- Chimera-users - RBVI Mailing Lists

structure matching
by Bala subramanian 04 Mar '09

04 Mar '09

Hello all, 1) I have to superimpose two protein structures based on sequence matching say prot1 and prot2. Precisely matchmaker. My prot1 is a cryo electron microscopy structure, the structure is not continuous, it has missing residues and hence its pdb contains 3 Chains. My prot2 is a crystal structure, having one chain. I need your suggestion in superimposing these two structure wherever the sequences are matching. What i tried: I opened pro1 pdb and changed all chain names as A ( it contains chain A,B,C). Then i tried to superimpose with prot2, but matchmaker doesn work. 2) when i open molecules one by one, i need all the molecules appear in the center of the chimera window. How to set this in chimera. After opening the first pdb, when i open the second one, it is invisible. Thanks, Bala

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matchmaker output
by Karan Uppal 03 Mar '09

03 Mar '09

Hello, I want to simplify the question I asked yesterday. Is there any way to store the output of Match Maker, specifically the RMSD values for every residue and the list of residues in the alignment regions in an external file from command line? Thank you -Karan

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Web Access Data
by Thiruvarangan Ramaraj 03 Mar '09

03 Mar '09

Hello All, I created a session and saved it under .chimerax extension. I have a link to this session on a web page. When I click on this link I wanted the session to open directly using the chimera program. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… I tried to follow the instructions given in the above link, still I am unsuccessful in figuring it out. Any suggestions/ideas would be greatly appreciated. Thank You Thiru

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save image with --nogui
by Mark Moll 03 Mar '09

03 Mar '09

I'd like to load some pdb files, change the view/colors/representation/ etc., and save the resulting view as an image. If possible, I'd like to do this in the background without the GUI. This doesn't seem to work. The latest daily build gives the errors below when using this simple script: import Midas Midas.copy(file='test.png', format='PNG', width=600, height=400) Should I be using a different command? > /Applications/Chimera.app/Contents/MacOS/chimera --nogui foo.pdb test.py Opening foo.pdb... Executing test.py...Rendering high resolution image... Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/ __main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/chimeraInit.py", line 420, in init chimera.openModels.open(a, prefixableType=1) File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/chimera/__init__.py", line 1368, in open File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/chimera/__init__.py", line 802, in _openPython File "test.py", line 10, in <module> Midas.copy(file='test.png', format='PNG', width=600, height=400) File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/Midas/__init__.py", line 1049, in copy File "/var/tmp/chimeraBuild_AGL/build/install/Chimera.app/Contents/ Resources/share/chimera/printer.py", line 1176, in saveImage AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' Error while processing test.py: AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' (see reply log for Python traceback info) -- Mark

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Saving MultAlign Viewer header information using python
by Karan Uppal 02 Mar '09

02 Mar '09

Hello, I am trying to write a Python script to extract the header information from the MultAlign Viewer tool. Are there any command-line commands to interface with this tool and save the header information without manually using the toolbar. Thank you -Karan Uppal

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finding salt bridges
by Elaine Meng 28 Feb '09

28 Feb '09

> Hi everybody, I just realized my previous suggestion would not include the positively charged histidines, and I have not been able to think of a selector for just those nitrogens. > Example commands to first select by atom type and then find the H- > bonds: > > sel O2- | O3- | N3+ | Ng+ > findhbond selRestrict both saveFile ~/mydir/myfile Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Reverse of AddH
by Francesco Pietra 27 Feb '09

27 Feb '09

Hi: Is it possible to remove all hydrogens by command, without intervening manually on the pdb file? I have to rmsd the starting (no H) pdb with the final structure after MD (with H). AddH command to the starting structure would place H not optimized, while MD has also changed the C-backbone conformation. Thanks francesco pietra

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solvent accessible area
by Bala subramanian 27 Feb '09

27 Feb '09

chimerians, I want to calculate the solvent accessible surface area for each atom and write it in the pdb file, kindly tell me how to do it. This is something i used to do with GRASP. it calculates the sasa for each atom and it can be written as a pdb file with sasa in the last column. Thanks, hve nice weekend Bala

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solvent accessible area
by Boaz Shaanan 27 Feb '09

27 Feb '09

Hi Bala, The program areaimol in the ccp4 package will do just that (i.e. generate a pdb file with the sasa value in the b-factor column). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Multiscale model of RNAP : fibrous aspect
by Damien Larivière 27 Feb '09

27 Feb '09

Dear Elaine, I used the Multiscale Model tool to create a low resolution surface of the PDB 1L9U (TAQ RNA polymerase). The attached image is what I got with a resolution 4 : a fibrous structure. So, I wonder what such a fibrous aspect means or whether it means the tool has some difficulties to create the surface with this specific protein ? Thanks for your help Damien

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How to refer to Chimera in a Newsletter
by Gary Newton 26 Feb '09

26 Feb '09

Hello... I am writing a newsletter for the SER-CAT synchrotron beamlines sector 22 at APS - the newsletter is called the "SER-CAT Spectrum" and is distributed primarily to beamline users. I have included a simple protein drawing produced by CHIMERA and indicated that the drawing was produced by CHIMERA. Should I include a trademark symbol or perhaps a copyright symbol after the name? Thanks for any advice. Best, Gary Newton University of Georgia Athens, GA

