- Chimera-users - RBVI Mailing Lists

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

1 0

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 > = > = > = > ====================================================================== > = > = > = > ====================================================================== > > >

1 0

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 >

1 0

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

2 1

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

2 1

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

4 4

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 ========================================================================= =========================================================================

2 1

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

3 3

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

1 0

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

6 11

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

2 1

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

5 7

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 <<< ------------------------------------------------------------------------> >>

2 1

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

2 1

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 > >

1 0

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

2 1

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

2 1

[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

2 1

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'

2 3

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

3 2

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

2 1

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

2 1

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

3 2

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

2 2

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

2 1

high quality pictures for publication
by Fabian Glaser 25 Jun '09

25 Jun '09

Hi all, I am trying to produce high quality figures for publication with chimera, and despite I am working some time with it, I am not quite satisfied with the result I get. I don't know if I can send figures to this list, just as example I send these two. They are fine, but they are not gorgeus as I would like. I don't know they are produced with and without the pov-ray in linux, with 300 dpi, etc. Could somebody try to help me how to improve them? Thanks a lot in advance, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

3 4

Re: [Chimera-users] Surface Creation
by Eric Pettersen 23 Jun '09

23 Jun '09

On Jun 23, 2009, at 2:25 PM, Thiruvarangan Ramaraj wrote: > Hi, > > I tried to create two surfaces, one for the Antibody and one for the > Antigen for an Antibody-Antigen complex (1A14.pdb). I am able to > create two surfaces as two models in one session. But when I try to > save this session it gives me an warning > "Cannot save surfaces without associated structure. > Surface will not be saved." This happens when you close the structure that a surface is based on. Sessions don't store vertex/triangle information for surfaces (which would be voluminous) but instead just the parameters that were used to generate the surface -- and the surface is regenerated when the session is restored. But if the underlying structure is gone then that won't work. > Then when I try to open the saved session there is only surface that > I could see. > > Is there any way that I could have both surfaces saved in one session. > > Any help would be greatly appreciated. Well, obviously one approach is to not close the underlying structure. FYI, you can get separate surfaces on the antigen/antibody without using multiple copies of the structure. You need to get the antigen and antibody into separate "surface categories" (as described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/msms.html ). Here is a sequence of commands (Favorites->Command Line) that gets the antigen (chain N) into its own surface category named "antigen" and then surfaces both the antigen and antibody: surfcat antigen :.n; surf antigen; surf --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Saving image and rendering
by Ibrahim Moustafa 23 Jun '09

23 Jun '09

Dear Chimera team, Recently, I have some trouble saving images with POV-RAY option ³true². The process of rendering is too slow (both on the mac and windows version). To give the feeling of how slow: rendering an image with 1700 lines takes 7 hrs (with quality 9 in pov-ray options) and 2 hrs (quality 5). I used to get the images rendered much faster than that (with older versions; however, I¹m not exactly sure of when I started to see such a slow rendering behavior). There is another related problem but only with the windows version: If I want to save an image, with depth cue, using the fast mode (POV-RAY false), the image output lacks any depth used in the model, with poor quality and darker than it should be. Somehow, the camera orientation is messed. In addition, the depth cue will be no longer available for the rest of the session (I have to restart over again). To get the depth cue I want, I need to turn the POV-RAY option ³true²....but then too slow to create a good figure. I¹d appreciate any comment or explanation from Chimera people; and what is the best way to overcome this problem? P.S. I have the PPC version for the MAC running OSX 10.4; the PC running Windows XP. Many thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

4 5

New surface coloring command
by Thomas Goddard 22 Jun '09

22 Jun '09

I added a Chimera command "scolor" that can color surfaces radially or according to volume data values such as electrostatic potential. This command is the equivalent of the Surface Color dialog. A few examples: scolor #0 geometry cylindrical colors the surface by distance from a cylinder axis (default z-axis) with default coloring red-white-blue ranging from minimum to maximum surface radius. scolor #0 geom radial cmap 100,gray:150,blue:200,purple colors radially with colors gray,blue,purple at radii of 100,150,200. scolor #0 volume #1 cmap -10,red:0,white:10,blue colors surface #0 using volume data #1 with colors red,white,blue for volume data values -10,0,10. Here's a summary of the full command syntax. Detailed documentation will be available in the manual before the next Chimera release. scolor <surfaceSpec> [volume <vspec>] [gradient <vspec>] [geometry radial|cylindrical|height] [color <color>] [center <x,y,z>|<atomspec>] [axis x|y|z|<x,y,z>|<atomspec,atomspec>] [coordinateSystem <modelid>] [cmap <v,color>:<v,color>:...|rainbow|gray|redblue|cyanmaroon] [cmapRange <min,max>|full] [reverseColors true|false] [colorOutsideVolume <color>] [autoUpdate true|false] [capOnly true|false] [perPixel true|false] Tom

1 0

Getting Delphi
by Yasser Almeida Hernandez 22 Jun '09

22 Jun '09

Hi all... Where can i download the Delphi executable to run in Chimera...? Thanks ---------------------------------------------------------------- Correo FENHI

2 1

Electrostatics
by Gawronski, Alexander 20 Jun '09

20 Jun '09

Hello, I'm a student at Carleton University and I need to create meshes with electrostatic coloring for all the proteins in the pdb. I need a way of automating this process with scripts but I can't figure out how. Is this possible to do this through command line? How do I call chimera commands from a script? Any help would be greatly appreciated! Thanks, Alex Gawronski

4 3

Re: [Chimera-users] 3D mouse - connexion
by Nils Becker 18 Jun '09

18 Jun '09

Hi Thomas, I'm also using it (recently, on a daily basis, on Mac OS X). It works very nicely, and it's cheap. Also, try the keyboard shortcuts na, nz etc... cheers, Nils

1 0

3D mouse - connexion
by Thomas C. Marlovits 18 Jun '09

18 Jun '09

Hi, the Chimera documentation indicates that the 3D mouse from Connexion (Space navigator) is supported. I have just asked the company, but they didn't know anything about Chimera. I am wondering, whether you have some good experience using it, or whether you have an alternative mouse model that would work nicely together with Chimera. Tx -Thomas Here is the link at your documentation site: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#otherinput ------------------------------------------------------------------------------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

3 2

controling multiscale models from command script
by Marhoefer, R (Richard) 18 Jun '09

18 Jun '09

Dear Chimera Users, for the production of a movie file I like to control some attributes of a multiscale model e.g. the style and the surface transparency through a Chimera command file. Unfortunately I couldn't find many commands allowing to do so in the documentation. How could that be done? 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. --------------------------------------

3 2

Minimize and solvate with a zinc ion
by Dr. Jean-Didier Maréchal 12 Jun '09

12 Jun '09

Dear all, I want to solvate then minimize (few steps) a structure with a zinc (Zn2+) ion. >From what I saw in the manual, zinc parameters are available in the actual version of the amber force field in chimera. However, I am stuck with troubles. When I solvate I have the following message: Could not determine charges for pre-existing solvent from added solvent for: Zn Zn What do I do wrong? All the 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

