- Chimera-users - RBVI Mailing Lists

hello !every one!
by gytjyb 27 Dec '09

27 Dec '09

can i load a file about force field into chimera. if it is ture,i could chose other force field in chimera! how can i do? i just come from china and am poor in english and knowledge. thank for you help!

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hello!every one!
by gytjyb 27 Dec '09

27 Dec '09

can i load a file about into chimera how can i do? i just come from china and am poor in english and knowledge

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perframe script
by Bala subramanian 23 Dec '09

23 Dec '09

Friends, I loaded a amber trajectory in chimera. I simply want to calculate the distance between two atom in each frame in the traj. and write it to a text file. I used the per-frame utility in MD movie tool. I chose interpret script as 'chimera commands' substitute text 001-200 (frame 1 to 200) In the script section i gave distance :163@CA :166@CA It reports to me the following in the reply log. Distance between GLY 163 CA and ARG 166 CA: 5.083 Problem in per-frame script: Distance monitor already exists Problem in per-frame script: Distance monitor already exists Problem in per-frame script: Distance monitor already exists How should i actually use the perframe option so that the analysis will be done in each frame and reported output file will hve the distance values for every frame. Thanks, Bala

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Grouping models
by Tom Goddard 23 Dec '09

23 Dec '09

-------- Original Message -------- From: Thomas C. Marlovits To: Tom Goddard Date: 9/22/09 2:04 AM > HI Tom, > > I was wondering, whether one can "group" a few models in chimera. At > the moment, I have more than 40 models open simultaneously, some of > which I would like to group in order to make coloring, selection, etc > ... more easily. It might be that the feature is present, but > couldn't spot it so far. > The other thing that I would appreciate, if there is a simple way to > assign the model nr manually (at the moment it is done automatically, > and it appears that the order is somewhat random ...) > Best, > Tx, > -T. > Hi Thomas, You can used "named selections" to give a short name to several models or to any combination of selected items. Use menu entry Select / Name Selection... You can use the names in Chimera commands or use the "Select / Named Selection / name" menu entry. I don't know of a command to name a selection. Is there such a command (other Chimera developers)? You can set the model number if you open your models with a command, for example, open 5 twisty.pdb to open a model as model number 5. After the model number has been assigned it unfortunately cannot be changed. Tom

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Grouping of bonds/atoms
by Dipl.-Ing. Thomas Mitterfellner 23 Dec '09

23 Dec '09

Hello! I'd like to group a certain set of bonds (or atoms), so that I can select them quickly without having to select each item manually every time I decide to change a property like size, style or color. I know that selecting a pseudobond and pressing the UP key selects all pseudobonds. Is it possible to do that for a user-defined subset of bonds too? Thank you, Thomas P.S.: Merry Christmas to the Chimera team!

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Linewidth in images
by Dipl.-Ing. Thomas Mitterfellner 22 Dec '09

22 Dec '09

Hello! I am making large images (4096x3072) which use silhouette edges and dashed wire-style bonds. When I increase the width of the silhouette edges, I do see that on the screen, but the output image turns out the same regardless of this setting. The same is true for my dashed bonds. Is this some issue of graphics card (GeForce 6200) or am I missing something? Thank you, Thomas

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selecting zone, minimizing, docking
by Elaine Meng 22 Dec '09

22 Dec '09

On Dec 21, 2009, at 11:30 PM, gytjyb wrote: > hello,Mr meng ! > I have 3 questions. > <1> > I select one residues or animo acid > But how can I made a radius around this residues or animo acid, > I aslo can select neighbor residues or animo acid within some radius. > <2> > If I should add water for model minization and refine, > how can I refine for a new model. > I want to do a mutation,wether I must fix other residues when I do > minization. > <3> > how can I prepare for a docking, dose this software do docking? > thank you for your answer! Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly) and include something meaningful in the "Subject" line. Also, you can use "Help... Search Documentation" in the Chimera menu to look up information by keyword. (1) menu "Select... Zone." You can also specify zones in commands. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones > (2) That is up to your own scientific judgement. As mentioned in an earlier reply, the minimization capabilities in Chimera are rather limited. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… > (3) Chimera does not do docking calculations. You can move two structures together by hand... of course that is only approximate. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html> However, Chimera does have tools that are related to docking: "Dock Prep" for preparing structures for docking or other calculations (with other programs outside of Chimera) and "ViewDock" for looking at docking results output by other programs, mainly DOCK. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.… > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h… > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> Here is the Web site for DOCK. <http://dock.compbio.ucsf.edu/index.html> They also have tutorials: <http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm> 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

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identifying residues in a surface
by Elaine Meng 22 Dec '09

