December 2009 - Chimera-users - RBVI Mailing Lists

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 --------------------------------------------------------

2 2

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

3 3

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

3 8

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 > ********************************************* >

3 2

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!

5 4

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.

2 1

(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

2 1

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

1 0

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

3 2

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!

2 1

Chimera-users December 2009