2 1

Morphing Code Request!
by Eric J. Choi 11 Jun '09

11 Jun '09

Hello, chimera-users, Hi, my name is Eric Choi and currently I am interning at the Ren Lab at mission bay for Dr. Ren. For one of my assignments, I was to make a video of a conformation change of PPAR-GAMMA, from open to closed structure with the addition of a ligand. Upon trying to make this happen, I realized that I need the morphing python code(I believe it is) to be able to complete this step. This is what the movie making tutorial told me in the part "Ligand Flying into Unbound Conformation". If I could get the command to make the morph(python code) that would be great. Thank you! -Eric Choi

2 1

map saving
by Jean-Paul Armache 09 Jun '09

09 Jun '09

hello, i would like to ask you a question concerning map manipulations. sometimes i need to manually fit a map into another map, but when saving the map in the new position, it doesn't retain the coordinates. it simply overlays with the original, unmoved maps. is there something i need to do in order to save it in the new position afore hand ? best regards, jean-paul armache

2 1

movie making
by Schulz-Gasch, Tanja 09 Jun '09

09 Jun '09

Hi there, I used Chimera so far only for making pictures. Now I am doing the first movie steps. I want to combine features like hide, show, rock,... with the MD Movie module to show a morph between different protein conformations. How can this be done? The movie should start with the display part (using hide, show, rock,...) followed by the morphing. However, when using the MD movie module the morph starts at frame 1. Thanks, Tanja __________________________________________ Dr. Tanja Schulz-Gasch F. Hoffmann-La Roche Ltd Pharmaceuticals Division PRCBLM Bldg. 92/2.10D CH-4070 Basel Switzerland Tel. +41(0)61 68 88309 Fax. +41(0)61 68 86459 http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html <http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html> Email: tanja.schulz-gasch(a)roche.com <mailto:tanja.schulz-gasch@roche.com> "The information transmitted in this message is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you receive this message in error, please contact the sender and delete the material from any computer."

3 4

loading chimera
by Bala subramanian 08 Jun '09

08 Jun '09

Friends, I installed chimera 1.4 ( build 27677) build in Fedora 10. The installation was successful but when i run chimera, chimera opens with the following message. ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: ignored. In addition, when i try to capture a high resolution image (300 dpi), chimera closed itself with following message. X Error of failed request: GLXBadPbuffer Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) Serial number of failed request: 75435 Current serial number in output stream: 75437 Locking assertion failure. Backtrace: #0 /usr/lib/libxcb-xlib.so.0 [0x19e767] #1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0x19e90e] #2 /usr/lib/libX11.so.6 [0xb690e9] #3 /usr/lib/nvidia/libGL.so.1 [0x6536ffd] Kindly write me what is going wrong. Thanks, Bala

2 1

Segementation Fault
by Kshatresh Dutta Dubey 08 Jun '09

08 Jun '09

Respected Sir, I am using chimera since five months. It was running without any error. But today when i am starting chimera it is giving error like segmentation fault. Kindely help me for this problem. Thanks in advance. Kshatresh Dutta dubey

2 1

Displaying surface residues...
by Yasser Almeida Hernandez 05 Jun '09

05 Jun '09

Hi all... I want to know if its possible display surface residues via python script. The idea is import the chimera module inside the script, and it receive (the script), the pdb file to analyze. The script is to run in a classical bash terminal... Thanks.. ---------------------------------------------------------------- Correo FENHI

3 2

chimera on GM945
by Dmytro Kovalskyy 04 Jun '09

04 Jun '09

Hi there, I experience porblems with chimera running on Lenovo X60t in Linux. graphics: intel GM945 I have two installations on the notebook: WinXP and Linux (ALT Linux 4.1.1). Chimera's benchmark under Windows returns preety nice values (see http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, pre-pre last line, Lenovo ThinkPad X60 Tablet 6363WDP). However under linux I can not get even something reasonable to post Surf - 1 Mesh - 26 Contouring 149 Solid 1 Recoloring 5 Is it natural or due to some bugs in Linux drivers/X/kernel? Thanks in advance Dima -- ----------------------------------------------------- Dmytro Kovalskyy, PhD D.Kovalskyy(a)enamine.net Molecular Modelling Group Leader tel.: +38 044 537 32 18 Enamine ltd. fax : +38 044 537 32 53 23, Matrosova str. 01103 Kiev, Ukraine

3 2

Residues that interact with active site
by Abeer Shokeer 03 Jun '09

03 Jun '09

Hello I have a model structure of my protein and I would like to determine which residues that could take part in active site. Can I do that with Chimera? Thanks for your help Abeer

2 1

Deleting parts of secondary structures
by Anindito Sen 03 Jun '09

03 Jun '09

Dear All I have a Chimera session in which I have 6 sets of PDB files (ribbon representation) showing variability in the structures. However I wish to display only few of the subunits. Questions are: 1. How do I delete undesired subunits from all the chains on the command line 2. How do I select particular residues from specific chains (not all the 6).. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

2 1

ribbon transparency
by hsosa＠aecom.yu.edu 02 Jun '09

02 Jun '09

Hi, Is there a command to control the transparency of a ribbon representation or the whole model ?. I'm trying to fade in an out a molecule (in ribbon + wire atom representation) in movie. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

3 3

Python -send command and IDLE
by cdlau＠ucsd.edu 29 May '09

29 May '09

Hi, I have 2 questions: 1. Is it possible to use send python scripts (with arguments) to an already running Chimera instance? I know that it is possible to use to use the --send feature, however I wasn't able to send argument in with my python script (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html) I want to be able to pass arguments to a already running instance of chimera similar to the --script feature (but this feature forces a new instance of chimera to open). 2. Along the same lines as the first question, is it possible to use terminal and python commands to manipulate color, rotation, etc. in place of using the IDLE? Currently I am working on a project to that requires communicating with a computer running Chimera through "ssh"ing into the computer. I want to be able to use terminal commands to do basic manipulations of the molecules from the other machine. Thanks for all your help in advanced, Chris

3 2

Re: [Chimera-users] Identifying surface residues
by Elaine Meng 29 May '09

29 May '09

On May 29, 2009, at 11:34 AM, Soumya Ghosh (Systembiologie) wrote: > Dear Dr. Elaine Meng, > Thanks a lot for your kind help.Your suggestions helped me a lot. I > tried to ask you another question. If I want to see the > Vanderwaal's interaction between the two molecules, is it also > possible with this software? Can you kindly suggest me how I should > proceed further. Also if I want to see different type of bondings > like intramolecular / intermolecular: covalent or ionic or any > sorts is it possible to see with this CHIMERA. > Eagerly waiting for your kind reply, > Thanks with regards, > Soumya Dear Soumya, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me directly, unless you are including private data. You can use Chimera to show all kinds of interactions, but it may be necessary to take a little time to become familiar with the tools and with Chimera in general. You can use "Help... Search Documentation" to look for topics such as "find interactions". See the tools "FindHBond" (equivalent command "findhbond") and "Find Contacts/Clashes." Both tools are under "Tools... Structure Analysis" in the menu. You can click the "Help" button on each tool to see its manual page. Both tools provide ways to control whether you are looking at intermolecular or intramolecular interactions. These tools are also used in the Structure Analysis and Comparison tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> Of course, covalent bonds are shown as connections in the graphics window. Metal coordination bonds are shown with dashed pseudobonds. FindHBond identifies hydrogen bonds, which could include both polar and charged groups. To only find salt bridges (H-bonds between charged groups), you could either get the total results and filter them yourself, or you can select only charged groups beforehand and then tell FindHBond to only use the selected atoms. More detailed instructions can be found in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/ 003602.html> Find Contacts/Clashes finds contacts of all kinds. To only find some subset of those, you could either filter the output, or limit the input, similar to the situation for FindHBond described above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu 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