22 Dec '09

On Dec 21, 2009, at 5:14 PM, gytjyb wrote: > hello:meng! > thank you for your help! > i want to make a surface about protein. > i want to do lipophilicity and electrostatics surface,we had better > label some amino acid on the surface,how can i do? > or i just use differrent color for different amino acid category. > i think the color must be very different from each. > so i can recognize each other,and find out some important different > between homology protein. > thank you very much! > Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly) and include a short description in the "Subject" line. You can show lipophilicity on the surface with menu item "Presets... Interactive 3 (hydrophobicity surface)" where orange is most lipophilic and blue is most hydrophilic. You can show Coulombic electrostatic potential on the surface with "Tools... Surface/Binding Analysis... Coulombic Surface Coloring" The regular labels are not that good when you are showing a surface. They are usually partly inside the surface so you can't read them. If it is for a figure, you can put labels anywhere you want with "2D Labels" (under Tools... Utilities), but those do not move when you rotate the structure. Also, there are pop-ups that say what is under your mouse, but they only show the detailed information when you are not showing the surface. Sometimes I like to use color-coding, a different color for each amino acid type. Of course, you can't have that as the same time as the lipophilicity or electrostatic coloring. There is a command file (rescol.com) linked to the User's Guide that does my favorite residue color-coding: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile > You would save that file to your computer as plain text and just open it (file named *.com) in Chimera to apply the residue color-coding. 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

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Re: [Chimera-users] hide dashed lines
by Elaine Meng 21 Dec '09

21 Dec '09

Hi Vijay, There are a few ways to hide these "missing segments" pseudobonds. Method 1: Ctrl-click to select one of the dashed lines, click magnifying glass on lower right corner of Chimera window to open Selection Inspector, Inspect "Pseudobond group," change "displayed" to "false" Method 2: open PseudoBond Panel (under Tools... General Controls), choose "missing segments" from the left side and click "hide" on the right side Method 3: "setattr" command, e.g.: setattr g display false but that turns off all pseudobonds, not just missing segment. You could also use the setattr command to only undisplay certain pseudobonds but that would require selecting or naming the endpoint atoms in the command, so if you want to retain other pseudobonds the first two methods will be easier. 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 Dec 21, 2009, at 10:52 AM, Vijay S. Reddy wrote: > Hello, If the there is break in the structure, it is shown by dahsed > lines in the Chimera, How can I hide them or turn them off. I am > deliberately trying to show different regions that are not > sequentially contiguous. Thanks very much, > Vijay

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center of molecule
by Bala subramanian 18 Dec '09

18 Dec '09

Friends, Is is possible to find the central x,y,z coordinates of a pdb file in chimera. Bala

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[Chimera] #7448: show axes/major ellipses for thermal ellipsoids
by Dipl.-Ing. Thomas Mitterfellner 18 Dec '09

18 Dec '09

Hello! > #7448: show axes/major ellipses for thermal ellipsoids Thanks for the implementation of this feature! There's just one thing: the major ellipses are displayed very thinly. The ellipse size factor does not seem to change the size of the ellipses (I supposed them to become larger than the ellipsoid with increased scaling factor so that they extend beyond the surface). Can the thickness or the size of the major ellipses be altered? Thomas

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price quote for chimera software
by Yong You 18 Dec '09

18 Dec '09

Dear Sir,/ Madam, I am emailing to inquire about a single user/computer license for the Chimera software for Molecular Modeling. Can I get the price quotes for using it in Windows 32-bit OS (Windows XP) and in Linux 64-bit OS? Thanks a lot! Sincerely, Yong You Integrated DNA Technologies, Inc. 1710 Commercial Park, Coralville, IA 52241 (319) 626 -9606

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single-component calculation
by Bala subramanian 17 Dec '09

17 Dec '09

Friends, When i try to show the surface sometimes, i get a chimera warning that ' calculation of some surface components failed, falling back to single component calculation'. The message in reply log is as follows. Kindly enlighten me on what is causing the problem. Calculation of some surface components failed. Falling back to single-component calculation. /home/cbala/chimera/bin/mscalc 1.400000 2.000000 0 MSMSLIB 1.3 started on RAMANA Copyright M.F. Sanner (March 2000) Compilation flags WARNING: check_SES_edge: weird case, 1 probe full1 and not full2 WARNING: class_arete2: warning hole in a reentrant face 2119 WARNING: classe_aretes2: No cycle in face 3781 (nba=-6) WARNING: classe_aretes2: No cycle in face 11830 (nba=-4) WARNING: classe_aretes2: No cycle in face 19652 (nba=4) WARNING: classe_aretes2: No cycle in face 19653 (nba=-1) WARNING: classe_aretes2: No cycle in face 19663 (nba=-3) RESTART FROM SES: 1 radius of atom 1220 goes from 1.625000 to 1.725000 radius of atom 1221 goes from 1.000000 to 1.100000 radius of atom 1665 goes from 1.700000 to 1.800000 radius of atom 1666 goes from 1.000000 to 1.100000 radius of atom 3490 goes from 1.500000 to 1.600000 radius of atom 3618 goes from 1.000000 to 1.100000 radius of atom 3620 goes from 1.500000 to 1.600000 radius of atom 3621 goes from 1.000000 to 1.100000 radius of atom 5103 goes from 1.625000 to 1.725000 radius of atom 5106 goes from 1.000000 to 1.100000 Partial mode WARNING: class_arete2: warning hole in a reentrant face 2119 RESTART FROM TRI: 2 radius of atom 470 goes from 1.700000 to 1.800000 radius of atom 4231 goes from 1.700000 to 1.800000 radius of atom 4250 goes from 1.480000 to 1.580000 Partial mode Surface black.pdb, category main, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 16352.1 Total solvent accessible surface area = 17959.3

