- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
by Jaime Rodríguez-Guerra 23 Sep '16

23 Sep '16

Hi! Since you are getting lists of atoms back, you only need to do some attribute access (rather than method calling)! Every chimera.Atom object has an attribute called molecule: a reference to its parent chimera.Molecule. chimera.Molecule objects have an attribute called 'name', but sometimes this is not very informative (depends on your input), so you need to resort to the pdb filename, stored in the first element of the openedAs tuple. In code, this looks like this: for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): molecule1 = atoms1[0].molecule # any atom from the list will do molecule2 = atoms2[0].molecule print molecule1.name, "\t", molecule2.name, "\t", rmsd # molecule1.openedAs[0] will also work here I don't know if atoms1 comes consistently from the reference molecule, but I'd guess it does. Hope it helps!

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Saving scenes
by Tom Goddard 22 Sep '16

22 Sep '16

Hi Josh, Chimera session files (menu File / Save Session) save the data, views, colors, display styles, what is hidden and shown. The savepos and reset commands save and restore the positions of models and clip planes and view direction and zoom, just in memory (e.g. “savepos view1”, “reset view1”). Positions saved this way are also saved in sessions so after reloading a session you can use the reset command to get those positions back. Savepos does not save the colors, display styles, or what is hidden and shown. “Scenes” are created by the “Animation” tool (menu Tools / Utilities / Animation) and the “scene” command and include positions, camera view, colors, display styles, what is hidden and shown. Scenes try to capture exactly how the scene looks so they are like sessions but no file is used (although the are preserved in session files). So to save the current scene use command “scene s1 save” and to restore it “scene s1 reset”. Like savepos/reset you can save as many scenes as you want with different names. Scenes are a more recent feature and are not completely reliable — they don’t record everything and sometimes the cause errors saving sessions. Tom > On Sep 22, 2016, at 5:38 AM, Broyde, Joshua E. wrote: > > Dear Tom, > I hope you are well. I was wondering how to save a particular view (i.e. with specified zoom, atoms displayed and angle of view) in Chimera? Currently, I simply save this as a different session, but I was wondering if there is a better or easier way? > > Josh >

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Re: [Chimera-users] Chimera-users Digest, Vol 161, Issue 19
by Healey, Joe 22 Sep '16

22 Sep '16

Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: chimera.openModels.open(top_hit, type="PDB") # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + model_path) rmsd_file = '{0}.tsv'.format(rmsd) with open(rmsd_file, "a") as rmsd_output_file: for j in len(model_list): match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) runCommand(match_cmd) # <somewhere in here retrieve the rmsd and append to a result file> or the other option would be to do the above but avoiding the string synthesis step with something like: chimera.module.mmaker() If the module can be accessed directly? If so which module is the mmaker function within? Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? Looking at your Match script the rmsd was the 3rd value of the tuple in the line: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] Would the same be true for mmaker? (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) Thanks again for all your help Joe Healey M.Sc. B.Sc. (Hons) 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> ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu <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: 20 September 2016 19:30 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 161, Issue 19 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: Recursive structure matching and acquisition of descriptive numbers (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Tue, 20 Sep 2016 11:30:38 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: "Healey, Joe" <J.R.J.Healey(a)warwick.ac.uk> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42(a)cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" Hi Joe, I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#opti… <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#opti…> I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. ?Eric > On Sep 20, 2016, at 5:07 AM, Healey, Joe <J.R.J.Healey(a)warwick.ac.uk> wrote: > > Hi again, > > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. > > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options> > > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html> > > But I can't quite unwrap the options specified in the command for my uses. > > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? > > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 <http://pastebin.com/6k9cew55> incase it gives you some indication of what I'm attempting to do. > > Many thanks > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > 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> > From: Greg Couch <gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> > Sent: 08 September 2016 22:43:55 > To: Healey, Joe; chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. > > -- Greg > > On 09/08/2016 11:53 AM, Healey, Joe wrote: >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> 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> >> From: Greg Couch <gregc(a)cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu> >> Sent: 07 September 2016 19:49:19 >> To: Healey, Joe; chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b>, for how to install other software into Chimera. Other parts of the FAQ may help you too. >> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html>, and came up with pychimera, https://pypi.python.org/pypi/pychimera <https://pypi.python.org/pypi/pychimera>. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >> >> HTH, >> >> Greg >> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >>> Hi Eric, >>> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >>> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >>> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >>> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >>> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >>> >>> Do you have any advice about how best to proceed? >>> >>> Many thanks, >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> 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> >>> >>> From: Eric Pettersen <pett(a)cgl.ucsf.edu> <mailto:pett@cgl.ucsf.edu> >>> Sent: 31 August 2016 18:23 >>> To: Healey, Joe >>> Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >>> Hi Joe, >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >>> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html> >>> >>> ?Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe <J.R.J.Healey(a)warwick.ac.uk <mailto:J.R.J.Healey@warwick.ac.uk>> wrote: >>>> >>>> Hi, >>>> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >>>> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >>>> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >>>> >>>> Thanks >>>> >>>> Joe Healey >>>> >>>> >>>> M.Sc. B.Sc. (Hons) >>>> 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>_______________________________________________ >>>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >>> >>> _______________________________________________ >>> 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> > >