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searching chimera archieve
by Bala subramanian 26 Feb '09

26 Feb '09

Dear Elaine, Long time back, I posted a question on *searching chimera archive for a keyword*. Just for an example, i gave "salt bridge" as a key word in the following link, but it dose nt show me the queries on salt bridge in chimera archive. I dnt undertand why ?. It would helpful for chimera loves like me not to repeat same queries and also to understand all ways of analyzing salt bridge based on previous queries. I am sorry if this question is not relevant to chimera technical issues. http://www.cgl.ucsf.edu/chimera/docs/feedback.html Cheers, Bala

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how to quickly delete several markers
by Juha Huiskonen 26 Feb '09

26 Feb '09

Dear Chimera developers & users, I am visualizing template matching results of volume data in Chimera, and I have to discard hundreds of false positives matches, represented as markers. Now I select some markers and then delete the selected markers from the Volume Path Tracer menu. This is quite slow, and for me it would be really handy, if I could delete (all linked) markers just by clicking (one of them) them. Maybe "delete markers with mouse" feature could be added to Volume Path Tracer module? Or is there already a faster way to do this? Thanks a lot in advance for your suggestions! Juha -- Dr. Juha Huiskonen Max Planck Institute of Biochemistry Department of Molecular Structural Biology Am Klopferspitz 18 D-82152 Martinsried Germany Tel: +49 89 8578-2632 Fax: +49 89 8578-2641 GSM: +49 176 20786875 E-mail: huiskone(a)biochem.mpg.de http://www.helsinki.fi/~huiskone/

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angles after match
by julien(GWDG) 25 Feb '09

25 Feb '09

Dear all, thank you for the very nice software. I continuously like it. I have the following problem. For different molecules, I would like to know what are the transformation that link them. I can do for example match #0 #1 matrixget - From this matrix I have the rotation information and the translation information. I would like to extract the angles. For that I need to know what convention you used. I guess those are Euler angles (?), but I need to know what is the order of rotation xyz, xzy... Finally how do you get ride of the gimbal lock problem if you use Euler angles. Thank you for your constant help. (Sorry if this question is a duplicate) many greetings julien

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slab representation of nucleic acid
by Bala subramanian 25 Feb '09

25 Feb '09

The slab representation of nucleic acid under Depiction is not working. I made the following settings *show backbone as* atoms/bonds, *show sugar as* atoms/bonds, *show base* as slab. But the representation is not displayed on the screen. What could be the reason. I myself have used it before and i am not aware why this happens now. Regards, Bala

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finding salt bridges
by Elaine Meng 24 Feb '09

24 Feb '09

On Feb 24, 2009, at 1:51 PM, Jeremy Schmit wrote: > Does Chimera have a tool for identifying salt bridges? I was able > to use the findHbond tool to count intermolecular H-bonds in the > lysozyme crystal, but I can't seem to find an analogous tool for > salt bridges. In fact, the term "salt bridge" does not yield a > single result on the Chimera site. > Thanks, > Jeremy Hi Jeremy, There isn't a tool for specifically finding salt bridges, but you can consider them as a subset of hydrogen bonds. You could select only atoms in charged functional groups and then limit H-bond detection to that selection. Example commands to first select by atom type and then find the H-bonds: sel O2- | O3- | N3+ | Ng+ findhbond selRestrict both saveFile ~/mydir/myfile If the subunits of interest are different chains in the same model (same input file), you could then postprocess the output (for example, with "grep" on unix) to count only those between the chains. If each subunit is opened as a different model, you could add "intramodel false" to the findhbond command. There are analogous options on the FindHBond graphical interface: "Only find H-bonds with both ends selected" and find just the "inter-model" bonds. findhbond command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> findhbond GUI: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon… > atom types: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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copy in a file the distance on the screen
by fabriceg＠univ-reunion.fr 24 Feb '09

24 Feb '09

Dear Users, When analyzing a trajectory file, I would like to monitor a distance (or series of distances) and save it to a file for each frame (getting a time series). I can do it but the values remain on the screen only! I am sure there is a simple script for making this. Thanks for any answer. Best wishes. Fabriceg

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Sequence vs Sequence plot using minrms....
by Sergio Garay 24 Feb '09

24 Feb '09

Hi all I run minrms with defaults values on my two proteins and I was able to obtain many useful alignments. But when I load the results on chimera, it doesn´t show me the sequence vs sequence plot. Is there any particular way to do that? Or there is any special minrms command (option) to obtain this? All the other plot were right (rms vs sequece and the alignment plot). Any help will be appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Match -> Align used with a pair of homodimers
by E. Merkley 24 Feb '09

