- Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] missing chimera-users email
by Eric Pettersen 17 Jul '09

17 Jul '09

I see what happened to the mail now. Cao is not a subscriber to chimera-users so her mail was held up for moderator approval. I'll fix that now... --Eric On Jul 16, 2009, at 5:46 PM, Greg Couch wrote: > So it's not in the archive nor does Tom Goddard have it, so you'll > have to forward it to me :-). > > - Greg

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Re: [Chimera-users] Chimera-users Digest, Vol 75, Issue 17
by Burkhard Heil 15 Jul '09

15 Jul '09

Liebste, hab jetzt auch AB abgehört:-) und warte auf meine gesättigte oder essende Sarah:-) Knutschknutsch! Küsse Dein Burkhard On 14.07.2009, at 21:00, chimera-users-request(a)cgl.ucsf.edu wrote: > 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. suggestion/transform molecule coordinates (Dougherty, Matthew T.) > 2. Re: suggestion/transform molecule coordinates (Thomas Goddard) > 3. Re: sequence viewer (Eric Pettersen) > 4. Re: sequence viewer (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jul 2009 15:30:21 -0500 > From: "Dougherty, Matthew T." <matthewd(a)bcm.tmc.edu> > Subject: [Chimera-users] suggestion/transform molecule coordinates > To: <chimera-users(a)cgl.ucsf.edu> > Message-ID: > <B5CA7C88183F884CB316B04DCD343849013465D6(a)BCMEVS13.ad.bcm.edu> > Content-Type: text/plain; charset="iso-8859-1" > > relating to the apply, close & help buttons > > 1)"reset" button > The reset would remove prior transformations > > 2) "apply once" button. > The apply once would function the same as a reset and apply in > sequence. > > 3) display sum of current transformation (Euler & shift) > > > Matthew Dougherty > 713-433-3849 > National Center for Macromolecular Imaging > Baylor College of Medicine/Houston Texas USA > = > = > = > ====================================================================== > = > = > = > ====================================================================== > > >

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Re: [Chimera-users] [chimera-dev] Non-standard residues
by Elaine Meng 15 Jul '09

15 Jul '09

Hi Alex, The calculation requires parameters for all of the atoms present regardless of whether they are frozen during minimization or not. The frozen atoms still exert forces on the movable atoms. Unfortunately there is a hard limitation on which metal ions can be handled. Possible workarounds have been discussed on chimera-users, for example: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004066.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003682.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 http://www.cgl.ucsf.edu/home/meng/index.html On Jul 14, 2009, at 4:56 PM, Alex Gawronski wrote: > Hello, > > I used :/!isHet for the "spec" option for "minimize" and I'm still > getting "Unable to find GAFF type for #0:155.A@FE " for 101M. I > thought this would skip the heme, but I guess not. How can I avoid > this error? > > Thanks again! > > Alex >

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dragging a displayed object
by justin oppenheim 15 Jul '09

15 Jul '09

Hello: I am displaying two or more very similar objects, but they are shifted one with respect to another. How can I drag/move/align them on the display to correct for the relative shift? Many thanks, JO

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Some problem with volume coloring
by MAG 14 Jul '09

14 Jul '09

Good day for you, Would be so kind and help me. The problem is I want to color two parts of my volume. So, I have put markers inside of it, color two parts, but now I want to save this colored volume, such that after I would be able to duplicate it and use as a normal volume, but colored. Thank you in advance, Best, Alex

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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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suggestion/transform molecule coordinates
by Dougherty, Matthew T. 13 Jul '09

13 Jul '09

relating to the apply, close & help buttons 1)"reset" button The reset would remove prior transformations 2) "apply once" button. The apply once would function the same as a reset and apply in sequence. 3) display sum of current transformation (Euler & shift) Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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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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no bug reports
by Eric Pettersen 09 Jul '09

09 Jul '09

Since mail to chimera-bugs eventually gets delivered to crick and crick is down, we won't be receiving any bug reports until crick comes up. --Eric