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Two open positions on molecule visualization and virtual reality in Paris
by baaden＠smplinux.de 21 Sep '16

21 Sep '16

Dear Colleague, It's already 2,5 years since Faraday discussion #169. I hope this message finds you well. Because of your interest for molecular visualization, I thought I share the following in the hope you can circulate it, or even direct candidates towards me :) Thanks in advance! We have two open positions in Paris, France, both relating to molecule and network visualization developments in Unity3D, and one specifically to VR. We are looking to hire ASAP and funds are available. The first position is for a postdoc on Development and Application of a Virtual Reality Immersive Modelling Platform for Enabling Drug Discovery. You can find an html version at [1] and PDF at [2]. The second position is for an engineer (or postdoc) on Computational Analysis, Visualization and Modeling of Redox Signaling Networks. You can find an html version at [3] and PDF at [4]. Thank you, Marc [1] http://www.baaden.ibpc.fr/ns16/pdoc1.html [2] http://www.baaden.ibpc.fr/ns16/pdoc1.pdf [3] http://www.baaden.ibpc.fr/ns16/inge1.html [4] http://www.baaden.ibpc.fr/ns16/inge1.pdf -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

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Recursive structure matching and acquisition of descriptive numbers
by Healey, Joe 20 Sep '16

20 Sep '16

Hi, I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? Thanks Joe Healey M.Sc. B.Sc. (Hons) 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>

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Chimera input from command line
by José Almeida 15 Sep '16

15 Sep '16

Hello, I am a beggining Chimera user and was wondering if it was possible to run, all in the same command, something that enabled me to use a function (e.g. hbonds) without utilizing the console or the gui. I am trying to include this into a program so that I can calculate H-Bond data on several proteins in order to automatize the procedure, but I haven't been able to do so. Already thanking any attention given to this problem, Best regards, José Guilherme de Almeida

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Problem in installing Chimera in Linux
by Chau Phi DINh 14 Sep '16

14 Sep '16

Dear my friends, I tried to install Chimera on Ubuntu. I followed the instruction in Release Note of UCSF. I typed in Terminal command the following: chmod +x chimera-installer.bin chimera-installer.bin but it shows me : chimera-installer.bin: command not found Can you tell me how I can do to install it ? Regards, Phi Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=dinhchauphi@…>

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RMF Viewer and Resolution Selection
by Chemmama, Ilan 14 Sep '16

14 Sep '16

Dear developers, I am trying to select hierarchical features based on resolutions (for example to show or hide). Using the resolution sliders does not seems to work however. I could not find anything in the documentation page though. Is there an easy way (command line would be the best) to select a given resolution? Thanks, Ilan

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Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
by Jaime Rodríguez-Guerra 09 Sep '16

09 Sep '16

Joe, If admin permissions are an issue, you can always install the Miniconda 2.7 distribution, which will install all packages in your user folder, virtualenvs included. I cannot recommend it enough! Greg, I have not come across any problems without that windowsize command, so I guess it just works? I posted a gist which shows how to render images programatically for a bunch of pdb files. Let me know if it works! https://gist.github.com/jaimergp/09104ca2bbccb81ff430374f9c2522a7 Cheers!

