- Chimera-users - RBVI Mailing Lists

x,y coordinates of the Chimera screen
by Jan Kosinski 13 May '14

13 May '14

Hi, When I load a model in Chimera I can move the model on the plane of the screenwith the move command along the x,y axes. Is it possible to get the current range of the coordinates of the x and y axes of the screen, so I could automatically (without setting positions with savepos) move my models to particular points on the screen? For example, move to left upper corner in a movie... Or move the model outside the screen and create nice fly-in effect in movies. Thanks, Jan

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1.9 production release
by Eric Pettersen 13 May '14

13 May '14

Hello everybody, A new production release of UCSF Chimera (version 1.9) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). New features include multiple sequence alignment using Clustal Omega or MUSCLE web services, building double-helical nucleic acids, "colorkey" command, "struts" command to reinforce structures for 3D printing, "vseries" volume series playback and processing options, more efficient save/restore of coordinates in sessions, Dynameomics amino acid rotamer library, WMV2 movie output, COLLADA export. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.9.html Display, Interface: * icon for menu selection mode: Append, Intersect, Replace, Subtract * distance monitor line style and color can be saved as preferences * silhouette outlines can be controlled per-model * Axes/Planes/Centroids objects can be recolored with Actions menu * "colorkey" command implementation of Color Key tool Structure Analysis and Modeling: * new Align Chain Sequences tool for multiple sequence alignment of structure chains using a Clustal Omega or MUSCLE web service (these can also be called to realign the sequences in an existing Multalign Viewer window) * "mda" command to Blast-search and retrieve structures similar to a query sequence, lay them out left->right by N->C along the query * APBS interface omits explicit solvent by default * "coulombic" command allows specifying atoms/charges to use for ESP calculation independent of the surface to color * Build Structure tool allows generating nucleic acid double helices, specifying phi angle when joining peptides * "adjust" command to change bond angle or length * MD Movie session support for partly loaded trajectories * Morph Conformations pairs chains by ID if the sets of IDs are same * "ramachandran" command can assign probabilities as attributes * Rotamers/swapaa include Dynameomics rotamer library (Daggett group) Volume Data (density maps, ESP maps): * "vop" volume operations to take pointwise maximum or multiply maps * "vseries" command options to open and close volume time series, jump playback to a specific frame, perform various processing such as alignment, normalization, cropping, compressing, save to file * new volume input format VTK structured points (ASCII) General, I/O: * some Preferences reorganization, new categories: Labels, Selection * more efficient save/restore of coordinates in sessions * new output movie format WMV2 * new export formats COLLADA, VTK * "struts" command to add strengthening bonds for 3D printing * "leap" command for using Chimera with a Leap Motion Controller Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to get translation and rotation vectors for move and turn commands
by Jan Kosinski 13 May '14

13 May '14

Hi, I have the same model loaded in Chimera twice. One model has been moved to a different position and rotated manually using mouse. How can I get x,y,z coordinates for the centers of the to models to calculate x,y,z axis definition compatible with the move command? And how to get rotation information for turn command? I tried with cofr command but it seems to give coordinates in different reference frame. I would like to avoid using savepos/reset/fly commands in this case. Python solution would be fine. Thanks in advance for your help, Jan

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EM density map rescaling issue???
by Christian Geiss 13 May '14

13 May '14

Dear Chimera User list, I have a fundamental problem when loading pdb structures and EM density maps as *.em. The scale doesn't fit at all, with other words my pdb structure is tremendously bigger than the EM structure. One work-around is to resample the EM structure from current 64 px boxsize with 8.6 A pixelsize to 1 A pixelsize, giving ~ a 500 pixel volume, but then the volume gets quite big und my chimera gets really slow in handling those structures (pdb and big EM map at once)...is there any other way to solve this issue like scaling the EM structure on the fly in not such a memory consuming way...I also wonder if there is any information about the pixelsize in the EM header, because then the scaling should be done usually automatically??? Thanks in advance, Chris P.S. I couldn't find anything related to this in the chimera archive... -- *Christian Geiss, M.sc.* Universitaet Frankfurt BMLS Frangakis Group Max-von-Laue-Strasse 15 D - 60438 Frankfurt am Main Phone: +49-(0)69-79842597 Fax: +49-(0)69-79846467 geiss(a)biophysik.org

