- Chimera-users - RBVI Mailing Lists

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 06 May '14

06 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 01 May '14

01 May '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 30 Apr '14

30 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 30 Apr '14

30 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 29 Apr '14

29 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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Re: [Chimera-users] [chimera-dev] read file by python script and color pdb file with script
by Eric Pettersen 22 Apr '14

22 Apr '14

Hi Sariya, Your "check" file contains this (one) line: 67 23 which means that the residue range you generate is ":67-23" which contains nothing. You want "check" to contain "23 67" so that your residue range becomes ":23-67". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 21, 2014, at 8:33 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > > I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. > I have chimera in my ~/bin/ > System specs: ubuntu 64 bit, 13.10, 4gb ram > > Below is the command I have used for script-chimera communication > > $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb > > > I am storing values in listu and want to use them for coloring my file loaded. > > rc("color blue :"+listu[0]+"-"+listu[1]) > > This works well, if hard coded > rc ("color red :55-86") > > I do not get any error. The particular protein length is not colored. > > attached 3 files. > Kindly suggest, how do I proceed. > > > -- > Regards > Sariya > > <Q6UXT6.pdb><y.py><check>_______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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read file by python script and color pdb file with script
by Sanjeev Sariya 22 Apr '14

22 Apr '14

Hello Chimera team, I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram Below is the command I have used for script-chimera communication $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb I am storing values in listu and want to use them for coloring my file loaded. rc("color blue :"+listu[0]+"-"+listu[1]) This works well, if hard coded rc ("color red :55-86") I do not get any error. The particular protein length is not colored. attached 3 files. Kindly suggest, how do I proceed. PS: I had sent the same mail to chimera-dev(a)cgl.ucsf.edu <chimera-dev(a)cgl.ucsf.edu>; Sorry, I didn't find this mailing list before. -- Regards Sariya

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Structure editing: add charge
by George Tzotzos 21 Apr '14

21 Apr '14

Hi everybody, I’m trying to add to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999. Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. Is there a way to force the charge on the ligand to be +1.000? Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). Regards George

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Problem with charges when writing mol2 file with a python script.
by jiserte＠unq.edu.ar 21 Apr '14

21 Apr '14

I'm trying to write a simple python script to open a mol2 file with a ligand, add hydrogens, add charges and write it into another mol2. The script is this: ----------------------------------------- import chimera #1 from chimera import runCommand #2 runCommand('open ligands/lig_in.mol2') #3 runCommand('addh') #4 runCommand('addcharge') #5 runCommand('write format mol2 #0 lig_out.mol2') #6 ------------------------------------------ The result mol2 file does no contain any charges. However, if a run another script that is exactly like this but does not contain the last line (#6), and then execute the command 'write format mol2 #0 lig_out.mol2' manually, the mol2 file contains charges. I don't understand why there is a difference with both methods. best regards. javier

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how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix)
by ashok rout 21 Apr '14

21 Apr '14

Hi, I have a transmembrane domain of a protein (20 amino acid long, single helix). The NMR derived structure comes out as a coiled-coil trimer. So can you please assists me how to calculate the core diameter of this trimer. Regards, Ashok -- thanks & regards, Ashok

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Chimera-crashing-ubuntu
by Prasanth Kumar 18 Apr '14

18 Apr '14

Dear Sir/Madam, I have been using chimera for past 3 months. In the past two days, when i load my saved sessions (.py files), chimera is getting hanged and my ubuntu 12.04 OS is also getting hanged. So please help me on how to fix the problem. Chimera has been a really useful tool in my research. Waiting for your reply. Thank you, Yours Truly, *PRASANTH*, Undergraduate Department, Indian Institute of Science, Bangalore-560012. Contact:- prasanth.311994(a)gmail.com, prasanth(a)ug.iisc.in.

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Rendering into 3d
by Rebecca Swett 18 Apr '14

18 Apr '14

Hey All, I'm looking at rendering some movies output from chimera as a 3d movie for viewing with nvidia 3d vision pro glasses. From everything I've read as long as the left/right eye frames are sequential, making the movie with ffmpeg should work fine. The problem I'm having is that ffmpeg has no way to alternate between 0-left.ppm 0-right.ppm 1-left.ppm 1-right.ppm, which is how chimera saves images when recording movies in stereo mode. If those same images were named 1.ppm 2.ppm 3.ppm 4.ppm, there would be no problem. Is there a quick fix that can be inserted to change the naming of the recorded frames? Any other suggestions? Rebecca Swett

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morphs
by Moses Adenaike 17 Apr '14

17 Apr '14

Hello Chimera users, Is there a way to make a morph between two PDBs that don't have the same amount of atoms or chains. For example, I want to morph between an enzyme bound to DNA and one without DNA. Moses

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call file-> open gui popup from script ?
by Katrina Lexa 17 Apr '14

17 Apr '14

Hello All, I’m wondering if there is a way to call the file->open popup within chimera when running a python script? I know that it’s possible to run the script on the command line and read the desired arguments in that way, and obviously the files I want could be coded in and then changed every time I want to look at something new, but I’m not seeing an obvious option from the mailing list or in the runCommand list for writing in a mid-script call for the user to select a file. Is such a thing possible? Thanks for your help, -- Katrina

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Doubts regarding building a structure using Build Structure option
by Garg, Ayush A. 16 Apr '14

16 Apr '14

Dear Developer I was working with with UCSF Chimera. I was trying to reproduce structure 1V4S - Glucokinase structure using the Build Structure option under the tab Structure Editing in Tools. I have the sequence of the 455 amino acids and also know the sequence which is alpha helix, beta helix but the sequence of connectors between these structures is not a secondary structure. I was wondering how to reproduce those using your structure builder option. I have attached a word file with the sequence and the image of 1V4S in UCSF Chimera. I hope that will help you understand my doubt better. Thank and Regards Ayush Arpit Garg Graduate Student Ohio State University

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Working with several proteins
by Navya Shilpa Josyula 16 Apr '14

16 Apr '14

Hi, I am working on a set of 400 proteins and for all these proteins I have specific list of amino acid residues. I wanted to know if there is any available script or a command to get the following 1. atomic areaSAS 2. atomic B-factor values 3. CASTp identified pocket residues and 4. CASTp identified pocket volumes for all the residues of these 400 proteins to be written in a single file. Kindly help me at your earliest. Thank you in advance for your help. Regards, Navya

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Relevant interacting amino acids between molecules
by Ogunniyan, Abisola 16 Apr '14

16 Apr '14

Hi, My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. Please, I will really appreciate it if this is made clearer to me. Thank You. Best Regards, Abisola Abisoye-Ogunniyan.

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Structure editing: addH
by George Tzotzos 11 Apr '14

11 Apr '14

Hi everybody, I’ve been trying to add hydrogens to a ligand (7-octenoic acid) obtained from docking. Hydrogens are added but not on the carboxyl group. I’m attaching the ligand.pdb for easy reference. I’d appreciate any suggestions regarding this behavior Best regards George

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Request for guidance
by MUHAMMAD RAMZAN MANWAR 08 Apr '14

08 Apr '14

Dear Dr. Ferrin, Hope this email finds you the best of your health. First of all, I did appreciate the effort that You and Your team did in the form of UCSF Chimera. Being the part of academic/government university, I have used Chimera tool for protein modeling and cited in my two articles: one published in JCB-Wiley and other in Hundawi in 2014. Current email I am sending to request for guidance about how can I substitute an amino acid (wild type to mutant residue) within protein 3D model by using Chimera. I will be thankful for your guidance, if possible. With regards Hussain MR PACER-HD, KAU, KSA

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Surprising "measure symmetry" result
by ingvar 08 Apr '14

08 Apr '14

Hello, I fetched entry EMD-2463 from EMDB and issued: measure symmetry #0 nMax 24 and got the result "Symmetry emd_2463.map: C13, center 64 64 37" Increasing the number of sampling points does not change the result, but if I increase the correlation criteria a little, to say 0.992, I get the expected C12 symmetry. Also if I change the contour level to 0.05, the author recommended level, I get C12 again. Looking at the volume at several different contour levels, it is difficult to see how it could be considered C13, and also how it would go from C13 to C12. Kind Regards, Ingvar Lagerstedt -- Ingvar Lagerstedt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Tel: +44 (0)1223 492533

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Docking ligands and protein using Chimera
by Sook Wong 08 Apr '14

08 Apr '14

Good morning, I am currently doing research with a professor for protein-ligand structure and would like to dock the receptor molecule (pdb file of the protein) and ligands (pdb file of the sugars). Since I have both the structure files from Chimera, how would I predict and assume which orientation bound to each other forming a stable complex? Looking forward to hear from you. Thank you so much! Sincerely, Sook Y Wong Chemical and Biomolecular Engineering '14 A. James Clark School of Engineering University of Maryland, College Park, MD 20742 swong18(a)terpmail.umd.edu

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Calculating SAS and SES with Chimera-MSMS wrap
by Jaime Rodríguez-Guerra 08 Apr '14

08 Apr '14

Dear Chimera dev team, I am trying to use your MSMS wrapper to compute some SAS/SES values for a given set of atoms. As suggested in a previous post in this list, I've taken a look into Measure.measure.buried_area() and I think I've got it, but just wanted to make sure. Here is my current procedure: ``` import chimera, Measure, MoleculeSurface atoms = chimera.selection.currentAtoms() xyzr_data = Measure.measure.atom_xyzr(atoms) surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data) for i, a in enumerate(atoms): print "Atom: {0}, SAS: {1}, SES: {2}".format(a.name, surfaces[3][i,0], surfaces[3][i,1]) ``` Is this OK? I don't know how to handle all that output that MSMS is giving back! Thanks in advance, Jaime.

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Re: [Chimera-users] Reaction Mechanism Movie
by Eric Pettersen 07 Apr '14

07 Apr '14

On Apr 5, 2014, at 1:06 PM, Moses Adenaike wrote: > Dear Dr. Pettersen, > I am wondering how I would go about making a moive detailing a biochemical reaction. For example, I want to show a DNA polymerase reaction, essentially a ligation between the backbone of two nucleotides. How would I go about doing so? I know chimera has a make new bond function but I haven't been too successful at getting that to work. Hi Moses, It is typically better to send questions like this to the chimera-users mailing list than to me directly so that others can benefit from the answer and in case others on the list have more expertise on the topic than I do. The simplest method is to decide which frame# you want the bond to start existing and use the "Define script…" entry in MD Movie's Per-Frame menu to define a one-command script to execute at that frame. For example, if you wanted a bond between :337.A@P and :338.A@O3' to exist starting with frame 53, in the Per-Frame dialog you would set "Interpret script as" to "Chimera commands" and enter as your script: #53 bond :337.A@P :338.A@O3' There is also a hidden capability in Chimera to compute all bonds on a per-frame basis. I can tell you how to access that if it turns out you really need it. However, for the purpose of making a movie it might be nice to have a more "continuous" representation of the bond forming than just the binary on/off that the above approaches give you. I have attached a Python script that you can use the Per-Frame dialog (with "Interpret script as" set to Python, and reading in the script with the "Insert text file…" button) to have a bond form (by starting out very thin and becoming thicker) as two designated atoms approach each other. There are some values at the top of the script that you can edit to make it work best in your situation. There is a distance value for when the bond begins to exist (noBond, default 3.5) and when it reaches full size (fullBond, default 2.0). There is a two-member list of residue IDs (resIDs) for the atoms involved in the bond, and a list of atom names (atomNames). Let me know if you need more help than this. Hmmm, this all assumes you have a trajectory of the reaction. You may have to use the Morph Conformations tool to create such a trajectory if you don't have one already. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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presets-interactive 3-hydrophobicity surface- those water molecules stay!
by Ying-Chieh Sun 06 Apr '14

