- Chimera-users - RBVI Mailing Lists

surface area
by yan zhang 27 Sep '10

27 Sep '10

Hi sir , I used StrucTools server of Area/Volume from Web to calculate the buried surface of ligand . The ligand and protein was docked with glide , and then, i saved the complex into the form of pdb.I calculate the protein, ligand and complex area respectively , but the values of protein and complex were the same . The Surface probe size is 1.5 and Atoms to use is 'atoms+hetatms' . Is there something wrong with the pdb file of the complex or my operation? Thanks, Sweety

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modify structure
by Francesco Pietra 26 Sep '10

26 Sep '10

Hello: New to modify structure. I would like to modify a peptide by changing ARG to VAL. As I wanted to start from the conformer containing ARG, I tried to delete bonds, in the hope to finally change one H to CH3. None worked in my hands. Thanks for suggestions. francesco pietra

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Problem: Electrostatic surface coloring
by Nitesh Sule 24 Sep '10

24 Sep '10

Hi, I am having trouble getting chimera to open .phi files, with the following reply: "Error reading file xyz.phi, format delphi Parameter record size 284 must be 16 or 20 or 36" The .phi file was generated using delphi, and works fine when opened with Grasp2. Can someone please help me with this? On a slightly related note, I am also unable to use the delphi controller in Chimera, with the message: "Delphi exited with status -1073741794". I am not sure if this is a bug. I can provide more details from the log. Chimera version: 1.4.1 (build 29977) Thanks Nitesh.

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Re: [Chimera-users] cover art
by Eric Pettersen 24 Sep '10

24 Sep '10

On Sep 24, 2010, at 3:49 PM, Friedman, Simon H. wrote: > Hey Eric, > Here is a mockup of the cover. I have a question for you: If you > look at the helix, there are some very funky shadows that ended up > very blocky. Other shadows are completely smooth. The helix was > rendered in pov using default everything (from Chimera). Any > insights into the blocky shadows? They are on one strand only! Hi Simon, That's because right now the ribbons are being represented by a bunch of triangles. One of the things on Greg's to-do list is to have them represented by NURBS curves, which POV-ray would be able to shadow smoothly, but that hasn't happened yet. For now, you can mitigate the blockiness by upping the subdivision quality to 5 or higher. Control of the subdivision quality is in the "Effects" tab of the side view. --Eric

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Stereo 3D for teaching
by Nadir T. Mrabet 24 Sep '10

24 Sep '10

Hi, I had addressed previously the question about which equipments would perform best to display molecular structures in 3D for teaching purposes. Greg Couch had offered to keep me up on the latest technologies offered at the last SIGGRAPH conference. But nothing so far. Can anyone help me with that? Many thanks in advance. Nadir -- Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet<at> medecine.uhp-nancy.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.

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movie command with headless Chimera
by Tom Goddard 23 Sep '10

23 Sep '10

Hi Masako, You want to create a movie by running Chimera in the background (no windows, no console). You are trying the right approach, using "headless" Chimera. I'm afraid the movie command may not work with headless (ie background, no windows) Chimera. Headless Chimera can't create any dialog windows and it may be that the movie command internally relies on the Movie Recorder dialog. I don't know for sure. Your error is caused by the movie command trying to monitor changes in the Chimera graphics window (which does not exist). I can fix that and see if there are subsequent errors. I'll try this today or tomorrow. Image saving works with headless Chimera, but I have not tried background movie recording in the past -- obviously useful though. Tom > Hi, Tom. I hope you had a nice vacation :) > > I was able to run very simple command script with headless chimera, but I > am getting these errors trying to save a simple spinning movie... > > reading final.mrc 2.2 Mb 0% > Done reading final.mrc > final.mrc opened > reading final.mrc 18 Mb 0% > Done reading final.mrc > Traceback (most recent call last): > File "/home/mterada/opt/UCSF/Chimera-headless/share/chimeraInit.py", > line 422, in init > chimera.openModels.open(a, prefixableType=1) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/chimera/__init__.py", > line 1510, in open > models = func(filename, *args, **kw) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/ChimeraExtension.py", > line 32, in func > processCommandFile(cmdFile) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 104, in processCommandFile > _processFile(f, emulateRead, filename) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 135, in _processFile > if makeCommand(line): > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 65, in makeCommand > f(c, args) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/ChimeraExtension.py", > line 25, in doMovieCmd > doExtensionFunc(MovieRecorder.processMovieCmd, args) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/Midas/midas_text.py", > line 426, in doExtensionFunc > extFunc(*tuple(processedArgs), **kw) > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/__init__.py", > line 207, in processMovieCmd > director = getDirector() > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/__init__.py", > line 342, in getDirector > director = Director.Director() > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/Director.py", > line 69, in __init__ > top = chimera.tkgui.app.winfo_toplevel() > AttributeError: 'module' object has no attribute 'tkgui' > Error while processing makeimage.cmd: > AttributeError: 'module' object has no attribute 'tkgui' > > File > "/home/mterada/opt/UCSF/Chimera-headless/share/MovieRecorder/Director.py", > line 69, in __init__ > top = chimera.tkgui.app.winfo_toplevel() > > See reply log for Python traceback. > > > This same command script saves spinning movie with no problem, so I am > guessing it's headless chimera not having GUI... Is there a way around > it? > > Thanks, > > Masako >

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Mutagenesis
by r charbel maroun 23 Sep '10

