- Chimera-users - RBVI Mailing Lists

Query
by Gurudeeban Selvaraj 28 Sep '17

28 Sep '17

Dear Support Team, Thanks for the academic free of Chimera. I have a doubt, how can I visualize H-bonding interactions of docked structure of protein-protein interaction. I used FireDock for docking studies. While running on FindHbond on structure/binding tool it says no H-bonds, but i click both shows something.....How can i see protein-protein interacting HBond and label it? For the reference, I enclosed two files. Thanks in advance! ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China

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High Sierra fix
by Eric Pettersen 28 Sep '17

28 Sep '17

We have fixed the problem where interfaces that also showed 3D graphics (Rapid Access/main window; side view) weren’t working correctly on Mac OS X 10.13 (High Sierra). The fix is in the current daily build and the very latest version of the 1.12 release candidate. If you get either of those then it will be safe to upgrade to High Sierra, at least as far as Chimera is concerned. ;-) —Eric Eric Pettersen UCSF Computer Graphics Lab

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Time evolution of the crossing angle between helices during MD trajectories
by George Tzotzos 27 Sep '17

27 Sep '17

In Chimera’s Structure Measurement tool, for a given protein, clicking on the Define axes gives the Cartesian coordinates of the centre of each helix as well as its direction. Selecting two helices (say helix 5 and 6) gives the angle and distance between these helices. I take it that the distance is defined as that between the centroids of the centre of mass of the two helices. The question is whether it is possible to work out the time evolution of the crossing angle between to helices during an MD trajectory. MD Movie/Analysis/Plots/Angles plots the angle between three atoms rather than the crossing angle of the chosen helices. Am I right? Missing something? Thanks in advance for your help George

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Re: [Chimera-users] Calculating AreaSES/AreaSAS without a molecular surface?
by Tom Goddard 27 Sep '17

27 Sep '17

Hi Oliver, ChimeraX does not yet have coloring by atom attributes and the “measures sasa” command isn’t saving a per-atom attribute. But you could tweak the code a bit and get the values in the bfactor column of a PDB file. For instance, I added two lines to the ChimeraX Python code for measure sasa in file ChimeraX.app/Contents/lib/python3.6/site-packages/chimerax/core/commands/measure_sasa.py after line 32 areas = spheres_surface_area(atoms.scene_coords, r) add two lines that set the atom bfactor areas = spheres_surface_area(atoms.scene_coords, r) for a, ar in zip(atoms, areas): a.bfactor = ar Then use the command “save areabfactors.pdb” to get those area values in the bfactor column. Some day we will putting the Chimera rangecolor command into ChimeraX so coloring and measure sasa will set an atom attribute enabling the coloring in ChimeraX without code tweaks. Tom > On Sep 27, 2017, at 11:42 AM, Oliver Clarke wrote: > > Hi Tom, > > Thanks! But ChimeraX doesn’t assign it as a per-residue attribute, or am I missing something? > > Is there any way to write out that parameter in ChimeraX per residue or atom, e.g. by replacing the B-factor column? > > Cheers > Oli > >> On Sep 27, 2017, at 2:37 PM, Tom Goddard wrote: >> >> Hi Oliver, >> >> The Chimera solvent accessible and solvent excluded surface area calculations are done by the MSMS surface calculation code, so if it fails you cannot get those numbers. The secret “grid” option in Chimera does not allow computing areas. >> >> ChimeraX computes the areas analytically (command “measure sasa”) and does not create a surfaces (and the ChimeraX surface calculation never fails). >> >> Tom >> >> >>> On Sep 27, 2017, at 11:20 AM, Oliver Clarke wrote: >>> >>> Hi, >>> >>> Is it possible to calculate the areaSES/areaSAS attributes without a molecular surface? For most large complexes, it is only possible to calculate surfaces using the `grid option` (because msms fails), but this does not automatically generate the SES/SAS attributes. >>> >>> Cheers >>> Oli >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

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Calculating AreaSES/AreaSAS without a molecular surface?
by Oliver Clarke 27 Sep '17

27 Sep '17

Hi, Is it possible to calculate the areaSES/areaSAS attributes without a molecular surface? For most large complexes, it is only possible to calculate surfaces using the `grid option` (because msms fails), but this does not automatically generate the SES/SAS attributes. Cheers Oli

