- Chimera-users - RBVI Mailing Lists

Can eraser position be defined by coordinates?
by Kelly Dryden 16 May '11

16 May '11

Hi, I would like to place the origin of the eraser to correspond with the center of my map but haven't found a way to define its position based on coordinates, only by moving it with the mouse. Is there a line command or other menu option that allows me to set the position more precisely? Thanks, Kelly

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rigid body rotation of subunit
by Dhiraj Srivastava 13 May '11

13 May '11

Hi I have the structure of two homologous protein. These proteins are dimeric. when I am superimposing chain A of one protein on to the chain A of other, it looks like chain B of one protein is related to chain B of other protein by rigid body rotation. How can I calculate the angle of rotation in chimera? Is there any way, I can draw a vector along beta sheet? Thank you. Dhiraj

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shape factor
by maznar 13 May '11

13 May '11

Hello, We are using Chimera to classify viruses. We use pdb files from viper. We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it? Thank you.

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square of density volume
by 仁田亮 12 May '11

12 May '11

Hi chimera users, I want to calculate the square value for the volume of the electron density because I want to calculate the variance map. Do anyone know whether we can calculate the square value of the volume by chimera? And if we can, could you teach me how to calculate? Thanks for your time and help, Ryo

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Pseudobonds disappearing during morphing movie
by Alan Cheung 12 May '11

12 May '11

Hi there - i'm scripting a complex movie and am having problems with pseudobonds during morphing. Script is pasted at the end. Part of the movie contains a morph between two structures, both of which are missing the same amino acid segment. Loading the two structures show the pseudobond for the missing residues and the resulting morph also contains the same pseudobond. I've been changing the thickness of the pseudobond with : setattr g lineWidth 8 and while the two static structures and the morph in the chimera window have a thicker pseudobond, the resulting movie (encoded to .mov) does not. Am i doing something wrong? Alan p.s. incidentally, when morphing by script, if one includes "nogui true" with the "morph movie" command, pseudobonds aren't kept in the morph at all. A bug? p.p.s. can someone explain to me the difference between "setattr g" and "setattr p"? I've read the manual but i don't understand why only the former seems to work for me. ## movie script open model1.pdb open model2.pdb morph start #0 frames 50 name morph1 method linear morph interpolate #1 name morph1 morph movie name morph1 coordset #2 1,1 setattr g lineWidth 8 ~modeldisplay # movie record supersample 3 directory ~/TEMP/ modeldisplay #2 coordset #2 1,51 ; wait 51 movie stop movie encode output morph1.mov

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How to show an icosahedral cage
by Tom Goddard 11 May '11

11 May '11

Hi Yen-Chywan, The Chimera "hkcage" command makes a cage of pentagons and hexagons to show virus symmetry. For example, open emdbID:1058 hkcage 1 1 radius 170 orient 222r linewidth 4 color blue The hkcage command has options for the lattice parameters for your virus, its radius, what icosahedral coordinate system is being used. Here's the documentation. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icosca… The meshmol command can make the edges of the cage cylinders instead of lines. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html The HHMI virus viewer Chimera tool is not part of the standard Chimera distribution. It was made for a CD distributed by the Howard Hughes Medical Institute http://wwwtest.cgl.ucsf.edu/Outreach/ViralOutbreak/index.html http://www.hhmi.org/catalog/main?action=product&itemId=366 We don't distribute it separately. Tom > Dear Tom, > > I attend Scripps cryoEM workshop before and meet you there. > > Attach please find a screen capture of a virus. But there is a > icosahedra cage. My question is how to display that cage with my virus > volume? > > I did find it in HHMI virus viewer demo movie. But where can download > this viewer? > > Thanks > > Yen-Chywan >

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constructing a dimer
by uzma saqib 11 May '11

11 May '11

Hello, I want to totally freeze the movement of one protein (which is a homology model) and open another molecule of the same protein, which I want to keep movable, so that I can make a dimer out of this at my chosen place on the first protein molecule. Plz help . thanks uzma

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System Compatiblility
by Satterlee, James D 11 May '11

11 May '11

Hello, I've not yet downloaded or used Chimera, but I am contemplating it. I am looking for Windows System compatibility information for the various newer versions of Chimera. To me it wasn't obvious on the Chimera home site. I do not use Window's 7 and I'm wondering which version might be most trouble-free for a Windows XP version with all service packs installed. Thanks, Jim Satterlee James D. Satterlee Professor of Chemistry Washington State University Pullman, WA 99164-4630 hemeteam(a)wsu.edu 509.335.8620

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color side chain only
by Zhou, Ming (NIH/NCI) [C] 11 May '11

11 May '11

Hello, this is Ming Zhou at NCI-Frederick, Maryland. I am trying to use Chimera to make some ribbon structure figures. I am wondering how I can display only side chain (without backbone) for a specific residue. Usually, if I display the residue, select the residue at the Atom specifier and color it. The color would be partially on the ribbon structure too since the backbone of that residue is on the ribbon. How do I avoid coloring backbone, only color the side chain? Thank you very much. Ming

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Morphing volumes
by Burgoyne, Thomas 10 May '11

10 May '11

Hi, I have two 3D-EM volumes that I wish to use the morph option for. I can align the two maps in chimera by hand so that they sit well together but the problem is I want to be able to create a morph video from the maps new positions. When I use the morph option it only allows me to create a morph from the original set starting positions of each volume. Is there a way to get around this? I would be very thankful for any help or guidance. Tom