23 Sep '10

Dear Chimera users, Please correct me if I'm wrong, but neither in Chimera nor in the user's list did I find any info on mutating a residue. Is this a missing functionality ? Greetings -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

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Saving new coordinates after superimposing structures
by Sujata 22 Sep '10

22 Sep '10

Hi, After I superimpose two structures using MatchMaker, I would like to save the coordinates of #1 after being superimposed with #0. When I save the PDB with the new coordinates and open #0 and #1 PDBs again, they do not superimpose. Can this be done? What is the best way to achieve this? (Elaine, I have a third fragment I want to bond to the previously bonded one and since the first-second has moved now, I want to do this so that they are on the same axis). Thanks, Sujata

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technical questions about volume viewer in chimera
by Alex Shkumatov 22 Sep '10

22 Sep '10

Hallo Perhaps, this has been on the forum before, but I could not find the answers to my questions: 1. Some EM density maps have a header. I wonder how Chimera recognizes it and calculates map dimensions? 2. Does chimera take default voxel size from header of EM file? Thanks in advance Alex ---------------------------------------------------------------------- Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY -- Building 25A Notkestraße 85 -- 22603 Hamburg -- Germany tel: +49 40 89902 178 fax: +49 40 89902 149 Email: shkumatau(a)embl-hamburg.de ----------------------------------------------------------------------

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Re: [Chimera-users] Joining fragments in a peptide bond
by Elaine Meng 21 Sep '10

21 Sep '10

Hi Sujata, I'll answer the easy part first: you can specify the axis cylinder radius as an Angstrom value in the Define Axis dialog (opened from the Axes/Planes/Centroids tool) or if you are using the "define" command, with the "radius" keyword, see the general options in that page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> I see you have a left-handed polyproline helix which also has a superhelical twist, and you wish to extend its length maintaining the same helicity and superhelicity. Then you have assembled three of these into a triple helix. This problem is not really something you want to attack with Build Structure; instead, you need to figure out the symmetry operations to extend this structure, then apply them to additional copies of the identical structure to extend it. One way would be to figure out BIOMT matrices and add those to the PDB file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#biomt> However, it can be difficult to figure out the correct values and edit them in using the correct format, so I'll describe a different way that just uses commands. The two fragments you sent are identical (I know you know this, I'm just explaining to the others), and I matched the first half of one copy to the second half of the other copy to try to figure out the symmetry operations. Command: match #1:1-15@ca #0:16-30@ca <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> This match looked pretty good to me, so next I used the measure command to tell me the transformation that had been used to generate this match: measure rotation #0 #1 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> Actually that command will display another axis cylinder, and I don't think you can control the size of that one, but you can just close or hide it with the Model Panel (under Favorites in the menu). The transformation information is given in the Reply Log (also under Favorites in the menu): Position of #1 relative to #0 coordinates: Matrix rotation and translation -0.00777505 -0.89851915 -0.43886545 45.94850252 0.89297961 -0.20375330 0.40133777 -0.02182236 -0.45002996 -0.38877748 0.80394347 -26.28870812 Axis -0.40352597 0.00570191 0.91495042 Axis point 17.07887792 12.85324577 0.00000000 Rotation angle (degrees) 101.75881858 Shift along axis -42.59440324 Then I reset so that the two fragments were again exactly superimposed (since they are identical ), using the command: reset <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> Then I applied TWICE the reported translation and rotation because the match was of 15 residues, but the whole fragment is 30 and I want to join the ends. I used the axis given in the Reply Log as the axis of movement and the axis point as the center of rotation, and applied twice the rotation angle with the "turn" command and twice the shift with the "move" command: turn -0.40352597,0.00570191,0.91495042 203.5 models #1 coord 0 center 17.07887792,12.85324577,0 move -0.40352597,0.00570191,0.91495042 85.188 models #1 coord 0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> At this point it looks like they are in a pretty good position to just add the bond and delete the extra atoms at the ends. Since you already have the models in position, don't use Join Models in Build Structure. Instead use "copy/combine" in the Model Panel (or the "combine" command) to merge the two fragments to create another model, and in that model, select the extra atoms that you want to delete (probably all hydrogens on N-term N and one of the oxygens on the C-term carboxyl of the other fragment), use command "del sel" to delete them, then select the two atoms to be bonded, and use command "bond sel". The bond will look a little strained, but this whole approach is going to get you an APPROXIMATE model. You could use command "addh" if you cared about the presence of the amide hydrogen at the join. This approximate model is good enough for a figure, or as a starting point for a simulation in some other package like Amber. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html> Actually, it might have been better to start with the trimeric fragment with all 3 chains, use residues from all 3 chains for the match, etc., and then there would be three bonds to form, rather than repeating only the single strand and then trimerizing. Hard to know without trying. Sorry, it is a rather laborious process. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 20, 2010, at 10:31 AM, Sujata wrote: > Hello Elaine, > Thank you for the email below. It was very helpful. > > But, I would like the second fragment to be on the same helical axis as the first one. When I join them this way, by defining the torsion angle, the second one does not stay on the same axis as the first one. So is there a way that I can fix the two peptides to be on the same axis when I fix the bond length and the torsion? > > I am attaching the two individual files and the combined one. > > Also when one defines axis, is there a way to reduce the thickness of the displayed axis. Due to its thickness, the atoms are not visible. > Thank you. > > Regards, > Sujata >

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