1 0

Supersample
by hsosa＠aecom.yu.edu 27 May '09

27 May '09

When using using supersample > 1 to record a movie the movies are not saved correctly (black or random color images) In the command script below the saved movies are OK if the option supersample 3 is eliminated and wrong if included. reset p1 movie record supersample 3 reset p2 reset p8 10 movie stop movie encode output test2.avi mformat avi I'm I doing something wrong ?. I'm running the daily build version of Chimera (May 25). Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

4 7

Request for advice on Protein Structure Alignment
by Elaine Meng 27 May '09

27 May '09

On May 26, 2009, at 8:46 AM, Madhura Rale wrote: > Dear Dr. Meng, > I am a post-doctoral researcher working in the the Lab of Prof. W. > D. Fessner, Technical University of Darmstadt, Germany. We work in > the area of Biocatalysis and I am an organic chemist by training. > > We are currently looking for an online software / tool to compare > the active sites of two proteins whose structures are already known. > Our work focuses mainly on the utility of these protein catalysts > for chemoenzymatic syntheses. > > My query is that, if the structures of these two proteins has > already been determined by XRD, is it possible to align their active > site sequences to highlight the similarities of the substrate > binding sites? Would the tools mentioned on your website (list of > online resources for structure superposition) be useful for this > purpose and if so, would it be possible for you to advice on which > would be the best one and how one could go about it? > Our need is to more or less obtain a pictorial comparison of the two > active sites to emphasise on the substrate specificites and > preferences of both the catalysts. I have no experience in such > determinations and I hope that my query is not too unappropriate. > > Thank you. Hoping to be excused for my ignorance and hoping to hear > from you soon, > With warm regards, > Madhura Rale. Dear Dr. Rale, It is a good question -- Unfortunately, there is no simple answer to what is the best method for comparing known structures or active sites -- it generally depends on the specific structures you are comparing! If the two proteins are rather closely related, it is an "easy" case and probably most of the methods will do a fine job. If they are distantly related, it may be that some methods will work and others will not, and which programs are successful will be different for different input proteins. It also depends what you already know, and what you are trying to prove. If you already know that in structure A, residues 10, 12, and 15 correspond to residues 48, 50, and 52 in structure B, then you would simply use any molecular modeling program to superimpose A and B using just those residues. Or, if you already have a sequence alignment of the two proteins, some programs can use that alignment to superimpose the 3D structures. I would just use Chimera to match specific residues, or use a sequence alignment, or even to guess the sequence alignment and then use that to superimpose the structures. I work with Chimera and familiar with it, and know it can do these things. Chimera is not a web server, but can be downloaded free for noncommercial use (Mac, Windows, Linux): <http://www.cgl.ucsf.edu/chimera/index.html> Discussion of how to superimpose structures in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Structure comparison tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> If you try using Chimera and run into difficulties, you can contact me for more specific help. My "online resources" web page <http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html > is separate from Chimera and is specifically limited to: (a) Web servers and databases (there are other programs, e.g. Chimera, that you could download and then use on your own computer) (b) comparisons based on overall structures (there is another large set of programs that instead focus on binding or active site patterns) Thus if you are more interested in comparing the active sites and not so much the overall structure, a general molecular modeling program may be more useful than the servers in that page, but if your proteins are an "easy" case, probably any of the above would be fine. The active site methods mentioned above are mostly for finding other proteins with a similar active site starting with your one structure of interest (not superimposing two proteins you already know about), so they are probably not very relevant to your situation. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu 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

1 0

starting chimera
by Bala subramanian 26 May '09

26 May '09

Friends, I downloaded the latest chimera build and installed it successfully without any error. When i give chimera in command line, i get the following error. But when i start the chimera 1.3 version, it works without any problem. I am using the latest build in Fedora 10. Traceback (most recent call last): File "/usr/local/chimera_new/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/usr/local/chimera_new/share/chimeraInit.py", line 374, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "CHIMERA/share/chimera/tkgui.py", line 2587, in initializeGUI File "/usr/local/chimera_new/lib/python2.5/site-packages/PIL/__init__.py", line 309, in checkConfig File "/usr/local/chimera_new/lib/python2.5/site-packages/Togl.py", line 27, in __init__ Tkinter.Widget.__init__(self, master, "togl", cnf, kw) File "/usr/local/chimera_new/lib/python2.5/lib-tk/Tkinter.py", line 1930, in __init__ (widgetName, self._w) + extra + self._options(cnf)) _tkinter.TclError: couldn't choose pixel format Couldn't configure togl widget Thanks, Bala

2 1

Chimera API
by christopher lau 26 May '09

26 May '09

Hi, Does anyone have any documentation on the chimera API? I want to familiarize myself more with the commands that can be used in the Chimera IDLE and python scripts. I have looked at the Example tutorials ( http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/) but aside from the commands used in the tutorial I do not know how to perform other actions on the molecule. One of the commands I would like to run is to rotate the molecule ("roll", in the command line) using IDLE commands. Thanks for your help, Chris

3 2

nmrclust additional request
by Austin B. Yongye 22 May '09

22 May '09

Hi chimera-users/developers, Is there a way to save all the structures (not only the representative structures) of all the clusters identified from an ensemble cluster analysis into their respective clusters? The g_cluster tool of gromacs does these, but I don't think it uses Kelley values to determine the optimal number of clusters. Any help will be greatly appreciated. I would like to perform further analyses on each cluster. Thanks, Austin-

3 2

define attribute error
by Roberto Kopke Salinas 22 May '09

22 May '09

Dear All, I am trying to color code a structure according to HetNOE. When I load the attribute list using "Define Attribute" via the "Structure Analysis" menu the program does not automatically open the "Render by Attribute" menu. If I click and open the "Render by Attribute" menu, the program does not show my file in the attributes list for residues. Does anyone have an idea of why this happen? I have pasted my attribute's list below. Thank you, Roberto attribute: teste recipient: residues :377.000000 0.842818 :378.000000 1.273292 :379.000000 0.763398 :384.000000 0.852818 :387.000000 0.999787 :388.000000 0.572572 :389.000000 1.016109 :393.000000 0.950908 :397.000000 0.761818 :399.000000 0.712411 :402.000000 0.388721 :403.000000 0.495060 :408.000000 0.460664 :411.000000 0.973597 :412.000000 1.036187

2 2

Aspect ratio
by hsosa＠aecom.yu.edu 21 May '09

21 May '09

Is there a way to specify the aspect ratio of the display window. Let say that I want to make sure that it is 4 by 3 or 16 by 9. I want to make chimera movies that are easy to merge with still images using some video editing programs (e.g. Windows MovieMaker) and these programs assume some standard video formats (with a given aspect ratio). The results when using movie clips and images created with arbitrary and different aspect ratios is not very good (jumpy transitions) so I would like to create all images and movie clips with the same (standard) aspect ratio. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

