- Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] What is the default of ribbon?
by Elaine Meng 20 Aug '16

20 Aug '16

Hi Root, You cannot change this preset, but you can control what is shown “manually," for example hiding all atoms and then displaying residues within 5 angstroms of ligand and 3.2 angstroms of ions with commands: ~disp disp ligand z<5 disp ions z<3.2 To make a more simple one-step action, you can make an “alias” combining several commands, and that could be listed in an Aliases menu. This is sort of like “make your own preset”. For examples, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007230.html> I hope this helps, Elaine On Aug 19, 2016, at 1:03 AM, 郭尚哲 <b02b02049(a)ntu.edu.tw> wrote: > Dear Elaine, > I have another question. How can I change this 3.6 Å criteria, if it is possible? > Root > ________________________________________ > 從: Elaine Meng [meng(a)cgl.ucsf.edu] > 寄件日期: 2016年8月19日上午 12:54 > 至: 郭尚哲 > 副本: chimera-users(a)cgl.ucsf.edu > 主旨: Re: [Chimera-users] What is the default of ribbon? > > Hi Root, > It is described in the “preset” documentation: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets> > > … specifically, > "Interactive 1 (ribbons) - shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.” > > In other words, if the amino acid residue has any atom within 3.6 Å of what Chimera thinks is “ligand” or “ion” the whole sidechain will be shown, except any H atoms attached to C atoms. > > You do not need to search on the net, you can just look at the manual included with your download, using menu: Help… Search Documentation. For example, you could search for “presets” or “ribbon interactive preset”. The information you found is explaining something different: why the backbone atoms are not shown. > > 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 Aug 17, 2016, at 11:13 PM, 郭尚哲 <b02b02049(a)ntu.edu.tw> wrote: >> >> Hi all, >> I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below: >> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo… >> It says "By default, when ribbon is shown for a residue, the mainchain atoms of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)." >> I can't get more imformation, and still don't understand. >> What is the rule chimera follow to show the sidechain of certain residues? >> Thanks, >> Root > >

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segmenting cryoEM maps
by giulia palermo 20 Aug '16

20 Aug '16

Dear all, I am new to chimera and I am working with density maps. I have segmented my cryoEM map successfully. I want now to group some of the segmented regions in a single region and subequently save the obtained map. Is there a way of doing it? Thank you very much Best wishes Giulia Palermo

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Re: [Chimera-users] Add Hydrogens - non standard residue - protonation state
by Elaine Meng 19 Aug '16

19 Aug '16

Hi Subha, This is out of my area, since I don’t know python. (We always recommend sending questions to the chimera-users list, CC’d here, since you are more likely to get a good answer by asking multiple people!) I can only say that as far as I know if it works in the command line, then you should be able to use python to run the same command, as described in this page in the Chimera programmer’s guide: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Best, Elaine On Aug 19, 2016, at 1:57 PM, Subha Kalyaanamoorthy <kalyaana(a)ualberta.ca> wrote: > Hi Elaine, > > Just another question, > > Is there anything I need to import for using setattr in a python script. I get an error when I use it as a part of script. But, it works fine when I type it on the command-line of Chimera gui. Not sure what I am missing. > > Thanks and Best Regards, > Subha >

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Default contour level in Volume Viewer
by MICHAEL POTEAT 19 Aug '16

19 Aug '16

Hello all, How is the default contour level in the Volume Viewer calculated when you first open up a .mrc file? I've tried the average density, and the root-mean-square of all voxels, but both do not match Volume Viewer's default level. I've tried looking here [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame…] for documentation on this, but it does not mention it. Thanks, Mike

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Add Hydrogens - non standard residue - protonation state
by Subha Kalyaanamoorthy 18 Aug '16

18 Aug '16

Hi There, Can anybody please suggest me how to use 'setattr' (or any other function) to assign a protonation state for an atom in a non-standard residue. I have a ligand and I am using a python script to add hydrogens and charge to the ligand molecule using chimera no-gui. I see that chimera adds an extra hydrogen to a nitrogen atom in the ligand and assigns a charge of +1 to the molecule. Removing this hydrogen using GUI is simple but not practical for large set of molecules. So, it would be helpful if somebody suggest me a command-line to set specific protonation states for atoms (in non-standard residue). Thanks and Best Regards, Subha