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Re: [Chimera-users] building large size polymer
by 윤홍민 05 May '11

05 May '11

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Re: [Chimera-users] imgCIF files
by Tom Goddard 04 May '11

04 May '11

HI Mattia, Chimera can save MRC2000 format which is nearly identical to CCP4 format. Any software that reads CCP4 will likely read the MRC output from Chimera as CCP4, but the origin of the map is specified differently. The MRC format allows a floating point origin specification which is not part of the CCP4 format and Chimera uses that. So alignment of the Chimera written MRC and atomic models may not work right in other software. A basic problem with CCP4 is that the origin has to lie on a crystallographic lattice point, which isn't so good for electron microscopy or maps from non-crystal sources. Chimera doesn't know about a SAXS bead radius in PDB header remarks. Also Chimera may try some heuristics to connect up the beads as if they were actual atoms. You'll have to try and see. You can adjust the sphere radius for the beads by selecting them and using Selection Inspector (green button in lower right of main Chimera window) or a command setattr a radius 5 #0 For making a simulated map with the Chimera "molmap" command the atom radius is not used. It simply adds 3-dimensional Gaussians centered at each atom. The Gaussian width is calculated by the resolution value used in the molmap command molmap #0 8 See the documentation for details. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html Tom > > Dear Elaine, > > thanks for your very fast and informative answer! I missed that option > in the list of Chimera commands. I will try it out tomorrow (I'm at > home now...). Perhaps it would be nice to add it to one of the > pull-down menus (in the Volume options?). Is there a way then to save > the map, say in ccp4 format? > > As for the SAXS file, yes, for instance the DAMMIN/DAMMIF-generated > files are in PDB format. But will Chimera read in the correct radius > for the beads, which is stored in the file header? (or is there a way > to externally enter the radius?). > > Thanks again - Mattia > > At 09.32 04/05/2011 -0700, Elaine Meng wrote: >> Dear Mattia, >> You can make a density map from atomic structures (or their parts) in >> Chimera using the "molmap" command: >> >> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> >> >> For example, commands: >> >> open 2gbp >> molmap ligand 4.5 >> molmap protein 5 >> >> ... would make a map of resolution 4.5 for the ligand part of the >> structure (glucose) and another map of resolution 5 for the protein >> part of the structure. You could also specify the whole structure, >> particular chains, etc. >> >> If the SAXS model was in the form of a PDB file with the beads as >> "atoms," perhaps you could use a similar procedure. >> >> 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 May 4, 2011, at 7:44 AM, Mattia Rocco wrote: >> > >> > To the developers of Chimera: is there any intention of implementing >> the uploading of imgCIF density maps files? Such files can be >> generated by RasMol starting from either atomic structures or >> low-resolution bead models (e.g. SAXS-derived models). >> > >> > Conversely, it would be nice if density maps could be generated >> within Chimera... >> > >> > Best - Mattia >> > >

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solvent exposed charged resides
by George Feldman 04 May '11

04 May '11

Hello Chimera community, I am rather new to Chimera, but in general familiar with PyMol. I switched to Chimera for the added functionality and general "free-ness," and so far I like it, but I'm having difficulty getting started. What I really need to do is identify the solvent exposed (SAS) residues that are charged. In particular I would like to identify exposed lysines, arginines, glutamic acids, and aspartic acids. All I need to do is identify and count them, is there a way to do this without slowly going over the entire molecular surface? Please bear in mind that I am capable of typing in commands, but I am no programmer. If it is too complex, I will simply, and sadly, have to do it manually. My fear with the manual approach is that I will miss something or miss-classify it. Your advise and help is greatly appreciated. PS. I've tried to do Render by Attribute -> areaSAS, but that doesn't seem to be working for me even after I tell it to calculate the surface. I'm not sure what I'm doing wrong if this is the approach that I am supposed to be taking. Best regards, George

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imgCIF files
by Mattia Rocco 04 May '11

04 May '11

To the developers of Chimera: is there any intention of implementing the uploading of imgCIF density maps files? Such files can be generated by RasMol starting from either atomic structures or low-resolution bead models (e.g. SAXS-derived models). Conversely, it would be nice if density maps could be generated within Chimera... Best - Mattia Dr. Mattia Rocco Biopolimeri e Proteomica Istituto Nazionale per la Ricerca sul Cancro (IST) c/o Centro per le Biotecnologie Avanzate (CBA) IST c/o CBA, Largo Rosanna Benzi 10 I-16132 Genova, Italy Phone: +39-0105737-310 Fax: +39-0105737-325 e-mail: mattia.rocco(a)istge.it ATTENZIONE. Il presente messaggio ed i suoi allegati devono intendersi ad uso esclusivo dei suoi destinatari e sono confidenziali. Persone diverse dal destinatario, anche ai sensi del D.Lgs. n. 196/2003 , non debbono prendere visione dei contenuti, copiare od inoltrare l'e-mail a terzi. Se ricevete questo messaggio per errore, Vi preghiamo di cancellarlo, di distruggerne ogni copia e di informarci immediatamente. La mail non è un protocollo sicuro, pertanto IST declina ogni responsabilità in caso di intercettazione o modifiche del presente messaggio. WARNING. This message and any attachments is intended solely for the use of the intended addressees and is confidential. Any unauthorized review, use, disclosure or distribution is prohibited. If you receive this message in error, please delete it, destroy all copies and immediately notify us. Mail is not a secure protocol, therefore IST will not be liable for interception or amendment of this message.