06 Apr '14

Hi, I did a simulation using Amber package and saved a snapshot into its pdb file, and use Chimera to open it. The pdb file contains a protein-ligand complex plus a box of about 20000 TIP3P water molecules. When I pressed presets-interactive 3-hydrophobicity surface, there are 8 water molecules stayed close to the ligand binding site. I am wondering how these 8 water molecules were determined? The reason I ask is because we are trying to find a way to determine 'crystal (or say, ordered) water molecules'. This presets-interactive 3-hydrophobicity surface seems to perform this function in some way. Thank you for your help. Ying-chieh Ying-Chieh Sun, Professor of Computational Chemistry Chemistry Department National Taiwan Normal University Taipei, Taiwan 11617 Tel: +886-2-7734-6215 Fax: +886-2-2932-4249

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Resolution of .stl file of ribbon representatiom
by Gavin Whittaker 04 Apr '14

04 Apr '14

Dear all, I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I /can/ now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? thanks! Gavin

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query
by Bhaskar Bagchi 04 Apr '14

04 Apr '14

Respected Sir I want to calculate surface area of different atoms in a molecule. Is it possible in chimera? Please help me. Thanking you Yours faithfully, Bhaskar Bagchi Research Scholar Raiganj University College Email: bhaskarbagchi(a)gmail.com

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ellipsoid main axis alignment ?
by Hugo J Bohorquez 04 Apr '14

04 Apr '14

Hi, I am writing a script in python for generating a series of ellipses linking the nuclei a molecule. Every ellipsoid should be positioned at a specific location *P* = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-*A*, *B*, *C*. However, when I create an ellipsoid with shape_command it gets located correctly at *P* but it is aligned with the global axis. I can't find a general way to reorient an object so its original axes point along the vectors *A*, *B*, and *C*. I will appreciate any suggestion how to do it. -- Hugo J Bohórquez <https://sites.google.com/site/hugojbohorquez/home>, PhD *Investigador* Grupo de Biofísica Fundación Instituto de Inmunología de Colombia TEL. +57 +1 -3158920 Ext. 122 CEL. +57 315-6169069 *The Pauli energy grows exponentially with the electronic localisation <http://dx.doi.org/10.1080/00268976.2013.836605>*

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resampling maps
by Jason Kaelber 03 Apr '14

03 Apr '14

Hi all, I decided to do a rough alignment of density maps manually and resample onto a common coordinate system to feed the output mrc files into my fine aligner. But, when I vop resample #1 onGrid #0, I get, TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' What might I be doing wrong to get this error? As far as I know, all the maps should be uint8 since they were most recently operated on by David Mastronarde's newstack command which outputs them as unsigned bytes. Thanks, Jason <type 'exceptions.TypeError'> Exception in Tk callback Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x276b2d88>> (type: <type 'instancemethod'>) Args: (<Tkinter.Event instance at 0x276a2ea8>,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "/opt/UCSF/Chimera64-1.8.1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_ui.py", line 283, in processCommand midas_text.makeCommand(cmdText) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/ChimeraExtension.py", line 24, in vop_cmd vop_command(cmdname, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 91, in vop_command doExtensionFunc(func, fargs, specInfo = spec) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 435, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 553, in resample_op boundingGrid, False, None, modelId) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 168, in add_operation scale = scale[i]) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values <type 'exceptions.TypeError'>: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' ================================================ Event contents: char: delta: 36 height: ?? keycode: 36 keysym: Return keysym_num: 65293 num: ?? send_event: False serial: 39103 state: 16 time: 139539396 type: 2 widget: .59791048.661335648.802317088.802317376.802317448 width: ?? x: 159 x_root: 524 y: 9 y_root: 988 TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values See reply log for Python traceback. -- National Center for Macromolecular Imaging, N420 Baylor College of Medicine, MS BCM125 1 Baylor Plaza Houston, TX, USA

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Is there a way to save animation editing process?
by Li, Leon 03 Apr '14

03 Apr '14

Dear all, I'm try to save all my editing of animation, it seems that 'save session' can't save 'scenes', 'timelines', etc. I wonder is there a way to save all the process, so that I can re-open it to edit. Thanks, Leon

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combining different chains
by faeze mohajer 01 Apr '14

01 Apr '14

good day I have modeled heavy and light chains of myosin now I want to combine them through chimera, would you plz help me on that your faithfully *FAEZE SADAT MOHAJERPhD Student * *Faculty of Bioscience and Medical Engineering (FBME)* *Universiti Teknologi Malaysia (UTM)* Buzzdock ads <http://www.buzzdock.com/setting/V2hpbG9raWk=> Search ResultsFaculty of Biosciences & Medical Engineering<http://fbme.utm.my/>

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Re: [Chimera-users] Chimera Shutting Down
by Tom Goddard 31 Mar '14

31 Mar '14

Hi Joshua, Glad to hear that the new graphics driver fixed the Chimera side view crash on your Ubuntu 12.04 system. Maybe this will help some other Chimera users. Tom On Mar 31, 2014, at 12:33 PM, Joshua Broyde wrote: > Dear Tom, > I installed a new graphics driver, so now it works. In case anybody else has this same problem, I installed the Gallium Radeon driver and it worked fine. I followed step 2 from this link: > http://arstechnica.com/civis/viewtopic.php?f=16&t=1137372 > > Thanks for the tip. > Sincerely, > Joshua Broyde > ----- Original Message ----- > From: "Tom Goddard" <goddard(a)sonic.net> > To: "Joshua Broyde" <jb3401(a)c2b2.columbia.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Sent: Thursday, March 27, 2014 12:58:50 AM > Subject: Re: [Chimera-users] Chimera Shutting Down > > The crash is due to a buggy graphics driver and the only fix is likely to be installing a working graphics driver. Sometimes some trick like starting the side view before opening models as described in the post you referenced avoids the problem, but usually there is no way to avoid a graphics driver crash other than replace the driver with one that doesn’t have the bug. > > Tom > > > On Mar 26, 2014, at 6:05 AM, Joshua Broyde wrote: > >> Hi, >> I am using the Chimera Linux 64-bit (chimera-alpha-linux_x86_64.bin), and Chimera shuts down when I try to open the Side View option. I tried the workaround mentioned here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008765.html but it is not working for me. >> >> OS: Ubuntu 12.04 >> Version of Chimera: Linux 64-bit Daily Build (Mar 24, 2014) >> >> >> For what it's worth, on another computer where I am running Ubuntu 12.10, with Chimera Linux 64-bit Daily Build (July 10, 2013), I did not have this problem. >> Is there another workaround that I could do to open the side view? >> >> Thanks! >> >> 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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Binding pocket surface command script not working
by Markus Heller 28 Mar '14

28 Mar '14

Hello, I'm trying to reproduce the Binding Pocket Surface image from the Gallery with a different pdb file. I can successfully reproduce with the pdb used in the example (2zcp), but not with 2v5z. Running latest Chimera. Steps to reproduce: open 2v5z delete :.b split atoms :sag surface measure contactArea #0.2 #0.1 3 slab -.1,0 color tan gives an error: error: Array must be 2-dimensional, got 1-dimensional File "C:\Program Files\Chimera 1.8.1\share\MeasureVolume\__init__.py", line 60, in surface_area area = surface_area(varray, tarray) See reply log for Python traceback. Why, and would it be helpful to file a bug report? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist 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<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CF49BD.0097D1F0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> 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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Chimera surface error
by Elaine Meng 28 Mar '14

28 Mar '14

On Mar 28, 2014, at 4:27 AM, Uzma Saqib wrote: > Hi Elaine, > Chimera is not showing me the surface of my protein file and gives the attached eror. > i tried what it suggested, but no improvement. > plz help. > attashed , is the pdb. This is a common problem in Chimera. Some explanation and all of our ideas for possible solutions are in this page (no use for me just to repeat that information here): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> #3 and #4 in that page will always work because they use different methods instead of the standard molecular surface calculation. Sorry for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. better to send chimera questions to chimera-users(a)cgl.ucsf.edu, unless including private data

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Measuring surface area of region
by Anindito Sen 28 Mar '14

28 Mar '14

Dear all, I was wondering if there is any way one can measure the surface area with a threshold higher than its neighbouring region in a TEM micrograph ? Thanks Andy Dr. Anindito Sen (Ph.D) >

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Chimera Shutting Down
by Joshua Broyde 27 Mar '14

27 Mar '14

Hi, I am using the Chimera Linux 64-bit (chimera-alpha-linux_x86_64.bin), and Chimera shuts down when I try to open the Side View option. I tried the workaround mentioned here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008765.html but it is not working for me. OS: Ubuntu 12.04 Version of Chimera: Linux 64-bit Daily Build (Mar 24, 2014) For what it's worth, on another computer where I am running Ubuntu 12.10, with Chimera Linux 64-bit Daily Build (July 10, 2013), I did not have this problem. Is there another workaround that I could do to open the side view? Thanks! Sincerely, Joshua Broyde

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Viewing Gromacs 4.6.5 trajectories
by William McDonald 26 Mar '14

26 Mar '14

Hello Chimera users, I recently upgraded my gromacs simulation software from 4.5.5 to 4.6.5; however, when I attempt to load a new simulation trajectory (either a .xtc or .trr file), Chimera allocates ~13GB RAM causing my machine to swap, and Chimera never loads the trajectory. The old trajectories from gromacs 4.5.5 load with out any problems. Has anyone else experienced this? I am using 64 bit Chimera 1.8.1 on a dual quad-core Mac Pro running OS 10.6.8. The simulation has ~50000 atoms of protein, lipid, and water and is 1ns long. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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selection color
by George Tzotzos 26 Mar '14

26 Mar '14

Hi everybody, I’ve conducted Principal Component Analysis on a trajectory and generated an ensemble of structures (see attachment, pc2.pdb). There should be a way of coloring (occupancy?) the most mobile regions of the protein (e.g. residues 67 - 72). I haven’t found a way to do this. Any help would be much appreciated. Best regards George

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stereo3D
by Dougherty, Matthew T 26 Mar '14

26 Mar '14

I have a toshiba qosmio x875-7390 S3D laptop, which is based on the NVidia NVision 3D. Toshiba structured the device to be user unfriendly, limiting stereo3D for bluray and youtube 3d via adobe flash. coming across a pymol S3D post I see there is a workaround, for a different Toshiba model. http://nanonan.wordpress.com/2012/03/28/pymol-and-coot-3d-stereo-on-qosmio-… http://coxcoppes.nl/3DScreenActivator/index.php?pagina=1 Any comments about chimera using S3D on NVidia NVision 3D? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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(no subject)
by Francesco Pietra 23 Mar '14

23 Mar '14

Hello: About stereo drawings with chimera (GNU Linux), I received from the editorial staff: All stereoview illustrations have been drawn in the cross-eye mode, i.e. the > picture for the right eye is on the left and vice versa. > Has this been chosen deliberately? In our opinion, the parallel-eye mode > seems to be used more often. > Please let us know whether we should switch the figures (you would not need > to send new ones) or not. They did the job of transformation to parallel-eye. Next time, I would like to be able to do that myself, while I don't see the parallel-eye mode in chimera. Which is the equivalent? thanks francesco pietra

