September 2017 - Chimera-users - RBVI Mailing Lists

STL File export size
by Healey, Joe 22 Sep '17

22 Sep '17

Hi Chimera team, I'm dealing with some protein structures that vary quite a lot in size. I'd like to make 3D printable versions, so I'm exporting STL files. Is there any way to reduce the file size of the exported STLs? How might one control the level of detail (triangulation) of the exported file - I suspect the defaults are including a lot of detail that a 3D printer wouldn't even be able to replicate in the first place. Many thanks Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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center a map
by C.J. 19 Sep '17

19 Sep '17

Hi specialists, I want to color a map by radius. But for some maps, it failed. I found that that "center"(Volume Viewer -> Features -> Coordinates) button(not the one at bottom of Volume Viewer dialog) can center a map to color by radius. Is there a command-line to do that function? And why some maps need to be center before color by radius? I have 2 C1 map with spherical shape reconstructed from the same data, but one need to and the other one needn't. Thank you in advances! Best regards! Jianhao

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COX inhibitor demo discrepancy
by simon chapman 18 Sep '17

18 Sep '17

Hi, I'm very impressed with Chimera as a user of only 3 weeks so far Trying out the various facilities has been a very useful exercise for completing my Masters in MedChem. However, when I emulated the tutorial covering COX 1 and 2 inhibition, inputting the molecules fluribrofen and SC558 I generated via DS Visualiser bind at the outside edge of the enzymes. Not centrally as displayed in the video. I also noted the molecular data in ViewDock, ie: energies etc, is missing. The table is blank other than the molecule number. Selecting 'Column' etc has no effect. The 'H-bonds' option does display however. I've probably done something wrong, hey ho...but can you enlighten me? Best wishes Simon

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ubuntu 14.04 problem - further information
by Boaz Shaanan 18 Sep '17