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pause during morph conformations
by Charles Greenberg 04 May '11

04 May '11

I have a 3-state structure and I'm currently using morph conformations to interpolate between them. This works very nicely, but I'd like the output movie to pause for half a second (a few frames) during each of the three key states. Anyone know how to do this? I know you can add behaviors during particular frames, but I don't know how to make it pause. Thanks! --Charles

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Using Chimera to look at confocal data
by Thomas Burgoyne 04 May '11

04 May '11

Hi, I've been using Chimera for a few years now to look at electron tomography data and I have to say I think the software is absolutely superb. Recently I have started looking at 3D-confocal data and I discovered with a bit of work I can open the data using chimera. I open each colour channel as a separate image stack which works quite nicely. The only problem I encounter is when viewing the data using solid rendering only one channel is visible. Is there a way to view three image stacks at the same time using the solid rendering? Thanks, Tom

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partial failure in addH BUG?
by Francesco Pietra 04 May '11

04 May '11

Hello: i had partial failure in addH to a natural product. H at a quaternary, chiral C was not added in spite of repeated attempts. All Hs were added by my favorite drawer (for organic compounds); however, this changes the coordinates, which is not what I want. I solved the issue by transferring the chimera pdb output to vmd, adding the missing H with Molefacture. On the other hand, Molefacture, if asked to add all Hs, resulted in incorrect stereochemistry at -O-CH3 and some -C-CH3 (inverted umbrella, which could not be reversed). francesco pietra

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building large size polymer
by 윤홍민 02 May '11

02 May '11

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kindly help
by preetam nayak 02 May '11

02 May '11

Respected sir, I am using chimera for the first time.I just want to ask that after successfully removing all clashes/contacts in my pdb file using commandline arguement selectively,I am unable to save this modified pdb file even after trying many a times.Everytime I am saving my pdb file after modifications,the changes are not at all saved and again when I am opening the pdb file ,it is showing the same clashes/contacts.Sir,please help by providing the required steps as to how to save the changes one has made in the pdb file.

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Information request
by Francesco Burresi 30 Apr '11

30 Apr '11

Hi, I've docked a ligand with a receptor and I get a pdb with1 chain (chain A) I'd like to separate recpetor-ligand in two different chians (chain A e chain B). How can I do that in Chimera? regards

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Information request
by elisa carli 28 Apr '11

28 Apr '11

Hi, I'm trying to model a TM protein using a Fugue approach. This method involves to divide a transmembrane protein in fragment (Nter, TM1,LOOP1and so on) Each fragments is predicted separatly. I'd like to assembly and join fragment, superimposing the backbone of a fragment with that of the correspondent segment in the structure of my protein. How can I achieve this goal with Chimera? regards

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Re: [Chimera-users] Chimera: Myosin thick filament movie
by Tom Goddard 28 Apr '11

28 Apr '11

Hi Rogelio, The myosin thick filament movie in the Chimera animation gallery was made in 2006 using a 700 line python program I wrote. Fortunately Chimera animation capabilities are much better now, so I've made a Chimera command script that makes the same movie in Chimera 1.5.2 (Jan 2011), about 150 commands. I've attached the script. It of course requires the myosin data files to work. So I've put the script and data files in myomovie.zip and put a link to that in the animation gallery with the myosin animation (will appear after web site is rebuilt tonight). http://www.cgl.ucsf.edu/chimera/animations/animations.html To create the movie you open the myomovie.py Chimera session then open the myomovie.cmd command script. Rendering this movie takes about 15 minutes (for about 70 seconds of final video, 1760 frames) using the high quality supersample 3 option set in the script. The myosin movie is somewhat complex. There are about a half dozen simpler movie making command scripts with links on the animation gallery page. We don't have a separate movie scripts web page, although that is a nice idea. There is a movie making tutorial on the Chimera tutorials page http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html and there are details about all the commands in the Chimera User's Guide http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html Tom > Hi Tom, > > I have been recently looking at the animation gallery of Chimera and I > was wondering if I could get a copy of the script used to make the > Myosin movie, > Do you guys have a repository of scripts used for the displayed movies? > > I am working with a helical map and I would like to try to implement a > similar animation for my maps, > > thanks a lot for your help and consideration > > ROGELIO > > > -- > Rogelio A. Hernandez Lopez > Leschziner Lab > Harvard University > 305.G NWB > 52 Oxford Street, Room 305 > Cambridge, MA 02138 > > http://www.mcb.harvard.edu/Leschziner/

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Information request
by elisa carli 28 Apr '11

28 Apr '11

Hi, I'm working with a pdb file, that have two atoms in an ARG residue , not allowed by Charm H Polar force fields Is it possible to fix the problem with Chimera? Residues: ARG 251 1HH1 ARG 251 2HH2 Regards

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how to write log file in Chimera
by Rogelio A. Hernandez-Lopez 27 Apr '11