24 Feb '09

Hello chimera friends: I am trying to get a structure-based sequence alignment for a pair of homologous proteins that are homodimers. If I proceed as described in the tutorial and in the 2006 BMC Bioinformatics paper, by first using Matchmaker, then using Match -> align, the Match -> Align fails to produce a reasonable alignment. The sequence identity from the Matchmaker output is 26.5%, but only 1.0 % from the Match -> Align step. If I delete the second monomer from each protein, Match -> Align works quite well. However, it seems like this alignment won't take into account any differences in the tertiary structure between the two proteins. That is, I think I want the global alignment of the whole dimer for the structural alignment, since the active sites is are at the interface. Any suggestions? I'm using version 1.2540, and my two proteins are PDB codes 1ds7 and 1nox (1nox dimer built from BIOMT matrix in Chimera and hand-edited to be 1 model with A and B chains). Thanks yet again, Eric

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Fwd: stereo view
by Francesco Pietra 24 Feb '09

24 Feb '09

It was a bad idea. What Jason initially suggested (save left-eye and right-eye) should work. What I have to manipulate images is only gimp, with which I am not very familiar. But it seems to have the capability of arranging the two saved files so as to get a stereo effect. There is even a (unofficial) plugin to remove unwanted space around. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Tue, Feb 24, 2009 at 9:31 AM Subject: Re: [Chimera-users] stereo view To: Elaine Meng <meng(a)cgl.ucsf.edu> Hi Elaine: That makes problems as the referee just wants a stereo view of details of the binding site, which requires magnifying the figure. Is it any way to save a pdb file of the magnified zone alone? (to start from there to build a stereoview). Of course, the normal pdb saving of a magnified figure saves the coordinates for the whole. The only way I can conceive to get the coordinates of the binding site, and nothing else, is manually deleting rows from the pdb file. A tricky route because the chains start and return to the starting point and the binding site is on both strands. thanks francesco On Tue, Feb 24, 2009 at 1:27 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > I guess you could also save separate left eye and right eye images and put > them farther apart. That might also mess up the stereo effect, though. > Elaine > > On Feb 23, 2009, at 4:26 PM, Elaine Meng wrote: > >> Hi Francesco, >> There is a certain separation needed or else your eyes cannot form the >> stereo image. You could try zooming out so the atoms don't take up the >> whole window, or adjusting parameters in the Camera tool (under Tools -> >> Viewing Controls) but I usually don't mess with those camera parameters >> because you could disrupt the stereo viewing if you change them very much. >> Elaine >> >> >> On Feb 23, 2009, at 3:06 PM, Francesco Pietra wrote: >> >>> Hi Elaine: >>> Is it any direct way to save stereoimages from magnified images? By >>> the normal route, the wall-eye couple of images are saved adjacent to >>> one another, with no space in between them. >>> >>> thanks >>> francesco >>> >>> On Tue, Feb 17, 2009 at 1:43 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> Hi Francesco, >>>> All of Jason's suggestions are good (thanks Jason!), and I only wanted >>>> to >>>> add a few things: >>>> >>>> (1) while the window will always be a rectangle, you could resize it so >>>> that >>>> there is a different ratio between height and width. If your long >>>> molecule >>>> is oriented across, you could resize the window to be less tall so that >>>> the >>>> width:height ratio is greater. Don't worry if the window is then >>>> filling >>>> less of your screen -- you can specify as high a resolution as you want >>>> in >>>> the File... Save Image dialog. Of course, with a given window size, you >>>> should scale up your molecule(s) to fill it as much as possible. In >>>> agreement with Jason, I think usually a white background is better than >>>> black for publication purposes. How to change background color is >>>> described >>>> near the top of the "Tips on Preparing Images": >>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> >>>> >>>> (2) There is a section on saving stereo images near the bottom of that >>>> "Tips >>>> on Preparing Images" page (by the way, you can use "Help... Search >>>> Documentation" to look for help topics such as "stereo image"). I think >>>> journals usually show the "wall-eye" type of stereo, which can be >>>> achieved >>>> by saving one image in the wall-eye stereo mode, or by saving separate >>>> left >>>> and right views and placing them side by side with the left-eye view on >>>> the >>>> left and the right-eye view on the right. >>>> >>>> (3) just show the surface, adjust clipping and depth-cueing as Jason >>>> suggested, and use your artistic and scientific judgement as to whether >>>> it >>>> improves your image! There are additional suggestions for improving >>>> surface >>>> appearance in the "Tips on Preparing Images" page. >>>> >>>> Best, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >>>> UCSF Computer Graphics Lab and Babbitt Lab >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> http://www.cgl.ucsf.edu/home/meng/index.html >>>> >>>> >>>> >>>> On Feb 16, 2009, at 2:04 PM, odonnell(a)chem.fsu.edu wrote: >>>> >>>>> Hi Francesco, >>>>> A couple of cents before the professionals respond with (very >>>>> likely) better ideas: >>>>> >>>>> In response to 1) Black is best for contrast but uses a lot of ink and >>>>> money. >>>>> White should be fine. >>>>> >>>>> n response to 2) If you go to TOOLS=>VIEWING CONTROLS=>CAMERA, you can >>>>> select various camera modes. CROSS-EYE stereo will put your chimera >>>>> graphic into cross-eye stereo. You can save an image as it is >>>>> displayed on the screen. But i find saving two images, stereo left eye >>>>> and stereo right eye better. Place these side by side in another >>>>> graphic program, (e.g Adobe illustrator) and voila, stereo viewing. >>>>> With two single images you can switch them around to alternate between >>>>> wall-eye and cross-eye. Also, with two images its easier to make the >>>>> distance between them a certain length, as journals are usually >>>>> stringent about how the stereo images are displayed. >>>>> >>>>> In response to 3)I'd to go TOOLS=>VIEWING CONTROLS=> SIDE VIEW and >>>>> slide the back and front yellow planes. This will create a slab >>>>> through your object removing other structural elements which might >>>>> complicate the image. Also, >>>>> try DEPTH CUEING under TOOLS=>VIEWING CONTROLS=> EFFECTS. tweak the >>>>> "start ratio and yon intensity to further remove emphasis on unwanted >>>>> objects. The Depth effects can make some really neat graphics >>>>> >>>>> Hope this helps. >>>>> >>>>> -Jason >>>>> >>>>> Quoting Francesco Pietra <chiendarret(a)gmail.com>: >>>>> >>>>>> Hi: >>>>>> >>>>>> I would greatly appreciate advice about the following requests >>>>>> (between "".."") by the referees (interaction between two proteins; >>>>>> graphics by chimera): >>>>>> >>>>>> 1) "there is way too much wasted black space in figures". >>>>>> >>>>>> As the complex of proteins is elongated along one axis, I found it >>>>>> unavoidable to have wasted space around. Perhaps using a white >>>>>> background in the hope that white is less offending than black? Or is >>>>>> it a way to tailor the background according to the shape of the >>>>>> object? >>>>>> >>>>>> 2) "a stereoview might be helpful for better understanding". >>>>>> >>>>>> How to fulfill this request with chimera I have no idea. >>>>>> >>>>>> 3) "a molecular surface representation of the docking site would be >>>>>> useful". >>>>>> >>>>>> I read on passing about molecular surfaces on this forum. Is that >>>>>> feasible for the highly complex situation of 3D perspective with so >>>>>> many atoms at different "layers"? >>>> >>>> >> > >