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splitting and surfaces
by A G Szabo 18 Aug '16

18 Aug '16

I am working on a large multi subunit structure (4CR2). Originally I selected one of the subunits, and received the error message that suggested I should use the split command. Which I did and obviously I must have been successful in splitting the subunits. Each of the subunits is now labelled as being split, i.e. (#0.14) etc. I was successful in showing the surfaces of 4 subunits, and colored them differently. However, when I tried to show the surface of one of the subunits with 437 residues, (several residues cannot be resolved) I received this error message One subunit which I successfully was able to show the surface in the image had 467 residues and also had a large number of residues that were not resolvable. So I am stuck! Your help would be appreciated. AGSzabo

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further
by A G Szabo 18 Aug '16

18 Aug '16

Further to my last message regarding surfaces it would be highly convenient to have the url listed at the bottom of the error message open as a link. Secondly it is not even possible to copy it and paste it into my browser. ags

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What is the default of ribbon?
by 郭尚哲 18 Aug '16

18 Aug '16

Hi all, I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo… It says "By default, when ribbon is shown for a residue, the mainchain atoms<https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)." I can't get more imformation, and still don't understand. What is the rule chimera follow to show the sidechain of certain residues? Thanks, Root

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Joining models
by Jie, Jing 16 Aug '16

16 Aug '16

Hi all, Is there a way in chimera to fix the position of one model when creating a peptide bond between two models? I selected 'move atoms on C side' but the N side chain still moves. Thanks in advance! Jing

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Problem
by Kari Boyett 15 Aug '16

15 Aug '16

I have alot of these Chimera Modules on my phone that I didn't authorize and I need to know how to remove them please.

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measure rotation command questions
by Joseph Atherton 15 Aug '16

15 Aug '16

Hi, When I use the command 'measure rotation' I get a matrix in the reply log. 1) The fourth column is 'translation'. At most the translation I see is 5 Angstrom, so how do I get these numbers (see below)? I also have a shift along axis reported, which seems a more reasonable number, but what if the shift is in a a different vector to the axis? 2) I can get depiction of the rotation axis, but can I also get a depiction of the translation vector? Cheers, Joe Position of model2 (#20) relative to model1.pdb (#1) coordinates: Matrix rotation and translation 0.98820614 -0.14982292 -0.03165001 43.44553134 0.14930460 0.98862441 -0.01816347 -23.90940685 0.03401127 0.01322376 0.99933396 -9.65968865 Axis 0.10195507 -0.21328736 0.97165512 Axis point 180.93496764 275.63881775 0.00000000 Rotation angle (degrees) 8.85455905 Shift along axis 0.14318049

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chimera crashing upon opening of trajectory
by Natesh Singh 12 Aug '16

12 Aug '16

Dear Sir/Madam, I am unable to open a trajectory (50 ns and about 25 gb size) in a chimera GUI. I am getting a python crash error after some time of initial message of 'reading PDB...' and then chimera shuts down. Is it the large file size that is causing the python to crash? Looking forward for the guidance. Best regards, Natesh

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Re: [Chimera-users] Selecting specific atoms in MD Movie
by Thomas Faour (x2013gua) 12 Aug '16

12 Aug '16

Hi Elaine, I thought about sending the data but was hoping there was an easy solution to something I was doing wrong... Which there was! Using :52.water worked perfectly. Thanks a ton! Thomas On Aug 12, 2016 14:49, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Thomas, It's difficult to answer questions like this without the data... I only have one low-confidence guess, which is to try :52.water instead of :52 ...as mentioned in the "subcategories" section of <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> If that doesn't work, you would have to send us the data (or a smaller sample, if possible). You could send it to just me if you don't want to send to the whole list. Best, 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 Aug 11, 2016, at 4:46 PM, Thomas Faour (x2013gua) <x2013gua(a)stfx.ca> wrote: > Hello there, > > I study water/ice systems and I have an algorithm which reads my trajectories and tell me if a certain water molecule can be considered "liquid", "hexagonal ice" or "cubic ice". So I can label each molecule at each frame as such. I am hoping to be able to use this data to create a movie where each group is coloured differently, and should a molecule change groups be re-coloured accordingly. > > I attempted this by running a PER-FRAME script which reads my labels from a data file, and colours the molecules. However I ran into a problem, running either of the following commands: > > colour blue,a :52 > select :52 > > in the PER-FRAME script, or even just on the command line during an MD Movie does NOT work for me. This works for a single configuration file, but not during a movie. The command: > > color blue,a @OW > > however does work. I am currently using XTC trajectories, in case that is relevant. > > What might fix my problem? Or is there a better way I could be doing this? > Cheers, > Thomas