18 Sep '17

Hi, I picked up from the list of old versions this version from November 2016 chimera-1.11.2-linux_x86_64.bin and it works fine. My recollection is also that last version I worked with, the nightly build from June 2017 also worked fine. I thought you might be interested in this piece of information. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Monday, September 18, 2017 6:30 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 173, Issue 14 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: COX inhibitor demo discrepancy (Elaine Meng) 2. morph & ligands (Hernando J Sosa) 3. ubuntu 14.04 - issue with latest chimera 64 bit (both production and recent nightlly build) (Boaz Shaanan) 4. Do you recieve image submissions? (Frank Irby) 5. Re: morph & ligands (Hernando J Sosa) ---------------------------------------------------------------------- Message: 1 Date: Sun, 17 Sep 2017 09:54:37 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: simon chapman <rowanlodge19(a)gmail.com> Cc: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] COX inhibitor demo discrepancy Message-ID: <375AFBD6-1B2D-4C2A-8677-B1F7E210D9C9(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Hi Simon, (1) There are lots of molecular dynamics programs: AMBER, GROMACS, NAMD etc., and the list of input formats for the Chimera ?MD Movie? tool shows which of those programs? results it can handle: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> Chimera itself even has a Molecular Dynamics SImulation tool (see Tools? MD/Ensemble Analysis) but it is relatively slow. Be aware that there is a learning curve to running MD simulations. Garbage in gives garbage out, so you have to take some time to learn about the technique and its limitations. There are many input options and parameters, and just taking all the defaults isn?t usually the path to success for any given molecular system. There are textbooks on the subject and running a decent simulation could be a project in itself. Or if you just wanted a conformational ensemble rather than a trajectory, there are a whole host of other programs that do some normal mode analysis based on network models. Those seem simpler than MD to use, but the results are more limited; that?s just a general impression? I?m not an expert on the topic. Even simpler is if you have two different conformations of some protein, you can morph between them in Chimera and show the results in Chimera. For example, see the ?superpositions and alignments? tutorial starting at ?different conformations of the same protein" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html> (2) References to the papers about the data are given in the MD Movie tutorial. Part 1 uses MD results (probably from AMBER but you?d have to read the paper to doublecheck) and part 2 uses an NMR ensemble. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html> (3) the browser is showing the text of 1plx.pdb ? you just need to save it as plain text, just like you did for ras.mol2 . Alternatively, you can get the same file from RCSB PDB, Download Files -> PDB Format: <http://www.rcsb.org/pdb/explore/explore.do?structureId=1plx> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 16, 2017, at 2:04 PM, simon chapman <rowanlodge19(a)gmail.com> wrote: > > Thank you Elaine...that did it! Couldn't save as Plaintext, but it still worked as Notepad. > > I am very pleased with the MD Movie tutorial...it worked for me without too many changes, and is suitably impressive. Did the authors supplying the data derive them from AMBER? How can I supply data relevant to the molecules I'm studying to produce the appropriate MD Movie? > > Also, and I hope it's OK to bother you again, the attached screenshots show the result of trying to download 1plx.pdb. I've tried several formats, but the message "no pdb structures found" appears every time. Clicking " 1plx.pdb" in the tutorial leads to the page shown. Selecting "save as..." leads to the other two pop-ups in screenshot 1. Downloads lists the file as Tutorial FrameSet, and contains the four files shown in screenshot 2. Feel like I'm going round in circles with this one. > > Thanks in advance...despite the challenges, Chimera is very impressive, and should enhance my MSc thesis which commences next month > > Best wishes Simon > ------------------------------ Message: 2 Date: Mon, 18 Sep 2017 00:00:22 +0000 From: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> To: chimera List <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] morph & ligands Message-ID: <F0E461AAE34D0448B6EE7D31E433B70801236B9246(a)AEWEXCPM21.yuad.uds.yu.edu> Content-Type: text/plain; charset="utf-8" Is there a way to keep & show the ligands in the Morph between structures?. In the morphs that I've tried the ligands do not show up. Thanks H. ------------------------------ Message: 3 Date: Mon, 18 Sep 2017 14:51:15 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] ubuntu 14.04 - issue with latest chimera 64 bit (both production and recent nightlly build) Message-ID: <4B2A491F685D1E4FBBF985E193095AAF012F4BC7A7(a)hawk3.auth.ad.bgu.ac.il> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170918/113b…> ------------------------------ Message: 4 Date: Sun, 17 Sep 2017 15:39:00 +0000 (UTC) From: Frank Irby <fourpaws3(a)yahoo.com> To: <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Do you recieve image submissions? Message-ID: <295279869.3724177.1505662740916(a)mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 https://mandelscape.deviantart.com/art/Luciferase-firefly-703808245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home is a handmade web: http://dreamscape.myartsonline.com/ Fractals Rule! http://mandelscape.deviantart.com/ Love the EARTH, Love yourself. https://www.thespiritsgarden.com/ ------------------------------ Message: 5 Date: Mon, 18 Sep 2017 15:30:28 +0000 From: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> To: chimera List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] morph & ligands Message-ID: <F0E461AAE34D0448B6EE7D31E433B70801236B989E(a)AEWEXCPM21.yuad.uds.yu.edu> Content-Type: text/plain; charset="us-ascii" Sorry that was an old question and here was the answer. ---------------------------------------------------------- As I had understood it (and had written in the documentation) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#…>: "HET residues such as ligands and ions are only included if they are present in both structures and attached to the same atom(s) in the paired chains by at least one "covalent" bond (which can be an unrealistic bond added manually, e.g., with the command bond, and subsequently undisplayed) or ion coordination pseudobond. Once residues are paired, atoms in common within those residues are paired. In paired residues of the same type, atom pairing is straightforward. In paired residues of different types, only atoms with the same names are paired, and only a single connected fragment is kept per residue." I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco -----Original Message----- From: Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Hernando J Sosa Sent: Sunday, September 17, 2017 8:00 PM To: chimera List Subject: [Chimera-users] morph & ligands [This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing] Is there a way to keep & show the ligands in the Morph between structures?. In the morphs that I've tried the ligands do not show up. Thanks H. _______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Subject: Digest Footer _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ End of Chimera-users Digest, Vol 173, Issue 14 **********************************************

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FW: ubuntu 14.04 - issue with latest chimera 64 bit (both production and recent nightlly build)
by Boaz Shaanan 18 Sep '17