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Letter Reference for Amino Acid Atoms
by Sarah Himes 23 Feb '09

23 Feb '09

Hi, My name is Sarah Himes. I'm a graduate student at the University of Maryland. I'm researching alkaline phosphatase for an advanced course. I'm using the file 1ALK in Chimera. I'm pretty familiar with Chimera but I had a question regarding the letter notation of amino acid atoms when you scroll over them. Here are some examples: His370 (NE2) Ser102 (CB) Ser102 (N) Asp327 (OD1) Asp327 (OD2) Glu322 (OE2) My question is, what do the letters in parentheses mean, what do they correspond to? When these letters show up in Chimera, there are no parentheses. I look forward to hearing from you shortly. Thank you for your time. Sincerely, Sarah Himes shimes(a)umd.edu 240-285-1251

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drawing parallelepiped
by Elaine Meng 23 Feb '09

23 Feb '09

On Feb 23, 2009, at 3:31 AM, Francesco Pietra wrote: > > For mono view figures, I wonder whether Chimera allows enclosing the > model in a parallelepiped. This would confer a sense of depth to a > very complex model (a complex of two proteins, partly in a lipidic > membrane. Hi Francesco, There are a few different possibilities: (a) make a PDB file with "atoms" at the corners and the desired bonds (described in CONECT lines), show as wire or stick. The Crystal Contacts tool uses that trick, but is unlikely to generate what you want in this case. You could try creating it interactively with markers and links using Volume Tracer, but probably just creating a PDB file in a text editor would be easier. (b) make a file in BILD format describing the parallelpiped outlines -- requires similar information as the above: coordinates of points at the corners and which points should be connected <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> both (a) and (b) require you to figure out coordinates for the corners yourself... (c) a devious but easy way if you don't mind a rectangular box (all angles 90 degrees) is to use the "molmap" command to create a density map from the displayed atoms, but hide that map's contour surface and just show the box around it. For example, use the command: molmap @/display 2 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> Then in the Volume Viewer dialog that appears, choose "Features... Data display options" and turn on "Show outline box" and also choose "File... Remove Surface." In that dialog you can also specify the color and linewidth of the outline. For conveying depth, you can also try adjusting the clipping planes in the Side View. If you put the back one closer to the atoms, the depth cueing "fog" will be more obvious. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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coloring the clipped surface
by Elaine Meng 22 Feb '09