27 Apr '11

Hi, Is there any way to create a log file to store all the actions performed by the user during a chimera session, either using the menus or command line? I want to write a script for a movie and it would be very useful to copy and paste commands from such as file thanks, ROGELIO -- Rogelio A. Hernandez Lopez Leschziner Lab Harvard University 305.G NWB 52 Oxford Street, Room 305 Cambridge, MA 02138 rhernand(a)fas.harvard.edu (617)-872-5399 http://www.mcb.harvard.edu/Leschziner/

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trying to add charges
by Irene Newhouse 27 Apr '11

27 Apr '11

I'd like to do a PDB2PQR run of my protein with its 'ligands' - actually substrates & am having problems getting the server to recognize my mol2 file. So I thought I'd use chimera to add charges & write, hopefully, a compatible mol2 file. I'm having problems with that as well. This is a pdb of the ligands:HETATM 8225 MG MG A 291 25.874 25.146 58.617 1.00 0.00 Mg2+ HETATM 8226 C4 FPS A 292 25.754 19.949 62.737 1.00 0.00 C HETATM 8227 C3 FPS A 292 26.088 21.273 63.475 1.00 0.00 C HETATM 8228 C2 FPS A 292 26.021 22.571 63.132 1.00 0.00 C HETATM 8229 C1 FPS A 292 25.656 23.447 61.998 1.00 0.00 C HETATM 8230 S1 FPS A 292 27.204 24.181 62.219 1.00 0.00 S HETATM 8231 P1 FPS A 292 27.928 23.762 60.771 1.00 0.00 P HETATM 8232 O1 FPS A 292 28.873 24.955 60.385 1.00 0.00 O HETATM 8233 P2 FPS A 292 28.554 26.180 59.405 1.00 0.00 P HETATM 8234 O2 FPS A 292 28.206 25.713 57.968 1.00 0.00 O HETATM 8235 O3 FPS A 292 27.331 26.943 59.830 1.00 0.00 O HETATM 8236 O4 FPS A 292 29.622 27.136 59.149 1.00 0.00 O HETATM 8237 O5 FPS A 292 26.862 23.528 59.683 1.00 0.00 O HETATM 8238 O6 FPS A 292 28.976 22.661 61.190 1.00 0.00 O HETATM 8239 C5 FPS A 292 26.754 21.192 64.778 1.00 0.00 C HETATM 8240 C6 FPS A 292 26.118 20.990 66.155 1.00 0.00 C HETATM 8241 C7 FPS A 292 27.084 20.015 66.840 1.00 0.00 C HETATM 8242 C8 FPS A 292 28.144 20.342 67.618 1.00 0.00 C HETATM 8243 C9 FPS A 292 28.586 21.777 67.991 1.00 0.00 C HETATM 8244 C10 FPS A 292 28.618 19.212 68.506 1.00 0.00 C HETATM 8245 C11 FPS A 292 27.622 19.162 69.634 1.00 0.00 C HETATM 8246 C12 FPS A 292 27.899 18.054 70.615 1.00 0.00 C HETATM 8247 C13 FPS A 292 28.127 18.187 71.942 1.00 0.00 C HETATM 8248 C14 FPS A 292 28.131 19.492 72.723 1.00 0.00 C HETATM 8249 C15 FPS A 292 28.358 16.835 72.549 1.00 0.00 C HETATM 8250 H4 FPS A 292 24.677 19.881 62.580 1.00 0.00 H HETATM 8251 H5 FPS A 292 26.263 19.931 61.773 1.00 0.00 H HETATM 8252 H1 FPS A 292 25.472 22.838 61.113 1.00 0.00 H HETATM 8253 H11 FPS A 292 24.694 24.092 62.300 1.00 0.00 H HETATM 8254 H14 FPS A 292 28.310 18.659 67.618 1.00 0.00 H HETATM 8255 H15 FPS A 292 29.626 18.910 68.790 1.00 0.00 H HETATM 8256 H141 FPS A 292 28.344 19.287 73.772 1.00 0.00 