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threshold level problem
by 李智海 13 May '14

13 May '14

Hello, I am a freshman for Chimera, sorry for a possibly stupid question but i seem to be confused by the difference between threshold level in volume view and the sigma value that is used to contour the density map in some articles. please help me out! Thank you very much! Zhihai Li

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help with surface coloring
by Benda, Christian 09 May '14

09 May '14

Hello, sorry for a possibly stupid question but I seem to have a problem getting a molecular surface colored the same way as the atoms or ribbons of the underlying structure. Here’s what I did: - selected two domains of a larger protein separately (sequence viewer) and colored each domain differently (say green and blue, ribbons and atoms are in the respective color) - then selected the molecule in the model panel and clicked surface main - I get a surface, but it is either transparent grey or a solid color (pink) of the color well displayed in the model panel (not the domain colors I selected). - when opening the attributes of the surface, I can toggle between color source “atoms" or “model" but that only toggles between transparent gray and pink. I tried all kinds of combinations and clicks but I don’t manage to get the surface colored in the colors of the two domains. Any hint? It would be highly appreciated! Many thanks! Christian

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! 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 Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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Enquiry: Match Maker
by Anna Hernandez 06 May '14

06 May '14

Hi, I have a question regarding structural alignments with Match Maker. I would like to know if there is any way to obtain a list of all possible alignment solutions (or a subset) tested by Match Maker, instead of only the "best" one, so that I can further assess the different options manually. Specifically I am trying to find an homologous substructure/motif from my template structure within a query structure. The pattern to be searched is rather small as compared to the whole protein and it can be aligned in multiple positions. I would like to assess each of the possibilities more carefully based on the biological knowledge of the protein. Thank you in advance. Best wishes, Anna Hernandez

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Re: [Chimera-users] how to save distance to a file
by Eric Pettersen 05 May '14

05 May '14

On May 5, 2014, at 4:07 PM, chang YG <changyg2008(a)gmail.com> wrote: > Hi Eric, > > Thank you very much for the quick response. I can't wait to try the script you provided. > > For the RMSD, I have two conformers for the same sequence. If I encounter any problem, I will give it my best shot before posting questions. In that case it should be easy: from chimera import openModels, Molecule m1, m2 = openModels.list(modelTypes=[Molecule]) import Midas rmsd = Midas.rmsd(m1.atoms, m2.atoms) etc. --Eric > > Yonggang > > > On Mon, May 5, 2014 at 3:59 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > On May 5, 2014, at 3:57 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > >> print>>f, a1, a2, diet > > Stupid auto-correct spelling. "diet" should be "dist". > > --Eric > >

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how to save distance to a file
by chang YG 05 May '14

05 May '14

Hi, Thanks for taking time to answer the questions. Could you advise me of how to save distances using a python script. Here is what I have: from chimera import runCommand as rc rc("open 1t4y") rc("distance :33@H :34@H") #how to save distance. Another related question: how to save "rmsd" of two structures using a python script? Thanks, Yonggang

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patching ACE NME
by Francesco Pietra 05 May '14

05 May '14

Hello; In parameterizing a new metal cluster, I would like to patch the various amino acids (which stand isolated from one another) with what are called by AMBER ACE and NME. I would like to do that within the whole block, not for each amino acid isolated from the block. Also, I would like to avoid tleap, which gets into troubles here. I could do that by modifying structure, but a problem arises of residue names, i.e, the original residue takes the name ACE or NME, or viceversa the capping groups take the name of the amino acid being capped. Is there a specific tool with chimera? thanks francesco pietra

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A question on tunnelling chimera through ssh between a linux server and OSX client
by Miguel Ortiz Lombardía 30 Apr '14

