- Chimera-users - RBVI Mailing Lists

patching ACE NME
by Francesco Pietra 05 May '14

05 May '14

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

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

30 Apr '14

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

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

30 Apr '14

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

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

29 Apr '14

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

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

29 Apr '14

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

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

29 Apr '14

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

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

29 Apr '14

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

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

28 Apr '14

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

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

28 Apr '14

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

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(no subject)
by Joshua Broyde 28 Apr '14

28 Apr '14

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

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