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Detection of Internal water along MD trajectory
by James Starlight 20 Mar '14

20 Mar '14

Dear Chimera users! I've performed md simulation of water soluble protein having water-assessable channel in its interior. I'd like to perform analysis of average number of water molecules detected within the protein interior during MD trajectory with the possible visualization of such internal water binding sites. Does SASA calculation which I've seen in vmd could provide me with additional insights? I'd be thankful if you provide me with some Chimera tools suitable for such task. Many thanks for help, James

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Chimera Sequence alignment window
by meginir urestal 20 Mar '14

20 Mar '14

Hi, I was wondering if there was a way of printing the contents of the chimera alignment window. If not, could anyone suggest something for printing saved aligned fasta sequences. Thanks

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Morph conformation - conformation collapsing
by Helge.Paternoga＠bzh.uni-heidelberg.de 18 Mar '14

18 Mar '14

Hello, I'm trying to morph two structures which have two chains each. The problem is that if I just add the two confirmations one chain will turn the wrong way, because it is taking the shortest distance to the final position. What i did now is I used this initial morphing to extract 4 frames of the movement of the other chain and inserted the movement of the smaller chain in each of these structures by hand (so the movement is in the right direction and happening at the same time as the other chain). But when I now add these 4 structures in my morph confirmation list like this: Start confirmation frame 1 frame 2 frame 3 frame 4 End confirmation It nicely starts moving in the right way but then at a transition to a new frame the whole structre collapses, bonds get distorted, it somehow shrinks and then extends again later to end up at the final confirmation... I think this is independent of which frame i use (I tried to simplify it by using only 2 intermediates) Do you have any idea what is causing this collapse? The initial confirmation has the same number of chains as the end confirmation (with the same names) but they have a different number of atoms (which i don't quite understand because they are the same macromolecules...) Could this be part of the problem? best regards, Helge

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Recording movie with simultaneous map morph and PDB morph conformation
by Joel Meyerson 17 Mar '14

17 Mar '14

Hi, Is it possible to record a movie that shows both an MRC map morph and PDB conformation morph happening simultaneously? Joel

2 1

residue number in Gromacs tpr file
by Mario Dejung 17 Mar '14

17 Mar '14

Hi all, I am experimenting with Gromacs a little bit and try to open the tpr file and the corresponding trajectory in chimera. Works fine, but the numbering is completely wrong. The residues get numbered continuous and not starting at 1 for the next chain. Not sure if the problem is in the tpr file or in chimera. I have 4 chains in my pdb file and all have a chain identifier, O P g and h and they are separated by TER I have also 4 .itp files with names like “topol_Protein_chain_O.itp” My topol.top file say 4 molecules [ molecules ] ; Compound #mols Protein_chain_O 1 Protein_chain_P 1 Protein_chain_g 1 Protein_chain_h 1 and ; Include chain topologies #include "topol_Protein_chain_O.itp" #include "topol_Protein_chain_P.itp" #include "topol_Protein_chain_g.itp" #include “topol_Protein_chain_h.itp" I create my tpr file with grompp Has anybody experience with this kind of issue? Kind regards Mario

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Chimera and XP?
by Boaz Shaanan 13 Mar '14

13 Mar '14

Hi, For some reason, I couldn't get Chimera (1.8.1 and the 12/3 daily build) to work today on my laptop running XP (32bit). It gets stuck in 'initializing graphics'. See attached screen shot of run with --debug. Chimera worked for years on this machine. Other programs work fine (spdbv, Coot, etc.). I can't imagine it has to do with the imminent downfall of XP support, or maybe it does? Please advise. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-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: Wednesday, March 12, 2014 9:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 131, Issue 13 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. match-align using just selected protein areas ? (Marek Maly) 2. Re: match-align using just selected protein areas ? (Elaine Meng) 3. Re: surface failures (Elaine Meng) 4. Re: match-align using just selected protein areas ? (Marek Maly) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Mar 2014 02:53:47 +0100 From: "Marek Maly" <marek.maly(a)ujep.cz> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] match-align using just selected protein areas ? Message-ID: <op.xck57xhvlc8gdf(a)pocitadlon.ujep.cz> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes Hello, I would like to know if it is possible in Chimera align two proteins let say protein A and protein B, but just using selected subsequences A_sel, B_sel (i.e. just the selected subsequences are going to be optimally matched and the rest of both proteins is not involved in the matching process/calculation) ? Thank you in advance ! Best wishes, Marek -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ ------------------------------ Message: 2 Date: Wed, 12 Mar 2014 09:35:39 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "Marek Maly" <marek.maly(a)ujep.cz> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] match-align using just selected protein areas ? Message-ID: <67EFA59C-7032-4F2A-8517-6D32E11C4F2D(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Marek, Yes, if you mean MatchMaker (Match->Align does not align the structures, it just makes a sequence alignment from a structural alignment you already made). In the MatchMaker GUI, there is a "Further restrict matching to current selection" setting: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> In the matchmaker (mmaker) command, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> ... it is similar but you instead specify the residues directly instead of selecting them: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> 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 Mar 11, 2014, at 6:53 PM, Marek Maly wrote: > Hello, > I would like to know if it is possible in Chimera > align two proteins let say protein A and protein B, > but just using selected subsequences A_sel, B_sel > (i.e. just the selected subsequences are going to be > optimally matched and the rest of both proteins is not involved > in the matching process/calculation) ? > Thank you in advance ! > Best wishes, > Marek ------------------------------ Message: 3 Date: Wed, 12 Mar 2014 09:51:04 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Julian Marzi <julian.marzi(a)googlemail.com> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] surface failures Message-ID: <91C53A76-7F10-4123-9752-0AE5F5C58689(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii On Mar 12, 2014, at 6:46 AM, Julian Marzi wrote: > Dear Eric, > I tryed the command surfcat c1 and surfcat c1 :.1 & ~:ohx, but this will also not work on my mac... The mac show for short time an activity, but nothing happens. The comand from Elaine molmap :.1&~:ohx 5 worked and it looks great! Is there also a possibility to select a part of the sequence in the "surface" (molmap) presentation to show it in an other color? I select one part on the 25S-rRNa in green, but the molmap view covers it in grey and if I make a higher transparency, the selected part will be seen. But it would be better, if the selected part is colored in the molmap view. This would allow the marked spot directly recognize without transparency. If there is an answer for my question, please let it me know. If not, is not bad, you two have helped me incredibly much. > Thank you so much > Regards > Julian Hi Julian, The "molmap" surface can be colored to match atoms with the Color Zone tool. The atoms can be hidden, it is just a step to the surface coloring that you want. After you color some atoms (for example, some part of the RNA that you selected) you can also color the part of the surface that is near the currently selected atoms with Color Zone (in menu under Tools... Depiction). Color Zone is mentioned along with molmap in #3 in the surface workarounds page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzo…> Also, you could color the molmap surface any overall color you want first, it doesn't have to be the default grayish color. You could just click the color square on the Volume Viewer tool (that appears when you create the molmap surface) and then use the Color Editor, or you can select the surface directly in the main window and use the Actions... Color menu. I hope this helps! P.S. please send chimera questions to the chimera-users address instead of our individual addresses (to allow others to see the Q & A) - thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco ------------------------------ Message: 4 Date: Wed, 12 Mar 2014 19:44:27 +0100 From: "Marek Maly" <marek.maly(a)ujep.cz> To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] match-align using just selected protein areas ? Message-ID: <op.xcmg0dxylc8gdf(a)pocitadlon.ujep.cz> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes Dear Elaine, thank you very much for your help ! Best wishes, Marek Dne Wed, 12 Mar 2014 17:35:39 +0100 Elaine Meng <meng(a)cgl.ucsf.edu> napsal/-a: > Hi Marek, > Yes, if you mean MatchMaker (Match->Align does not align the structures, > it just makes a sequence alignment from a structural alignment you > already made). > > In the MatchMaker GUI, there is a "Further restrict matching to current > selection" setting: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> > > In the matchmaker (mmaker) command, > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> > ... it is similar but you instead specify the residues directly instead > of selecting them: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict> > > 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 Mar 11, 2014, at 6:53 PM, Marek Maly wrote: > >> Hello, >> I would like to know if it is possible in Chimera >> align two proteins let say protein A and protein B, >> but just using selected subsequences A_sel, B_sel >> (i.e. just the selected subsequences are going to be >> optimally matched and the rest of both proteins is not involved >> in the matching process/calculation) ? >> Thank you in advance ! >> Best wishes, >> Marek > > > __________ Informace od ESET NOD32 Antivirus, verze databaze 9532 > (20140312) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > > > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 131, Issue 13 **********************************************

2 1

'Old-style' silhouette edges?
by Thomas Mitterfellner 13 Mar '14

13 Mar '14

Hello! It seems that somewhere between 1.6.2 and 1.7, the way silhouette edges are drawn has changed. Most of the silhouette edges are now drawn in white regardless of the color I set (presumably due to some smart algorithm?). In my opinion, the old way gave a much clearer appearance of the molecule on different backgrounds and it gave it a 'cartoonish' flavor which made it look quite distinguished from the images other software produces and I really loved that. So my question is: is there any way to get back the 'old-style' (pre 1.7) silhouette edges in 1.7+ releases? Kind regards, Thomas

2 2

editing selected dihedral angles
by Francesco Pietra 13 Mar '14

13 Mar '14

Hello: I would appreciate receiving instructions on changing selected dihedral angles in a peptide. Imagine that the initial and final stretches are alpha-helices, while in the middle, dihedral angles are such that two alpha-helix coiled portions make an angle different from 180 degrees. In all that, all dihedrals in the alpha-helix portions should not be modified. Thanks francesco pietra

2 1

anti aliasing
by George Tzotzos 12 Mar '14

12 Mar '14

Hi everybody, I’m trying to produce images of a protein for publication. However, using the publication presets, I get jagged edges in ribbons/helices. Is there a way to set up the anti aliasing. Thank you in advance for any suggestions Regards George

2 1

match-align using just selected protein areas ?
by Marek Maly 12 Mar '14

12 Mar '14

Hello, I would like to know if it is possible in Chimera align two proteins let say protein A and protein B, but just using selected subsequences A_sel, B_sel (i.e. just the selected subsequences are going to be optimally matched and the rest of both proteins is not involved in the matching process/calculation) ? Thank you in advance ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