H HETATM 8257 H142 FPS A 292 28.897 20.155 72.320 1.00 0.00 H HETATM 8258 H143 FPS A 292 27.155 19.970 72.638 1.00 0.00 H HETATM 8259 H91 FPS A 292 29.470 21.732 68.628 1.00 0.00 H HETATM 8260 H92 FPS A 292 28.821 22.333 67.083 1.00 0.00 H HETATM 8261 H93 FPS A 292 27.779 22.279 68.525 1.00 0.00 H HETATM 8262 H7 FPS A 292 26.852 18.977 66.652 1.00 0.00 H HETATM 8263 H61 FPS A 292 26.054 21.948 66.670 1.00 0.00 H HETATM 8264 H62 FPS A 292 25.117 20.575 66.036 1.00 0.00 H HETATM 8265 H51 FPS A 292 27.451 20.354 64.779 1.00 0.00 H HETATM 8266 H52 FPS A 292 27.298 22.117 64.967 1.00 0.00 H HETATM 8267 H4 FPS A 292 26.087 19.103 63.338 1.00 0.00 H HETATM 8268 H12 FPS A 292 27.905 17.074 70.162 1.00 0.00 H HETATM 8269 H151 FPS A 292 28.547 16.946 73.646 1.00 0.00 H HETATM 8270 H152 FPS A 292 27.455 16.195 72.388 1.00 0.00 H HETATM 8271 H153 FPS A 292 29.246 16.355 72.064 1.00 0.00 H HETATM 8272 H111 FPS A 292 27.646 20.103 70.183 1.00 0.00 H HETATM 8273 H112 FPS A 292 26.622 19.003 69.230 1.00 0.00 H HETATM 8274 H2 FPS A 292 26.305 23.333 63.843 1.00 0.00 H HETATM 8348 O3 IPE A 586 21.257 22.023 59.139 1.00 0.00 O HETATM 8349 C1 IPE A 586 21.725 22.610 60.331 1.00 0.00 C HETATM 8350 C2 IPE A 586 21.891 21.539 61.401 1.00 0.00 C HETATM 8351 C3 IPE A 586 22.135 21.746 62.732 1.00 0.00 C HETATM 8352 C4 IPE A 586 22.476 23.125 63.351 1.00 0.00 C HETATM 8353 C5 IPE A 586 22.090 20.534 63.651 1.00 0.00 C HETATM 8354 P1 IPE A 586 22.541 22.279 58.101 1.00 0.00 P HETATM 8355 O1 IPE A 586 23.289 23.718 58.505 1.00 0.00 O HETATM 8356 O2 IPE A 586 23.635 21.031 58.224 1.00 0.00 O HETATM 8357 O7 IPE A 586 21.980 22.381 56.596 1.00 0.00 O HETATM 8358 P2 IPE A 586 22.517 20.944 55.933 1.00 0.00 P HETATM 8359 O4 IPE A 586 24.120 21.122 55.494 1.00 0.00 O HETATM 8360 O5 IPE A 586 22.398 19.740 57.082 1.00 0.00 O HETATM 8361 O6 IPE A 586 21.597 20.552 54.601 1.00 0.00 O HETATM 8362 H6 IPE A 586 20.970 20.939 61.359 1.00 0.00 H HETATM 8363 H7 IPE A 586 22.711 20.896 61.047 1.00 0.00 H HETATM 8364 H4 IPE A 586 22.660 23.213 64.432 1.00 0.00 H HETATM 8365 H5 IPE A 586 22.534 24.017 62.710 1.00 0.00 H HETATM 8366 H1 IPE A 586 21.090 20.076 63.606 1.00 0.00 H HETATM 8367 H2 IPE A 586 22.843 19.801 63.329 1.00 0.00 H HETATM 8368 H3 IPE A 586 22.303 20.848 64.684 1.00 0.00 H HETATM 8369 H11 IPE A 586 22.687 23.089 60.148 1.00 0.00 H HETATM 8370 H12 IPE A 586 21.008 23.356 60.675 1.00 0.00 H END When I try to add charges, chimera chews on it for a bit, then gives me a message that amber has stopped running, check the log file. When I click on the log file, the only message is that I've had a crash. In the older version of chimera I was running, I also tried this with only the IPE & got the same behavior. Are my compounds just too nonstandard? Thanks! Irene Newhouse