2 1

povray error using surfrepr mesh
by Sebastian Kruggel 20 May '09

20 May '09

Dear Chimera-users and team, I tried to generate a POV-Ray image making use of mesh style surface by > surfrepr mesh When I go to 'save image' with activated POV-Ray option, I get the attached error message. I tried several versions ('stable' and daily build, linux and windows) and different molecules but it doesn't work out. Isn't it possible to get raytraced mesh-surface pictures in chimera or do I miss anything? Thanks in advance and best regards Sebastian Kruggel -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel +49 (0)40 42838-3626 (-3484) kruggel(a)chemie.uni-hamburg.de Surface ANP_in_1j1bB, category main, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 345.475 Total solvent accessible surface area = 606.13 running "/usr/local/chimera/bin/povray" "/home/kruggel/chimera/4wiebke/image.ini" "+I/home/kruggel/chimera/4wiebke/image.pov" "+O/home/kruggel/chimera/4wiebke/image.png" "+V" povray: cannot open the user configuration file /home/kruggel/.povray/3.6/povray.conf: No such file or directory Persistence of Vision(tm) Ray Tracer Version 3.6.1 (g++ -pipe -ansi -pthread -fPIC -I/home/chimera/chimeraBuild_X11/build/build/include 3.3.4 @ i686-pc-linux-gnu) This is an unofficial version compiled by: UCSF Chimera <chimera(a)cgl.ucsf.edu> The POV-Ray Team(tm) is not responsible for supporting this version. POV-Ray is based on DKBTrace 2.12 by David K. Buck & Aaron A. Collins Copyright 1991-2003 Persistence of Vision Team Copyright 2003-2004 Persistence of Vision Raytracer Pty. Ltd. Primary POV-Ray 3.5/3.6 Developers: (Alphabetically) Chris Cason Thorsten Froehlich Nathan Kopp Ron Parker Contributing Authors: (Alphabetically) Steve Anger Eric Barish Dieter Bayer Steve A. Bennett David K. Buck Nicolas Calimet Aaron A. Collins Chris Dailey Steve Demlow Andreas Dilger Alexander Enzmann Dan Farmer Mark Gordon Christoph Hormann Mike Hough Chris Huff Kari Kivisalo Lutz Kretzschmar Jochen Lippert Pascal Massimino Jim McElhiney Douglas Muir Juha Nieminen Bill Pulver Eduard Schwan Wlodzimierz Skiba Robert Skinner Yvo Smellenbergh Zsolt Szalavari Scott Taylor Massimo Valentini Timothy Wegner Drew Wells Chris Young Other contributors are listed in the documentation. Support libraries used by POV-Ray: ZLib 1.2.3, Copyright 1995-1998 Jean-loup Gailly and Mark Adler LibPNG 1.2.16, Copyright 1998-2002 Glenn Randers-Pehrson LibJPEG 6b, Copyright 1998 Thomas G. Lane LibTIFF 3.8.0, Copyright 1988-1997 Sam Leffler, 1991-1997 SGI Redirecting Options All Streams to console..........On Debug Stream to console.........On Fatal Stream to console.........On Render Stream to console........On Statistics Stream to console....On Warning Stream to console.......On Parsing Options Input file: /home/kruggel/chimera/4wiebke/image.pov (compatible to version 3.61) Remove bounds........On Split unions.........On Library paths: /usr/local/chimera/share/povray-3.6 /usr/local/chimera/share/povray-3.6/ini /usr/local/chimera/share/povray-3.6/include /usr/local/chimera/share/fonts Output Options Image resolution 1730 by 1280 (rows 1 to 1280, columns 1 to 1730). Output file: /home/kruggel/chimera/4wiebke/image.png, 24 bpp PNG Graphic display......Off Mosaic preview.......Off CPU usage histogram..Off Continued trace......Off Tracing Options Quality: 9 Bounding boxes.......On Bounding threshold: 1 Light Buffer.........On Vista Buffer.........On Draw Vista Buffer....Off Antialiasing.........On (Method 1, Threshold 0.300, Depth 3, Jitter 1.00) Clock value: 0.000 (Animation off) 0:00:00 Parsing File: /home/kruggel/chimera/4wiebke/image.pov Line: 92 Parse Warning: Should have at least 2 objects in csg.

2 1

POV-RAY tracing in Mac OSX (a workaround)
by Miguel Ortiz Lombardia 20 May '09

20 May '09

Hi, I'm almost sure that this problem has been reported here... but couldn't find anything about it. When I try to ray-trace [Chimera 1.3 build 2572 (Darwin/aqua)] I consistently get this error: File Context (5 lines): } object { text { ttf "verdana.ttf" "$" 0.01, 0 texture Parse Error: Cannot open font file. It appears even if I have no labels on the image. I managed to solve the problem but only when I asked for the povray intermediate files not to be deleted and then manually edit them: A) image.ini file: I changed the line: Library_Path="/Applications/Chimera.app/Contents/Resources/share/fonts/" to Library_Path="/Applications/Chimera.app/Contents/Resources/share/fonts/ freefont/" B) image.pov file: All calls to verdana.ttf were changed to FreeSans.ttf It would be great if you point me to an easier solution or if you could make such changes in the code. Thanks! Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

2 1

residue order for match/rmsd
by Klaus Kopec 19 May '09

19 May '09

Hi everybody, at first I would like to thank you for Chimera, it's the best structure viewer I am aware of! Now to my question: I would like to match residues in two structures, but not in the numerical order. My expectation was that if I run "match #0:1,2,3@CA #1:3,2,1@CA" I would end up with least squares fitted coordinate pairs (#0:1, #1:3), (#0:2, #1:2) and (#0:3, #1:1). What I get, however, is a least-squares fit of pairs (#0:1, #1:1), (#0:2, #1:2) and (#0:1, #1:3). Is it possible to use the order of coordinate pairs given in the command line (e.g. pair first specified coordinate of protein 1 with first specified coordinate of protein 2, second with second, etc.) instead of the numerical order of the residue numbers? I would be really glad if someone could help me out on this! Klaus PS: I use Chimera 1.3.2577 under a 64-Bit Kubuntu. I also tried some older (1.2.something) version which gave the same results.

2 2

2d labels and pov-ray option
by Bala subramanian 19 May '09

19 May '09

Friends, I opened a molecule, made some 2d labels and saved the image in jpeg format. But the 2d labels are not apperaing in the final picture. What could be the reason for the same ? When i try to set POV-RAY as True and save the image, the POV-RAY progress till 98% and stays for longtime but dosent save the image. Has anyone come across such problems before ? Thanks, Bala

2 1

residue order for match/rmsd
by Klaus Kopec 19 May '09

19 May '09

Hi everybody, at first I would like to thank you for Chimera, it's the best structure viewer I am aware of! Now to my question: I would like to match residues in two structures, but not in the numerical order. My expectation was that if I run "match #0:1,2,3@CA #1:3,2,1@CA" I would end up with least squares fitted coordinate pairs (#0:1, #1:3), (#0:2, #1:2) and (#0:3, #1:1). What I get, however, is a least-squares fit of pairs (#0:1, #1:1), (#0:2, #1:2) and (#0:1, #1:3). Is it possible to use the order of coordinate pairs given in the command line (e.g. pair first specified coordinate of protein 1 with first specified coordinate of protein 2, second with second, etc.) instead of the numerical order of the residue numbers? I would be really glad if someone could help me out on this! Klaus PS: I use Chimera 1.3.2577 under a 64-Bit Kubuntu. I also tried some older (1.2.something) version which gave the same results.

