- Chimera-users - RBVI Mailing Lists

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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find the barycenter of a model
by mljin 11 Sep '17

11 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. Appreciate for the effort you've done! Best regards, Mingliang Jin NCPSS, SIBCB, CAS

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Re: [Chimera-users] Chimera-users Digest, Vol 173, Issue 3
by Pu Qian 08 Sep '17

08 Sep '17

Dear Chimera developers, I'm using Chimera to estimate molecular weight from cryo-em map through volume viewer/tools/measure volume and area/ The value of the volume I got is in e3 unit. What dies this e3 mean. This e3 unit is used for area as well, which confused me. The version I'm using is 1.12. It seems that the e3 equals nm3, but I'm not sure. It would be a great appreciated if you could help me to make it clear. Thanks Best regards Qian On 7 September 2017 at 16:44, <chimera-users-request(a)cgl.ucsf.edu> wrote: > 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. COX inhibitor demo discrepancy (simon chapman) > 2. longbond command documentation? (Oliver Clarke) > 3. Re: Batch mode for Chimera (Elaine Meng) > 4. Re: COX inhibitor demo discrepancy (Elaine Meng) > 5. Re: longbond command documentation? (Elaine Meng) > 6. Re: COX inhibitor demo discrepancy (simon chapman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 6 Sep 2017 12:17:56 +0100 > From: simon chapman <rowanlodge19(a)gmail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] COX inhibitor demo discrepancy > Message-ID: > <CAJPu8_4y4xVjZiXnT3TRXOj7XDnAtg2D7T-VuOQ7BTV3NdVteQ@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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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Color palettes - ColorBrewer support?
by Oliver Clarke 08 Sep '17

08 Sep '17

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

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Re: [Chimera-users] Batch mode for Chimera
by James Starlight 08 Sep '17

