September 2016 - Chimera-users - RBVI Mailing Lists

segmentation and resolution
by Kristin Parent 23 Sep '16

23 Sep '16

To whom it may concern, I am currently working on segmenting a high resolution cryo-EM map (~4Å by the ³gold standard FSC²) to phase crystallography data. After the segmentation, my colleague doing the phasing tells me that map appears more like 12Å resolution and I am worried I am doing something wrong during the process and somehow distorting my original data. I believe the 4Å of the original map based on structural features that I can clearly see. And the segmented density does not appear as defined. Therefore it appears that there has been some changes. In order to begin the process, I did some manipulations before I started. This is an icosahedral virus map created through Auto3dem. I am only using an small quadrant of the original map, and since it was in pif format originally, I used proc3d to convert to mrc and invert the contrast to be compatible with segger. Before segmentation the map visually looked the same as the original pif map when both were displayed in chimera. The procedure I followed after segmentation was: "Save selected regions to .mrc file... save density map masked by the selected <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html> segmentation regions to an MRC file (map dimensions set to the minimal box containing the regions)². I have made sure that the correct binning has been applied during segmentation. Any help would be much appreciated. Kristin -- Kristin N. Parent, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology Michigan State University 603 Wilson Road Room 519 Biochemistry Building East Lansing, MI 48824 Office phone: (517) 432-8434 https://kparentlab.natsci.msu.edu/

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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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Chimera-users September 2016