1 0

Principal axis of inertia
by A. Di Fenza 18 May '09

18 May '09

Hi Tom, I saw your message on the web and I tried to use your script on Chimera 1.3. Unfortunately it does not work, it give me the following message: 0 models opened Do you think it is because of the Chimera version? Do you have suggestion? Thank you very much, Armida Oops. That script I posted for calculating the inertia of a molecule had some problems. The printed matrix of axes was transposed though the correct axes were used for the displayed ellipsoid. Also I was using inertia matrix I_ij = sum_over_k(m_k*r_ki*r_kj) omitting the diagonal term. Should have been I_ij = sum_over_k(m_k*(|r_k| - r_ki*r_kj)). And finally I incorrectly computed the ellipsoid size along each axis. Everything was a little bit wrong. Here's the fixed version. Tested in Chimera version 1.2500 but should work with earlier versions. Tom

5 6

multiple morphs
by Charles Midgett 18 May '09

18 May '09

Dear Chimera developers, I am trying to make a movie of how we think domains of our complex interact. Essentially, there will be three morphs, made from different pdb files, that need to be displayed simultaneously. How can I get the three trajectories to happen at the same time? Sincerely, Charles Midgett

2 1

Saving Render by Attribute Values
by Kevin Wu 18 May '09

18 May '09

Hi all, I'm having trouble saving some data to the session. I've rendered a figure using the "render/select by attribute" by either the occupancy or beta field in a pdb file. However, when I save session and restore it, the colors that I've chosen seem to be erased, and need to be reset again. Is there a way to save this data? Thanks in advance! Kevin Wu

4 4

fit map --nogui
by sean connell 18 May '09

18 May '09

Hello, I am having some problems using/adapting a script I found by searching the mailing list. The script is pasted below but to summarize it should print out the transformation matrix used to fit one map to another. In principle I would like to do the same but in addition to writing out the matrix I would also like to apply it and save the resulting map. I am currently using chimera 1.4 build 27496 (Aqua on OSX 10.5.7) the first problem I have is just invoking the python interpreter..... if I use: Chimera.app/Contents/MacOS/chimera --nogui fittomap.py Executing fittomap.py... Traceback (most recent call last): File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ __main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimeraInit.py", line 407, in init chimera.openModels.open(a, prefixableType=1) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimera/__init__.py", line 1357, in open models = func(filename, *args, **kw) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimera/__init__.py", line 794, in _openPython loadFunc(sandboxName, fileName, f) File "fittomap.py", line 70, in <module> fit_map_in_map(p1, p2) File "fittomap.py", line 24, in fit_map_in_map from VolumeViewer import Data_Region, full_region, Rendering_Options ImportError: cannot import name Data_Region Error while processing fittomap.py: ImportError: cannot import name Data_Region (see reply log for Python traceback info) # ----------------------------------------------------------------------------- # Example script for fitting one map in another without the graphical user # interface. # # chimera --nogui fitnogui.py # # It can also be run using the graphical Chimera interface using File/ Open. # def fit_map_in_map(map1_path, map2_path, initial_map1_transform = None, map1_threshold = None, ijk_step_size_min = 0.01, # Grid index units ijk_step_size_max = 0.5, # Grid index units max_steps = 100, optimize_translation = True, optimize_rotation = True): # Files have to have file suffix indicating volume format. from VolumeData import open_file data1 = open_file(map1_path) data2 = open_file(map2_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map1 = Data_Region(data1, full_region(data1.size), '', ro) map2 = Data_Region(data2, full_region(data2.size), '', ro) if initial_map1_transform: from PDBmatrices.matrices import chimera_xform xf = chimera_xform(initial_map1_transform) map1.surface_model().openState.globalXform(xf) use_threshold = (map1_threshold != None) from FitMap import map_points_and_weights, motion_to_maximum points, point_weights = map_points_and_weights(map1, use_threshold) if len(points) == 0: if use_threshold: print 'No grid points above map threshold.' else: print 'Map has no non-zero values.' return move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps, ijk_step_size_min, ijk_step_size_max, optimize_translation, optimize_rotation) if initial_map1_transform: from PDBmatrices.matrices import multiply_matrices move_tf = multiply_matrices(move_tf, initial_map1_transform) header = ('\nFit map %s in map %s using %d points\n' % (map1.full_name(), map2.full_name(), stats['points']) + ' correlation = %.4g, overlap = %.4g\n' % (stats['correlation'], stats['overlap']) + ' steps = %d, shift = %.3g, angle = %.3g degrees\n' % (stats['steps'], stats['shift'], stats['angle'])) print header from FitMap.gui import transformation_description tfs = transformation_description(move_tf) print tfs # ----------------------------------------------------------------------------- # Example call fitting map into itself. # p1 = p2 = '/usr/local/src/chimera-demos/volume/examples/groel.mrc' fit_map_in_map(p1, p2)

2 1

Solvent Occupancy Calculation
by Saikumar Ramadagu 18 May '09

18 May '09

Hi Elaine, I know people in the past have asked a question about the solvent Occupancy Calculation, but please help me. I have an oligosaccharide simulaiton trajectory from AMBER9. I used a 100ps trajectory for solvent occupancy calculation using Chimera. Everything looks absolutely fine. The questions I have are as follows: I have 0-220 in my levels section of volume viewer. If I fix the level of 80, what does that mean? When I'm sliding the bar of levels from left-right what information about solvent density am I obtaining? For example does a value of 80 mean low density when compared with a value of 70? or is it the other way? When I have two different oligosaccharide simulations and I want to say that oligosaccharide 1 has more water density around it, what value of levels should I choose? What I mean by this statement is do I select same value of levels? or do I calculate the percentage i.e., 80/220 for first model gives me 36% and for second sugar if the levels are 0-300 the i should choose a level of 109 which gives 36%? Also is there any reference paper by which Chimera calculates the solvent occupancy? Thanks very much for your time Sai

2 1

Formation of coordination bond
by Enrico Morelli 18 May '09

18 May '09

Dear all, We would like to know if is it possible, when we have two molecules docked together, to form a coordination bond between a metal ion present in one of the two molecules and a donor atom of the other molecule, in such way forming a covalent bond between the two proteins. Thanks -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

3 2

A request
by Soumya Ghosh (Systembiologie) 18 May '09

18 May '09

Dear Chimera, Thanks for giving such a wonderful software for molecular modelling. I am a PhD student in Germany and using the CHIMERA programme for my molecule. I want to increase the font and the font size of the highlighted amino acid in my protein and thats why I was trying in the Command: Tools - Utilities - Colour key where there is a option for font size but so far remain unsuccessful. Can you kindly advise me how I should proceed. Waiting eagerly for your kind reply, Soumya Ghosh, TUM, Freising, Germany