30 Apr '14

Hi all, I understand that this is not a typical use of chimera, so I don't expect much support, but I would appreciate if someone can give me a clue to solve the issue... We have a GNU/Linux server (Debian wheezy) with some EM software installed on it. One of these programs calls at some point chimera to show something on which the user has to act upon (or just check, not sure, I'm not the user as you've guessed) This machine is accessed from client OSX machines via ssh. All permissions are set so X11 is seamlessly tunnelled between them (checked with many graphical programs) Now, for a OSX client running on 10.6.8 (snow leopard) and using Apple's X11 the whole process works without problems. But for a OSX on 10.7.5 (lion) with a parallel installation of Apple's X11 and Xquartz 2.7.5 the first small window opens and then the chimera process hangs (it can be killed via Ctrl-C, which returns the control to the program that launched chimera and things can proceed, though without the information provided by chimera) If I connect to the Linux server from the lion machine and directly execute chimera I make a different observation: the first small window opens but then chimera crashes leaving this error in the terminal: Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1360 Current serial number in output stream: 1360 Now, I would appreciate any clues on the meaning and possible solution of this error or at least any directions on how to properly remove both Apple's X11 and Xquartz (they are supposed to be able to work side-by-side but I presume that a possible source of problems could arise from some conflict between them) AND re-install them to test them in a fresh install. Downgrading the lion machine to snow leopard does not seem to be an option... Thank you! Cheers, -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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Preparation of the protein-ligand system for the amber simulation
by James Starlight 30 Apr '14

30 Apr '14

Dear Chimera Users, I wounder to know if it's possible to use combination of the amber ff with the cgenff for the both parametrization of the small ligands in complex with the proteins using amber tools built in Chimera's? Does it possible to use some scripts instead of GUI for such tasks ? I'll be thankfull for some tutorial or example Thanks for help, James

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multi-channel solid rendering
by Nick Walter 29 Apr '14

29 Apr '14

Hello, I've been attempting to create a movie in Chimera using multiple data files in solid style volume rendering, and I have been running into an issue where Chimera consistently shows the last channel to be loaded on top, regardless of the spacial position of the data with respect to the other solid channels. I found this message ( http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006329.html) which explains that multi-channel solid rendering was removed in 2008. I was wondering, if there are any plans to reinstate this feature, or if you were aware of any work-arounds that would work well for creating movies. Thank you for your time, Nick Walter

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related with Fit in map option
by SRDA.DRAKULIC.599589 29 Apr '14

29 Apr '14

Hi, I have a question related to Fit in Map option and how to evaluate subsequently given results. I have a EM map at 19 ang. resolution of protein at yet non-characterised activity state, and there are two atomic structures of homologue of that protein, at clenched and open, active state. I would like to relate that state to one of the atomic structures, thus, both of them were fitted in my EM map and for the clenched state I got following values: cross correlation: 0.8447; average map value 9.526; and number of atoms outside the contour: 1709/7621 (or 22.42%) For the open state: cross correlation: 0.8385; average map value 9.085; and number of atoms outside the contour: 2064/8124 (or 25.42%) Are those differences big enough to say with certainty that my protein is at conformation similar to the clenched one or due to the EM map resolution this can not be said. Sincerely, Srdja Drakulic

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Saving ribbons as PDBs?
by Maja Divjak 29 Apr '14

29 Apr '14

Hello Chimera Gurus, Is there a way to save ribbon structures as PDBs for import into Maya? I've found only the surface structures are saved in the PDB, even though I am working with the ribbon structure in chimera initially. If there is a way to do this, I would be mightily pleased! I used to export chimera domains as vrml files and then convert them to maya files and both the ribbon and surface structures would be included. You can reply to my work email at divjak.m(a)wehi.edu.au if you prefer. Thank you so much and best wishes, Maja Divjak, PhD Biomedical Animator Walter and Eliza Hall Institute of Medical Research

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select zone & rename script
by Michael Garton 29 Apr '14