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Selecting specific atoms in MD Movie
by Thomas Faour (x2013gua) 12 Aug '16

12 Aug '16

Hello there, I study water/ice systems and I have an algorithm which reads my trajectories and tell me if a certain water molecule can be considered "liquid", "hexagonal ice" or "cubic ice". So I can label each molecule at each frame as such. I am hoping to be able to use this data to create a movie where each group is coloured differently, and should a molecule change groups be re-coloured accordingly. I attempted this by running a PER-FRAME script which reads my labels from a data file, and colours the molecules. However I ran into a problem, running either of the following commands: colour blue,a :52 select :52 in the PER-FRAME script, or even just on the command line during an MD Movie does NOT work for me. This works for a single configuration file, but not during a movie. The command: color blue,a @OW however does work. I am currently using XTC trajectories, in case that is relevant. What might fix my problem? Or is there a better way I could be doing this? Cheers, Thomas

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APBS mobile ion option
by Eita Sasaki 12 Aug '16

12 Aug '16

Hi, I'd like to run APBS command with mobile ions (150 mM NaCl). I tried the following command, but it did not work. apbs molecule #1 ion true _posion 1,0.15,1.16 _negion -1,0.15,1.67 If I typed just "apbs molecule #1" it works (without mobile ions). I am wondering my command was perhaps wrong but don't know the right one. I hope you could help me to solve the problem Thank you in advance. Eita

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(no subject)
by Karel W. F. de Pourcq 09 Aug '16

09 Aug '16

Dear Chimera team: I am a student of a Msc. in Bioinformatics at the Autonomous University of Barcelona. I am using Chimera to prepare visual representations of molecular events, and I write in order to ask if there is a straightforward way in which to: a) Create a sphere of a certain diameter: Yes, I found how to do it already: with the "shape" command. This is solved. b) In an orderly and distributed way, cover that sphere with a number of copies of a molecule chain, anchored over the sphere's surface by one of their ends (and the other end of the molecule protruding towards the outside). I believe I could do it manually for a small system. Is there some kind or automated and more convenient way to do this for a large sphere, linking its surface with hundreds of molecules of -for instance- dodecane? I could not find explicitly a way to do something similar to what I am trying to do. I attach an image of a 2-d representation of something similar to what I would like to represent. The difference is that I would like to cover the surface. [image: Imágenes integradas 1] I thank you a lot in advance for your time. Kind greetings from Barcelona, Spain, Karel De Pourcq

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chimera minimize script
by Bylund, Tatsiana (NIH/NIAID) [F] 09 Aug '16

09 Aug '16

Dear all, I need to minimize a lot of protein complexes and am trying to do it with a script. I have a protein complex structure without Hydrogens, but when they are added in Chimera, it outputs error Non-standard atom names: ASN HA2 (:33.K@HA2) ASN HA3 (:33.K@HA3) Total charge for #0: 32.039 Total charge for #0: 32.039 The following residues had non-integral charges: :33.K 0.039 Correct charges are unknown for 2 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log Dock prep finished Error while processing chimera_mini.py: No MMTK name for atom "HA3" in standard residue "ASN" When I delete residue K 33 (which DOES NOT have H in pub file) chimera runs minimization. Would you have any suggestions? Thank you! Kind regards, Tatsiana

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UCSF
by Amali Guruge 05 Aug '16

05 Aug '16

Dear All, What is UCSF referring to? Is it University of California San Francisco ? Thank you.