22 Feb '09

On Feb 22, 2009, at 4:48 PM, Harinathachari Bahudhanapati wrote: > Dear Elaine, > Chimera is getting more exciting to work with than > ever. I think you guys are the best in the field. > About per-model clipping... > > When I tried, I was not able to find how to color the clipped plane > based on atom B-factors? I was able to give a color (single color) > only > but not based on atom B-factors or other attributes like SAS, SES, > electropotential. > I am not sure if modeled PDB files still have B-factor details. I saw > an image on the chimera website on the feature highlights (B-factor > coloring) and I wondered if I can get few more details on this > feature. > I am trying to make a few pictures for my paper. > Thank you elaine, > sincerely, > Hari > Dear Hari, Thanks for your kind words! Yes, there is a trick to coloring planar surface caps by B-factor or some other attribute, as in that figure: <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> First, color the atoms by the attribute (Tools... Depiction... Render by Attribute), which would also color the actual molecular surface but not the planar cap where it is clipped. Then, select the atoms and use Color Zone (also under Tools... Depiction) to color the planar cap to match the nearby atoms. Render by Attribute: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render> Color Zone: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/ colorzone.html> I've been wanting to write a tutorial on how to make that figure, but haven't had the time! I also increased the "mesh subdivision factor" in the Surface Capping dialog to 3. Coloring by electrostatic potential is different than coloring by an atom attribute. To color the planar cap by electrostatic potential, you would use Electrostatic Surface Coloring, but it requires a potential map previously created with some other program such as DelPhi. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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multiple coloring
by Anindito Sen 19 Feb '09

19 Feb '09

Dear All Please share with me as how to put multiple color to several pdb structures docked in a density map. Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Re: [Chimera-users] defining a putative binding site
by Elaine Meng 18 Feb '09

18 Feb '09

Hi Francesco, If you want detailed information about which atoms contact which, and the distances between them, use the "Find Clashes/Contacts" tool, or its command version "findclash", as discussed in several previous posts: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003260.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/ 003163.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/ 003183.html> There are links in those posts to the manual pages and a tutorial with an example. Some of those discussions were about finding contacts for a ligand, but the findclash feature is general and can be used on whatever set of atoms/residues you want. Again, you can save results to a file or write them to the Reply Log. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 18, 2009, at 10:55 AM, Francesco Pietra wrote: > Hi Elaine: > > By doing as indicate in your and my post, only residues (45 residues) > for model 0 (the bigger protein) are listed. Then I also commanded: > > sel #1:1701-1793 & 0:20,30-40,55 z<5 > > i.e., inverting the order of the two models. That gave a list of > residues (18 residues) for only model 1 (the smaller protein). > > Probably all that is useful information. But, is any way (one touch, > as above) to get information about which-to-which? > > I am not too lazy, I am prepared on the basis of the above two > listings, to use the zone command residue per residue, should this be > the way. > > (the numbers for the above residues are just for a split example; > actually I set all residues - even for areas that I knoe are not > involved - in the zone command for both proteins) > > Thanks > francesco >

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defining a putative binding site
by Francesco Pietra 18 Feb '09

18 Feb '09

Hi: I need to define a putative binding site for a smaller protein upon a larger one. The task is creating a table of likely interactions between residues of the larger proteinseparated by less than 5 A from those of the smaller protein. Deriving from molecular dynamics, all residues for both proteins are in the same pdb file, alongside lipid, water, etc. I wonder whether the most appropriate way is to separate in two different pdb files the lines belonging to the two different proteins. Then: sel #0:20,30-40,55 & #1:1701-1793 z<5 where "0" is the larger and "1" is the smaller protein. If OK, can the results be obtained in a table form? Thanks francesco pietra

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Re: [Chimera-users] color changes
by Elaine Meng 17 Feb '09

17 Feb '09

On Feb 17, 2009, at 1:15 PM, Jean-Paul Armache wrote: > hello, > i have one question concerning color manipulation in chimera. > every pdb file one opens gets a specific color (if set so). so, > having a few of them open, one can distinguish > between them color-wise. > now, when one selects the files, it is possible to change the color > via actions->color. this indeed changes all > of the things selected, and if the whole pdb was selected, all the > chains there. when one looks then into the > model panel, the old colors are still there - untouched. this would > be reasonable in the case when only parts > of the pdb were selected and re-colored. however if one selects > whole files and changes the colors - is it > possible to have these colors changed also in the model panel? and > is it possible to revert to the old color > once changed through this action menu? > > best regards, > jean-paul armache Hi Jean-Paul, It is because there is a coloring hierarchy: the Model Panel shows the model color, but you can also set atom colors, whichoverrule and hide the model color. As you found, Actions... Color and the "color" command set the atom colors (otherwise you would not be able to make different parts of the same model different colors). If you already colored the atoms of a model, you can "uncolor" some or all of them to reveal the model color using the command "~color". Another way is to choose "Actions... Color... from editor" and then click the "No Color" button in the Color Editor. (The Color Editor can be found in the menu under Tools... Utilities) You can change the model color with the command "modelcolor" or by clicking on the square color wells in the Model Panel to call up the Color Editor. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/coloring.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/hierarchy.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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surface view of large file in chimera
by G.-Q. Hu 17 Feb '09

17 Feb '09

Hello, I am trying to show a large file by surface view in chimera. But I found that the structure lost the detail and the surface was smoothed. I guess there is a sampling problem for large file. Is there any way to view the large file at the original resolution? Thanks. Guiqing

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Volume->Fit in Map question
by Keren Lasker 17 Feb '09

17 Feb '09

hello, Is there a way to fit a density map to a pdb rather than a pdb to a density map ? Or in other words, that in the end of the fitting procedure the map would move to best fit the model rather than the other way around. thank you, Keren Lasker.