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error running large iterative script (return code 3)
by Sumitro Harjanto 16 Dec '09

16 Dec '09

Hi, I was trying to run the following script (below), which calculates RMSDs between 39 pdb models. Total iteration will be 741 with about 3000 match commands. After it has run for about 10 mins chimera will crash with an error: Chimera failed abnormally; the exit code was 3. I've printed the debug lines below the script: Any suggestions..? Cheers, Sumitro -------------------------------------------------------- open d:\result\pdb\1B0G.pdb open d:\result\pdb\1DUZ.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 open d:\result\pdb\1EEY.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 open d:\result\pdb\1EEZ.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 open d:\result\pdb\1HHG.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 open d:\result\pdb\1HHI.pdb match #0:1-9.C@ca #1:1-9.C@ca match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o close #1 ... ... ... -------------------------------------------------------- initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions CloneMenu failed inside of MenuAddOrInsert. This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. Return code: 3 Press return or enter to to exit --------------------------------------------------------

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size limits on bild geometric primitives?
by Kristina Furse 16 Dec '09

16 Dec '09

Hi- I like to use Chimera as a front end to povray to make high resolution images of molecules. I'm starting to work with other types of data, and was wondering if I could still use it. I have some network data--20,000 nodes with 32,000 connections. I translated the data into drawing instructions in bild format--spheres for the nodes and cylinders for the connections. Small test data sets work (300 nodes with 500 connections or 20,000 spheres with vectors instead of cylinders) but the full data set of spheres and cylinders crashes Chimera. Is there a limit somewhere I could raise or is this a hard wall for bild shapes? Would it be less memory intensive to create a "pdb" of the node locations and create the connections as bonds? Thanks! Kristina Kristina Furse Davis, Ph.D. Visualization Scientist Center for Research Computing University of Notre Dame P.O. Box 539 Room 122 Information Technology Center Notre Dame, IN 46556 kristina.davis(a)nd.edu

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how to create surface from volume tracer path
by jinghua＠ucsd.edu 16 Dec '09

16 Dec '09

When I try to create a tube by tracing two planes, the surface it makes is more like a cone. Do I need connect all the markers from two different planes? Thank you for your help! Jinghua

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Surfnet command line
by Jean Didier Pie Marechal 15 Dec '09

15 Dec '09

Dear All, is there a command line equivalent for surfnet applied to atom selection (not interfase)? Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dilluns, Desembre 14, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 80, Issue 14 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. help in installation of chimera-1.4-linux_x86_64.exe > (Dr Muhammad Nadeem Kardar) > 2. Re: help in installation of chimera-1.4-linux_x86_64.exe > (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 14 Dec 2009 10:45:22 +0500 > From: Dr Muhammad Nadeem Kardar <drmnkardar(a)ciitlahore.edu.pk> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] help in installation of > chimera-1.4-linux_x86_64.exe > Message-ID: > <38c1a890912132145o18302b67r6fc153793de8d76d(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > chimera-1.4-linux(2).exe > > chimera-1.4-linux.exe > chimera-1.4-linux_x86_64.exe > > I have three files of chimera but unable to execute chimera kindly > help > Kardar > > -- > M. Nadeem Kardar, PhD > Assistant Professor > Department of Chemical Engineering > COMSATS Institute of Information Technology > Defence Road Off Raiwind Road, Lahore, Pakistan > Cell# +92-300-2414231 > Email: drmnkardar(a)ciitlahore.edu.pk > Website: > http://www.ciitlahore.edu.pk/researchgroups/bcrg/page/kardar.html--- > ----------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://www.cgl.ucsf.edu/pipermail/chimera- > users/attachments/20091214/5abbdcee/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Mon, 14 Dec 2009 08:45:21 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Dr Muhammad Nadeem Kardar <drmnkardar(a)ciitlahore.edu.pk> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] help in installation of > chimera-1.4-linux_x86_64.exe > Message-ID: <92B97B1E-8164-4CC4-AD10-6161D911791F(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Kardar, > The *exe file is not Chimera itself but an installer. Please click > > the appropriate "Instructions" link on the download page to see how > to > install Chimera from the *exe file. > > <http://www.cgl.ucsf.edu/chimera/download.html> > > 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 Dec 13, 2009, at 9:45 PM, Dr Muhammad Nadeem Kardar wrote: > > > chimera-1.4-linux(2).exe > > > > chimera-1.4-linux.exe > > chimera-1.4-linux_x86_64.exe > > > > I have three files of chimera but unable to execute chimera > kindly > > help > > > > Kardar > > > > > > > > > > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 80, Issue 14 > ********************************************* >

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thank you ,thank you very much!
by gytjyb 15 Dec '09

15 Dec '09

Thank you very much for you answer. My english is not very well,Because I just come from china. My major subject is gene structure,So I am not good at protein structure. But ,I think this is very useful for me to analyze protein structure and asure their structure. So,I must thank for you first! You means: If I get a homologous model structure from swissmodel which I just align with PDB stucture,i must minimize structure ,at first。 But before i do minimization,I should add water or not.so this is a question.Which condition should I add water? Secondly,I get a stable structure after minimization.If I want to do mutation, I should do minimization for every time mutation about this structure. Thank you very much! Thank you very much! BEST WISHES FOR YOU!