2 6

Verify integer/non-integer charges in mol2
by Francesco Pietra 18 May '09

18 May '09

Hi: I assigned Amber ff99SB charges to a proven pdb file of standard amino acids and capping groups (ACE NME), saving as mol2. Conversion to a pdbqt file with ATD (autodock tool) resulted in non-integer charge (-5...). Unless something occurred that escaped my attention, the protein has -5.00000 charge. My question: how to verify a posteriory the total charge in the Chimera-written mol2 file, in order to trace back were I have blurred things? I don't see the total in the mol2 file. Thanks francesco pietra

2 2

Morphing with two models
by Enrico Morelli 18 May '09

18 May '09

Dear all, I'm a new chimera user and I'm asking about morphing. I've two models and I'm able to move one to contacts the other. But what if I need to move both to converge on a specific center? There is some shortcut? Thanks to all -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

2 4

apple ui
by Nils Becker 15 May '09

15 May '09

hi, just a quick user interface suggestion: it would be great if mouse-over over all directory listings (when choosing files to load etc) could activate the mouse wheel for both x and y scrolling. right now, only placing the cursor directly over the scroll bars allows scrolling by mouse wheel, and there is only one mouse wheel axis to scroll with. i am on mac is x 10.5.6 and using a recent native snapshot cheers, nils

3 3

Floating exception
by hsosa＠aecom.yu.edu 14 May '09

14 May '09

Hi, I am having the following problem with the latest production version of Chimera (1.3) on a linux computer. Chimera crash and exit after doing some actions like rotating a molecule several times or simply trying to open the side-view window. After the program ends there is a Floating exception message in the console. The problem occur with the latest production release (1.3) and daily build versions but not with an older production version of chimera (1). I installed the latest nvidia driver but this didn't solve the problem. I am running the old linux 2.4 kernel (Suse 9.0) and I am not sure if this has anything to do with the problem . I am hesitant to upgrade the OS and break all the other programs that now work in this machine (you got to love linux :-)) Thanks Hernando Computer: Dual Xeon processor. Graphic card: NVIDIA Quadro4 XGL 9800 OS: Linux Suse 9.0 UCSF Chimera 1.3 Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

2 1

DMS citation
by Ben Keshet 14 May '09

14 May '09

Hi, I have used DMS to calculate accessible surface prior to the usage of Dock6. Is there any specific citation for the DMS application? Thank you, Ben Keshet Chemical Engineering UMBC

1 0

surface spanning multiple models
by Nils Becker 14 May '09

14 May '09

Hi, is it possible to define surfaces that seamlessly span multiple models? when i define a surface category spanning multiple models, i always get distinct surfaces around each model. saving as a single pdb and re-importing does not help, since then i have the same problem with multiple submodels... thanks for any help! cheers, nils

2 1

Multiple sequence alignment
by Avner Schlessinger 13 May '09

13 May '09

Dear Chimera experts, Once I create multiple structure alignment i was wondering how I can view the corresponding multiple sequence alignment. when I try to view it through the MultiAlignViewer it shows all possible pairwise alignments with the sequence of the first structure rather than all the sequences together. Thanks! Avner -- Avner Schlessinger, Ph.D. Department of Bioengineering and Therapeutic Sciences Mission Bay, Byers Hall 1700 4th Street, Suite 501 University of California, San Francisco San Francisco, CA 94158-2330 Tel +1 (415) 514-4258 Fax +1 (415) 514-4231