08 Sep '17

Hi Greg, I am using Ubuntu with Nvidia driver. I have updated all those packages and copy files to chimera_batch lib dir but it was the same effect. then I found that the problem was hidden in my batch script! "preset apply pub 2" produced that crash ! but if I change it to "preset app int all" everything is fine. P.S. as I found in the resulted images on the default the protein is aligned along its Z vector. Is it possible to turn it via some command to display in-front or in the pseudo-isometrical projection? Thanks!! Gleb 2017-09-04 10:08 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: > Hi Greg, > > I am using Ubuntu with Nvidia driver. > > I have updated all those packages and copy files to chimera_batch lib > dir but it was the same effect. > > then I found that the problem was hidden in my batch script! > "preset apply pub 2" produced that crash ! > but if I change it to "preset app int all" everything is fine. > > P.S. as I found in the resulted images on the default the protein is > aligned along its Z vector. Is it possible to turn it via some command > to display in-front or in the pseudo-isometrical projection? > > Thanks!! > > Gleb > > 2017-09-03 2:58 GMT+02:00 Greg Couch <gregc(a)cgl.ucsf.edu>: >> My guess is it is a graphics driver problem. >> >> We haven't updated the software OpenGL driver that is bundled with the >> headless Chimera in ages (Mesa 7.6.1), but we have updated Chimera's use of >> OpenGL. Chances are that your Linux server has newer version. So assuming >> you don't have a graphics driver installed, you should try moving aside the >> libGL.so* and libOSMesa.so* files in your >> /home/gleb/.local/UCSF-Chimera64-batch/lib directory so chimera will use the >> system versions. You might need to install those libraries on your system. >> On CentOS/RHEL, they are the mesa-libOSMesa and mesa-libGL packages. On >> Debian/Ubuntu, they are the libosmesa6 and libgl1-mesa-dev packages. >> >> If you have an AMD/NVIDIA graphics driver installed, then you will want to >> copy the Mesa versions of libGL.so and libOSMesa.so to your >> /home/gleb/.local/UCSF-Chimera64-batch/lib directory. On CentOS/RHEL, the >> AMD/NVIDIA installers should have moved the Mesa versions aside somewhere, >> so they could be restored with the driver is uninstalled -- it will take >> some detective work to find them. On Ubuntu, the libGL.so* files are in >> /usr/lib/x86_64-linux-gnu/mesa/. >> >> HTH, >> >> Greg >> >> >> >> On 9/1/2017 1:23 AM, James Starlight wrote: >>> >>> now the errors of the execution of the script using headless chimera: >>> >>> Opening rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb... >>> The following problems occurred while reading PDB file for >>> rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb >>> warning: Ignored bad PDB record found on line 2 >>> >>> Opened rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb containing 1 model, 903 >>> atoms, and 301 residues >>> Rendering high resolution image... >>> ./run.sh: line 113: 14479 Segmentation fault (core dumped) >>> chimera_batch $pdb "${temp}"/script_${name}.cmd >>> >>> >>> the same with a pow-ray render >>> >>> Opened rmsf_visu_AT1_wat_Na.3rep.step7_1.pdb containing 1 model, 903 >>> atoms, and 301 residues >>> Generating POV-Ray data file >>> Exporting POV-Ray data to >>> >>> /home/gleb/Desktop/Scripts/MegaAnalysis/output/plots/rmsf/rmsf_AT1_wat_Na.3rep.pov >>> Ignoring CHIMERA environment variable >>> Parse error at line 1: >>> no element found >>> >>> >>> here is my script: >>> >>> preset apply publication 2 >>> rangecolor bfactor 2 blue 30 red 50 yellow >>> copy file >>> /home/gleb/Desktop/Scripts/MegaAnalysis/output/plots/rmsf/AT1_wat_apo.3rep.png >>> png width 800 height 600 >>> >>> >>> I have made the same images in chimera GUI and it worked very well. >>> >>> Is it possible to run same script using in chimera-gui but from batch >>> mode? >>> >>> 2017-08-31 22:04 GMT+02:00 Greg Couch <gregc(a)cgl.ucsf.edu>: >>>> >>>> You must have the given the "key" argument to the rangecolor command. >>>> That >>>> option tries to display the Color Key tool which want you to use the >>>> mouse >>>> to position the color key in the graphics window. That is not possible >>>> in >>>> batch mode. You'll need to add the color key afterwards with an image >>>> editor if you need it. >>>> >>>> HTH, >>>> >>>> Greg >>>> >>>> >>>> >>>> On 08/31/2017 01:00 AM, James Starlight wrote: >>>>> >>>>> Thanks Eric! >>>>> >>>>> Everything works fine with the exception of the copy command. On the >>>>> rendering stage I have: >>>>> >>>>> >>>>> Opened AT1_dry_apo.1rep.step7_1.pdb containing 1 model, 57791 atoms, >>>>> and 12661 residues >>>>> Traceback (most recent call last): >>>>> File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimeraInit.py", >>>>> line 683, in init >>>>> chimera.openModels.open(a, prefixableType=1) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", >>>>> line 1951, in open >>>>> models = func(filename, *args, **kw) >>>>> File >>>>> >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/ChimeraExtension.py", >>>>> line 31, in func >>>>> processCommandFile(fileName) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", >>>>> line 108, in processCommandFile >>>>> _processFile(f, emulateRead, filename) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", >>>>> line 143, in _processFile >>>>> if makeCommand(line): >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", >>>>> line 69, in makeCommand >>>>> f(c, args) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", >>>>> line 1786, in doRangeColor >>>>> showKey=key) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/__init__.py", >>>>> line 2526, in rangeColor >>>>> from Ilabel.gui import IlabelDialog >>>>> File "/home/gleb/.local/UCSF-Chimera64-batch/share/Ilabel/gui.py", >>>>> line 13, in <module> >>>>> from chimera import tkgui, chimage, CLOSE_SESSION >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py", >>>>> line 74, in <module> >>>>> import Togl >>>>> ImportError: No module named Togl >>>>> >>>>> Error while processing >>>>> >>>>> >>>>> /home/gleb/Desktop/Scripts/MegaAnalysis/temp/script_AT1_dry_apo.1rep.step7_1.pdb.cmd: >>>>> ImportError: No module named Togl >>>>> >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py", >>>>> line 74, in <module> >>>>> import Togl >>>>> >>>>> See reply log for Python traceback. >>>>> >>>>> I have found that it is due to some conflict in PYTHONPATH from my >>>>> bash since I am running Chimera directly from BASH. The people also >>>>> wrote that Its related to setting transparency- which was not a case >>>>> there - I did not set in my script. Anyway how to fix it? >>>>> >>>>> Thanks you! >>>>> >>>>> James >>>>> >>>>> 2017-08-30 22:54 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >>>>>> >>>>>> Hi James, >>>>>> First, if you want to save images without showing the Chimera GUI then >>>>>> you >>>>>> have to use the “headless” version of Chimera, available on the >>>>>> download >>>>>> page. To do the other things you want, just put the equivalent >>>>>> commands >>>>>> in >>>>>> a file that ends in “.cmd” and just add that file to your invocation of >>>>>> Chimera, e.g.: >>>>>> >>>>>> chimera $pdb script.cmd >>>>>> >>>>>> The easiest way to handle the image file name is probably to used a >>>>>> fixed >>>>>> name in the Chimera “copy” command, and then in your bash script move >>>>>> that >>>>>> file to the final name you want. Also, "preset” is the command to >>>>>> apply >>>>>> presets — “help preset” in Chimera for more info. >>>>>> >>>>>> Hope this helps. >>>>>> >>>>>> —Eric >>>>>> >>>>>> >>>>>> Eric Pettersen >>>>>> UCSF Computer Graphics Lab >>>>>> >>>>>> >>>>>> On Aug 30, 2017, at 8:40 AM, James Starlight <jmsstarlight(a)gmail.com> >>>>>> wrote: >>>>>> >>>>>> Dear Chimera Users! >>>>>> >>>>>> My simple bash script loops the folder with the pdbs and open it in >>>>>> Chimera >>>>>> >>>>>> for pdb in ${output}/xtc_proc/*.pdb ; do >>>>>> name=$(basename "$pdb") >>>>>> echo "I am sending ${name} to Chimera!" >>>>>> chimera $pdb >>>>>> done >>>>>> >>>>>> My question - can I use with chimera some batch file which will >>>>>> apply the following commands to each of the loaded pdbs without >>>>>> opening of Chimera GUI: >>>>>> >>>>>> 1- Apply "publications-2" preset >>>>>> >>>>>> 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb >>>>>> according to b-factor provided in the pdb file >>>>>> >>>>>> 3- make a screen-shot of the colored cartoon figure in the selected >>>>>> output folder. >>>>>> >>>>>> >>>>>> I thanks so much for the example of batch file and the syntax accepted >>>>>> by chimera from the linux shell. >>>>>> >>>>>> James >>>>>> _______________________________________________ >>>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>>>>> Manage subscription: >>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> 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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longbond command documentation?
by Oliver Clarke 06 Sep '17