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thermal ellipsoids
by Michael K. Gilson 08 Jul '09

08 Jul '09

Hi, Chimera and PyMol are showing very different thermal ellipsoid orientations for the same PDB file, and I have reason to believe that the PyMol display is the right one. Here are the first two lines of the PDB file I am reading in: Atom 1 O1 CUC 1 3.345 1.613 0.172 ANISOU 1 O1 CUC 1 619 156 528 150 43 -6 ATOM 2 O2 CUC 1 -1.699 0.125 2.792 ANISOU 2 O2 CUC 1 497 355 848 128 -68 204 I would appreciate help with this because Chimera appears to provide more detailed control of the coloring of the ellipsoids than PyMol does. I'll be happy to provide screenshots or other information. Regards, Mike

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Model translation
by David Chenoweth 08 Jul '09

08 Jul '09

Hi, Can anyone tell me the easiest way to translate an entire model by a defined amount (angstroms) in a defined direction. I have a slice of a nanotube and I would like to open it several times, translate each section, and make bonds between the translated sections in order to create a longer nanotube and then save the new coordinates as a new model. Thanks, Dave

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Re: [Chimera-users] Display Molecule Name
by cdlau＠ucsd.edu 08 Jul '09

08 Jul '09

Hi, Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible? Thanks, Chris On Thu, 2 Jul 2009, cdlau(a)ucsd.edu wrote: Hi, I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great. Thanks for your help, Chris Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name. - Greg

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Thermal ellipsoids
by Michael Day 07 Jul '09

07 Jul '09

Hi, I see thermal ellipsoid rendering was just enabled. This is another point (in a long list of points) in favor of using Chimera. Is there a plan to be able to display ellipsoid axis or octants as in ortep type renderings. This would be extremely useful in small molecule work. I've been using Chimera as an alternate when reporting structures in my lab and it has been very well received. The first question asked when I distributed a report today was about the axis and/or octants. Great work. Keep it up! Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------> >>

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Display of a vector in Chimera
by Charles Letner, Ph.D. 07 Jul '09

07 Jul '09

Hello, Is there a way to display a vector between two sets of coordinates in Chimera? If the approach is to write a python, any chance I could get a nudge in the right direction on chimera commands to work with? I've written a minimal amount of python code but not related to Chimera. Cheers, Chuck Charles Letner, Ph.D. Alpharetta, GA 30004 Email: chuck(a)theletners.com

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Re: [Chimera-users] minmize small molecule
by Elaine Meng 06 Jul '09