2 1

a small suggestion
by Jean Didier Pie Marechal 13 May '09

13 May '09

Hello everyone, just a small suggestion to the team. Could it be possible that, when clicking on a given angle/torsion in the Structure measurments panel, the involved atom/bond get selected in the visualizer? cheers 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: Dimarts, Maig 12, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 13 > 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: chimera performance (Greg Couch) > 2. adding pseudo bonds (Jean Didier Pie Marechal) > 3. Re: adding pseudo bonds (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 11 May 2009 14:32:22 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] chimera performance > To: Bala subramanian <bala.biophysics(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0905111420070.1959390(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > I have had bad luck with NVidia drivers packaged as RPMs. Instead > I > recommend that you uninstall the RPM you got from rpmfusion.org and > install the NVidia driver from NVidia at > <http://www.nvidia.com/Download/index.aspx>. The "Nvidia.com > Binary > Installer" option given the webpage you cited. As mentioned there, > the > disadvanatge of NVIdia's driver is that you need to reinstall it > every > time your update your kernel -- otherwise the X server won't start. > After > a successful install (and reboot), glxinfo should tell you which > OpenGL > renderer you have and chimera should work too. > > Good luck, > > Greg > > On Fri, 8 May 2009, Bala subramanian wrote: > > > Dear Greg, > > After installing nvidia graphics drivers, i am not able to open > chimera. I > > have attached the xconfig file and the output of glxinfo as text > files.> > > *[cbala@ramana ~]$ chimera > > 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 309, in checkConfig > > > > File "/usr/local/chimera/lib/python2.5/site-packages/Togl.py", > line 27, in > > __init__ > > Tkinter.Widget.__init__(self, master, "togl", cnf, kw) > > File "/usr/local/chimera/lib/python2.5/lib-tk/Tkinter.py", line > 1930, in > > __init__ > > (widgetName, self._w) + extra + self._options(cnf)) > > _tkinter.TclError: could not create rendering context > > Couldn't configure togl widget* > > > > I installed the nvidia driver as follows. I installed it based on > the> information given in the nvidia install guide in the following > link.> > > http://www.mjmwired.net/resources/mjm-fedora-nvidia.html#pci_id > > > > su -c 'rpm -ivh > > http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release- > stable.noarch.rpm> ' > > su -c 'rpm -ivh > > http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree- > release-stable.noarch.rpm > > ' > > su -c 'rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-rpmfusion-*' > > su -c 'yum install kmod-nvidia' > > > > Then i gave the following command > > > > nvidia-xconfig as root. Then i restarted the system. Now i am > able to see > > nvidia display setting. When i give chimera, it dosent work. > > > > Bala > > > > On Thu, May 7, 2009 at 8:44 PM, Greg Couch <gregc(a)cgl.ucsf.edu> > wrote:> > >> Looking at your chimera benchmark scores and at the scores on > the web page, > >> http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, it > looks like > >> you don't have the NVidia graphics driver installed. And that > would make a > >> *huge* difference. To double-check, run the glxinfo command and > look at the > >> "OpenGL renderer string:" line, it should have NVIDIA in it > instead of Mesa. > >> To get the NVidia drivers, go to < > >> http://www.nvidia.com/Download/index.aspx>. > >> > >> - Greg > >> > >> > >> On Thu, 7 May 2009, Bala subramanian wrote: > >> > >> Dear Greg, > >>> You are right. Previously it was normal but now it is slow. I > havent>>> updated > >>> the kernel. I checked and noticed that i dnt have any memory > intensive>>> background jobs also. > >>> > >>> I did benchmarks with two chimera versions 1.3 (attached file > chim_test)>>> and > >>> chimera 1.4 (attached chim_test1). > >>> My graphics card is nVIDIA GETFORCE 9300MG, VRAM: 256 MB. I dnt > know how > >>> to > >>> compare and judge what is going wrong. I wud appreciate your > help on the > >>> same. > >>> > >>> Thanks, > >>> Bala > >>> > >>> So it was formerly fast on the same computer? This could > happen on a > >>> Linux > >>> > >>>> computer if you updated the kernel and forgot to reinstall the > graphics>>>> driver (from ATI or NVidia, the open source 3D drivers > still need work, > >>>> but > >>>> are improving). Another possibility, on all operatings > sytems, is that > >>>> there is a background process that is using a lot of CPU or > memory, so > >>>> chimera doesn't have the resources it used to. > >>>> > >>>> If you just want to check the graphics performance, then you > can use the > >>>> Benchmark tool in Tool / Utilities to guage the current > performance. And > >>>> then you can compare to the reported scores to see if your > graphics>>>> performance is reasonable (the Show button in the > Benchmark tool brings > >>>> up > >>>> the web page). > >>>> > >>>> - Greg > >>>> > >>>> > >>> > > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 May 2009 17:19:46 +0200 > From: Jean Didier Pie Marechal <JeanDidier.Marechal(a)uab.cat> > Subject: [Chimera-users] adding pseudo bonds > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <165553c1104b.4a09afb2(a)uab.es> > Content-Type: text/plain; charset=iso-8859-1 > > Dear all, > > what is the way to add pseubond between metal and chelating atoms? > if you could tell me what are the "mouse driven" and "script > driven" manner I'll be very pleased.... > all the best, > JD > > > Dr. Jean-Didier Mar?chal > Lecturer > Computational Biotechnological Chemistry @ Transmet > Unitat de Qu?mica F?sica > Departament de Qu?mica > Universitat Aut?noma 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: Diumenge, Maig 10, 2009 9:00 pm > Assumpte: Chimera-users Digest, Vol 73, Issue 11 > > > 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. Protonate heteroatoms only (Francesco Pietra) > > 2. Re: Protonate heteroatoms only (Eric Pettersen) > > > > > > ------------------------------------------------------------------ > -- > > -- > > > > Message: 1 > > Date: Sat, 9 May 2009 23:35:37 +0200 > > From: Francesco Pietra <chiendarret(a)gmail.com> > > Subject: [Chimera-users] Protonate heteroatoms only > > To: chimera <chimera-users(a)cgl.ucsf.edu> > > Message-ID: > > <b87c422a0905091435q4a1671e2td61284cf092e7fb6(a)mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Hi: > > Is there a command in Chimera to protonate (Sybyl-type) the > > heteroatoms only (or deprotonate the other elements from a fully > > protonated protein)? > > thanks > > francesco pietra > > > > > > ------------------------------ > > > > Message: 2 > > Date: Sat, 9 May 2009 15:27:55 -0700 > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Subject: Re: [Chimera-users] Protonate heteroatoms only > > To: Francesco Pietra <chiendarret(a)gmail.com> > > Cc: chimera <chimera-users(a)cgl.ucsf.edu> > > Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30(a)cgl.ucsf.edu> > > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > del HC > > > > will delete all hydrogens bonded to carbons (their IDATM types > are > > HC). > > --Eric > > > > Eric Pettersen > > USCF Computer Graphics Lab > > > > On May 9, 2009, at 2:35 PM, Francesco Pietra wrote: > > > > > Hi: > > > Is there a command in Chimera to protonate (Sybyl-type) the > > > heteroatoms only (or deprotonate the other elements from a fully > > > protonated protein)? > > > thanks > > > francesco pietra > > > _______________________________________________ > > > Chimera-users mailing list > > > Chimera-users(a)cgl.ucsf.edu > > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > ------------------------------ > > > > _______________________________________________ > > 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 73, Issue 11 > > ********************************************* > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 12 May 2009 08:39:11 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] adding pseudo bonds > To: JeanDidier.Marechal(a)uab.es > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <06B51782-B5EB-487A-B770-ACA04AA2D738(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi JD, > The "user interface" (i.e. no programming) way is to create a text > file listing the desired pseudobonds and their colors and read it > in > with PseudoBond Reader. The tool and file format are described here: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.… > > > > I don't know the python way, but perhaps looking in the code for > PseudoBond Reader will help ( share/PBReader/ within your Chimera > installation). > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > 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 May 12, 2009, at 8:19 AM, Jean Didier Pie Marechal wrote: > > > Dear all, > > > > what is the way to add pseubond between metal and chelating atoms? > > if you could tell me what are the "mouse driven" and "script > driven" > > manner I'll be very pleased.... > > all the best, > > JD > > > > ------------------------------ > > _______________________________________________ > 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 73, Issue 13 > ********************************************* >

2 1

Compiling chimera from source code
by cdlau＠ucsd.edu 13 May '09

13 May '09

Dear Madam/Sir, I am currently involved in a project which requires compiling the Chimera source code from scratch. I have been using: http://www.cgl.ucsf.edu/chimera/sourcecode.html for reference, and I understand that surfacing library is not available due to licensing issues. Because I am not interested in using this feature, I wanted to know if it was still possible to compile the Chimera source code. I know that it will be difficult but any knowledge or past experience that may help me would be greatly appreciated. Thanks in advance, Chris

2 1

adding pseudo bonds
by Jean Didier Pie Marechal 12 May '09

12 May '09

Dear all, what is the way to add pseubond between metal and chelating atoms? if you could tell me what are the "mouse driven" and "script driven" manner I'll be very pleased.... all the 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: Diumenge, Maig 10, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 11 > 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. Protonate heteroatoms only (Francesco Pietra) > 2. Re: Protonate heteroatoms only (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Sat, 9 May 2009 23:35:37 +0200 > From: Francesco Pietra <chiendarret(a)gmail.com> > Subject: [Chimera-users] Protonate heteroatoms only > To: chimera <chimera-users(a)cgl.ucsf.edu> > Message-ID: > <b87c422a0905091435q4a1671e2td61284cf092e7fb6(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi: > Is there a command in Chimera to protonate (Sybyl-type) the > heteroatoms only (or deprotonate the other elements from a fully > protonated protein)? > thanks > francesco pietra > > > ------------------------------ > > Message: 2 > Date: Sat, 9 May 2009 15:27:55 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Protonate heteroatoms only > To: Francesco Pietra <chiendarret(a)gmail.com> > Cc: chimera <chimera-users(a)cgl.ucsf.edu> > Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > del HC > > will delete all hydrogens bonded to carbons (their IDATM types are > HC). > --Eric > > Eric Pettersen > USCF Computer Graphics Lab > > On May 9, 2009, at 2:35 PM, Francesco Pietra wrote: > > > Hi: > > Is there a command in Chimera to protonate (Sybyl-type) the > > heteroatoms only (or deprotonate the other elements from a fully > > protonated protein)? > > thanks > > francesco pietra > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > _______________________________________________ > 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 73, Issue 11 > ********************************************* >

3 2

chimera performance
by Bala subramanian 11 May '09

11 May '09

Friends, Is there any way to check the performance of chimera. I have been using chimera without any problems but now it is very slow, in opening even a small dna molecule and manipulating. Is there any way that i can check the root of the problem. Thanks, Bala

2 6

any aid for dock3.5 score?
by Francesco Pietra 11 May '09

11 May '09

Hi: I am considering to use dock3.5 score in DOCK6.2, which makes use of Delphi. Is any aid in chimera for builing the grid? thanks francesco