2 2

Re: [Chimera-users] surface failures
by Elaine Meng 12 Mar '14

12 Mar '14

On Mar 12, 2014, at 6:46 AM, Julian Marzi wrote: > Dear Eric, > I tryed the command surfcat c1 and surfcat c1 :.1 & ~:ohx, but this will also not work on my mac... The mac show for short time an activity, but nothing happens. The comand from Elaine molmap :.1&~:ohx 5 worked and it looks great! Is there also a possibility to select a part of the sequence in the "surface" (molmap) presentation to show it in an other color? I select one part on the 25S-rRNa in green, but the molmap view covers it in grey and if I make a higher transparency, the selected part will be seen. But it would be better, if the selected part is colored in the molmap view. This would allow the marked spot directly recognize without transparency. If there is an answer for my question, please let it me know. If not, is not bad, you two have helped me incredibly much. > Thank you so much > Regards > Julian Hi Julian, The "molmap" surface can be colored to match atoms with the Color Zone tool. The atoms can be hidden, it is just a step to the surface coloring that you want. After you color some atoms (for example, some part of the RNA that you selected) you can also color the part of the surface that is near the currently selected atoms with Color Zone (in menu under Tools... Depiction). Color Zone is mentioned along with molmap in #3 in the surface workarounds page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzo…> Also, you could color the molmap surface any overall color you want first, it doesn't have to be the default grayish color. You could just click the color square on the Volume Viewer tool (that appears when you create the molmap surface) and then use the Color Editor, or you can select the surface directly in the main window and use the Actions... Color menu. I hope this helps! P.S. please send chimera questions to the chimera-users address instead of our individual addresses (to allow others to see the Q & A) - thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

surface failures
by Julian Marzi 11 Mar '14

11 Mar '14

Dear Chimera, I try to show the surface of the 60S in yeast (PDB: 3O5H), but it doesn't work. Mscalc returned code 11 is shown. If I split the 60S every chain show the surface except the first strain (25S). How can I show the surface from the first chain? Thank you very much Best regards Julian Marzi

3 4

Editing named selections
by Yasser Almeida Hernández 10 Mar '14

10 Mar '14

Hi all, It is possible to edit (rename, remove, etc.) named selections? Regards Yasser -- Yasser Almeida Hernández, MSc. Center of Molecular Immunology (CIM) System Biology Department 216 St. & 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3127 almeida(a)cim.sld.cu --------------------------------------------------- [http://5.cim.co.cu/cim.gif]

2 1

Visualizing trajectory
by Yasser Almeida Hernández 10 Mar '14

10 Mar '14

Hi all, I have a MD trajectory from GROMACS and I want to visualize it in Chimera using MD Movie tool. My protein move inside the water box. How I cant fix the protein to see the its dynamics in each frame? I have used VMD for this task, using the RMSD trajectory calculator plugin. Here the trajectory is loaded and then press the Align button. The protein coordinates in each frame is superposed on those from the first frame. Whith this the protein stay in a fixed position. It is this possible in Chimera? On the other hand, It is possible load the trajectory just by every N frames? I have a trajectory with 2 000 000 of frames, and I want to load the trajectory every 100 frames. Thanks in advance Yasser -- Yasser Almeida Hernández, MSc. Center of Molecular Immunology (CIM) System Biology Department 216 St. & 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3127 almeida(a)cim.sld.cu --------------------------------------------------- [http://5.cim.co.cu/cim.gif]

3 3

To get CHIMERA to work: "with stereo viz on new samsung "3D" LCD and quadro card"
by Peter Engelhardt 08 Mar '14

08 Mar '14

Dear Chimera, Sorry - Specification - We naturally meant: CHIMERA to WORK with "stereo viz on new samsung "3D" LCD and quadro card" > Dear Chimera, > > We recently got a mail on instruction to install correct parameters > to get VMD-L to work: > > "vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card" > > Now we ask, do you have any suggestions to get "Samsung "3D" LCD and > quadro card" and to get CHIMERA work not only for: > > 1. Linux (Ubuntu) with "quadro card" > > but also and on: > > 2. MacPro/Mavericks with "a quadro card" > > We thank you in advance > > Cheers > Peter et al. > > Quoting John Stone <johns(a)ks.uiuc.edu>: > > [Hide Quoted Text] > Carlos, > Ah, I had missed the startup message you included when I read > your first note. All of the VMD stereo modes other than "QuadBuffered" > are implemented by rendering code within VMD itself, and they do not > depend on the graphics driver or any special hardware capabilities. > So, the fact that you are able to use the "SideBySide" or other modes > just indicates that your TV can work with the VMD-supplied mode, but > that's separate from the issue of having the Quadro's stereo sync and > other features working. > > The VMD "QuadBuffered" stereo mode relies entirely on the GPU and > its driver for stereoscopic display. This is the best mode to use > if you want the IR or RF stereo emitter to remain in proper sync with > the displayed images, but it requires that the GPU drivers and windowing > system be configured correctly, and that the GPU and driver will actually > support the target display. If you're running on Linux, then the thing > to do is to check the contents of /var/log/Xorg.0.log and look for > the word "Stereo". Here's an example of the kinds of output you're looking > for, as seen on a couple of our machines: > (**) NVIDIA(1): Option "Stereo" "10" > (**) NVIDIA(1): Option "ForceStereoFlipping" "true" > > Here's a machine that has stereo enabled: > (II) Setting vga for screen 0. > (II) Setting vga for screen 1. > (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(0): RGB weight 888 > (==) NVIDIA(0): Default visual is TrueColor > (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(0): Option "MetaModes" "2560x1600 +0+0" > (**) Feb 17 16:21:29 NVIDIA(0): Enabling 2D acceleration > (II) Feb 17 16:21:29 NVIDIA(0): Display (Samsung SyncMaster (DFP-0)) > does not support NVIDIA > (II) Feb 17 16:21:29 NVIDIA(0): 3D Vision stereo. > (II) Feb 17 16:21:29 NVIDIA(0): NVIDIA GPU Quadro 7000 (GF110GL) at > PCI:8:0:0 (GPU-0) > (--) Feb 17 16:21:29 NVIDIA(0): Memory: 6291456 kBytes > (--) Feb 17 16:21:29 NVIDIA(0): VideoBIOS: 70.10.4a.00.01 > (II) Feb 17 16:21:29 NVIDIA(0): Detected PCI Express Link width: 16X > (--) Feb 17 16:21:29 NVIDIA(0): Valid display device(s) on Quadro > 7000 at PCI:8:0:0 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-0 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-1 > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0) > (boot, connected) > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): CRT-1: 400.0 MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): Internal > Dual Link TMDS > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): 330.0 > MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: Internal Single Link TMDS > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: 330.0 MHz maximum pixel clock > (**) Feb 17 16:21:29 NVIDIA(0): Using HorizSync/VertRefresh ranges > from the EDID for display > (**) Feb 17 16:21:29 NVIDIA(0): device Samsung SyncMaster > (DFP-0) (Using EDID frequencies > (**) Feb 17 16:21:29 NVIDIA(0): has been enabled on all display devices.) > (II) Feb 17 16:21:29 NVIDIA(0): Validated MetaModes: > (II) Feb 17 16:21:29 NVIDIA(0): "2560x1600+0+0" > (II) Feb 17 16:21:29 NVIDIA(0): Virtual screen size determined to be > 2560 x 1600 > (--) Feb 17 16:21:29 NVIDIA(0): DPI set to (101, 101); computed from > "UseEdidDpi" X config > (--) Feb 17 16:21:29 NVIDIA(0): option > (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(1): RGB weight 888 > (==) NVIDIA(1): Default visual is TrueColor > (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(1): Option "Stereo" "10" > (**) NVIDIA(1): Option "ForceStereoFlipping" "true" > (**) Feb 17 16:21:29 NVIDIA(1): USB IR emitter stereo requested > (WW) Feb 17 16:21:29 NVIDIA(1): For stereo to work with Xinerama, > stereo X configuration > (WW) Feb 17 16:21:29 NVIDIA(1): option should be enabled on all > X screens in the X server. > (WW) Feb 17 16:21:29 NVIDIA(1): Stereo is disabled on one (or > more) X screens, while > (WW) Feb 17 16:21:29 NVIDIA(1): Xinerama is enabled. Stereo > visuals will not be > (WW) Feb 17 16:21:29 NVIDIA(1): available. > (**) Feb 17 16:21:29 NVIDIA(1): OpenGL stereo forced > (**) NVIDIA(1): Option "MetaModes" "nvidia-auto-select +0+0" > (**) Feb 17 16:21:29 NVIDIA(1): Enabling 2D acceleration > (II) Feb 17 16:21:29 NVIDIA(0): Display (Acer HN274H (DFP-0)) > supports NVIDIA 3D Vision > (II) Feb 17 16:21:29 NVIDIA(0): stereo. > (II) Feb 17 16:21:29 NVIDIA(1): NVIDIA GPU Quadro 7000 (GF110GL) at > PCI:9:0:0 (GPU-1) > (--) Feb 17 16:21:29 NVIDIA(1): Memory: 6291456 kBytes > > > Here's a machine that has stereo disabled currently: > (II) Setting vga for screen 0. > (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(0): RGB weight 888 > (==) NVIDIA(0): Default visual is TrueColor > (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(0): Option "Stereo" "0" > (**) NVIDIA(0): Option "nvidiaXineramaInfoOrder" "DFP-3" > (**) Feb 17 17:20:19 NVIDIA(0): Stereo disabled by request > (**) NVIDIA(0): Option "MetaModes" "DFP-0: nvidia-auto-select > +2560+520, DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +2560+0, > DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +0+0, DFP-3: > nvidia-auto-select +1920+0" > (**) Feb 17 17:20:19 NVIDIA(0): Enabling 2D acceleration > (II) Feb 17 17:20:21 NVIDIA(0): Display (Acer HN274H (DFP-0)) > supports NVIDIA 3D Vision > (II) Feb 17 17:20:21 NVIDIA(0): stereo. > (II) Feb 17 17:20:21 NVIDIA(0): Display (HP ZR30w (DFP-3)) does not > support NVIDIA 3D Vision > (II) Feb 17 17:20:21 NVIDIA(0): stereo. > (II) Feb 17 17:20:21 NVIDIA(0): NVIDIA GPU Quadro K6000 (GK110BGL) > at PCI:131:0:0 (GPU-0) > (--) Feb 17 17:20:21 NVIDIA(0): Memory: 12582912 kBytes > (--) Feb 17 17:20:21 NVIDIA(0): VideoBIOS: 80.80.16.00.01 > (II) Feb 17 17:20:21 NVIDIA(0): Detected PCI Express Link width: 16X > (--) Feb 17 17:20:21 NVIDIA(0): Valid display device(s) on Quadro > K6000 at PCI:131:0:0 > (--) Feb 17 17:20:21 NVIDIA(0): CRT-0 > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0) (boot, connected) > (--) Feb 17 17:20:21 NVIDIA(0): DFP-1 > (--) Feb 17 17:20:21 NVIDIA(0): DFP-2 > (--) Feb 17 17:20:21 NVIDIA(0): HP ZR30w (DFP-3) (connected) > (--) Feb 17 17:20:21 NVIDIA(0): DFP-4 > (--) Feb 17 17:20:21 NVIDIA(0): DFP-5 > (--) Feb 17 17:20:21 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): Internal Dual Link TMDS > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): 330.0 MHz > maximum pixel clo > -- ___________________________________________________________ Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/ Department of Pathology lab. tel: (+358-9)-19126729, 19126442 EM-lab, Tel: (+358-9)-19126261 Fax: (+358-9)-19126700 (Dept. of Pathology) Nanomicroscopy Center, Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358400193342

2 1

CHIMERA: help with stereo viz on new samsung "3D" LCD and quadro card
by Peter Engelhardt 07 Mar '14

