefeldt Lab > > Department of Chemistry and Biochemistry > > Utah State University > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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how to turn molecule centering a specific atom in ChimeraX
by Shin Inchul 07 Jul '20

07 Jul '20

Hi, I was trying to turn molecule around specific atom. Since I am a beginner of ChimeraX, I would like to have some working examples in the command line. Without it, I have difficulties in applying the usage as appeared in the user guide. In PyMOL, mouse middle button click on a atom sets the centering on the atom then use rotate command. I appreciate all the supports provided. Thank you. Inchul

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Re: [chimerax-users] session file sizes
by Tom Goddard 07 Jul '20

07 Jul '20

To close molecular surfaces surface close #1 or just surf close If instead you do ~surface that hides the surface. I discourage use of these obscure "~" commands that Chimera used. Use "surface hide #1" or "surface close #1". If you just hide the surfaces they are still in the session file. You can also see the surface models in Model Panel by clicking the little triangle and the left of the model name to show submodel of your molecule. And you can choose those surface models and close them. Tom > On Jul 7, 2020, at 2:48 PM, Melissa Jurica <mjurica(a)ucsc.edu> wrote: > > That was my first guess, so I turned off the surface view. However, no change in file size. I don’t see how to delete the surface that I calculated- still trying to get the hang of ChimeraX after switching from Chimera. > > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > Melissa S. Jurica, Ph.D. > Professor, Molecular, Cell & Developmental Biology > Center for Molecular Biology of RNA > University of California, Santa Cruz > 1156 High Street > Santa Cruz, CA 95064 > > Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs > Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 > http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > >> On Jul 7, 2020, at 2:41 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Melissa, >> >> Molecular surfaces make session files very large because they save all the surface triangles. Did you have a molecular surface in that large session? I have considered not saving the molecular surfaces and just recomputing them although that will make restoring the session slower as it tries to recompute the surface. >> >> Tom >> >> >>> On Jul 7, 2020, at 2:28 PM, Melissa Jurica <mjurica(a)ucsc.edu <mailto:mjurica@ucsc.edu>> wrote: >>> >>> What deterimines the file size of saved ChimeraX sessions (.csx files)? I saved a session of one structure (6Y5q) at 4 MB, and another structure (6y50) at 2.6 MB. However, when I saved a session with both structures open, it was a whopping 120.6 MB. Is there a way to reduce that file size? >>> >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>> Melissa S. Jurica, Ph.D. >>> Professor, Molecular, Cell & Developmental Biology >>> Center for Molecular Biology of RNA >>> University of California, Santa Cruz >>> 1156 High Street >>> Santa Cruz, CA 95064 >>> >>> Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs >>> Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 >>> http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>> >>> _______________________________________________ >>> 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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session file sizes
by Melissa Jurica 07 Jul '20

07 Jul '20

What deterimines the file size of saved ChimeraX sessions (.csx files)? I saved a session of one structure (6Y5q) at 4 MB, and another structure (6y50) at 2.6 MB. However, when I saved a session with both structures open, it was a whopping 120.6 MB. Is there a way to reduce that file size? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064 Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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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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