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

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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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