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3D labels
by matheus froeyen 26 Apr '11

26 Apr '11

Dear all, I try to change the size of the 3D labels in my structure via the preferences/background menu but there is no effect! Strange but changing the font type & bold, italic etc works. I tried a previous version of chimera and there I have the same problem. The font is always small (about 12?) The 2D labels I can change font size without problem. But I know it has worked before. I have no idea what is going on. I work on A Macintosh G5 with Leopard. Thanks for any suggestions mathy

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labels
by Jean-Paul Armache 26 Apr '11

26 Apr '11

hello, i was wondering, whether there is a way to make the 2d labels appear slowly, stepwise (meaning, through some rounds of opacity to the normal text) ? best regards, jean-paul

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how to make simmetric dimer
by Francesco Biagi 26 Apr '11

26 Apr '11

Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results.I would like to know if there is a method or a script that can help me. Thanks to all.Francesco

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PDB reference frame
by Roberto Kopke Salinas 25 Apr '11

25 Apr '11

Dear All, Is there a way to draw and visualize the three axes of the PDB reference frame in Chimera? Thank you for your help, Roberto

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Re: [Chimera-users] Changing charge of protein
by Elaine Meng 22 Apr '11

22 Apr '11

Dear Monisha, If you get a Chimera daily build (version 1.6, whereas you probably have 1.5), there will be AddH options for all those residue types I mentioned. The options in AddH are for the side chains. The N-terminus of the backbone will already get a +1 charge, and the C-terminus -1. If the backbone N is not the N-terminus, it is in an amide group and will not be formally charged. However... There is a limit as to what total charge is reasonable for a given protein sequence. If you just arbitrarily increase positive charges everywhere to try to reach some value (why??), it will become less representative of reality. Another approach you might consider if you are trying to make your "system" more neutral is to add counterions (see Tools... Structure Editing... Add Ions). 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 22, 2011, at 11:47 AM, Monisha Hajra wrote: > Dear Elaine, > > Thank you for your reply. > > However I find in AddH option, its only Histidine specific, what should I do if I want to alter specific protonation state of Lys, Arg. > > Also, read from the link that you had send is that > "lysine positive or neutral > • charges for the neutral LYN residue are assigned if the atom named NZ has atom type N3 and thus two attached hydrogens rather than three" > Is that mean that I can't create +2 charge for Lys, by adding another H to N (which is attached to alpha C)? > > I tried even by command line " addh #0: 34@N", its showing error, though chain #0: 34@N is showing the N atom. > > Kindly provide some solution. Right now charge of my protein is -22, I have to bring it up to +10. Really appreciate on general comment of yours on how do do that? > > Regards > Monisha > > On Fri, Apr 22, 2011 at 9:38 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Dear Monisha, > The charge of the protein is the sum of the charges of its residues, but charges are not saved in PDB format. > > Maybe you mean you want to control the protonation state and thus the formal charges of certain residues (for example, specifying which histidines should be positive and which should be neutral)? That can be done when you are adding hydrogens. In the AddH tool (under Tools... Structure Editing) there is "Protonation states for" setting for controlling protonation states of histidine, glutamic acid, aspartic acid, lysine, and cysteine residues. You would have to decide yourself which residues should be in which states. You could indicate that by editing the input PDB file to contain special residue names, or just choose "specified individually" for it to go through and ask you about each one. Details: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> > > Then, you could save the PDB file including the hydrogens using "File... Save PDB" in the Chimera menu. > > Charges are a somewhat separate matter, and are not saved in PDB files. There would not be any charge assignments until after you used Add Charge (under Tools... Structure Editing). Then, you could see the atom and residue charges in histograms in Render by Attribute, or save them to a file using that tool. If you really meant you wanted to assign specific charges to specific atoms yourself, you could do that with Define Attribute or the command setattr. You can label atoms with their charges as described here > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharg…> > but we don't have that for whole residues. > > 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 22, 2011, at 5:20 AM, Monisha Hajra wrote: > > > Dear User, > > Is there any way to increase or decrease total charge of the protein in Chimera? Can I see the residue wise (not atom wise) charge and modify, and should be able to save the modified protein in pdb. Trying to look to add charge / "render by attribute" section, but didn't get much help. > > Any help will really be appreciated. > > Regards > > Monisha > >

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Why sym # group h did't work
by Fang, Shunming (NIH/NIDDK) [C] 22 Apr '11

22 Apr '11

Hello, There, I tried several time to use the commend sym #1(or 2,3..), group h, 11.75, 101.32 to my em map, it always show errors saying unknown keyword 11.75, 101.32? Please help me, Thanks Shunming

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Changing charge of protein
by Monisha Hajra 22 Apr '11

22 Apr '11

Dear User, Is there any way to increase or decrease total charge of the protein in Chimera? Can I see the residue wise (not atom wise) charge and modify, and should be able to save the modified protein in pdb. Trying to look to add charge / "render by attribute" section, but didn't get much help. Any help will really be appreciated. Regards Monisha

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Command line
by Ryan Doherty 21 Apr '11

21 Apr '11

I searched the online documents and was unable to find out how to perform certain actions via the command line. Can you let me know how to perform the following commands via the command line: Color secondary structure (and set color for Helix, Strand & Coil) Create a text file with a summary of attributes (ie. # of ions, # of ligands, # of chains, areaSAS for each selected residue) Color surface based on hydrophobicity Thanks! Ryan

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help with command line selections
by Corey Fugate 21 Apr '11

21 Apr '11

I'm having a hard time figuring out how to select secondary structural elements from the command line. Can someone help me with this? Corey

2 2

Command line
by Ryan Doherty 20 Apr '11

20 Apr '11

I searched the online documents and was unable to find out how to perform certain actions via the command line. Can you let me know how to perform the following commands via the command line: Color secondary structure (and set color for Helix, Strand & Coil) Create a text file with a summary of attributes (ie. # of ions, # of ligands, # of chains, areaSAS for each selected residue) Color surface based on hydrophobicity Thanks! Ryan

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dock prep error in chimera
by Daron Standley 20 Apr '11

20 Apr '11

Hi- I just submitted the following bug report to chimera. Sorry if this is a redundant report, but I thought perhaps an experienced chimera user could identify my problem, since I am new to using this tool. I am trying to prepare a ligand for docking. I want to prepare the 4 ribonucleotide monophosphates AMP, GMP, UMP, and CMP. First, I tried extracting these from the Zinc database, but I kept getting related but not quite correct molecules. So, I then tried preparing the molecules in Chimera. My procedure was: 1. Chop up an RNA molecule from the PDB (e.g., 2xnz.pdb) into 'residues' (that is, a single ribonucleotide monophosphate) using a simple perl script. 2. Optional step 2 (I tried both with and without this step): add an oxygen fromt the previous residue to the phosphate and name it ' OP3'. 3. Save each molecule as an individual pdb file (e.g., 2xnz-G-1.pdb for the first GMP) 4. Read one of the newly created pdb files into chimera 5. run Tools->Structure Editing-> AddH In either case (with or without step 2) I get the error below. I have attached both pdb files (bug.zip) for reference. ####################### Error Log ####################### Error in ':ALA': underlying C++ Selectable object is missing Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 346, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 564, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/AddH/gui.py", line 265, in Apply hisScheme=hisScheme, okCB=self.cb) File "/Applications/Chimera.app/Contents/Resources/share/AddH/unknownsGUI.py", line 272, in initiateAddHyd okCB() File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 194, in <lambda> cb=lambda pap=_postAddPrep, mols=mols, kw=kw: pap(mols, **kw)) File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 259, in _postAddPrep method=method, cb=lambda ur, uc, m=mols, kw=kw: File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 117, in initiateAddCharges chargeModel=chargeModel, nogui=nogui, showCharges=labelStandard) File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 199, in addStandardCharges for r in m.residues: ValueError: underlying C++ Molecule object is missing ValueError: underlying C++ Molecule object is missing File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 199, in addStandardCharges for r in m.residues: See reply log for Python traceback. ####################### End Error Log ####################### Best regards, Daron