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Programmer's Guide feedback....
by Will Moore 15 Dec '09

15 Dec '09

Hi, I am just trying to get started coding some plugins to Chimera, by following the Programmer's Guide 1.3. I have limited programming experience, and the points below were where I got stuck... Not sure if the guide is generally aimed at those with more or less developer skills? Starting with the examples (writeMol2.py) it isn't clear that all these commands should be typed in the IDLE window. I see that it is mentioned previously in the text, but it would be helpful to make clear that this is not in the command line or python prompt. When you've downloaded 4fun.pdb and saved it somewhere, does it matter where you save it, and how should you specify this in commands like opened = chimera.openModels.open('4fun.pdb') E.g. this would have made it more clear that you don't just put the file in a particular place that Chimera knows were to look: opened = chimera.openModels.open('Users/username/Downloads/4fun.pdb') Actually, this point was more relevant to the command: execfile("backbone.py") which I was working on earlier. I was trying to save backbone.py in one of the Chimera.app/Contents/Resources folders, and hoping that Chimera would find it with the above command: When really the command should be more like: execfile("Users/username/Desktop/backbone.py") Running chimera from the command line: A note that it is necessary to add the Chimera bin to the PATH variable would have been handy, especially for novice developers. export PATH=$PATH:/Applications/Chimera.app/Contents/Resources/bin/ ToolbarButton.py I got errors when running this script unless I put the import statements in the mainchain function like this import os import chimera def mainchain(): import re import chimera MAINCHAIN = re.compile("^(N|CA|C)$", re.I) for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: a.display = MAINCHAIN.match(a.name) != None chimera.tkgui.app.toolbar.add('ToolbarButton.tiff', mainchain, 'Show Main Chain', None) Otherwise I got errors like: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/ __main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/ chimeraInit.py", line 434, in init tkgui.eventLoop() File "/Applications/Chimera.app/Contents/Resources/share/chimera/ tkgui.py", line 2885, in eventLoop app.mainloop() File "/Applications/Chimera.app/Contents/Frameworks/ Python.framework/Versions/2.5/lib/python2.5/lib-tk/Tkinter.py", line 1023, in mainloop self.tk.mainloop(n) File "/Applications/Chimera.app/Contents/Frameworks/ Python.framework/Versions/2.5/lib/python2.5/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/ toolbar.py", line 191, in <lambda> command=lambda func=callback: _guard(func)) File "/Applications/Chimera.app/Contents/Resources/share/chimera/ toolbar.py", line 28, in _guard func() File "ToolbarButton.py", line 8, in mainchain MAINCHAIN = re.compile("^(N|CA|C)$", re.I) NameError: global name 're' is not defined Error in toolbar callback: NameError: global name 're' is not defined (see reply log for Python traceback info) This is just my feedback, which I hope is useful Cheers, Will.

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(no subject)
by Bala subramanian 15 Dec '09

15 Dec '09

Friends, I have a RNA structure. I want to calculate hydrogen bonds between the bases (for which i used findhbond menu). Then i want to show the ladder representation for those base-pairs which form atleast two hydrogen bonds. How can i do the same. Hope i am clear. Cheers, Bala

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Re: [Chimera-users] matching peptides with altenate locations
by Elaine Meng 15 Dec '09

15 Dec '09

Hi Sumitro, I work on a Mac and cannot open the winmail.dat file. Can you just send the two PDB files as attachments, or if they are in the public database, tell me what the PDB ID codes are? Thanks, Elaine

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FindHBond
by Greg Friedland 14 Dec '09

14 Dec '09

Hello, I'm new to Chimera and just discovered the FindHBond tool. This tool seems very useful, but unfortunately it draws hbonds between the heavy atoms even when I have hydrogens added. Is there a way to configure this behavior? I'd like the hydrogen bonds to be drawn between the hydrogen and the acceptor atom. It looks rather strange now, especially for the hbonds with relaxed constraints that deviate significantly from the angle made by the hydrogen. See the attached tiff for an example. Also, I'm curious what cutoffs are used. I looked at http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon… but I was hoping for more details. I.e what numbers from the paper are used for the proton-acceptor distances, donor-proton-acceptor angle and the corresponding dihedral angle. Thanks! Greg Friedland Postdoc Joint BioEnergy Instute Sandia National Lab Formerly of Tanja Kortemme's lab at UCSF

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hello!
by gytjyb 14 Dec '09

14 Dec '09

hello! i am a fleshman for this software! can you tell me about this software ,if all the thing is free? how can i minimize a energy and refine for a protein structure? i also want to do a mutation,how can i do? thank you very much!