29 Apr '14

Hi all, Can anyone show me a good way to select all residues that are <2Å from zinc atoms, then rename any selected CYS and HIS, to CYM and HIN respectively ... I'm trying to write a script to do this on ~300 files. Thanks!! Mike Here's what I have so far import os from chimera import runCommand as rc from chimera import replyobj # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: replyobj.status("Processing " + fn) # show what file we're working on rc("open " + fn) rc("select :ZNB zr<2") rc("writesel "reslist + fn") rc("close all") rc("stop now")

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Question About Using Chimera In Python Scripts with Other Features
by John Dougherty 28 Apr '14

28 Apr '14

Hello, I am not very computer savvy and very new to programming. I am using Windows 7, Python 2.7.3 32 bit I would like to know if it is possible to use features from Chimera in a python script. For example: from chimera import * from otherprogram import * otherprogram stuff runCommand('blah blah blah') Chimera does some things the other program does not and vice versa. My life would be made much easier if I could just integrate them into one script. I do not understand the instructions about this matter which are posted on the FAQs on the website. Sincerely, -- John J. Dougherty III Biomathematics Major Rutgers, New Brunswick (P) 856 981 9491

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Re: [Chimera-users] (no subject)
by Elaine Meng 28 Apr '14

28 Apr '14

Hi Joshua, The linewidth issue is mentioned in the supersampling documentation, but you wouldn't be expected to know that your problem was related to supersampling in the first place! Most people report encounter it as the lines being too thin rather than being completely invisible. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#supersampling> If you use the Image Save dialog, it reports near the bottom of the dialog the "effective maximum linewidth" given the specified level of supersampling and image pixel dimensions. Elaine On Apr 28, 2014, at 3:43 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Joshua, > I'm glad to hear it worked! And of course you're welcome. Don't hesitate to send other problems or concerns to the list, and I'm sure you're right that others will benefit from having the info Googlable from the list archive. > > --Eric > > On Apr 28, 2014, at 3:39 PM, Joshua Broyde <jb3401(a)c2b2.columbia.edu> wrote: > >> Dear Eric, >> Thank you so much. The first thing I did is change the supersampling from 3x3 to 1x1 and it worked! Thanks so much! >> >> Sincerel, >> Joshua Broyde >> p.s. feel free to share this email with others who have this problem. When I googled "dashed lines not saving chimera".Thanks again! >> >> ----- Original Message ----- >> From: "Eric Pettersen" <pett(a)cgl.ucsf.edu> >> To: "Joshua Broyde" <jb3401(a)c2b2.columbia.edu> >> Cc: chimera-users(a)cgl.ucsf.edu >> Sent: Monday, April 28, 2014 2:06:04 PM >> Subject: Re: [Chimera-users] (no subject) >> >> Hi Joshua, >> The first thing you should do is make sure you have the latest driver installed for your graphics card. Based on the info you provided, I believe the latest release for your card was 4/24/14 -- only 4 days ago! Go to the AMD drivers site here: >> >> >> Download Drivers >> >> >> and input the values for your system to get to the latest drivers. >> If that doesn't help, my best guess as to the issue is that the card/driver can't show dashed lines beyond a certain thickness and that the supersampling done while saving the image requires lines thicker than the card supports (each "tile" of the supersampled image is essentially a zoomed-in depiction of that part of the image and is later sampled down to its final size -- which reduces aliasing artifacts). Therefore the two things to try are to reduce the amount of supersampling as you save the image, or reduce the thickness of the dashed lines before you save the image. >> There is a "Supersample" control on the Save-Image dialog, and there is a "supersample" keyword to the "copy" command, if that's what you're using. >> You can reduce the line width of the hydrogen bonds by bringing up the PseudoBond Panel (in the General Controls tool category) and double clicking on the "hydrogen bonds" group (assuming you've made some hydrogen bonds). The "line width" control is in the lower part of the inspector that comes up. >> I hope one of these things work! :-) >> >> >> --Eric >> >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> >> >> On Apr 27, 2014, at 3:24 PM, Joshua Broyde < jb3401(a)c2b2.columbia.edu > wrote: >> >> >> Hi, >> >> >> I had a chimera-related problem. When saving images from chimera, chimera is not saving the dashed hbonds (I am NOT using POV-Ray), in the images, even though they appear on the screen. Does this have to do with the graphics driver, or is is there something internally in chimera that is likely causing this? >> I am using the AMD Radeon HD 6450 graphics driver on ubuntu 12.04. When I tried this on another computer with ubuntu 12.10 (using Gallium .04 graphics driver) , it worked fine and the image came out perfectly. This problem happens whether I use chimera 1.8, 1.8.1, or any release after that. >> >> Sincerely, >> Joshua Broyde >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > >