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animation
by Jean-Paul Armache 20 Apr '11

20 Apr '11

hello, i would like to ask a question about animation. i would like to achieve the following: 1. i have 3 different volumes, so when i put them next to each other, i would like to have each of them to rotate around it's own axis. an additional feature would be to start the rotation of each of the volume at a different point of time. 2. i would like to make certain parts of pdb appear slowly, either through change of colors from transparency or nucleotide/aminoacid at a time. 3. i would like the colors of a specific volume/pdb to "pulsate", meaning to start up with color nr 1, through 2 or 3 different colors to color nr 2. at the present moment i don't really know how to do those, would you have any hints ? thank you best regards, JP Armache

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trajectories for movie making
by Justin Pahara 20 Apr '11

20 Apr '11

Hello All, I am interested in learning how to write and implement code that defines a pathway through a molecular model in chimera (I want to make movies this way rather than moving and rendering frame by frame through the scene. I'm far more biochemist than computer scientist, so I'm hoping to find material that will allow me to learn from the basics. Q's that I have: 1)how do I define a trajectory start point and end point in the chimeraff 3D viewing space 2)how do I define movement and/or velocity through the 3D space (how do I find define particular reference points in 3D space using chimera) 3)how do I define the incremental steps in in the trajectory (so I can achieve high frame rate or low frame rate videos) 4)can I use the utility function to make a movie/export pov files of the pathway? I greatly appreciate all suggestions! thanks, Justin.

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measure volume for protein subsections
by Anke Mulder 19 Apr '11

19 Apr '11

Hi, I have used segger to divide my reconstruction into protein monomers, and I know how to measure the volume and other attributes of the protein monomer, however, I would like to be able to measure subsections of the monomer so that I can have an idea of what the volume of protein is that, for example, is buried in the lipid bilayer, etc. I thought that I could use clipping planes to do this, but from what I can tell the volume measurement still takes into account the volume of the entire protein. Thanks so much. Anke M.

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Adjust angle
by Thomas Mitterfellner 19 Apr '11

19 Apr '11

Hello! My question is: it possible not just to measure but to change the angle between three atoms (e.g. A1 and A2 fixed, A3 rotated in the plane spanned by A1-A2-A3 with radius A2-A3)? What I really like in Chimera (and miss in other molecular modelling software) is the possibility to move/rotate only the atoms selected, which is great e.g. for pre-aligning two molecular fragments when modelling transition states. I know chimera is actually rather intended to be used for large molecules but it could be a great tool for modifying/building structures if only it was easier to modify structural parameters like bond lengths, angles and torsions (which I saw is possible). Kind regards, Thomas Mitterfellner

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Re: [Chimera-users] Alteration of C-terminal AA-sequence within an X-ray model data set with Chimera
by Elaine Meng 14 Apr '11

14 Apr '11

Dear Heinrich, I can think of a couple possibilities. First you would open the structure and the density map. Opening the density map will automatically start Volume Viewer, in which you can adjust the display type (surface, mesh, etc.) and contour level by moving the slider on the histogram. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum…> Then... (A) you could select those 30 residues, then use "Movement Mouse Mode" (under Tools... Movement) "move selection" option to manually reposition them. However, that would not automatically fit the residues to density, it would just let you rotate and translate them as a rigid body yourself with the mouse, which can be difficult if you are trying to dock into density. The selecting could be done in several ways, such as by command (e.g. "select #0:356-end.a" to select model 0 chain A residues 356 to the end) or interactively in the Sequence tool (under Favorites in the menu). After the movement you could save the modified structure with "File... Save PDB" in the Chimera menu or the "write" command, and you would probably want to save "relative to" the map model. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> (B) you could make those 30 residues a separate model and then automatically fit them as a rigid whole into the density using "Fit in Map" (under Tools... Volume Data). You would delete the rest of the structure, for example with command "delete ~#0:356-end.a" to delete all atoms EXCEPT model 0 residues 356-end in chain A. Next, using the mouse, manually move it to an approximate position relative to the map. You can freeze the map and move only the structure by un-checking the "Active" box for the map model below the Command Line or in the Model Panel (both tools are under Favorites in the menu). Then use Fit in Map, which will perform a local optimization. You may want to run it a few times to see if the result improves. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht…> Saving a whole model is less convenient than in (A). You would need to open another copy of the structure, delete the opposite part (e.g. command "delete #0:356-end.a") and probably also fit that one into the density. You could either save both as PDB relative to the map model and then manually combine them into one PDB file, or in Chimera merge the models (see command "combine" or the "copy/combine" function in the Model Panel), possibly add the bond if you need it (see command "bond" or the Build Structure tool) and then save the PDB of the combined model relative to the map model. Even if method (B) is not too long for you, I can think of two problems: (1) It is not flexible fitting. Each part is treated as a rigid body, and you have to decide yourself how to split a structure into parts. (2) The parts do not "see" each other, there is nothing to stop them from bumping into each other or even going to the same place in the density map. In the Chimera daily builds, we have recently added a tool that addresses this problem: MultiFit (under Tools... Volume Data) will perform simultaneous fitting of multiple rigid structures. However, it currently assumes overall Cn (cyclic) symmetry, so it cannot be applied to your problem. We hope to have it working for structures without cyclic symmetry soon, but that is not yet available. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multifit/multifit.…> 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 14, 2011, at 2:01 AM, Heinrich Lünsdorf wrote: > Dear Elaine, > here I'm again to ask for your constructive help on another item. My question: Is it possible with Chimera functions and commands to pick up and activate an AA-sequence, i.e. the last 30 C-terminal AAs, and to 'move' or 'bend' them in parts or as a whole but without changing or moving the rest of the X-ray model to get the C-terminal AA-tail fit along with an overlaid EM-density model?? Can such alterations be stored for the original X-ray model? > Thank you cordially for your help in advance. > Sincerely yours, > Heinrich