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help in installation of chimera-1.4-linux_x86_64.exe
by Dr Muhammad Nadeem Kardar 14 Dec '09

14 Dec '09

chimera-1.4-linux(2).exe chimera-1.4-linux.exe chimera-1.4-linux_x86_64.exe I have three files of chimera but unable to execute chimera kindly help Kardar -- M. Nadeem Kardar, PhD Assistant Professor Department of Chemical Engineering COMSATS Institute of Information Technology Defence Road Off Raiwind Road, Lahore, Pakistan Cell# +92-300-2414231 Email: drmnkardar(a)ciitlahore.edu.pk Website: http://www.ciitlahore.edu.pk/researchgroups/bcrg/page/kardar.html

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File conversion question
by Miriam Gochin 12 Dec '09

12 Dec '09

I have a series of docked ligands produced by AutoDock (as .dlg files, containing more than one conformer per ligand) and I would love to be able to view these ligands using the ViewDock utility in Chimera. Is there a file conversion protocol? Thanks so much, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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image size
by Bala subramanian 11 Dec '09

11 Dec '09

Friends, What is the best way to generate an image of fixed size. Say i want to create an image of 4,4 (width, height) at 300dpi. I tried the following windowsize 1200 1200 When i go to save image--> I saw the pixel width and height changed as *1200, 618* ( I dnt understand why this changes although i set as 1200 1200). So i set the print unit as 'inches', then i entered width and height as 4,4. The final image that it produced has different width and height (4, 6.13). Thanks, Bala

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Curves+ output files
by David Chenoweth 10 Dec '09

10 Dec '09

Problem solved! Sorry, but it seems all I needed to do was show the atoms and bonds. Chimera is reading the file it just doesn't show anything until you tell it to show atoms and bonds. Another surprise with the new Chimera version is that it automatically displays my nucleic acid files with slab bases, filled sugars, and a backbone ribbon. Is there anyway to shut this off so I don't have to go in and manually do it each time I open a nucleic acid structure? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Curves+ output files
by David Chenoweth 10 Dec '09

10 Dec '09

Hi! I have been using a program called Curves for analyzing nucleic acid crystal structures for quite a while and I have always used Chimera to visualize the output pdb. One file shows the backbone splines and the vectors defining the nucleic acid groove widths (r+bdna_b.pdb) and the other file shows the nucleic acid helical axis (r+bdna_X.pdb). Chimera has always been able to read both of these files until the recent production release where it is no longer able to read the r+bdna_b.pdb file. I have attached the two files and the actual DNA pdb file. Can you please help me fix the problem with reading the r+bdna_b.pdb file in the new production release? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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creating additional coordinates to save from BIOMT records
by Irene Newhouse 09 Dec '09

09 Dec '09

I'm working with a pdb structure that's icosahedral. The surface is tiled with hexamers and pentamers of its single chain. The unit cell contains 4 chains, 3 from a hexamer and 1 from a pentamer. I need to compare the pentamer inter-chain contacts to those in the hexamer, so I immediately thought of Chimera. I can generate a pretty picture of hexamers & pentamers on screen, but what I can't seem to figure out how to do is to save additional coordinates for the other units of the pentamer, analogous to saving additional coordinates when you fill out a unit cell using the "Higher-order Structure" utilities. Thanks for your help! Irene Newhouse Res. Corp. U of Hawaii _________________________________________________________________ Windows 7: Unclutter your desktop. Learn more. http://www.microsoft.com/windows/windows-7/videos-tours.aspx?h=7sec&slideid…

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isosurface
by Bala subramanian 09 Dec '09

09 Dec '09

Friends, I have calculated the electrostatic-potential map using APBS program. I can use the 'electrostatic colouring' to colour my protein but i want to display the +ve and -ve isosurface. Kindly write me how to do the same. Thanks, Bala

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chimera help - calmodulin
by roach a.p.l. (aplr1g08) 07 Dec '09

07 Dec '09

Hi, I am a student trying to do a project on the protein calmodulin. I have just started using chimera and have gone though your tutorials and understood everything as it is very clear but i don't know how i would select the protein calmodulin and put it in the chimera display to make my images. I realise this is probably a simple step but this is all new to me and i would much appreciate your help. Thank you Annabel Roach

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Maximizing performance with large volume data maps
by Ryan Rochat 07 Dec '09

07 Dec '09

Hello, I was wondering how much video memory Chimera is capable of accessing. I currently have a 898Mb videocard that begins to slow down with a 550x550x550 map (at step size 1). This map is actually a downsample of the true 1100x1100x1100 map coming in at 5GB. I was contemplating going for a much larger video card at 4GB, however I was curious to what extent I could expect to see acceleration using Chimera with such a massive dataset (600+MB) and video card. Thank you, Ryan H. Rochat MS MD/PhD Candidate (Baylor College of Medicine) Graduate Student SCBMB (Baylor College of Medicine) Chiu Lab One Baylor Plaza N420 Alkek Houston Texas 77030