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Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
by Jaime Rodríguez-Guerra 08 Sep '16

08 Sep '16

Hi! Such an honor to see my name listed here! Yes, with pychimera you should be able to do it! All you need to do is to patch the environment so that Chimera can find its libraries and dependencies, and then initialize it. In practice, this means importing pychimera and calling pychimera.patch_environ() and pychimera.load_chimera() at module level. Then you can proceed as you'd do with a standard Python distribution. If you don't want (or are not able) to modify the script, pychimera also installs a binary that will patch and load Chimera for you, so you can just do "pychimera myscript.py" However, it's a bit buggy when it comes to parsing additional arguments for your script. That said, the binary is very useful to fiddle with Chimera internals from the command line, since it provides a patched python in which you can import chimera, and also hooks for ipython and jupyter notebook (with magic calls to render inline!). pychimera will do its best to locate your Chimera installation, but if it doesn't succeed, you can always provide it manually with the envvar CHIMERADIR, which is what you would probably need to load the headless edition of Chimera. Additionally, it will load your current Python distribution sys.path, which means it will be able to import already installed packages in such distribution. As a result, you don't need to install the packages again for Chimera. This is particularly useful if you are using virtual envs or conda envs! I think that's all. If further questions arise or something is not working as you'd expect, please report that in the issues page of GH ( https://github.com/insilichem/pychimera) or write to me directly. Cheers, Jaime.

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Re: [Chimera-users] Mesh points from volume data
by Elaine Meng 07 Sep '16

07 Sep '16

Hello, Sorry, I can’t help on this one, so I’m forwarding to the list! Best, Elaine On Sep 7, 2016, at 6:24 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > Hello, > > I'm almost home. There are several issues: > 1. I need not only points but also planes -> point triples from surface triangulation. > 2. I have quite a lot of points (more than 30 000). PDB file format fails in the CONNECT records: > > In the end of file they looks like this: > CONECT3051230171301923050530506 > CONECT3051230511 > CONECT3051330165301663018830508 > CONECT3051330514 > CONECT3051430188302133050830509 > CONECT305143051330515 > CONECT3051530213302163050930510 > CONECT305153051430516 > CONECT3051630193302163021830510 > CONECT305163051130515 > END > > Is there any walkaround? Preferably it would be best solution for me if I could access both points and planes (faces) programatically with python. Is it possible? > > -- > pozdrawiam serdecznie > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > > > On Sep 6, 2016, at 12:36 PM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > > > Works like a charm! :) > > > > -- > > pozdrawiam serdecznie > > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > > > > 2016-09-06 19:28 GMT+02:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > > Hi Michal, > > You can use the “meshmol” command to make the isosurface mesh into a fake molecule, where the the points are “atoms” and the mesh lines are “bonds” shown as sticks. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html> > > > > Although the new “molecule model” is suppressed from appearing in the File… Save PDB dialog, you can still save it to PDB from the command line with “write” … or save it as a marker set using the File menu of the Volume Tracer tool. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/…> > > > > Either of those formats will contain the coordinates. The marker format will do a better job of preserving the stick bonds and their radii, if that matters to you. > > I hope this helps, > > Elaine > > ---------- > > Elaine C. Meng, Ph.D. > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > > > On Sep 6, 2016, at 6:48 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > > > > > Hello, > > > > > > I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation. > > > > > > How can I do that? > > > -- > > > pozdrawiam serdecznie > > > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > > > >

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Mesh points from volume data
by Michał Kadlof 06 Sep '16

06 Sep '16

Hello, I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation. How can I do that? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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extracting chaing colors from session file?
by Melissa Jurica 06 Sep '16

06 Sep '16

I am analyzing a structure containing many individual chains that I have colored. I would like to transfer these colors to another structure of the same complex in a different conformation. Is there a way to extract the colors into a text file so that I can write a command file with the same color designations? For example: color #6168c8fb41bc #0.17 Also- How do I get that color to apply to the little square that shows up on the model panel? Melissa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064 Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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Bonds
by Igor Peixoto Rodrigues 06 Sep '16

06 Sep '16

Hi my name is Igor Peixoto, and I have a question. There is some way to count the number of bonds in molecule? Like how much bonds of kind B-C, C-C, B-N.... for example?

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secondary structure incomplete
by Ming 06 Sep '16

06 Sep '16

Dear Chimera team, I was using chimera to do some pdb editing and exporting the file for pymol printing. However after the editing with chimera the pdb file won't show secondary cartoon in pymol (It still shows perfect secondary structure in chimera). I used the file--export function in chimera and I have checked the pdb file and the secondary structure description in the pdb file is intact. Do you think if I export the file in a wrong way that caused the incomplete cartoon? If not what do you think could be the reason causing the issue? Thank you, Ming

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Command line doesn't work properly on Mac
by Li, Leon 04 Sep '16

04 Sep '16

Hello All, The command line in Chimera seems not working properly on my Mac. Any input in the command line will not show unless you select them. Does anybody experience this problem? Or any idea about this? Both versions of 1.11 and 1.11.1 have been tried. My mac is iMac (Retina 5K, 27-inch) OS X EI Capitan. Thanks, Leon