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rebuild DNA
by Damien Larivière 14 Apr '11

14 Apr '11

Dear all, Here is a PDB file of a DNA portion. It contains only the atoms of the backbone chain trace. Is there a way to rebuild the remaining parts (sugar,...)? Many thanks for your help Damien

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Problem for docking result analysis
by Bishwajit Das 12 Apr '11

12 Apr '11

Hi, I load a docking results in .pdb format,now how can i view inter-molecular bonding information with chimera. please help me. -- * BISHWAJIT DAS*** KOLKATA

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Merging of two pdb files
by Monisha Hajra 11 Apr '11

11 Apr '11

Hi, I have modeled one protein. I have pdb file of the protein. I want to merge the protein with one co-factor (I have the pdb file for the same). Can I merge them in one file using Chimera? If not, then any other tool can you suggest? Regards Monisha

2 1

NMR average structure
by Lucio Ferella 11 Apr '11

11 Apr '11

Hi all, I need to calculate an average structure (or select the most representative member of), from an NMR emsemble structures in Chimera. Is it possible? Thanks for any helps. Lucio

3 2

recording path through centroid
by Francesco Pietra 11 Apr '11

11 Apr '11

Hello: Is it anything new about recording path by the way of the centroid? I did not use it since September 2000. It worked nicely, though -being at illustrations for a candidate publication - my question is whether it has been improved further. thanks francesco pietra

2 2

Hydrophoic and Hydrophilic solvent accessible surface area
by Monisha Hajra 09 Apr '11

09 Apr '11

Hi Team, Can I calculate Hydrophoic and Hydrophilic solvent accessible surface area in Chimera? If so, let me know how? Really appreciate help. Regards Monisha

2 1

Labeling 3D structures in Chimera (and saving them as such)
by Bilal Asif 08 Apr '11

08 Apr '11

Hello, I am a senior undergraduate student at Stony Brook University, part of a team currently attempting to design an introductory biology lab for biology undergraduates. We are attempting to use Chimera as a way to introduce students to structural biology and research. However, we have run into a problem, one which we hope you can help us solve. We have discovered that if one attaches a label to a molecule in Chimera, one cannot save it as a .pdb, and open it again with the same labels attached. Is there a way to preserve labels attached to 3D structures, perhaps by saving it in a different file format? Thank you for your time and consideration. Any insight would be greatly appreciated. Bilal Asif Stony Brook University

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problems in chimera display
by manidip_rs＠iicb.res.in 08 Apr '11

08 Apr '11

  I have downloaded and installed chimera-1.5.3-linux_x86_64.bin, release date April 05,2011.  But after opening a volume data the volume is appearing as random slices.  I have checked all the other necessary requirements. I am using RHEL 5.4 and NVIDIA graphics.  Please suggest.                                                                                                                                                                                                      Thanks,                                                                                                                                                               Manidip Shasmal, Research Fellow,                                                                                                                                                               Indian Institute of Chemical Biology, kolkata -700032 Do not Remove: [HID]20110408124249826[-HID] **************************************************** VirusFree, Spamfree, power packed email service. ****************************************************

2 1

Controling the configuration of chiral atoms.
by vincent zoete 07 Apr '11

07 Apr '11

Dear Chimera team, We are very satisfied daily users of Chimera for drug design and protein engineering applications in our lab. Congratulations for your great work! I would like to come back on the point raised by Dr. Charbel MAROUN recently. Having the possibility to change the configuration of whatever chiral atom would be very useful for drug design applications. It's true that we can do it using other software like Pymol or HyperChem, to cite just two of them arbitrarily. But it would be much more convenient to rapidly and graphically do it in Chimera, without the need to switch to another program for that particular and single action. We are often working with D-amino acids and chiral small molecules. We apreciate a lot the "Build Structure" module to construct or modifiy such compounds, and allowing more control on the chiral center configuration would be very useful. Do you think you could consider adding such chirality inversion command in the future? Sincerely, Vincent Zoete, Molecular Modeling group - SIB www.click2drug.org =========================================================== Hello, Sorry, Chimera does not do that. I am pretty sure that SYBYL and probably some other programs will do it, but you may want to ask on a more general list such as CCL.net for a more certain and detailed answer about other programs. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 28, 2011, at 6:15 AM, R. Charbel Maroun wrote: > Hi everybody, > Is there an easy and quick way to invert the chirality of an atom, say a Ca ? > Greetings, > ----------------------------------------- > R. Charbel MAROUN, Ph.D., H.D.R.

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