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Re: [Chimera-users] To consult the Morph conformation
by Elaine Meng 07 Dec '09

07 Dec '09

Dear Jiraporn, Sorry, Morph Conformations only includes parts that are in both structures in the morphing trajectory. In your situation, I suggest text-editing one of the input PDB files (more details below). Morph Conformations maps residues in the starting structure to residues in the ending structure by creating a sequence alignment. Where the residue in the starting structure is aligned with the same type of residue in the ending structure, the whole residue will be included. Where the residue in the starting structure is aligned with a different type of residue, only the parts that are the same will be included, which will include the backbone and sometimes part of the sidechain. Where there are backbone atoms, you can show a ribbon. If the residue is aligned with a gap, it will not be included. Here is the explanation in the manual: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p… > Currently Morph Conformations will only use the sequence alignment it figures out itself. A future improvement will be to allow the user to provide the sequence alignment (perhaps avoiding some of the gaps), but that is not available yet. I took a look at your proteins, 3DRR and 3DRS. They are the same protein, and the only difference is that the 3DRR crystal structure has more residues at the C-terminal end, forming a helix. 3DRR ends at 557 and 3DRS ends at 548. I guess you want that end part shown in the morphing trajectory. The structures look nearly the same in the residues before the difference, so to do this I would just use a text- editor and add the end residues from 3DRR onto the 3DRS structure. For example, make a copy of the 3DRR PDB file, then edit it to replace 543-end with 543-end from the 3DRS PDB file. Then you would just open the new edited 3DRR with the longer tail and then morph from that to 3DRS. 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 Dec 5, 2009, at 1:29 AM, Nok :p wrote: > Dear Chimera teme, > > First of all, I would like to introduce myself. My name is Jiraporn > Yongpisanphop. Now, I am a master student of KMUTT university in > Bioinformatics field. > > My thesis topic involve in drug design. A part of my work is > concerning about overaly binding pocket of single mutant enzymes > (PDB file: 3DRR and 3DRS). And, I > > use Morph Conformation method. It is good but it not complete for my > work. Because the intermedate structure was generate from compare of > same amino acid > > of both structures. However, the difference amino acid was kept only > reference model. Therefore, I would like to consult you how I will > keep amino acid that > > differece of both structures into intermediate structure. > > Thank you very much for your kind. > > Best regards, > > Jiraporn

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Movie spinning and slicing a density map
by Thomas Goddard 06 Dec '09

06 Dec '09

Hi Andy, I've added an example movie spinning and slicing a virus EM density map to the Chimera Animations page. See the bacteriophage phi6 entry. There is also a link to the movie script. http://www.cgl.ucsf.edu/chimera/animations/animations.html Tom -------- Original Message -------- Subject: making a movie From: Anindito Sen To: Thomas Goddard Date: 12/2/09 5:50 PM > Hi Tom > > I am not sure if this email can be out on the general Chimera wiki. THe > following movie is from a published work of mine. Can you help me > getting the script for generating such a movie. There is a Chimera session in the > webpage but I think its a bit too much for me to understand. > > Please feel free to reframe the question and put it in the Chimera wiki > email list which may prove helpful to others. > > Thanks for your help. > > Best > > Andy > > > > http://emnavi.protein.osaka-u.ac.jp/emnavi_detail.php?id=1500 > > Dr. Anindito Sen (Ph.D) > >

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drawing elipsolids
by Keren Lasker 03 Dec '09

03 Dec '09

Dear Chimera team, Is there a way to draw ellipsoids in Chimera. The ellipsoid is defined by its center and 3 radii. Thanks for your help. Best, Keren.

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How to clip surface using mclip
by Marhoefer, R (Richard) 03 Dec '09

03 Dec '09

Dear Chimera Team and Users, I like to clip the surface of a model (but not the model itself) using the command mclip. Unfortunately, this command apparently is waiting for a model number and therefore works on the surface as well as the model itself. On the other hand, the interactive tool "Per Model Clipping" allows to clip the surface only. Because I like to use clipping in a movie, using the interactive interface is not an option. Does anybody know how this could be acomplished using the command line? Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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Re: [Chimera-users] missing ribbon loop
by klumpler＠sci.muni.cz 03 Dec '09

03 Dec '09

Dear Elaine, I think PDB is alright, I send it as a attachment. Could you help me with the editing? Thank you very much Tomas > Hello, > My guess is there is something strange about the structure or the format of the input file -- for example, maybe the residues don't all have the same chain ID, or the backbone atoms do not have the expected names (N,CA,C,O). If Chimera does not show a ribbon at that position even though you told it to show ribbons for everything, it is probably necessary to edit the input file to fix the problem. I couldn't be more specific without seeing the file. > 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 Nov 27, 2009, at 2:16 AM, klumpler(a)sci.muni.cz wrote: > >> Hallo, >> please, can you tell me how to create missing part of ribbon >> representation of loop? >> >> Using "ball and stick" representation is peptide chain complete without >> gap, but in "ribbon" representation is one residue missing and forms the >> gap. >> >> Thank you very much >