06 Sep '17

Hi, I want to use the longbond command to clean up display of a PDB file which has some ugly bits – missing TER cards etc - and which hence has unphysical bonds displayed. According to the manual `longbond` should be the command to use, but it doesn’t seem to work – it just displays and undisplays pseudobonds. If I attempt to use arguments as described in the docs, I get a message saying that longbond no longer takes arguments. Is there an updated description of this command? Or another command that does what longbond used to do? Cheers Oli

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3D-SNFG symbol representation for carbohydrate molecules
by Oliver Grant 06 Sep '17

06 Sep '17

Dear developers, The carbohydrate community has decided on a standard symbol representation for carbohydrates. The article is here <https://academic.oup.com/glycob/article-lookup/doi/10.1093/glycob/cwv091>, and the webpage is here <https://www.ncbi.nlm.nih.gov/books/NBK310273/>. Our group has created a 3D version <http://glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-…> of the symbols within the software VMD. Here's a video showing both versions. <http://glycam.org/docs/othertoolsservice/wp-content/uploads/sites/15/2016/0…> We have also worked with David Sehnal to implement this into LiteMol, here is an example <https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/?loadFromCS=5a6z>. I wanted to reach out and see if you are interested to implement this representation within Chimera? We can discuss the details if so. Regards, Dr. Oliver Grant Associate Research Scientist Complex Carbohydrate Research Center Athens, GA, USA.