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Volume and mesh data simultaneously? Coordinate space is different
by Marvin Albert 03 Aug '16

03 Aug '16

Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap). Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh? (this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3 <http://www.filedropper.com/cube_3>) Thanks a lot in advance, Marvin

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precalculated void representation as surface
by Michalska, Karolina M. 03 Aug '16

03 Aug '16

Hi, I have a precalculated cavity represented as a grid in the pdb format, where “atoms” are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface. I appreciate your help, Karolina

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APBS webservers not working
by Ursula Schulze-Gahmen 02 Aug '16

02 Aug '16

I used to run APBS from within Chimera. But recently, the webservers that are called for the APBS calculations are not working. Do I need to go to the APBS website directly or what is the solution? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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chimera 1.11 question
by Dixon, John 01 Aug '16

01 Aug '16

Hi I was wondering if you could help When I install chimera on my main physical PC I can use function left CTRL and mouse to highlight atoms in green in the graphics interface as below. [cid:image003.jpg@01D1E728.1FE9F730] However when I install chimera on a virtual PC, this function does not work. Any ideas on how to get around this issue? thanks John Dixon Application Integration Team Client Platform Services Information Services Division, UCL Tel: 02076799163 Ext: 09163

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help for make figures
by 陈柳青 30 Jul '16

30 Jul '16

HI How to make the figures in attachment, which highlight part of a structure. Thanks very much for advise. -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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help for make figures
by 陈柳青 30 Jul '16

30 Jul '16

HI How to make the figures in attachment, which highlight part of a structure. Thanks very much for advise. -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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UI suggestions - Save map
by Oliver Clarke 29 Jul '16

29 Jul '16

Hi, minor suggestion for Chimera, related to dealing with large numbers of maps: It would be really helpful if there was a 'Save map' dialog in the 'File...' menu, with similar dropdown menus to select the map one wants to save as for the 'Save PDB' dialog. Doing so via the volume viewer is a bit clunky when there are lots (e.g. 10+) of maps loaded. Even better would be if it included a 'Save relative to map' dropdown, analogous to the 'Save relative to model' drop down in the 'Save PDB' dialog, which would resample the map to be saved on the grid of the selected target map (perhaps warning of the potential for a modest loss of quality). This would be really helpful when one aligns many different conformations of a molecule (e.g. from 3D classification) to a reference subvolume and wants to save the resulting transformed maps. Cheers, Oli.

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Re: [Chimera-users] [chimera-dev] B factor
by Elaine Meng 28 Jul '16

28 Jul '16

On Jul 26, 2016, at 5:12 PM, Bashayer Althufairi <althufairib(a)mymail.vcu.edu> wrote: > Hello > As you know many crystallographers need to determine the ave. B factor of selected amino acids or sometimes they wanna know B factor of N-termius Vs. C-terminus of a protein. I'm working on a protein where I need to predict B factor of certain amino acids sequence as well as difference between the values for analysis. Is this possible by Chimera? If yes, I'd like to know Please the way step be step, If no, I wish you could recommend a simple way to do it by educational simple software like PyMol. > Thank You in Advance > -- > Bashayer Althufairi > Medicinal Chemistry department > Virginia Commonwealth University Hello Bashayer Althufairi, This is really a Chimera user question so I’m CCing the chimera-users mailing list. The chimera-dev list is for Chimera programming questions. Chimera doesn’t predict any B-factors, but you can see the B-factors from the PDB file for a structure, e.g. in a histogram in the Render by Attribute (in menu under Tools… Structure Analysis). This tool can color the structure to show the B-factor values. It also automatically calculates the average B-factor per residue (over the atoms in each individual residue so that each residue can have one number). It can also save the values to a file (see File menu of that tool) although of course the PDB file already contains the per-atom B-factor values. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> See also the tutorial for coloring by B-factor: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> But maybe you mean that you want to select several residues and then calculate a single average B-factor for them. You can do that with Attribute Calculator (in menu under Tools… Structure Analysis) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcul…> For example, you could select several residues and open Attribute Calculator, turn on the options to “Restrict formula domain to current selection” and “Show calculation results in Reply Log”, calculate a new attribute named whatever you want for “molecules” with formula: average(atom.bfactor). Click Apply to calculate a single average over all selected atoms, value reported in Reply Log. If you have predicted B-factor values you can also read them into Chimera as a custom attribute (see file format for doing that <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defi…> … it is the same format as used for the saving mentioned above). When you read in those values they are also available for use in Render by Attribute and in Attribute Calculator, and with the latter you could calculate the differences between the bfactor attribute from the PDB file and your custom attribute (the predicted values). The differences would then be another attribute also available for coloring using Render by Attribute. See also the attributes tutorial for examples of using Attribute Calculator and Render by Attribute: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html> I don’t use other programs so I don’t have any advice about using them for this purpose. 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

