June 2009 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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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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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

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sequence viewer
by Gatsogiannis, Christos 13 Jul '09

13 Jul '09

Hi all, i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks! -Christos ------------------------------- Christos Gatsogiannis Insitute of Zoology, Dpt. II cryoEM Lab, AG Markl Joh. v. Müllerweg 6 Johannes Gutenberg University Mainz, Germany +49-6131-3923091 ------------------------------- ________________________________________ Von: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] im Auftrag von chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Gesendet: Mittwoch, 17. Dezember 2008 21:00 An: chimera-users(a)cgl.ucsf.edu Betreff: Chimera-users Digest, Vol 68, Issue 22 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. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 2. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 3. possibilities to save parts of models (selection)? (Sebastian Kruggel) 4. Re: possibilities to save parts of models (selection)? (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Dec 2008 14:59:34 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids To: Tom Goddard <goddard(a)cgl.ucsf.edu> Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> Message-ID: <9A34751B-6356-4AF4-A8C7-31757E5FFBF1(a)cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii" On Dec 12, 2008, at 10:40 AM, Tom Goddard wrote: > Hi David, > > Ok I see now, it's a matter of choosing the size of each ellipsoid to > have a 50% chance of finding the atom in that volume. This > shouldn't be > too hard but I'll let Eric tackle it if he has time. Hi David, This is one of those things that I'll endeavor to get into Chimera's production version of thermal ellipsoids, but that I can't spare the time for until then. My guess is that the eigenvectors/values of the U matrix are at the 50% probability level, but verifying that would require some research. If you do look into and find that that's not the case, just change the setting of the 'scale' variable of the start of the script to change the ellipsoid sizes to whatever size encloses 50%. --Eric

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Faster raytracing
by "Bernhard Pätzold" 09 Jul '09

09 Jul '09

Hello I love Chimera and the only little bummer to me are the long rendering times for raytraced movies. I managed to get the PovRay version 3.7 which uses multiple cores running on our server. However now I am stuck and here comes my question. Is there away how I can get Chimera to use the newer Version of PovRay? Or can I somehow change my script so that I get only the .pov and .ini files for all the frames while the actual raytracing is skipped and I can do it subsequently with the newer Version? Currently the whole things has to happen on a windows system, but I hope that I'll get my ubuntu version soon up and running again, so hints and advices for both options are welcome. Thanks a lot in advance Berni -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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standalone programs for processing volume data
by Michele Lunelli 30 Jun '09

30 Jun '09

Dear all, I want to use the program combine.py to subtract two delphi potential maps. I have the most recent stable version of Chimera installed in /usr/local/chimera. Following the documentation, I set the PYTHONPATH variable with setenv PYTHONPATH /usr/local/chimera/share then I try to run the program with /usr/local/chimera/bin/python2.5 /usr/local/chimera/share/VolumeProcessing/combine.py but the result is always: Traceback (most recent call last): File "/usr/local/chimera/share/VolumeProcessing/combine.py", line 12, in <module> from VolumeData import Grid_Data File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 10, in <module> # File "CHIMERA/share/VolumeData/opendialog.py", line 70, in <module> File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 72, in <module> File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 15, in <module> ImportError: No module named _chimera How can I overcome this problem? Thanks in advance, Michele

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modeldisp
by cdlau＠ucsd.edu 29 Jun '09

29 Jun '09

Hi, I am currently using the modeldisp command on the command line to hide and view various molecules within a single mol2 file. I was wondering how I would be able to access how many total molecules there were in a single mol2 file. For example, if the mol2 file is loaded into model 0, I would be using modeldisp #0.$i etc in a large loop where $i is changing. What command can I use to return a value for the total number of molecules in the mol2 file so I can have this be the upper limit of $i? Thanks for your help, Chris

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GROMACS trajectory
by Dave Hassan 29 Jun '09

29 Jun '09

Hi All, I'm trying to generate an MD move from a gromacs trajectory. I used tools > MD/Ensemble Analysis > MD movie in the toolbar. I then get the following error message: VERSION 4.0.5 using floats version 58 generation 17 9975 atoms DICKERSON DODECAMER in water 17 atoms 456 residues <type 'exceptions.IndexError'> Exception in Tk callback Function: <function command at 0x10ecc870> (type: <type 'function'>) Args: () Traceback (innermost last): 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/baseDialog.py", line 244, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 458, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/EnsembleLoader.py", line 92, in Apply self.callback) File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble startFrame, endFrame, callback) File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble ensemble = Gromacs(topology, trajectory, startFrame, endFrame) File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, in __init__ self.topology = TprTopology(topology) File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py", line 68, in __init__ self._readTopology(version) File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py", line 181, in _readTopology for i in range(numResidues)] <type 'exceptions.IndexError'>: list index out of range attached are the .trr and .tpr I used. Any help would be greatly appreciated. Thanks, Dave Hassan

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where is 'glossy'
by Boaz Shaanan 25 Jun '09

25 Jun '09

Hi, I don't see 'glossy' in the Lighting panel (Tools / Viewing Controls / Lighting) that Tom mentioned (I'm using the latest production release, XP). Is this a recent development or what am I missing ? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Sending commands via terminal
by cdlau＠ucsd.edu 25 Jun '09

25 Jun '09

Hi, I was wondering if there was a simple way to send commands (such as "open 1zik" or "preset apply int 2" ) to an already running instance of chimera. I want to be able to send this command using 1 line of command. This means that "--start ReadStdin" would not work because it allows commands to be sent indefinitely. Potentially I could write the commands in a python script and use the --send command, however I would like to avoid this if I just want to send a single command to chimera. Thanks for your help, Chris Lau

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