- Chimera-users - RBVI Mailing Lists

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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