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configuration file for chimera
by Bala subramanian 17 Feb '09

17 Feb '09

Dear chimerians, Sorry if this question has been asked before. Where can i fix the default parameters for chimera. I explored the preferences option in favourites menu and set chose some preferences. In addition to that I want to the following like setting the color of carbon atoms as green as default setting the color of hydrogen atoms as white as default setting some macros setting the command line option when the chimera starts up (every time i go to favourites and click command line to invoke it) and other settings something like the configuration file used for vmd (.vmdrc ). Thanks in advance, Bala

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stereo view
by Francesco Pietra 16 Feb '09

16 Feb '09

Hi: I would greatly appreciate advice about the following requests (between "".."") by the referees (interaction between two proteins; graphics by chimera): 1) "there is way too much wasted black space in figures". As the complex of proteins is elongated along one axis, I found it unavoidable to have wasted space around. Perhaps using a white background in the hope that white is less offending than black? Or is it a way to tailor the background according to the shape of the object? 2) "a stereoview might be helpful for better understanding". How to fulfill this request with chimera I have no idea. 3) "a molecular surface representation of the docking site would be useful". I read on passing about molecular surfaces on this forum. Is that feasible for the highly complex situation of 3D perspective with so many atoms at different "layers"? Thanks indeed for answering francesco pietra

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Consurf .chimerax file under linux
by Boaz Shaanan 16 Feb '09

16 Feb '09

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Re: [Chimera-users] Chimera 3D labels
by Elaine Meng 16 Feb '09

16 Feb '09

On Feb 16, 2009, at 6:53 AM, nettles wrote: > > Dear Elaine, > I'm thinking this should be possible, but don't know how to do it. > Can the labeling function in Chimera could be made more spacially > flexible? > > An example is below. The residue label coordinates are anchored to > a fixed 3D point that may, or may not be desirable for a given > view. Can this be adjusted? > > It looks like these references may be set at centroids. Maybe one > could have a toggle switch that sets the anchor projected a certain > distance from a C-alpha along the viewing vector. That might give > quick access unified text float-over > > Thanks again for such a great tool. > Jim [attachment removed by Elaine] Dear Jim, I am frequently irked by the same issue. Currently residue labels are anchored at the centroid of the displayed atoms, whereas sometimes it would look better if they were anchored at the alpha- carbon. I've previously created a bug report about this. Longer term we would also like them to be movable with the mouse, but that also can't be done currently. Here is the bug/request tracking info: http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/6866 http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/167 One current workaround is that you can label some particular atom in the residue with residue information. However, currently that atom must be explicitly displayed (won't work to label some backbone atom if ribbon is shown and suppresses that atom... which I've also complained about!). Commands to do that: labelopt info residue la @ca [or if ribbon is shown, "la @cb" instead if you can live without the glycine residue labels] I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Animating a C-alpha chain trace
by Tom Goddard 13 Feb '09

13 Feb '09

Hi Matt, A Python script can make a chain trace movie with density display that adds one residue at a time. I've attached an example script and movie. I used the today's Chimera daily build that has a nice 1-layer transparency option. That won't work in earlier Chimera versions. Tom Matthew Dougherty wrote: > Hi Tom, > > Over the last couple years I have moved my animation off the > SGI/IrisExplorer to Chimera/Amira. > > I have one piece of code on Explorer that I have not moved; attached > is a typical animation. > > what is being accomplished is a demonstration of the folding of a > protein based on c-alpha backbone and related density. > starting at the first residue, it proceeds by adding one residue at a > time. > > How would you suggest to move this to chimera? > > Matt > > > > > > > > > > > > > > > # ----------------------------------------------------------------------------- # Trace C-alpha backbone adding one residue at a time and show simulated map. # pdb_path = '/usr/local/src/staff/goddard/pdb/pdb1fav.ent' resolution = 5.0 # Simulated density resolution, Angstroms map_color = (.6,.7,.8,.3) # red,green,blue,opacity. from chimera import runCommand # Open model from chimera import openModels as om m = om.open(pdb_path, 'PDB')[0] # Orient molecule runCommand('turn y 90') runCommand('turn x 30') # Color molecule and background runCommand('rainbow') runCommand('set bg_color white') # Create residue number label runCommand('2dlabel create rlab xpos 0.1 ypos 0.9') # Set display style. runCommand('repr stick #%d' % m.id) m.stickScale = 5.0 # Fatter sticks # Order residues by number and chain id. rlist = m.residues rlist.sort(key = lambda r: (r.id.position, r.id.chainId)) # Hide all atoms. for a in m.atoms: a.display = False # Show density adding one residue at a time. from MoleculeMap import molecule_map atoms = [] map = None for r in rlist: # Accumulate atoms from residue. atoms.extend(r.atoms) # Close previous map. if map: om.close([map]) # Make map. map = molecule_map(atoms, resolution, gridSpacing = .2*resolution, showDialog = False) map.set_parameters(surface_colors = [map_color], one_transparent_layer = True) map.show() # Display backbone atoms. for a in r.atoms: if a.name == 'CA': a.display = True # Update residue label text = 'chain %s residue %d' % (r.id.chainId, r.id.position) if r.isHelix: text += ' helix' elif r.isSheet: text += ' sheet' runCommand('2dlabel change rlab text "%s" color black' % text) # Draw one frame. runCommand('wait 1')