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keyboard input gone
by Zhou, Wei 02 Dec '09

02 Dec '09

Hi, Yesterday I installed the latest 1.4 32bit linux version of chimera into my opensuse 11.1. Soon after I fetched some pdb files and started to use it, at some point, I can no longer input any text into the program, such as typing another pdb id, or typing a command line, or type a file name to save it. I can still use mouse. Please help. I'm here at mission bay, rock hall. My extension is 60421. Thanks, Wei Zhou

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phenix map not reading in chimera
by Geoffrey Feld 02 Dec '09

02 Dec '09

Greetings, I'm trying to make a figure showing off my best density from a 2Fo-Fc map I generated using phenix.refine. The output file has a .map suffix. However, Chimera gives an error about the header, which I've included: MRC header value nsymbt (538976288) is invalid. How do I give Chimera a map with a header it can read? Thanks, -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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Chimera question with Mac
by Durga Velukumar 30 Nov '09

30 Nov '09

Hello, I'm an undergraduate student at the University of Georgia and I'm using your system, UCSF Chimera, for my powerpoint presentation. I'm having some problems with trying to create a movie. I have a MacBook Pro, which I just got this recent August, and downloaded the latest Chimera version for the Mac. I'm trying to save the commands in a separate file, like TextEdit, but I don't know what type of file to save it as. I'm hoping to be able to open the file through Chimera to play the movie. I tried saving the commands as "movie.cmd" but TextEdit is not allowing me to save that type of file. Any help would be greatly appreciated. Thank you, Durga

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Bond change
by Bruno Cramer 30 Nov '09

30 Nov '09

Hi After getting the conformations as *.sdf (or *.pdb) files with Macromodel (from Shroedinger) and/or Vconf(VeraChem) I use Chimera to add missing H's and add charges with amber 99. After these steps are completed, I split the sdf conformations-file into single *.mol2 files. All works fine except for the last step, that changes a single bond into a double bond in each molecule. I am correcting this manualy opening the *.mol2 file with Texd editors and changing the double bond into single bond the the benzene rings. Opening a chosen conformation from the *.sdf file it looks correct.So, the problem happens during conversion/splitting process. Question: How can this arbitrary bond change be avoided? Attached zip file with *.mol2 examples of one compound after splitting process. Thank you Regards Bruno

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missing ribbon loop
by klumpler＠sci.muni.cz 30 Nov '09

30 Nov '09

Hallo, please, can you tell me how to create missing part of ribbon representation of loop? Using "ball and stick" representation is peptide chain complete without gap, but in "ribbon" representation is one residue missing and forms the gap. Thank you very much

2 1

structure manupulation
by Haixin Sui 24 Nov '09

24 Nov '09

Tom and Elaine, Is there a simple way to manipulate part of a protein structure in Chimera? What I would like to do is the following. Let's say I have a molecular compose 8 helixes. 7 of them fit in the cryo-EM map perfectly but one short helix is off probably owing to conformational change. I would like to move the short helix into the density map manually. The difficult part is how to make a smooth transition for loop regions at both ends of the helix. Would you please give me some advice on this? Thanks! Haixin -- Haixin Sui, Ph.D. Wadsworth Center NYS Dept. of Health Empire State Plaza P.O. Box 509 Albany, NY 12201-0509 (518)474-4235 (office) (518)473-0309 (lab) 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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Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

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Display of double-bond in Chimera
by J H 24 Nov '09

24 Nov '09

Dear Chimera, Is there a way to display a molecule's double bond as double-bond (i.e., two lines between the atoms instead of one) in chimera? Thanks a lot. Best, Jules.

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Moving PDB between 3 orientations
by Thomas Goddard 23 Nov '09

23 Nov '09

Hi Chris, To show a molecular model moving between three orientations you would use Chimera commands savepos and reset and matrixcopy. Here's how I'd go about it. First put copies of the molecular model at all 3 positions. If you have saved these in 3 Chimera session files I would open all 3 sessions telling Chimera not to close the previous session when I open each new session. Now open a 4th copy of the molecule. Suppose the original 3 copies are model numbers #0, #1, #2 and the 4th copy is model #5. To align the 4th copy with #0 use matrixcopy #0 #5 (The matrix being copied is the positioning matrix, the rotation and shift that places the molecule in the scene.) Record the positions of all the models now with savepos p0 The name p0 could be anything. We'll use it later with the reset command. Also save positions with the 4th model in the other 2 states: matrixcopy #1 #5 savepos p1 matrixcopy #2 #5 savepos p2 Now to move the 4th model pack to position 0: reset p0 and to move it from position 0 to 1 over 50 frames reset p1 50 and then from 1 to 2 reset p2 50 In a movie recording command script remember to put a "wait 50" between these two commands so they don't both try to run simultaneously. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html There is a movie making tutorial that explains some of this: http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html Tom -------- Original Message -------- Subject: Re: [Chimera-users] how to link three EM confirmations in morph map From: Chris Arthur To: Thomas Goddard Date: 11/23/09 1:40 PM > Hi Tom, > I have one other question. I have a pdb (the same pdb loaded into > chimera 3 times), that I have docked into three distinct EM maps. I > would like to make a movie showing the rotation of the pdb as it goes > from one docked state to the next, to the next. I guess this would be > similar to the morph command but for pdb's instead of EM maps. Any > suggestions? > Thanks, > Chris > > > The Scripps Research Institute