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Batch mode for Chimera
by James Starlight 02 Sep '17

02 Sep '17

Dear Chimera Users! My simple bash script loops the folder with the pdbs and open it in Chimera for pdb in ${output}/xtc_proc/*.pdb ; do name=$(basename "$pdb") echo "I am sending ${name} to Chimera!" chimera $pdb done My question - can I use with chimera some batch file which will apply the following commands to each of the loaded pdbs without opening of Chimera GUI: 1- Apply "publications-2" preset 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb according to b-factor provided in the pdb file 3- make a screen-shot of the colored cartoon figure in the selected output folder. I thanks so much for the example of batch file and the syntax accepted by chimera from the linux shell. James

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B-Factor Difference Plot
by Amanda Evans Constantinides 31 Aug '17

31 Aug '17

Hello, I am plotting the B-factor differences between two similar structures. I do not understand why the plot is almost entirely on the positive side of the X-axis. If I open B factor putty models in PYMOL and in Chimera, there are some visible areas that should translate to negative B-factor differences on a quantitative plot. There is no way one structure is entirely more flexible than the other. Can you help explain this to me? Is there away to adjust the zero point to more accurately reflect these differences on the plot? Thank you, Amanda Constantinides Graduate Research Assistant Georgia State University

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Center on surface at mouse accelerator
by Daniel P Farrell 30 Aug '17

30 Aug '17

Hello, I found myself constantly needing to re-center on different regions of EM density maps, and I was originally just dropping spheres on the surface, centering on those, then deleting them. Finally I got sick of that and wrote this. It will center the window on the surface of whatever surface the mouse is currently overlaying. I found this to be a very helpful addition when looking at large EM maps, and was thinking other people might too, after using it for a while I feel as though it could be part of trunk since I use it so much. basically it would require the addition of this to standard_accelerators.py ... other accelerators.. ('zx', 'Center view on surface where mouse is located', center_on_surface_at_mouse), ... zx because it's close to where you rest your hands on the keyboard... def center_on_surface_at_mouse(): from chimera import selection, tkgui hits = [] w = tkgui.app.graphics x = w.winfo_pointerx() - w.winfo_rootx() y = w.winfo_pointery() - w.winfo_rooty() from Surface import surface_models import VolumePath.tracer as tracer hits.extend(tracer.surface_intercepts(x, y, surface_models())) xyz, model = tracer.closest_hit(hits) print(xyz) if xyz: print('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) chimera.runCommand('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) chimera.viewer.camera.center = xyz cheers! ~Dan

2 2

Adding ions with Amber
by George Tzotzos 30 Aug '17

30 Aug '17

I’ve loaded the prmtop and inpcrd of a protein in complex with a ligand (named DE3). I’ve tried to add ions to the complex using the Amber Tool. I received the following message (see Reply log below). I wonder if I erred, in which case I would be grateful for any suggestions, or there’s a bug in the program. Many thanks in advance George Assigning chain ID A to 125 residues, e.g. ASP Assigning chain ID B to 125 residues, e.g. ASP Model 0 (complex.inpcrd) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. /Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=1, right=1 + 'left=%s, right=%s') % (left, right)) Charge model: AMBER ff14SB Assigning partial charges to residue DE3 (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.in.mol2 -fi mol2 -o /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (DE3) (DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (DE3) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (DE3) Reason: image not found (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (DE3) (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (DE3) Total number of electrons: 104; net charge: 0 (DE3) (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (DE3) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue DE3 Check reply log for details

2 1

Rainbow command
by Mark Rosenberg 28 Aug '17

28 Aug '17

Please can you provide an example of using Rainbow with Command line for a specific chain so I can see how the nomenclature works. It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them to different situations. Thank you.

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