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Re: [Chimera-users] Command Line - Slecting Zone Parameters
by Elaine Meng 11 Feb '09

11 Feb '09

On Feb 11, 2009, at 2:54 PM, Thiruvarangan Ramaraj wrote: > Hi all, > I am trying to find all the atoms that lie within a certain > distance from a selected chains. I am able to do this by going to > select -> zone and giving the distance I want and selecting all the > atoms that met my criteria. I would like to do this on command > line. I am unable to figure it out. > Any help would be greatly appreciated. > Thank You > Thiru Ramaraj Hi Thiru, The following command would select all residues with any atom within 4.5 angstroms of your current selection: select sel z<4.5 You could use "za" instead of "z" if you want an atom-based cutoff instead of whole residues, > instead of < to get the atoms farther away, and of course, a different distance. Also, you don't have to use selections. For example, this would color all atoms within 5 angstroms of chain A red: color red :.a za<5 Description of command-line zone specification: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ atom_spec.html#zones> More examples appear in various tutorials: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ attributes.html#part2> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ squalene.html#surfaces> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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maps handling
by Benoit Zuber 11 Feb '09

11 Feb '09

Hi, I want to handle a large number of small density maps (around 1000 maps of approx 50x50x50 pixels). I need to group them (in around 5 groups). Then I need to treat all the maps of each group in a certain way. For example, I would like to change the level threshold for display, or the display style for every maps in a group at once. Also I would like to show or hide all maps of a group at once. The maps are not opened in an order related to their group. I remember someone recently suggested model 'folders' as a new functionality. Has this been incorporated in the latest versions of chimera? Even if it is the case, It would be too tedious to have to click on each individual model to assign it to a group. Similarly a simple command passed at the command line wouldn't be very elegant: I would have to write each volume number since they are unsorted. I suppose a python script would be much more appropriate. The script would have some functions to do tasks like those described above on each members of a group and a function to read group composition from a text file. I looked in chimera's programmer guide for a section on volume handling but I couldn't find much material on that. Did I miss it? What approach would you recommend? I guess I could use runCommand() but there are maybe better ways. Also the script would have to run in interactive mode. I suppose that IDLE would work for that purpose. How should I do that? Open IDLE and import my module? Where can you define the paths that chimera uses to look for packages? Thanks in advance! Ben -- Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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examples of python scripts
by Bala subramanian 11 Feb '09

11 Feb '09

Dear Chimerians, Can someone help me by providing examples of python scripts written for analyzing structures inside chimera. I have seen the chimera programmers guide but i need some more scripts written for different tasks to understand the way of accessing certain residues or atoms in a structure and extracting its attributes etc. Cheers, Bala

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making movies with CMM files
by Keren Lasker 06 Feb '09

06 Feb '09

hello, Is there a way to generate a movie out of a set of CMM files ( similar to MD Movie with PDB files)? thank you very much, Keren.

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Re: [Chimera-users] [chimera-dev] alias menu
by Eric Pettersen 05 Feb '09

05 Feb '09

On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote: > Dear Chimera Developers, > > Perhaps I have missed it, but I would find a menu for selected > aliases very useful. Having returned to Chimera from PyMol recently, > it would be great to have an option for the alias command that > allowed the particular alias to be listed in a separate window and > ran the alias by clicking on the alias name listed there. > > Best regards, > > Tim Hi Tim, As Elaine pointed out in her reply, aliases are frequently used as shorthands for long atom specs rather than as replacements for complete commands. However, the form of the alias command that uses '^' (so that matching only occurs at the start of the line) typically is used to define full command aliases. So my thinking is this: aliases defined with the '^' character would be placed in an 'Aliases' top-level menu (created on the fly as needed). Such aliases would automatically be remembered across Chimera invocations (and populate an Aliases menu). The menu could be torn-off (except on Aqua) to make a stand-alone window. Those aliases could be deleted as normal with the ~alias command (which would remove them from the menu and no longer remember then in subsequent Chimeras). Would this be good enough? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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script command for writing out areaSAS attribute?
by Julius Su 05 Feb '09

05 Feb '09

Hello, Does anyone know what script command could be used to output an "attribute assignment file" in Chimera, specifically for the areaSAS attribute? I am trying to show how the solvent accessible surface area on various residues changes over the frames of a multitrajectory PDB file. To do this I am trying to write a small script in "MD movie" that computes the solvent accessible surface for each frame, then outputs the areaSAS values. I was previously able to do this by loading in all the PDB geometries at once, then using the "Render attributes by ..." dialog, but this method does not scale well to very large proteins (the program runs out of memory trying to compute all the surfaces at once). Thus I am trying to do this task sequentially with a script. Thanks much! Julius