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Make volume have mean 0, standard deviation 1
by Thomas Goddard 23 Nov '09

23 Nov '09

Hi Terry, Chimera does not automatically scale density maps. You can use a command like vop scale #0 shift -8.0 factor 0.2 to shift map #0 values by -8.0 and then scale by 0.2. If the mean were 8.0 and standard deviation were 5.0 then this would normalize to mean 0 and SD 1.0. This creates a new volume data set. There is no capability to shift and scale an existing map without making a new volume data set. The Volume Filter dialog (menu Tools / Volume Data) can do the same thing. Python code to do the shift/scale is in chimera/share/VolumeFilter/scale.py There is a menu entry Tools / Volume Data / Volume mean, SD, RMS that reports the mean and SD and RMS about zero of the highlighted map in the volume dialog. There is no command equivalent (I should make the measure command do this). The Python code that does this is in chimera/share/VolumeStatistics/__init__.py Tom -------- Original Message -------- Subject: question about ccp4 formatted map density From: Terry Lang To: Tom Goddard Date: 11/23/09 11:39 AM > Hey Tom, > > I am looking into some new schemes for scaling electron map > density. I know you said that the scaling to a mean of zero and > standard deviation of 1.0 is implemented in the current release. > However, I can't seem to find where the code is located. I am really > interested in figuring out where exactly scaling happens and if it's > automatic or needs to be requested. Any input you can provide would be > greatly appreciated! > > Sincerely, > Terry >

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Re: [Chimera-users] [chimera-dev] Rotation about the axis of symmetry
by Elaine Meng 23 Nov '09

23 Nov '09

On Nov 23, 2009, at 2:06 AM, Liam Browne wrote: > I want to rotate a model by 90 degrees about the axis of symmetry, > but I seem to be having problems setting the axis correctly. > After two identical models are superimposed I use measure rotation > and get the following: > > Matrix rotation and translation > -0.04092271 -0.36724445 0.92922379 -82.20183653 > -0.91203666 0.39354649 0.11537022 -54.21831923 > -0.40806183 -0.84276490 -0.35104539 11.47082481 > Axis -0.55288898 0.77167664 -0.31437070 > Axis point -56.22800779 0.00000000 25.47389901 > Rotation angle (degrees) 119.94780111 > Shift along axis 0.00338820 > > What should I do to rotate the model at the same axis but by 90 > degrees? > > Many thanks, > Liam Hi Liam, You can just use the reported values -- the tricky part is remembering to indicate that they are in the coordinate system of the first model in the "measure rotation" command, and also using the reported axis point as the center of rotation. Let's say you used the command "measure rotation #0 #1". Then the values in the Reply Log are for the transformation of #1 relative to #0 expressed in the coordinate system of #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation > Now you can use the values in the Reply Log to rotate #1 further. Keep in mind that this transformation will be applied on top of any existing transformations. If you want only the new rotation and not prior transformations, you would need to "reset default" first. To rotate model #1 90 degrees about the reported axis and use the reported axis point as the center, the command would be: turn -.55288898,.77167664,-.31437070 90 center -56.22800779,0,25.47389901 mod #1 coord #0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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question
by Laura Packer 20 Nov '09

20 Nov '09

To whom it may concern: I am not sure if I am sending this inquiry to the correct e-mail address. If not, I apologize for any inconvenience. I am looking to acquire a list of atoms that are within a certain distance of a set other atoms. I have googled this question and have learned how to select these atoms: bfsdjf select <description of atoms/residues> z<5.0 # or zr<5.0 or select <description of atoms/residues> za<5.0 What I would like to know is how to get a list of these results. It is not appearing in my reply log as I thought it might. Thank you for your time. Sincerely, Laura Packer packer(a)bu.edu

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how to link three EM confirmations in morph map
by Chris Arthur 19 Nov '09

19 Nov '09

I am wondering what would be the best way to link three EM maps using Morph Map? I have three sequential conformations of a protein and I would like to show a movie morphing from 1 to 2 to 3 if possible. Thanks in advance for any tips. Regards, Chris Christopher Arthur Ph.D. Staff Scientist Milligan/Unwin Lab The Scripps Research Institute carthur(a)scripps.edu 858-784-7073

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