07 Mar '14

Sorry2 for a typo - now corrected: Dear Chimera, We recently got a mail on instruction to install correct parameters to get VMD-L to work: "vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card" Now we ask, do you have any suggestions to get "Samsung "3D" LCD and quadro card" to work - not only for: 1. Linux (Ubuntu) with "quadro card" but also and on: 2. MacPro/Mavericks with "a quadro card" We thank you in advance Cheers Peter et al. Quoting John Stone <johns(a)ks.uiuc.edu>: [Hide Quoted Text] Carlos, Ah, I had missed the startup message you included when I read your first note. All of the VMD stereo modes other than "QuadBuffered" are implemented by rendering code within VMD itself, and they do not depend on the graphics driver or any special hardware capabilities. So, the fact that you are able to use the "SideBySide" or other modes just indicates that your TV can work with the VMD-supplied mode, but that's separate from the issue of having the Quadro's stereo sync and other features working. The VMD "QuadBuffered" stereo mode relies entirely on the GPU and its driver for stereoscopic display. This is the best mode to use if you want the IR or RF stereo emitter to remain in proper sync with the displayed images, but it requires that the GPU drivers and windowing system be configured correctly, and that the GPU and driver will actually support the target display. If you're running on Linux, then the thing to do is to check the contents of /var/log/Xorg.0.log and look for the word "Stereo". Here's an example of the kinds of output you're looking for, as seen on a couple of our machines: (**) NVIDIA(1): Option "Stereo" "10" (**) NVIDIA(1): Option "ForceStereoFlipping" "true" Here's a machine that has stereo enabled: (II) Setting vga for screen 0. (II) Setting vga for screen 1. (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(0): RGB weight 888 (==) NVIDIA(0): Default visual is TrueColor (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(0): Option "MetaModes" "2560x1600 +0+0" (**) Feb 17 16:21:29 NVIDIA(0): Enabling 2D acceleration (II) Feb 17 16:21:29 NVIDIA(0): Display (Samsung SyncMaster (DFP-0)) does not support NVIDIA (II) Feb 17 16:21:29 NVIDIA(0): 3D Vision stereo. (II) Feb 17 16:21:29 NVIDIA(0): NVIDIA GPU Quadro 7000 (GF110GL) at PCI:8:0:0 (GPU-0) (--) Feb 17 16:21:29 NVIDIA(0): Memory: 6291456 kBytes (--) Feb 17 16:21:29 NVIDIA(0): VideoBIOS: 70.10.4a.00.01 (II) Feb 17 16:21:29 NVIDIA(0): Detected PCI Express Link width: 16X (--) Feb 17 16:21:29 NVIDIA(0): Valid display device(s) on Quadro 7000 at PCI:8:0:0 (--) Feb 17 16:21:29 NVIDIA(0): CRT-0 (--) Feb 17 16:21:29 NVIDIA(0): CRT-1 (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0) (boot, connected) (--) Feb 17 16:21:29 NVIDIA(0): DFP-1 (--) Feb 17 16:21:29 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock (--) Feb 17 16:21:29 NVIDIA(0): CRT-1: 400.0 MHz maximum pixel clock (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): Internal Dual Link TMDS (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): 330.0 MHz maximum pixel clock (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: Internal Single Link TMDS (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: 330.0 MHz maximum pixel clock (**) Feb 17 16:21:29 NVIDIA(0): Using HorizSync/VertRefresh ranges from the EDID for display (**) Feb 17 16:21:29 NVIDIA(0): device Samsung SyncMaster (DFP-0) (Using EDID frequencies (**) Feb 17 16:21:29 NVIDIA(0): has been enabled on all display devices.) (II) Feb 17 16:21:29 NVIDIA(0): Validated MetaModes: (II) Feb 17 16:21:29 NVIDIA(0): "2560x1600+0+0" (II) Feb 17 16:21:29 NVIDIA(0): Virtual screen size determined to be 2560 x 1600 (--) Feb 17 16:21:29 NVIDIA(0): DPI set to (101, 101); computed from "UseEdidDpi" X config (--) Feb 17 16:21:29 NVIDIA(0): option (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(1): RGB weight 888 (==) NVIDIA(1): Default visual is TrueColor (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(1): Option "Stereo" "10" (**) NVIDIA(1): Option "ForceStereoFlipping" "true" (**) Feb 17 16:21:29 NVIDIA(1): USB IR emitter stereo requested (WW) Feb 17 16:21:29 NVIDIA(1): For stereo to work with Xinerama, stereo X configuration (WW) Feb 17 16:21:29 NVIDIA(1): option should be enabled on all X screens in the X server. (WW) Feb 17 16:21:29 NVIDIA(1): Stereo is disabled on one (or more) X screens, while (WW) Feb 17 16:21:29 NVIDIA(1): Xinerama is enabled. Stereo visuals will not be (WW) Feb 17 16:21:29 NVIDIA(1): available. (**) Feb 17 16:21:29 NVIDIA(1): OpenGL stereo forced (**) NVIDIA(1): Option "MetaModes" "nvidia-auto-select +0+0" (**) Feb 17 16:21:29 NVIDIA(1): Enabling 2D acceleration (II) Feb 17 16:21:29 NVIDIA(0): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision (II) Feb 17 16:21:29 NVIDIA(0): stereo. (II) Feb 17 16:21:29 NVIDIA(1): NVIDIA GPU Quadro 7000 (GF110GL) at PCI:9:0:0 (GPU-1) (--) Feb 17 16:21:29 NVIDIA(1): Memory: 6291456 kBytes Here's a machine that has stereo disabled currently: (II) Setting vga for screen 0. (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(0): RGB weight 888 (==) NVIDIA(0): Default visual is TrueColor (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(0): Option "Stereo" "0" (**) NVIDIA(0): Option "nvidiaXineramaInfoOrder" "DFP-3" (**) Feb 17 17:20:19 NVIDIA(0): Stereo disabled by request (**) NVIDIA(0): Option "MetaModes" "DFP-0: nvidia-auto-select +2560+520, DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +2560+0, DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +0+0, DFP-3: nvidia-auto-select +1920+0" (**) Feb 17 17:20:19 NVIDIA(0): Enabling 2D acceleration (II) Feb 17 17:20:21 NVIDIA(0): Display (Acer HN274H (DFP-0)) supports NVIDIA 3D Vision (II) Feb 17 17:20:21 NVIDIA(0): stereo. (II) Feb 17 17:20:21 NVIDIA(0): Display (HP ZR30w (DFP-3)) does not support NVIDIA 3D Vision (II) Feb 17 17:20:21 NVIDIA(0): stereo. (II) Feb 17 17:20:21 NVIDIA(0): NVIDIA GPU Quadro K6000 (GK110BGL) at PCI:131:0:0 (GPU-0) (--) Feb 17 17:20:21 NVIDIA(0): Memory: 12582912 kBytes (--) Feb 17 17:20:21 NVIDIA(0): VideoBIOS: 80.80.16.00.01 (II) Feb 17 17:20:21 NVIDIA(0): Detected PCI Express Link width: 16X (--) Feb 17 17:20:21 NVIDIA(0): Valid display device(s) on Quadro K6000 at PCI:131:0:0 (--) Feb 17 17:20:21 NVIDIA(0): CRT-0 (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0) (boot, connected) (--) Feb 17 17:20:21 NVIDIA(0): DFP-1 (--) Feb 17 17:20:21 NVIDIA(0): DFP-2 (--) Feb 17 17:20:21 NVIDIA(0): HP ZR30w (DFP-3) (connected) (--) Feb 17 17:20:21 NVIDIA(0): DFP-4 (--) Feb 17 17:20:21 NVIDIA(0): DFP-5 (--) Feb 17 17:20:21 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): Internal Dual Link TMDS (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): 330.0 MHz maximum pixel clo On Tue, Feb 18, 2014 at 08:06:04AM -0500, Carlos Simmerling wrote: Hi John, thanks for the quick reply. I included VMD's output in my original post- yes, it says stereo, and I can indeed get VMD to do stereo if I pick side by side mode in VMD. I'm using win 7 pro (though I'd upgrade to win 8 if I knew that would solve the problem). The TV is HDMI only, unfortunately. The quadro card has only DVI outputs, so I'm using a DVI to HDMI cable. I'm hoping to find a way to do quad buffered stereo at a reasonable refresh rate. Carlos On Mon, Feb 17, 2014 at 12:53 PM, John Stone <johns(a)ks.uiuc.edu> wrote: Hi Carlos, I'm not familiar with the TV you're using, but I can say a few things that are broadly true of a wide range of HDTVs that support stereo that may also apply in your case. If a TV has a DVI input (unlikely), then one is sometimes able to use it just like any other stereo display. If the TV uses HDMI, then the options for stereo will depend somewhat on which operating system the computer is running what video card, and what driver are being used. In regards to the NVIDIA GPUs, the "Quadro" GPUs have the best support for stereoscopic display across all OS platforms. Last I knew however, HDTVs are considered a special case, and at least on the Windows platform there was/is a special driver that one had to use to allow stereoscopic display to an HDTV over HDMI (3DTV Play) for games and the like: http://www.nvidia.com/object/3dtv-play-overview.html I just looked up the NVIDIA web site regarding stereoscopic display, and they have clearly rewritten much of it since the last time I looked: http://www.nvidia.com/object/3d-vision-professional-users.html I would expect that the Quadro would have a good chance of working with a 3D HDTV, but you will likely have to set the NVIDIA driver's stereo mode to one that your TV agrees with. If you tell me which OS you're running, we can work through a few of the details there. The most important thing is to see if VMD lists "STEREO" during the OpenGL feature startup messages that it prints to the text console. Cheers, John Stone vmd(a)ks.uiuc.edu On Fri, Feb 14, 2014 at 02:25:25PM -0500, Carlos Simmerling wrote: Hi all, I'm trying to optimize my stereo viewing. I have windows 7 pro, a quadro fx-4600 and a samsung UN60F8000BF LCD TV (http://www.samsung.com/us/video/tvs/UN60F8000BFXZA) that came with active stereo glasses. I also have an old stereographics emitter with 3-pin DIN connector that plugs into my quadro card, along with some stereographics glasses. VMD tells me this at startup: Info) OpenGL renderer: Quadro FX 4600/PCIe/SSE2 Info) Features: STENCIL STEREO MDE CVA MTX NPOT PP PS GLSL(OVF) So, what I need help with is optimizing my 3D viewing. So far I can only get this setup to work when I select side by side 3D in VMD, and on the TV I also select side by side and use the glasses that came with it. It's ok, but the glasses are cheap and there's some bleed through, and of course I lose resolution. I suspect I'd be better off using the emitter and the expensive SG glasses. When I plug in the emitter, the red light goes on so it seems to be working. If I select stereo/quadbuffered in VMD, it looks like it's doing the right thing, but using the SG glasses doesn't seem to sync properly. A few other questions: 1) do the settings in the Nvidia control panel under "manage 3D settings" impact VMD? In there you can choose the 3D mode, antialiasing, etc. I don't know if that controls the openGL part. 2) Is it possible to send a >60HZ signal to these screens? It claims it is 240Hz, but I don't know if that's internal interpolation or accepts inputs >60Hz. thanks! -- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/ -- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/ -- -- ___________________________________________________________ Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/ Department of Pathology lab. tel: (+358-9)-19126729, 19126442 EM-lab, Tel: (+358-9)-19126261 Fax: (+358-9)-19126700 (Dept. of Pathology) Nanomicroscopy Center, Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358400193342

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CHIMERA: help with stereo viz on new samsung "3D" LCD and quadro card
by Peter Engelhardt 07 Mar '14