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Help with Autodock Vina
by Jonathan Y Wang 28 Jul '16

28 Jul '16

To whom it may concern, Hi, I was trying to dock a ligand into my receptor and all of the other ligands so far have worked and outputted a value, but this one compound never outputs a .pdbqt file. The other files such as the .conf and .pdb files have been created, the bottom of the screen no longer says "execution in progress", and the green box remains. I've looked at the tutorial for AutodockVina online and tried fidgeting around with it, but I seem to be extremely lost. I was wondering if you had any pointers, tips, or anything at all that could help me. All the best, Jonathan Wang

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Auto start and nogui option causing segmentation fault?
by Daniel P Farrell 26 Jul '16

26 Jul '16

Hello, I don't know if maybe i'm doing something wrong, or if there's a problem, but I'm on a mac el capitan 10.11.6 and I'm getting these weird errors when I try to start chimera in nogui mode. I usually set various tools to auto-start once I start chimera, but recently I was messing around and added a few, and now I'm getting these errors when i start chimera via --nogui. Problem is, I don't know which one is causing the seg fault, but I feel like it shouldn't be calling these gui options with the nogui options on anyway. Once I started getting these errors I went to Favorites->add to favorites/toolbar->reset & save, and now I don't get the segfault. I do get a few other errors if I adda few back to the auto start / on toolbar options. chimera production version 1.11 (build 41179) 2016-07-15 05:43:21 UTC with many auto-start options on """ >chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' [1] 1045 segmentation fault ~/Desktop/Chimera.app/Contents/MacOS/chimera --nogui """ after removing most auto-start options """ >chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' Starting extension 'Model Panel' failed Starting extension 'Keyboard Shortcuts' failed Starting extension 'IDLE' failed > """ should I be adding a different flag or something when I start chimera via nogui? Thanks, Dan

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Saving Attribute settings and Worm Radius Consistency
by Nicole Persky 26 Jul '16

26 Jul '16

Hi All, I've started using Chimera to map two different datasets onto structures. For one, we use color, and for the other we use worm radius. I've encountered two problems while trying to make figures for publications: 1- when I save my session the image is saved but when I go to "render by attribute" to tweak the settings a little, the threshholds under colors and worm radius have been reset. How to I get them not to reset, but to keep the thresholds? 2- I am trying to compare three different images with the same worm radius thresholds. For one of the images the lowest number of my attribute is LARGER than the lowest number I want to define on my threshhold (I would like to set the lower worm radius to 1 for a value of 1 however for this dataset my lowest value is 2. I cannot just set the value starting at 2 because there is a gradient to the largest value that gets thrown off). Yet, I cannot set the threshold lower than the lowest value of my attribute. Does anyone know a way around this? thanks so much, Sincerely, Nicky

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saving multiple models in Chimera
by Kamil Kuder 26 Jul '16

26 Jul '16

Dear Sirs/Madamme I have multiple PDB'a (ca.40) in the model panel. While trying to save each model in single file using option "Save multiple models in multiple files" I got this message: You must provide a file name that contains either $name or $number. I set the name to eg. A1_01 and/or A1_$01 but none of this works. How shall I manage that? Many thanks Kind regards Kamil J. Kuder, PhD Jagiellonian University Medical College Faculty of Pharmacy Department of Technology and Biotechnology of Drugs Medyczna 9 30-600 Krakow POLAND tel.: +48 12 602 55 86

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