18 Sep '17

Here is the plain text version (I keep forgetting about the html problem on your site. Sorry. Boaz Hi, I started to get the following error message on both the production and nightly build of the x86_64 versions. The Windows version is fine. Please advise. Thanks, Boaz >chimera Traceback (most recent call last): File "/home/boaz/chimera/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/boaz/chimera/share/chimeraInit.py", line 625, in init initialize_ssl_cert_dir() File "/home/boaz/chimera/share/chimeraInit.py", line 309, in initialize_ssl_cert_dir import ssl File "/home/boaz/chimera/lib/python2.7/ssl.py", line 97, in <module> import _ssl # if we can't import it, let the error propagate ImportError: No module named _ssl Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Do you recieve image submissions?
by Frank Irby 17 Sep '17

17 Sep '17

https://mandelscape.deviantart.com/art/Luciferase-firefly-703808245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home is a handmade web: http://dreamscape.myartsonline.com/ Fractals Rule! http://mandelscape.deviantart.com/ Love the EARTH, Love yourself. https://www.thespiritsgarden.com/

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residue.areaSES returns 0 for buried residues
by Kevin Jude 15 Sep '17

15 Sep '17

Hi Chimerans- I am trying to use Chimera to list percent accessible surface area by residue for a structure by calculating (solvent accessible area SAS) / (solvent excluded area, SES). For some reason, for residues that are completely buried, Chimera returns not only SAS=0, but also SES=0, and thus those residues aren't included in the percent accessible calculation. Does anyone have a clue for this behavior? My workflow is as follows: File>Open [choose pdb file] > Actions>Surface>Show > Tools>Surface/Binding Analysis>Measure Volume and Area > Tools>Depiction>Render by Attribute > > in the render by attribute window: > File>Save Attributes > > in the save window: > select attribute 'areaSAS' or 'areaSES' of 'residues' and save to a file > > to calculate % accessible: > Tools>Structure Analysis>Attribute Calculator > > in the attribute calculator window: > Calculate attribute "percentaccessible" for "residues" > Formula: > (residue.areaSAS)/(residue.areaSAS+residue.areaSES) > [check Save calculation results to file] Best wishes Kevin -- Kevin Jude, PhD Research Specialist in Structural Biology, Garcia Lab Departments of Molecular & Cellular Physiology and Structural Biology Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431

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Reading density files in xyz format
by George Tzotzos 14 Sep '17

14 Sep '17

I’ve run an Amber trajectory and generated grid data as a volumetric map. The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius. The format of the file is xyz (see head of the file below). 727 C 3.46464014 25.54114723 39.11305046 0.03241467 C 3.46464014 26.54114723 40.11305046 0.03353754 C 3.46464014 28.54114723 40.11305046 0.03223133 C 3.46464014 29.04114723 37.61305046 0.03259914 C 3.46464014 30.04114723 41.11305046 0.03254872 C 3.46464014 31.54114723 28.11305046 0.03995054 C 3.46464014 32.04114723 38.11305046 0.02878203 C 3.46464014 33.04114723 42.61305046 0.02801451 Is there a way to visualise in Chimera the protein together with volumetric map? Thank you in advance for any advice George

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barycenter of a model
by mljin 13 Sep '17

13 Sep '17

Dear USCF Chimera developers, I got a question here, how to find the barycenter of a model in UCSF Chimera? And the Model has a C2 symmetry, I can only find the symmetry axis. Best regards, Mingliang Jin NCPSS, SIBCB, CAS

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Re: [Chimera-users] [chimerax-users] Color palettes - ColorBrewer support?
by Elaine Meng 12 Sep '17

12 Sep '17

HI Oli, Thanks for the suggestion. I agree these would be great to have in ChimeraX, and we certainly haven’t ruled it out… but (as you know) many things are vying for developer time. I would certainly use those palettes if they were available. We’re aware of Colorbrewer and actually its palettes have been in Chimera’s Palette Editor for quite a while: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/palette.html> However, they never got interfaced with coloring by value and the only direct use was for gradient-coloring the background… admittedly not the best use of most multicolor schemes. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 8, 2017, at 8:35 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Hi, > > I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)? > > It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc. > > It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet. > > Cheers > Oli > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

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Chimera-users September 2017