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(no subject)
by Joshua Broyde 28 Apr '14

28 Apr '14

Hi, > I had a chimera-related problem. When saving images from chimera, chimera is not saving the dashed hbonds (I am NOT using POV-Ray), in the images, even though they appear on the screen. Does this have to do with the graphics driver, or is is there something internally in chimera that is likely causing this? > I am using the AMD Radeon HD 6450 graphics driver on ubuntu 12.04. When I tried this on another computer with ubuntu 12.10 (using Gallium .04 graphics driver) , it worked fine and the image came out perfectly. This problem happens whether I use chimera 1.8, 1.8.1, or any release after that. > > Sincerely, > Joshua Broyde

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Print selected
by m.maletta＠nki.nl 28 Apr '14

28 Apr '14

Dear all, I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds. I manage to do the first part with this command, but I do not manage to have a list of all the distances found. select #0:.A za<3.5 & #0:.B Is there a way to get the list? Best and thank you in advance Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta(a)nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029

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Multiscale models color
by Hernando J Sosa 26 Apr '14

26 Apr '14

Hi, How do you control the color of the surfaces generated by the multi-scale models command "Make models" so that the user can specify the color associated with each chain? I tried to follow the documentation on how to do this but still I don't get it right as I didn't manage to change the colors assigned by default. Thanks Hernando

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1.9 release candidate
by Eric Pettersen 24 Apr '14

24 Apr '14

Hi everybody, There is a release candidate of Chimera 1.9 on the download page. If you can, please try it out and let us know if you have any problems or questions. The differences between 1.9 and 1.8 are covered in the release notes. Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Export Pov-Ray file with a python script.
by jiserte＠unq.edu.ar 23 Apr '14

23 Apr '14

I'm writing a small python script to generate Pov-Ray with chimera. The script loads a pdb file containing a protein and a ligand, modifies the protein view to ribbon and the ligand to surface. Then exports the .pov file. However the image created by Pov-Ray shows only the surface of ligand. The image is shown correctly in the chimera GUI. If I run the commands one by one in the chimera command line, the .pov file generated is ok. The script is: ----------------------------------------- import chimera from chimera import runCommand runCommand('windowsize 800 600') runCommand('open ../../kinase.domain.2/A.4K9Y.pdb') runCommand('ribbon #0') runCommand('surf ligand') runCommand('export test.pov') ------------------------------------------ After running the script the ReplyLog contains: ----------------------------------------- A.4K9Y.pdb opened /opt/UCSF/Chimera64-1.7/bin/mscalc 1.400000 2.000000 1 MSMSLIB 1.3 started on hamal Copyright M.F. Sanner (March 2000) Compilation flags Surface A.4K9Y.pdb, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 436.845 Total solvent accessible surface area = 772.871 ----------------------------------------- Javier Iserte

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Transparency of selected atoms
by Chinaza Egbuta 23 Apr '14

23 Apr '14

Hi, Is there a way to change the transparency of selected atoms in a model? I am trying to visualize what is behind the plane of my model without using the surface capping function. Thanks! CE Chinaza Egbuta Ph.D. Candidate Department of Pharmacology & SUNY Upstate Cancer Research Institute SUNY Upstate Medical University Syracuse, NY 13210

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