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High Sierra
by Eric Pettersen 26 Sep '17

26 Sep '17

If you rely on Chimera for your work, you should avoid upgrading to Mac OS X 10.13 (High Sierra) for now. The interfaces that also show OpenGL 3D graphics (Rapid Access/main window; Side View) don’t work correctly. We are working on a fix/patch, but are uncertain how long it will take to develop one. ChimeraX works fine on High Sierra. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Chimera scripting question
by Oliver Clarke 25 Sep '17

25 Sep '17

Hi, I’d like to do the following (presumably with a python script): For each pair of Calphas in two identical structures A and B: Get list of other Calphas within distance cutoff of Calpha(0) for each conformation (say 10 Å); For each Calpha in list: Calc distance difference diff_dist between Calpha(0—>A), Calpha(0—>B) average(diff_dist) over list and assign to attribute So more or less, I think I need to (1) iterate through all Calphas of the first structure (this part I get); (2) check if there is an equivalent Calpha in the second structure (same residue number and chain I guess?); (3) get a list of nearby Calphas, merged between structures (not exactly sure about this but I think I found something in an example I can adapt) (4) calculate distances, then difference-distances between the paired structures, from each target Calpha; (5) assign the averaged difference distance to an attribute (I think I can figure out this bit) Any suggestions much appreciated (or if anyone can point me towards similar scripts I can adapt the would also be most welcome!) The intent of this is to generate an attribute representing local structural flexibility (independent of displacement) - to capture changes in the local arrangements of atoms, decoupled from rigid displacements of domains. The idea is this may be useful for highlighting hinge regions and regions that have undergone plastic deformation, without pre-aligning structures. Cheers Oli

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get near/far clip positions?
by Oliver Clarke 25 Sep '17

25 Sep '17

Hi, I would like to write a script to progressively go through the current scene in n depth steps, saving an image with depth cueing off at each step. I want to do this so I can manually apply depth cueing and DoF effects in post processing. For example, if the near and far clip position are at 0 and 100, and I want to split the scene into 4 depth slabs, I’d like to take images with (near,far)=(0,25),(25,50),(50,75),(75,100). Is there any way in the scripting interface to get the positions of the global clipping planes, so I can calculate how thick each slab should be? Cheers Oli Script (example pseudocode): scene tmp save set depth cueing off depth_steps=4 near_clip=0 (would like to get this position from current scene) far_clip=100 (would like to get this position from current scene) thickness=far_clip-near_clip thickness_per_step=thickness/depth_steps set far clipping plane to (near_clip+thickness_per_step) for i in range (1,depth_steps+1): save image_%i section thickness_per_step scene tmp reset.

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Re: [Chimera-users] Do you recieve image submissions?
by Elaine Meng 25 Sep '17

25 Sep '17

Hi Frank, Sorry for the slow response. I didn’t see your question from last week in my mailbox (might have gone to spam) but now I see it in the archive: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-September/013892.html> No, we don’t really have the manpower to put up other people’s images on the Chimera website currently (given other work demands), although we enjoy seeing them! However, this post mentions some biology-related image contests that may be of interest: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-September/013918.html> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] STL File export size
by Tyrwhitt-Drake, James (NIH/NIAID) [C] 25 Sep '17