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Is it possible?
by Ahir Utsav Pushpanath 04 Feb '09

04 Feb '09

Hello Dear Sir/Madam, I am very fond of chimera, and everytime I have looked at scripts for doign things, I find that chimera has them already inbuilt as features. There is one particular problem that I am sure chimera has the capability of doing but I am struggling to do it. 1) I want to use structural superposition servers such as Mammoth etc to produce a structural alignment of two proteins, 2nadA and 1ybaB. However, some of these servers do not produce a sequence alignment output in a format compatible with chimera (i.e such as .aln or aligned fasta). But they do produce a .pdb file showing the superposition. 2) If I load the .pdb onto chimera, sometimes in "model list" window, i see the two proteins, wheras in others I only see 1 model(yet there is clearly 2 models there) 3) I was wondering whether you can load the superposition onto chimera, and see the sequence alignment that gives rise to that structural superposition, so that I may save it as a .aln format using multialign viewer. How do I do this? Apologies if this is a very straightforward scenario. Thanks Ahir

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roll command:
by Bui Khanh Huy 01 Feb '09

01 Feb '09

Dear all, I tried the roll command with my model (EM map) open: roll z 30 1 center 50,50,50 Chimera showed msg "wait_frames argument not implemented". Just wonder how to implement that command without the error? Huy

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Calc buried surface area between 2 chains
by Tom Duncan 30 Jan '09

30 Jan '09

I saw an earlier post (Dec. 29, 2008; Digest vol. 68, issue 28) in which Elaine Meng described a procedure for calculating surface area for selected atoms. I did this for atoms on chain A that were selected as contacting atoms on neighboring chain B, but the sum(atom.areaSES) probably includes area buried within the chain A, not just between the 2 chains. I tried checking this by calculating the sum(atom.areaSES) for chain A (all atoms in A) in the whole model, then again for a model from which chain B was deleted before calculating the surface. However, the results indicated a larger areaSES for chain A in the absence of chain B! There were some errors reported in calculating the surfaces; perhaps this contributed. Is there a better way to calculate the buried surface on 1 chain due to contacts with a 2nd chain? Thanks, Tom Duncan

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error message
by Katherine Parra 28 Jan '09

28 Jan '09

Hello! I'm trying to get the hydrogen bonds between some selected residues during a trajectory, using per frame commands from tools. But when I get the possible hydrogen bonds formed between the selected residues I also get the following error message in the Reply Log: *Skipping possible acceptor with bad geometry: #0:2108@O Wrong number of grandchild atoms for phi/psi acceptor #0:2108@O *What could be happening? Thank you in advance. KP

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color zone on command line
by Giulia Zanetti 28 Jan '09

28 Jan '09

Hi all, I would like to make a movie in which areas of my map are coloured while the surface is rotating. Any idea how to use color zone from the command line? thanks Giulia

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fit in map output : coordinate representation of axis, axis point
by Hwang, Youngha,Ph.D. 27 Jan '09

27 Jan '09

Hi, could anyone explain to me what axis points mean in chimera? What unit is used for them? Is it related to the volume dimension? Is the rotation matrix based on Euler-angle representation? Thanks, Youngha. 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.

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3D on Chimera.
by ayassin＠wadsworth.org 27 Jan '09

27 Jan '09

Hello, I am trying to use Chimera to model pdb files into EM maps. When I select the red cyan stereo, the EM map is stereo but the pdb structure is not. -Is there anyway to display pdb in stereo in Chimera, how? -Is there another program that would allow me to do the same thing: fit pdb in EM density map-in stereo(other than "O")? -When I use Chimera on windows VISTA the side view panel does not appear and a message about graphic card appear, anyway to solve this? Thank you all very much. Aymen Yassin. Postdoc Research Affiliate Wadsworth Center, Albany,NY. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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marker coordinates
by Gabor Papai 27 Jan '09

27 Jan '09

Hi, I would like to do the following: I placed markers on density spots. I want to get their coordinates and excise a box around the marked density and save it as a separate file. For this I would like to know how I can retrieve the coordinates of a marker set and possibly how to position exactly a box around a marker to set a subregion (and of course how to set the dimensions of that box). This second feature existed before, but disappeared in the latest releases with the subregion selection tool in the Volume Viewer. Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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Volume information
by vamsee 26 Jan '09

26 Jan '09

Hello All, I am working on a virus and I am trying to figure out its volume. I would want to find out the volume of the nucleic acid and the water inside the virus capsid. That way, if I am thinking right, that should give me the total internal volume of the virus. This volume would be a constant even with the movement of water in and out. Is it possible to use chimera to calculate any of such data, with no prior information about how the nucleic acid is packed inside? Thanks in advance, Vamsee Graduate Student Dept of Chemistry and Biochemistry Montana State University Bozeman, MT - 59715

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suggested feature/model panel
by Matthew Dougherty 26 Jan '09

26 Jan '09

1) ability to create folders in the model panel so models can be grouped 2) ability to have a model in multiple folders 3) ability to show/hide in a folder by a a single checkbox 4) ability to name the folder

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