06 Jul '09

Hello, It looks like the Cu is part of the small molecule. Sorry, in my first reply I thought it was just a separate monatomic ion (not covalently bonded to anything) that happened to be near the small molecule, such as in the binding site of a protein. Covalent organometallic compounds cannot be minimized in Chimera. Chimera uses Antechamber/GAFF to assign parameters to nonstandard residues such as small molecules, and this process is only meant to handle organic molecules made of C, N, O, H, S, P, F, Cl, Br and I. To minimize this type of compound, you would need to use some other program, sorry. Elaine On Jul 6, 2009, at 12:48 PM, Venkataraman Kabaleeswaran wrote: > changed the atom type, but got the following error message? > > > Running ANTECHAMBER command: /net/earth/disk3/vk/pgm/chimera/bin/ > antechamber/exe/antechamber -i /tmp/tmpXaquvp/ante.in.mol2 -fi mol2 - > o /tmp/tmpXaquvp/ante.out.mol2 -fo mol2 -c gas -nc -1 -df 0 -j 5 -s 2 > (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ > bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f > ac -j part > (LIG) > (LIG) For atom[10]:Mg, the best APS is not zero, exit > (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ > atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > (LIG) > (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ > atomtype -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d "/net/ > earth/disk3/vk/pgm/chimera/bin/antechamber"/dat/antechamber/ > ATOMTYPE_GAS.DEF > (LIG) > (LIG) > (LIG) No Gasteiger parameter for atom[9]:Mg :DU, exit(0) > Failure running ANTECHAMBER for residue LIG > Check reply log for details > > Kabaleeswaran Venkataraman > > -------------------------------------------------------------- > Arise, Awake and stop not until goal is Reached > - Swami Vivekananda > -------------------------------------------------------------- > > > --- On Mon, 7/6/09, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] minmize small molecule > To: "Venkataraman Kabaleeswaran" <vkabs(a)yahoo.com> > Cc: chimera-users(a)cgl.ucsf.edu > Date: Monday, July 6, 2009, 8:07 PM > > Hello, > The "Minimize Structure" tool in Chimera uses MMTK. In general, it > works on (polyatomic) nonstandard residues because Antechamber is > can generate parameters for those, but unfortunately there is a hard > limitation on the types of monatomic atoms that are handled. > > From the Minimize Structure documentation: > "Only the ions in ff99 are handled: Na+, K+, Rb+, Cs+, Mg2+, Ca2+, > Zn2+, and Cl–" > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… > > > > You could change the Cu to one of those, say Mg, by editing your > structure input file or by using Build Structure (Modify Atom > section). If you are concerned about the effect on the nearby > atoms, you could make sure to freeze that part of the structure so > that it is not allowed to move during minimization. > > 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 > http://www.cgl.ucsf.edu/home/meng/index.html > > > On Jul 6, 2009, at 10:35 AM, Venkataraman Kabaleeswaran wrote: > > > > > Hi > > I wanted to optimize the geometry of small molecule by > minimization for docking. > > > > I have not seen any option in chimera but even I did tried with > the small molecule I have as nonstandard aminoacid, but it give me > error mmtrk could not Cu atom type. > > > > Is it any small script or through chimera I could able to optimize > the small molecule? > > thanks > > > > Kabaleeswaran Venkataraman > >

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building a backbone model from deposited Calpha coordinates
by Mark Girvin 06 Jul '09

06 Jul '09

I'm sure that this has been asked before, but with limited web bandwidth while traveling, and not finding it in the downloaded help, will ask again anyway (pls feel free to ignore) -- what would you suggest as the best way to coax a ribbon diagram out of deposited Calpha coordinates? Thanks either way, - Mark (further apologies if this turns into a double posting - seemed to bounce the first try). -- Mark Girvin Biochemistry Department Albert Einstein College of Medicine 1300 Morris Park Ave. Bronx, NY 10461 http://www.bioc.aecom.yu.edu/labs/girvlab

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minmize small molecule
by Venkataraman Kabaleeswaran 06 Jul '09

06 Jul '09

Hi I wanted to optimize the geometry of small molecule by minimization for docking. I have not seen any option in chimera but even I did tried with the small molecule I have as nonstandard aminoacid, but it give me error mmtrk could not Cu atom type. Is it any small script or through chimera I could able to optimize the small molecule? thanks Kabaleeswaran Venkataraman -------------------------------------------------------------- Arise, Awake and stop not until goal is Reached - Swami Vivekananda --------------------------------------------------------------

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[Chimera-Users] Display molecule name
by cdlau＠ucsd.edu 02 Jul '09

02 Jul '09

Hi, I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great. Thanks for your help, Chris

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chimera error
by Bala subramanian 02 Jul '09

02 Jul '09

Friends, I installed chimera in fedora10, installation was fine but starting chimera throws me the following error. Trying chimera version 1.3 Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 361, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "CHIMERA/share/chimera/tkgui.py", line 2525, in initializeGUI File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 321, in checkConfig File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 297, in checkForChange File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 52, in readGfxInfo KeyError: 'Pbuffer'

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Normal recalculation
by Damien Larivière 02 Jul '09

02 Jul '09

Dear Chimera team, I have open in Chimera a VRML file containing multiple copies of the FtsZ protein. The VRML file does not contain the smooth groups so that, at display, triangles appear at the surface of the proteins as shown in the attached image. I would like to get the surface smooth but not by increasing the number of triangles. Is there a way in Chimera to recalculate the normals as it can be done in 3DSMax for instance? My best regards, Damien

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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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