25 Sep '17

Hi Joe and David If you want to reduce the mesh density of a Chimera model before export, use the following two methods. These are much more elegant than mesh reduction after export, which can introduce errors. You can read our molecular 3D printing protocol in JoVE for detailed instructions of model generation and printing: https://www.jove.com/video/55427/3d-printing-of-biomolecular-models-for-res… https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.… Ribbon models * Open Tools>depiction>ribbon style editor * Select the ‘cross section’ tab * Change the ribbon cross section to something simpler. You may draw a square, octagon or (a good balance) hexadecagon. Drawing the shapes can be a little tricky, but the results are worth it! [cid:image003.jpg@01D33385.D40FF980] Surfaces * Instead of using the surface command from the menus, enter the following command in the command line” where ‘#0’ is the model number, and ‘0.5’ is the grid resolution in angstroms. Higher grid values give less detailed meshes * surf #0 grid 0.5 Regards, James Tyrwhitt-Drake Scientific Visualization Specialist Contractor, Medical Science and Computing, Inc. Bioinformatics and Computational Biosciences Branch (BCBB) NIH/NIAID/OD/OSMO/OCICB Building 31, 3B62 Bethesda, MD 240-593-7508 @NIAIDBioIT<https://twitter.com/niaidbioit> | @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Hurt, Darrell (NIH/NIAID) [E] Sent: Friday, September 22, 2017 6:48 AM To: Healey, Joe <J.R.J.Healey(a)warwick.ac.uk>; David Bhella <David.Bhella(a)glasgow.ac.uk> Cc: NIH 3D Print Exchange <3Dprint(a)nih.gov> Subject: Re: [Chimera-users] STL File export size Hi Joe and David, I encourage you to consider the NIH 3D Print Exchange (cc’d) as a place to easily create 3D-printable models of proteins of any size or complexity. We use Chimera as part of our toolchain, so the models will look familiar to you. Check out the “Submit” function of the website to upload a PDB file and get a model in return. Or simply type in a PDB accession code for your model in the “Quick Submit” box to generate a model. https://3dprint.nih.gov Full disclosure: I lead the team that maintains the Exchange. Cheers, Darrell -- Darrell Hurt, Ph.D. Chief, Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A50 North Bethesda, MD 20852 Office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: "Healey, Joe" <J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> Date: Friday, September 22, 2017 at 6:40 AM To: David Bhella <David.Bhella(a)glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] STL File export size Hi David, Thanks very much! I'm currently experimenting with MeshMixer's "Reduce" to do the same kind of thing - though I think that will only get me so far. I'll certainly have a look at that walkthrough though. I have just realised part of my problem however, was that I was exporting the surface and ribbon representations though without realising it, rather than just the surface, which would be totally redundant when printed. Joe 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<mailto:J.R.J.Healey@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 ________________________________ From: David Bhella <David.Bhella(a)glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Sent: 22 September 2017 11:24:55 To: Healey, Joe Cc: chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] STL File export size The free software package meshlab is very effective at reducing the complexity of 3D scenes for printing. There is a tutorial here: https://www.shapeways.com/tutorials/polygon_reduction_with_meshlab D. Dr David Bhella Director - Scottish Macromolecular Imaging Centre MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch > On 22 Sep 2017, at 10:38, Healey, Joe <J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> wrote: > > 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<mailto:J.R.J.Healey@warwick.ac.uk> > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Contests?
by ginn4711 25 Sep '17

25 Sep '17

Are there contests for chimera images? Sent from my MetroPCS 4G LTE Android Device

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Swapping models in an open structure
by Healey, Joe 22 Sep '17

22 Sep '17

Hi again Chimera Team, I have a large macromolecular structure, and I want to, at random, substitute some of the separate models for a variant form. Is it possible to do this through chimera, e.g. via python? It seems to me it would basically be a case of: 1. enumerate the list of open models 2. pick a model at random 3. either open a new model, fit it to that model, then close the old one, or somehow get the old models co-ords, close it, then open the new one in its place from a specified file path Any alternative suggestions if there's a better way to do this would be great as well. 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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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. 18 Sep '17

18 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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change the smoothness of a shape
by C.J. 12 Sep '17

12 Sep '17

Hi specialists, I make a shape and set color to it according to another map,but the color of the shape didn't look smooth. May I change the smoothness of the shape in command-line? Best regards! Jianhao

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Undo Move with movewholemolecules false
by Oliver Clarke 12 Sep '17

12 Sep '17

Hi, Undo move is really useful when one accidentally moves a model relative to another using fitmap. However, it doesn’t work when a part of one model is moved relative to another part – e.g `fitmap sel #1 movewholemolecules false`. Would there be a possibility of making `Undo Move` recognize intra-model movements, if not in Chimera then in ChimeraX? Cheers Oli

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Save PDB
by samaha th 12 Sep '17

12 Sep '17

Dear Sir/Madam, I would like to know how to save single protein-ligand complex pose using chimera. While saving I am getting an error message mentioning- "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". How to solve the issue.

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