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disabling previous state
by david gae 02 Sep '16

02 Sep '16

Dear Chimera Users, I am wondering if anyone can help me with this question: Whenever I start up CHIMERA. My previous settings and panels show up. Is there a way to prevent my previous preferences being saved? Thanks, David

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Deleting invisible structures?
by max taylordavies 31 Aug '16

31 Aug '16

Hello all, Is there any way to selectively delete the 'invisible' (undisplayed) parts of a structure and keep the visible parts without having to use the usual atom-spec approach? For example, if I run per-model clipping on a protein, is there any way to delete the part that has been rendered invisible by the clipping? If this isn't possible, is there a way to export only the visible/displayed components of a scene? Many thanks in advance, Max Taylor-Davies

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ETA ChimeraX
by Chris Sander 30 Aug '16

30 Aug '16

Just curious when ChimeraX will appear and what it will be able to do! Keep up the good work. Chris Sander www.evfold.org

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Integrating chimera into a database
by McCafferty, Caitlyn (NIH/NEI) [F] 29 Aug '16

29 Aug '16

Hi, I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed? Thank you, Caitlyn McCafferty Postbaccalaureate Fellow Ophthalmic Genetics and Visual Function Branch National Eye Institute Bldg. 10 Rm. 6-3350 Tel: (301) 402-7058 Email: caitlyn.mccafferty(a)nih.gov

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bond formation
by A G Szabo 26 Aug '16

26 Aug '16

I am working with a PDB file that has two proteins docked together. As this is a model the two proteins do not have a bond between them. The model number is the same for the two chains designated A and B. I have looked through the various tutorials, functions and tools to figure out how to actually place a bond between two residues that link the two chains. It is well established as to how the two proteins would be linked if the bond had been formed. The linkage is between the S of a Cysteine and carbonyl carbon at the C-terminal of the other protein. I think I have managed to select both atoms, but cannot determine how to include a bond. Your assistance is appreciated. Arthur Szabo

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Creating and saving Multiscale Models using Python functions
by Jon David 24 Aug '16

24 Aug '16

Hi Friends, I would like to use Python to perform operations equivalent to the following GUI operations; I'd like to be able to do this as a batch script (e.g., I don't want the Chimera GUI to appear because I don't want to have to close it.): 1) Open a PDB file (I know how to do this part). 2) Tools > Higher-Order Structure > Multiscale Models (this opens the MultiScale Models popup window). 3) Click on the "Make models" button. 4) File > Export Scene... (this opens the Export Scene popup window) 5) In the Export Scene popup window, select File type to be "OBJ [.obj]", enter file name "test.obj" 6) Click on the "Save" button. I have used Python to open a PDB file, and translate, and rotate it around before. But I don't know where to begin with selecting Multiscale Models' parameters. Any tips? Any help would be much appreciated. Thanks, --Jon

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volume viewer - planes
by Michael Elbaum 24 Aug '16

24 Aug '16

Hi. I'm using the volume viewer and the Planes function is extremely useful in order to see a subsection of the volume. Often I want to compare different processing or filtering of the same dataset. When I load several datasets, all the visualization parameters are set individually. Normally this is good, for example in setting different colors, but for Planes it's problematic. In order to switch among the various representations and see the same section of the volume I have to scan them individually, and when two are visible I can move only one. Is there a way to link the Planes among the maps? Perhaps there's a command line trick? thanks, Michael

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question
by A G Szabo 23 Aug '16

23 Aug '16

I recently downloaded the new version of Chimera. No issues with that so far. However, when I save a session it is still saved as a Chimera file, or a PYC file on my desktop. So when I went to my desktop file list, and tried to open one of the files I would click on "open with ." Two programs would be listed, Adobe, and Chimera. So I would select Chimera and the file would open satisfactorily. However, with the new version of Chimera, if I repeat the above, the only program that is listed is adobe. If the file type is listed as Chimera, then adobe would be listed, and there would be other programs listed but not Chimera. I can open the file in a round about way, but the former way was more efficient and user friendly. If I go to my programs list, there doesn't seem to be a way that I can conveniently open the file without first opening up Chimera. Your comments will be appreciated. Arthur G. Szabo

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Select Non-conserved residue
by Markus Heller 23 Aug '16

23 Aug '16

Hi all, I used matchmaker to align two homologues proteins, and to calculate the sequence alignment. How can I select all non-conserved residues, in one fell swoop? Thanks and Cheers Markus -- Markus Heller, Ph.D. Senior Scientist, NMR CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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