07 Mar '14

Sorry for the earlier mail the body text was not correct here a new mail with the original vmd-l mail included (see below) Dear Chimera, We recently got a mail on instruction to install correct parameters to get VMD-L to work: "vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card" Now we ask, do you have any suggestion how to get "Samsung "3D" LCD and quadro card not to work - not only for: 1. Linux (Ubuntu) with "quadro card" but also and on: 2. MacPro/Mavericks with "a quadro card" We thank you in advance Cheers Peter et al. Quoting John Stone <johns(a)ks.uiuc.edu>: > Carlos, > Ah, I had missed the startup message you included when I read > your first note. All of the VMD stereo modes other than "QuadBuffered" > are implemented by rendering code within VMD itself, and they do not > depend on the graphics driver or any special hardware capabilities. > So, the fact that you are able to use the "SideBySide" or other modes > just indicates that your TV can work with the VMD-supplied mode, but > that's separate from the issue of having the Quadro's stereo sync and > other features working. > > The VMD "QuadBuffered" stereo mode relies entirely on the GPU and > its driver for stereoscopic display. This is the best mode to use > if you want the IR or RF stereo emitter to remain in proper sync with > the displayed images, but it requires that the GPU drivers and windowing > system be configured correctly, and that the GPU and driver will actually > support the target display. If you're running on Linux, then the thing > to do is to check the contents of /var/log/Xorg.0.log and look for > the word "Stereo". Here's an example of the kinds of output you're looking > for, as seen on a couple of our machines: > (**) NVIDIA(1): Option "Stereo" "10" > (**) NVIDIA(1): Option "ForceStereoFlipping" "true" > > Here's a machine that has stereo enabled: > (II) Setting vga for screen 0. > (II) Setting vga for screen 1. > (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(0): RGB weight 888 > (==) NVIDIA(0): Default visual is TrueColor > (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(0): Option "MetaModes" "2560x1600 +0+0" > (**) Feb 17 16:21:29 NVIDIA(0): Enabling 2D acceleration > (II) Feb 17 16:21:29 NVIDIA(0): Display (Samsung SyncMaster (DFP-0)) > does not support NVIDIA > (II) Feb 17 16:21:29 NVIDIA(0): 3D Vision stereo. > (II) Feb 17 16:21:29 NVIDIA(0): NVIDIA GPU Quadro 7000 (GF110GL) at > PCI:8:0:0 (GPU-0) > (--) Feb 17 16:21:29 NVIDIA(0): Memory: 6291456 kBytes > (--) Feb 17 16:21:29 NVIDIA(0): VideoBIOS: 70.10.4a.00.01 > (II) Feb 17 16:21:29 NVIDIA(0): Detected PCI Express Link width: 16X > (--) Feb 17 16:21:29 NVIDIA(0): Valid display device(s) on Quadro > 7000 at PCI:8:0:0 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-0 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-1 > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0) > (boot, connected) > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1 > (--) Feb 17 16:21:29 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): CRT-1: 400.0 MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): Internal > Dual Link TMDS > (--) Feb 17 16:21:29 NVIDIA(0): Samsung SyncMaster (DFP-0): 330.0 > MHz maximum pixel clock > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: Internal Single Link TMDS > (--) Feb 17 16:21:29 NVIDIA(0): DFP-1: 330.0 MHz maximum pixel clock > (**) Feb 17 16:21:29 NVIDIA(0): Using HorizSync/VertRefresh ranges > from the EDID for display > (**) Feb 17 16:21:29 NVIDIA(0): device Samsung SyncMaster > (DFP-0) (Using EDID frequencies > (**) Feb 17 16:21:29 NVIDIA(0): has been enabled on all display devices.) > (II) Feb 17 16:21:29 NVIDIA(0): Validated MetaModes: > (II) Feb 17 16:21:29 NVIDIA(0): "2560x1600+0+0" > (II) Feb 17 16:21:29 NVIDIA(0): Virtual screen size determined to be > 2560 x 1600 > (--) Feb 17 16:21:29 NVIDIA(0): DPI set to (101, 101); computed from > "UseEdidDpi" X config > (--) Feb 17 16:21:29 NVIDIA(0): option > (**) NVIDIA(1): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(1): RGB weight 888 > (==) NVIDIA(1): Default visual is TrueColor > (==) NVIDIA(1): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(1): Option "Stereo" "10" > (**) NVIDIA(1): Option "ForceStereoFlipping" "true" > (**) Feb 17 16:21:29 NVIDIA(1): USB IR emitter stereo requested > (WW) Feb 17 16:21:29 NVIDIA(1): For stereo to work with Xinerama, > stereo X configuration > (WW) Feb 17 16:21:29 NVIDIA(1): option should be enabled on all > X screens in the X server. > (WW) Feb 17 16:21:29 NVIDIA(1): Stereo is disabled on one (or > more) X screens, while > (WW) Feb 17 16:21:29 NVIDIA(1): Xinerama is enabled. Stereo > visuals will not be > (WW) Feb 17 16:21:29 NVIDIA(1): available. > (**) Feb 17 16:21:29 NVIDIA(1): OpenGL stereo forced > (**) NVIDIA(1): Option "MetaModes" "nvidia-auto-select +0+0" > (**) Feb 17 16:21:29 NVIDIA(1): Enabling 2D acceleration > (II) Feb 17 16:21:29 NVIDIA(0): Display (Acer HN274H (DFP-0)) > supports NVIDIA 3D Vision > (II) Feb 17 16:21:29 NVIDIA(0): stereo. > (II) Feb 17 16:21:29 NVIDIA(1): NVIDIA GPU Quadro 7000 (GF110GL) at > PCI:9:0:0 (GPU-1) > (--) Feb 17 16:21:29 NVIDIA(1): Memory: 6291456 kBytes > > > > > > > Here's a machine that has stereo disabled currently: > (II) Setting vga for screen 0. > (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 > (==) NVIDIA(0): RGB weight 888 > (==) NVIDIA(0): Default visual is TrueColor > (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) > (**) NVIDIA(0): Option "Stereo" "0" > (**) NVIDIA(0): Option "nvidiaXineramaInfoOrder" "DFP-3" > (**) Feb 17 17:20:19 NVIDIA(0): Stereo disabled by request > (**) NVIDIA(0): Option "MetaModes" "DFP-0: nvidia-auto-select > +2560+520, DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +2560+0, > DFP-3: 2560x1600 +0+0; DFP-0: nvidia-auto-select +0+0, DFP-3: > nvidia-auto-select +1920+0" > (**) Feb 17 17:20:19 NVIDIA(0): Enabling 2D acceleration > (II) Feb 17 17:20:21 NVIDIA(0): Display (Acer HN274H (DFP-0)) > supports NVIDIA 3D Vision > (II) Feb 17 17:20:21 NVIDIA(0): stereo. > (II) Feb 17 17:20:21 NVIDIA(0): Display (HP ZR30w (DFP-3)) does not > support NVIDIA 3D Vision > (II) Feb 17 17:20:21 NVIDIA(0): stereo. > (II) Feb 17 17:20:21 NVIDIA(0): NVIDIA GPU Quadro K6000 (GK110BGL) > at PCI:131:0:0 (GPU-0) > (--) Feb 17 17:20:21 NVIDIA(0): Memory: 12582912 kBytes > (--) Feb 17 17:20:21 NVIDIA(0): VideoBIOS: 80.80.16.00.01 > (II) Feb 17 17:20:21 NVIDIA(0): Detected PCI Express Link width: 16X > (--) Feb 17 17:20:21 NVIDIA(0): Valid display device(s) on Quadro > K6000 at PCI:131:0:0 > (--) Feb 17 17:20:21 NVIDIA(0): CRT-0 > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0) (boot, connected) > (--) Feb 17 17:20:21 NVIDIA(0): DFP-1 > (--) Feb 17 17:20:21 NVIDIA(0): DFP-2 > (--) Feb 17 17:20:21 NVIDIA(0): HP ZR30w (DFP-3) (connected) > (--) Feb 17 17:20:21 NVIDIA(0): DFP-4 > (--) Feb 17 17:20:21 NVIDIA(0): DFP-5 > (--) Feb 17 17:20:21 NVIDIA(0): CRT-0: 400.0 MHz maximum pixel clock > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): Internal Dual Link TMDS > (--) Feb 17 17:20:21 NVIDIA(0): Acer HN274H (DFP-0): 330.0 MHz > maximum pixel clo > > > On Tue, Feb 18, 2014 at 08:06:04AM -0500, Carlos Simmerling wrote: >> Hi John, >> thanks for the quick reply. >> I included VMD's output in my original post- yes, it says stereo, and >> I can indeed get VMD to do stereo if I pick side by side mode in VMD. >> I'm using win 7 pro (though I'd upgrade to win 8 if I knew that would >> solve the problem). The TV is HDMI only, unfortunately. The quadro >> card has only DVI outputs, so I'm using a DVI to HDMI cable. >> >> I'm hoping to find a way to do quad buffered stereo at a reasonable >> refresh rate. >> Carlos >> >> On Mon, Feb 17, 2014 at 12:53 PM, John Stone <johns(a)ks.uiuc.edu> wrote: >> > Hi Carlos, >> > I'm not familiar with the TV you're using, but I can say a few >> > things that are broadly true of a wide range of HDTVs that support >> > stereo that may also apply in your case. >> > >> > If a TV has a DVI input (unlikely), then one is sometimes able to use it >> > just like any other stereo display. >> > >> > If the TV uses HDMI, then the options for stereo will depend >> > somewhat on which operating system the computer is running what >> > video card, and what driver are being used. >> > >> > In regards to the NVIDIA GPUs, the "Quadro" GPUs have the best support >> > for stereoscopic display across all OS platforms. Last I knew however, >> > HDTVs are considered a special case, and at least on the Windows platform >> > there was/is a special driver that one had to use to allow stereoscopic >> > display to an HDTV over HDMI (3DTV Play) for games and the like: >> > http://www.nvidia.com/object/3dtv-play-overview.html >> > >> > I just looked up the NVIDIA web site regarding stereoscopic display, >> > and they have clearly rewritten much of it since the last time I looked: >> > http://www.nvidia.com/object/3d-vision-professional-users.html >> > >> > I would expect that the Quadro would have a good chance of working with >> > a 3D HDTV, but you will likely have to set the NVIDIA driver's stereo >> > mode to one that your TV agrees with. If you tell me which OS >> > you're running, we can work through a few of the details there. >> > The most important thing is to see if VMD lists "STEREO" during the >> > OpenGL feature startup messages that it prints to the text console. >> > >> > Cheers, >> > John Stone >> > vmd(a)ks.uiuc.edu >> > >> > On Fri, Feb 14, 2014 at 02:25:25PM -0500, Carlos Simmerling wrote: >> >> Hi all, >> >> >> >> I'm trying to optimize my stereo viewing. >> >> I have windows 7 pro, a quadro fx-4600 and a samsung UN60F8000BF LCD >> >> TV (http://www.samsung.com/us/video/tvs/UN60F8000BFXZA) that came with >> >> active stereo glasses. I also have an old stereographics emitter with >> >> 3-pin DIN connector that plugs into my quadro card, along with some >> >> stereographics glasses. VMD tells me this at startup: >> >> Info) OpenGL renderer: Quadro FX 4600/PCIe/SSE2 >> >> Info) Features: STENCIL STEREO MDE CVA MTX NPOT PP PS GLSL(OVF) >> >> >> >> So, what I need help with is optimizing my 3D viewing. So far I can >> >> only get this setup to work when I select side by side 3D in VMD, and >> >> on the TV I also select side by side and use the glasses that came >> >> with it. It's ok, but the glasses are cheap and there's some bleed >> >> through, and of course I lose resolution. >> >> >> >> I suspect I'd be better off using the emitter and the expensive SG >> >> glasses. When I plug in the emitter, the red light goes on so it seems >> >> to be working. If I select stereo/quadbuffered in VMD, it looks like >> >> it's doing the right thing, but using the SG glasses doesn't seem to >> >> sync properly. >> >> >> >> A few other questions: >> >> 1) do the settings in the Nvidia control panel under "manage 3D >> >> settings" impact VMD? In there you can choose the 3D mode, >> >> antialiasing, etc. I don't know if that controls the openGL part. >> >> 2) Is it possible to send a >60HZ signal to these screens? It claims >> >> it is 240Hz, but I don't know if that's internal interpolation or >> >> accepts inputs >60Hz. >> >> >> >> thanks! >> > >> > -- >> > NIH Center for Macromolecular Modeling and Bioinformatics >> > Beckman Institute for Advanced Science and Technology >> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 >> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 >> > http://www.ks.uiuc.edu/Research/vmd/ > > -- > NIH Center for Macromolecular Modeling and Bioinformatics > Beckman Institute for Advanced Science and Technology > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 > http://www.ks.uiuc.edu/Research/vmd/ -- ___________________________________________________________ Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/ Department of Pathology lab. tel: (+358-9)-19126729, 19126442 EM-lab, Tel: (+358-9)-19126261 Fax: (+358-9)-19126700 (Dept. of Pathology) Nanomicroscopy Center, Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358400193342

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Re: [Chimera-users] Chimera-users Digest, Vol 131, Issue 5
by Peter Engelhardt 07 Mar '14

07 Mar '14

Dear Chimera, We recently got a mail on instruction to install correct parameters to get VMD-L to work: "vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card" Now we ask, do you have any suggestion how to get "Samsung "3D" LCD and quadro card not to work - not only for: 1. Linux (Ubuntu) with "quadro card" but also and on: 2. MacPro/Mavericks with "a quadro card" We thank you in advance Cheers Peter et al. Quoting chimera-users-request(a)cgl.ucsf.edu: > 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. surface failures (Julian Marzi) > 2. Re: surface failures (Elaine Meng) > 3. Area/Volume from Web not working (Hurt, Darrell (NIH/NIAID) [E]) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 4 Mar 2014 12:31:46 +0100 > From: Julian Marzi <julian.marzi(a)googlemail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] surface failures > Message-ID: <F372C2E9-7034-47D3-B94A-CBE2D6DEF470(a)googlemail.com> > Content-Type: text/plain; charset=us-ascii > > Dear Chimera, > > I try to show the surface of the 60S in yeast (PDB: 3O5H), but it > doesn't work. Mscalc returned code 11 is shown. If I split the 60S > every chain show the surface except the first strain (25S). How can > I show the surface from the first chain? > > Thank you very much > > Best regards > > Julian Marzi > > > ------------------------------ > > Message: 2 > Date: Thu, 6 Mar 2014 10:20:22 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Julian Marzi <julian.marzi(a)googlemail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] surface failures > Message-ID: <E468C80B-D21F-40B7-A569-B66126212530(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Dear Julian, > The surface failure is a numerical thing that may differ on > different machines, and there is not a consistent recipe for how to > solve the problem. Please see this page on possible solutions, > including showing some alternative types of surface instead of a > "molecular" surface: > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> > > 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 Mar 4, 2014, at 3:31 AM, Julian Marzi <julian.marzi(a)googlemail.com> wrote: > >> Dear Chimera, >> I try to show the surface of the 60S in yeast (PDB: 3O5H), but it >> doesn't work. Mscalc returned code 11 is shown. If I split the 60S >> every chain show the surface except the first strain (25S). How can >> I show the surface from the first chain? >> Thank you very much >> Best regards >> Julian Marzi > > > > > ------------------------------ > > Message: 3 > Date: Thu, 6 Mar 2014 19:48:26 +0000 > From: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh(a)niaid.nih.gov> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Area/Volume from Web not working > Message-ID: <CF3E3B45.E956%darrellh(a)niaid.nih.gov> > Content-Type: text/plain; charset="us-ascii" > > Hi Chimera friends, > > I'm trying to use "Area/Volume from Web", but I keep getting an > error about how the server is not giving the expected output. > > I'm using build 39297. > > Any hints? > > Thanks, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > Office: 301-402-0095 > Mobile: 301-758-3559 > Web: BCBB Home > Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> > Twitter: @niaidbioit<https://twitter.com/niaidbioit> > > Disclaimer: The information in this e-mail and any of its > attachments is confidential and may contain sensitive information. > It should not be used by anyone who is not the original intended > recipient. If you have received this e-mail in error please inform > the sender and delete it from your mailbox or any other storage > devices. National Institute of Allergy and Infectious Diseases shall > not accept liability for any statements made that are sender's own > and not expressly made on behalf of the NIAID by one of its > representatives. > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 131, Issue 5 > ********************************************* -- ___________________________________________________________ Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi URL: http://www.lce.hut.fi/~engelhar/ Department of Pathology lab. tel: (+358-9)-19126729, 19126442 EM-lab, Tel: (+358-9)-19126261 Fax: (+358-9)-19126700 (Dept. of Pathology) Nanomicroscopy Center, Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358400193342

1 0

Area/Volume from Web not working
by Hurt, Darrell (NIH/NIAID) [E] 06 Mar '14

06 Mar '14

Hi Chimera friends, I'm trying to use "Area/Volume from Web", but I keep getting an error about how the server is not giving the expected output. I'm using build 39297. Any hints? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

2 2

superimposition of DNA moleucles
by Urszula Uciechowska 05 Mar '14

05 Mar '14

Dear chimera users, I need to supeimpose a DNA molecule DNA-1.pdb into the protein-DNA complex. I was trying to do this using Mach Maker, but I am getting errors. I am not sure if I can do it using this tool and how should I do it. Thank you in advance for any help and suggestions... best regards Urszula ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/

2 5

exported as PDB, but structure is not the same upon reopening
by Stern, Alexander Thomas 03 Mar '14

03 Mar '14

Hello, I am attempting to attach a covalent (cysteine modifying) ligand to my protein, and I will later be optimizing/minimizing in another program. I opened my structure in Chimera, loaded the ligands, moved them roughly into place, and merged the models. I then added the bonds and exported the file as a pdb. Upon reopening that very same pdb in Chimera, the bonds I made are gone (however, the ligands are in the position I placed them in). Curious to understand what I am doing incorrectly here. Alex The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

Building protein-protein complex with known interacting residues
by fei.wu＠chem.utah.edu 03 Mar '14

03 Mar '14

Dear Chimera Team, I am studying the interactions between three enzymes with their biological assembly structures available in PDB. Using mass spectrometry, I have been able to identify interfacial residues, and what I want to do is build up a super complex (made of the three proteins) in a desired way that these proteins are oriented by interactions between experimentally-determined residues. Would you please tell me that, if I can make or draw this in chimera? And I am also trying to compare experimentally-proposed complex structure with simulated structure. Is there a specific way in chimera to simulate interactions between two or more proteins? I found that when I opened multiple protein files in one session, chimera would gave me a complex of these proteins (not always true with different pdb files). Is this an automatic generation of simulated protein complexes or just a superimposition of part of proteins? Thanks, Fei -- Fei Wu, Ph.D. candidate Shelley D. Minteer Group Chemistry Department University of Utah Phone: 385-234-0603 Email: fei.wu(a)chem.utah.edu

3 2

Expanding EMdatabank map to full map
by Jason C Porta 03 Mar '14

03 Mar '14

Greetings, I am searching for a way to take a map from the EMdatabank which is just a cut-out of an icosahedral asymmetric and generate the full map via the sym operators. I see there are similar options for generating sym-related models, but is there a way to do this for a section of a map in Chimera? Many thanks, Jason P

2 1

pocket cavity file produced by rdock
by Fabian Glaser 02 Mar '14

02 Mar '14

Hi all, I am trying to upload and examine the cavity file produced by the rbcavity program from rdock, an open source docking program. There are both a binary form and a regular file "RBT FFT GRID" but I am not able to upload or visualize them. Can you please help me to do it? Files are attached. Thanks a lot, Fabian

2 2

Using sym command to generate icosahedral cage
by Yen-Ting Lai 26 Feb '14

26 Feb '14

Hi, I noticed that the sym command can be used to generate icosahedral symmetry, but it requires that the molecule to be oriented in specific ways (222, 2n5, n25, ...), which requires aligning the symmetry axes to the X, Y or Z axes. I am wondering if there is a way to specify the symmetries axes by vectors (instead of aligning them to the three principal axes) and then use sym command to generate the whole icosahedral cage? Yen

2 6

Chimera hardware resources
by Derrick Smith 18 Feb '14

18 Feb '14

Hi Chimera users, I've been working with what are probably some pretty big files (400 MB - 3 GB) for ultramicrotomed sections of holograms. I've trimmed the volume down as well as I can while keeping it large enough to see what we ultimately were aiming for. However, I am running into some hardware resource issues. None of our computers in the lab can handle it, so I've been using my gaming rig at home to do it. I run a server off it also, so have some decent hardware to work with, but I cannot figure out how to reallocate the resources that Chimera seems to default to. I have 64 GB of system RAM available, and after recording 1-2 movies of rotations or a flythrough of clippings etc. Chimera has never used more than 1.5 GB. My graphics card has 4 GB. After filtering and post-processing, before any rotation or video capturing, the vid card has used around 2 GB already. During video capture, depending on if I'm rotating or clipping (clipping uses up a lot more faster), the vid card memory slowly gets eaten up, eventually crashing Chimera altogether. I can usually only get about 800-1000 frames before this happens on a smaller file (400 MB), and usually can't get through a whole 10s, or 250 framed, video on one of the larger files. I have pretty limited experience with this program, so I'm hoping it's a simple settings or otherwise fix I've overlooked. Any suggestions on this? Best, Derrick -- Derrick Smith Drexel University Soft Materials Group Philadelphia PA 19104 dms348(a)drexel.edu http://www.mse.drexel.edu/srg/

2 1

Receptor-Ligand bonding at the LBP
by Graziella Portelli 13 Feb '14

13 Feb '14

To whom it may concern I would like to ask if there is a function where the bonds with which the ligand binds inside the LBP of the receptor would be visualised, or whether one has to search the amino acids involved in binding with the ligand one by one? I thank you in advance for your time Graziella Portelli

3 2

Symmetry-aware segmentation?
by Joel Meyerson 13 Feb '14

13 Feb '14

Is it possible for Chimera to segment with an awareness of symmetry, such that the collection of segments in the asymmetric units are identical? For example, a molecule with C2 symmetry would have two copies of each segment. Also, is it possible to select a segment and then have Chimera further sub-divide that segment into additional segments? Thanks, Joel

2 1

when will NoResidueRotamersError be raised?
by Xiao-Bo Li 13 Feb '14

13 Feb '14

I would like to mutate one residue to another. So far, the only way I found is to use the rotamers of the other residues on the original. I'm using chimera's python script. I would like to know if the NoResidueRotamersError will only be raised for residues that don't have rotamers like GLY. If not, then how can I replace the amino acid residue that I want to mutate? I am using the "getRotamers" function, which returns this error. XBL

3 8

Problem in using BondRot
by amin＠imtech.res.in 13 Feb '14

13 Feb '14

Dear Chimera users, I am trying to write a script to change the phi and psi angle of a peptide. I am trying to adapt the code from http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-September/000456.html . I am trying to invert the angles so I am multiplying the angles by -1. My code is import chimera from chimera import selection, UserError, BondRot, replyobj opened = chimera.openModels.open('fun.pdb') mol = opened[0] RES_LIST = mol.residues for res in mol.residues: b = str(res.phi) if b != 'None': c = -1*float(b) atomsMap = res.atomsMap N = atomsMap['N'][0] CA = atomsMap['CA'][0] C = atomsMap['C'][0] CAmap = CA.bondsMap phiBond = CAmap[N] psiBond = CAmap[C] phiAnchor = N psiAnchor = CA phi = BondRot(phiBond) phi.setAngle(c, phiAnchor) When I run this script i get the error phi.setAngle(c, phiAnchor) AttributeError: '_molecule.BondRot' object has no attribute 'setAngle' Can someone please help me with this? Warm regards. Amin.

3 6

un-subscribe
by Ted Holman 13 Feb '14

13 Feb '14

hi there i made a mistake and signed up for the email questions on chimera to be copied to me. i tried to un-subscribe but it did not work. can you tell me how to do this? thanks ted ___ Ted Holman, Ph.D. Professor Chemistry and Biochemistry Department 250 PSB, Thimann Receiving University of California, Santa Cruz Santa Cruz, CA 95064 Phone: 831-459-5884 Email: holman(a)ucsc.edu

2 1

vrml lighting
by Dougherty, Matthew T 12 Feb '14

12 Feb '14

I have a multiple vrml models that vary by scale. 1, 10 & 100 I notice the lighting significantly drops off as the scale increases. When I have another model, say PDB, that is in approximate relation (ie, viewable in regards to the volume size similar to the vrml files volumes); the PDB file looks good regardless of size (eg, tRNA or ribosome). I can increase the brightness to compensate (10-20) but it washes out the PDB models when brightness goes beyond 2. is the lighting handled differently between these different types of models? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

2 1

superimposing two structures based on a specific selection
by David Martin 10 Feb '14

10 Feb '14

Chimera 1.8 on Windows I have been trying to align (superimpose) models based on a specific conserved region. Unfortunately Chimera doesn't seem to do what the documentation claims it does. I run (example): match #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA and get an RMSD calculation (more on this below), but no movement of the model occurs. I specify 'move true show true' as options. Still no movement but I have a transformation matrix. Unfortunately this is not in a form that can be understood by Transform Coordinates. How do I persuade my structures to superimpose on the specific atoms? The RMSD calculation appears to be broken. If I take the command rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-30@CA then I will get a number If I then run rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,21-31@CA I get exactly the same number. In fact, if I specify atom sets of different sizes (as long as it is not the first block) then I continue to get exactly the same number rmsd #0:5-15@CA,20-30@CA #1: 5-15@CA,20-35@CA This should fail but doesn't Have I completely misunderstood what Chimera should be doing here? ..d The University of Dundee is a registered Scottish Charity, No: SC015096

2 3

Query on introducing an external protein
by Aditya Padhi 06 Feb '14

06 Feb '14

Dear All, I want to place a protein molecule (appx. 20 kDa in size) into a viral capsid loop region which is about 7 amino acid long. What I want to do is to remove the 5 amino acids out from the loop region and place the 20 kDa protein, so that the loop region can accommodate the 20 kDa protein. I am finding it difficult as the co-ordinates of both the molecules are different. Although, this is not related to MD simulation or associated stuff, it would be grateful if I can get some suggestions. Thanking you, Regards Aditya.

2 3

Query on introducing a protein
by Aditya Padhi 05 Feb '14

05 Feb '14

Dear All, I want to place a protein molecule (appx. 20 kDa in size) into a viral capsid loop region which is about 7 amino acid long. What I want to do is to remove the 5 amino acids out from the loop region and place the 20 kDa protein, so that the loop region can accommodate the 20 kDa protein. I am finding it difficult as the co-ordinates of both the molecules are different. Although, this is not related to MD simulation or associated stuff, it would be grateful if I can get some suggestions. Thanking you, Regards Aditya.

1 0

Question about "Color Zone" and "Render by Attribute"
by Helge Paternoga 04 Feb '14

04 Feb '14

Hello, I have a question regarding the colouring of surfaces and their caps. I am trying to recreate the colouring by hydrophobicity on capped surfaces as shown in (on the right side): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.… So first I've opened the "Render by Attribute" dialog and assigned "kdHydrophobicity". This only coloured the surface and not the surface cap though. I am assuming this is done by "Color Zone"? Indeed this colours the surface cap but I have one problem: The colouring of the surface is different between "Render by Attribute" and "Color Zone" and I don't know why. The differences are small but I would like to know which one is more accurate (intuitively I would say the one from "Render by Attribute"). I've played around with the radius of "Color Zone" but this doesn't achieve the same colouring as "Render by Attribute". So my question is: How can I achieve the same surface colouring by "Color Zone" as in "Render by Attribute"? Does it have something to to with "bondzone" or the hierachy in which the atoms apply their respective colour in "Color Zone"? Thanks for reading! Helge

4 6

Question about opening mrc and PDB files
by Min Woo Sung 03 Feb '14

03 Feb '14

Hi, This is Min Woo Sung from Texas A&M University. I was using Chimera to see EM structure(.mrc file) and wanted to put a PDB file to fit that in EM map. I'm wondering if I can use Chimera to analyze the volume, size or domains of these two files for the purpose of analysis. I saw one PDB file seemed much bigger that EM map when I opened it in Chimera. Do I have to normalize the size of any files? If so, how can I do that? Any suggests would greatly appreciated. Best regard, Min Woo Sung

3 2

Creating output with IDATM naming
by Nikolay Igorovich Rodionov 03 Feb '14

03 Feb '14

Hi, Does anyone know a way to rename all of the atom names in a PDB file to their IDATM types, so that a new PDB file can be generated with the IDATM naming scheme? Best, Nikolay Rodionov

2 1

Zoom problem?
by Damien Larivière 03 Feb '14

03 Feb '14

Dear all, I try to zoom in the scene, to get very close to my model shown here below. I cannot be closer than in the image below, the zooming function is at its maximum. When zooming, I get the error message : /refocus to continue scaling/ I do not know whether it is a bug or something I'm doing wrong. Thanks for your help, Damien

5 5

Need help in Coulombic surface coloring
by Haresh Tukaram More 30 Jan '14

30 Jan '14

Hi, I tried to get the Coulombic surface coloring for one of the protein that I modified by removing certain residue at the C-termini and then mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine using Swisssidechin option. I am getting this error which I am not able to understand. Disabled GPU programs because a graphics driver bug was encountered while compiling a vertex shader. #0, chain A: COMP #0, chain B: COMP #0, chain C: COMP #0, chain D: COMP #0, chain E: COMP C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2 22 connected surface components Total solvent excluded surface area = 10393.6 component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059, 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549, 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319, 26.9429 Total solvent accessible surface area = 10372 component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165, 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737, 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394, 0.0674059, 0.0311705 No SEQRES records for combination (#-2147483648.-2147483648) chain A; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain B; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain C; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain D; guessing terminii instead No SEQRES records for combination (#-2147483648.-2147483648) chain E; guessing terminii instead Chain-initial residues that are actual N terminii: #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B, #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D, #-2147483648.-2147483648 MET 27.E Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B, #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D, #-2147483648.-2147483648 TFLE 67.E Chain-final residues that are not actual C terminii: 424 hydrogen bonds Hydrogens added Charge model: AMBER ff12SB Assigning partial charges to residue TFLE+TFLE (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (TFLE+TFLE) Cannot automatically determine charges for residue TFLE+TFLE; Run AddCharge tool manually to add charges and then rerun ESP Can someone please tell me a step by step procedure to make this work. Thanks & Regards, Haresh

4 13

Re: [Chimera-users] Coloring map by curvature
by Tom Goddard 29 Jan '14

29 Jan '14

Hi Joel, I don't think surface curvature will be helpful understand the differences between two EM maps. But I was curious what it would look like. So here's a Python script and an image on a simulated map at 15 Angstroms. You use the script by opening your map, selecting the surface (ctrl-click on it), then open the curvature.py script (menu File / Open…). Here's a description of the method it uses from the comments at the top of the curvature.py file. # Color selected surface pieces by mean curvature. # # Gray at the average curvature value over the surface, and blue and red # at +/- 3 standard deviations of curvature values across the surface. # # The curvature is estimated from the vertices and normals of the triangulated # surface in simple way which will show artifacts from non-isotropic meshes. # For each triangle edge it computes the normal vector rotation from one vertex # to the other divided by the edge length. The vertex mean curvature is the # mean of the curvatures computed for each edge. # And the steps to make the example image open 1grl molmap #0 15 grid 2 model #1 select #1 open ~/Desktop/curvature.py Tom On Jan 29, 2014, at 9:40 AM, Joel Meyerson wrote: > Hi Darrell, > Thanks for the tip! I hadn't considered mesh lab but that link you sent looks promising. I'll also wait to see if Tom has any further suggestions. > Joel > > > On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: > Hi Joel, > > I love Chimera and use it all the time. However, a quick-and-dirty solution to your problem might be to try Meshlab. It is kind of buggy software, but can be very useful. Here's a tutorial/blog entry that I found in a quick search. At the very least, it describes what I think Tom was communicating about enhancing surface shading: > http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-a… > > FWIW, > Darrell > > -- > Darrell Hurt, Ph.D. > Section Head, Computational Biology > Bioinformatics and Computational Biosciences Branch (BCBB) > OCICB/OSMO/OD/NIAID/NIH > > 31 Center Drive, Room 3B62B, MSC 2135 > Bethesda, MD 20892-2135 > > > Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > > From: <Meyerson>, "Joel [F] (NIH/NCI)" > Date: Tuesday, January 28, 2014 9:08 PM > To: Tom Goddard > Cc: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> > > Subject: Re: [Chimera-users] Coloring map by curvature > > Hi Tom, > I have cryo-EM maps for two conformations of a protein, both in the 15 Angstrom resolution range. The conformations are visibly different, but I am also interested in seeing where they differ in terms of their surface curvature, as it could have bearing on how I interpret the conformations. If there's any other info I can provide just let me know. > Thanks! > Joel > > > On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard wrote: > Hi Joel, > > No, Chimera does not compute surface curvature. It would not be too hard to make a Python script that computed it and used it to color a surface. The main trouble is defining numerically the curvature for a triangulated surface at each vertex. Why are you interested in this? Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter? Is the idea to try it on EM maps or molecular surfaces? > > Tom > > > On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote: > > > Hi, > > Is it possible to color a map based on surface curvature? > > Thanks, > > Joel > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > >

2 1

Coloring map by curvature
by Joel Meyerson 29 Jan '14

29 Jan '14

Hi, Is it possible to color a map based on surface curvature? Thanks, Joel

4 4

adding GalNac moiety on Threonine residue
by Elsa Marquez 28 Jan '14

28 Jan '14

Hi there! Do you guys know if I can add or somehow draw a carbohydrate moiety such as GalNac to a single Threonine in a protein complex? Thanks! Elsa Marquez University of Alberta

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