2 3

Protonate heteroatoms only
by Francesco Pietra 09 May '09

09 May '09

Hi: Is there a command in Chimera to protonate (Sybyl-type) the heteroatoms only (or deprotonate the other elements from a fully protonated protein)? thanks francesco pietra

2 1

changing diameter of the cylinders in bs representation
by Jean Didier Pie Marechal 08 May '09

08 May '09

Dear all, I know how to change the size of the balls using the vdwdefine, but I don't see the command/option to change the diameter of the cylinder in bs representation. Can I do this? 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: Dijous, Maig 7, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 7 > 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: chimera performance (Greg Couch) > 2. volume filtering (Thomas C. Marlovits) > 3. Re: volume filtering (Tom Goddard) > 4. Re: any aid for dock3.5 score? (Elaine Meng) > 5. Re: chimera performance (Bala subramanian) > 6. Re: chimera performance (Greg Couch) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 6 May 2009 12:23:38 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] chimera performance > To: Bala subramanian <bala.biophysics(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0905061215200.1920327(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Wed, 6 May 2009, Bala subramanian wrote: > > > Friends, > > > > Is there any way to check the performance of chimera. I have been > using> chimera without any problems but now it is very slow, in > opening even a > > small dna molecule and manipulating. Is there any way that i can > check the > > root of the problem. > > > > Thanks, > > Bala > > So it was formerly fast on the same computer? This could happen on > a > Linux computer if you updated the kernel and forgot to reinstall > the > graphics driver (from ATI or NVidia, the open source 3D drivers > still need > work, but are improving). Another possibility, on all operatings > sytems, > is that there is a background process that is using a lot of CPU or > memory, so chimera doesn't have the resources it used to. > > If you just want to check the graphics performance, then you can > use the > Benchmark tool in Tool / Utilities to guage the current > performance. And > then you can compare to the reported scores to see if your graphics > performance is reasonable (the Show button in the Benchmark tool > brings up > the web page). > > - Greg > > > ------------------------------ > > Message: 2 > Date: Tue, 5 May 2009 22:34:45 +0200 > From: "Thomas C. Marlovits" <marlovits(a)imp.ac.at> > Subject: [Chimera-users] volume filtering > To: <chimera-users(a)cgl.ucsf.edu> > Message-ID: <019F22EC-BFF8-4612-A1B9-BE4DDA9471E3(a)imp.ac.at> > Content-Type: text/plain; charset="us-ascii" > > HI, > > I am trying to look for the various filtering options as descibed > on > the Chimera webpage (guide to volume data display). Indicated are > Gaussian filtering, Fourier filter, Hide dust, etc ... > unfortunately, > I can only find the Gaussian filter option under TOOLS/VOLUME DATA > > but cannot find the others ... can you point me to these other > options, in particular the Fourier filter ? (am using version 1.3 !) > Tx. > -Thomas > > > > -------------------------------------------------------------------- > ----------- > > Thomas C. Marlovits, PhD, M.A.S. > Research Group Leader > > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences > (IMBA) > > Dr. Bohr-Gasse 3 > Room IMBA/6.02 > A-1030 Vienna > Austria, Europe > > fone: (++43-1) 79044-4630 > fax: (++43-1) 79044-4401 > email: marlovits(a)imp.univie.ac.at > > > > >

2 1

volume filtering
by Thomas C. Marlovits 06 May '09

06 May '09

HI, I am trying to look for the various filtering options as descibed on the Chimera webpage (guide to volume data display). Indicated are Gaussian filtering, Fourier filter, Hide dust, etc ... unfortunately, I can only find the Gaussian filter option under TOOLS/VOLUME DATA but cannot find the others ... can you point me to these other options, in particular the Fourier filter ? (am using version 1.3 !) Tx. -Thomas ------------------------------------------------------------------------------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

2 1

unable to install on SLES 11
by Rajendra P. OJHA 05 May '09

05 May '09

Dear Users, It gives the segmentation fault and icon disappear. How to rectify the problem. Thanks Ojha

2 1

Fwd: Coulombic Surface Coloring
by Francesco Pietra 04 May '09

04 May '09

---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Sun, May 3, 2009 at 11:01 PM Subject: Re: [Chimera-users] Coulombic Surface Coloring To: Eric Pettersen <pett(a)cgl.ucsf.edu> On Sun, May 3, 2009 at 10:50 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Francesco, > How did you find the page describing Coulombic Surface Coloring, did > you Google it? Yes, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi… Anyway, that tool is only in the daily build, and not in > whatever version you are using. You can get a daily build by going to the > Chimera home page (www.cgl.ucsf.edu/chimera) and following the "Daily > Builds" link. You can install in a location different from your current > version if you like. That way you can use the daily build for the surface > coloring, but use the other version if needed (i.e. if you run into a bug). I'll first see if a program to furnish data for Chimera's Electrostatic Surface Coloring is available. Any suggestion? I forgot that have both apbs and delphi executables as components of an installed docking program. > If your protein consists only of standard residues then I see no > reason for you to use your calculated charges -- the pre-computed Amber > charges should be fine. If there are non-standard residues then it's up to > you if you want to use Define Attribute to add the charges to the structure > or instead rely on Chimera's charge-computation capabilities. My "have a file with calculated charges" was misleading, It was a mol2 file saved with Chimera. thanks francesco > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > On May 3, 2009, at 12:07 PM, Francesco Pietra wrote: > >> Hi: >> I would like to simply color the surface of a protein by the Coulombic >> Surface Coloring method. I can show the surface, have a file with >> calculated charges if useful, but i am unable to implement the >> indications below >> >> >> "There are several ways to start Coulombic Surface Coloring, a tool in >> the Surface/Binding Analysis category. >> >> The molecular surface(s) should first be displayed (using Actions... >> Surface... show or the command surface) and then chosen from the list >> of Surfaces to color by ESP. " >> >> which tool should be opened from Surface/Binding Analysis? Of those >> related, I can only see Electrostatic Surface Coloring and that - in >> my hands - does not bring to the simple Coulombic method. >> >> Thanks for clearing >> francesco pietra >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

2 1

NMRCLUST
by Austin B. Yongye 04 May '09

04 May '09

Dear chimera users, Does the NMRCLUST algorithm in the Ensemble Cluster tool use Kelley penalty values (Kelley et al. Protein Engineering, 1996, 9(11), 1063-1065) to determine the optimum number of clusters during a clustering procedure? Thanks, Austin-

2 1

Merging models
by Elaine Meng 04 May '09

04 May '09

On Apr 30, 2009, at 1:45 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote: > Hi everybody, > > I'm working with a pdb file (http://www.rcsb.org/pdb/files/2vxi.pdb1.gz > ) made of two models. I need to merge this two models into one. How > can I do that? > > Thanks in advance, > > Maziar S. Ardejani > Lab 9, The Orner Lab > Division of Chemistry and Biological Chemistry > School of Physical and Mathematical Sciences > 21 Nanyang Link > Nanyang Technological University > Singapore 637371 > Hi Maziar, In general, you can merge models with the "copy/combine" button on the right side of the Model Panel (Favorites... Model Panel) or with the "combine" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> However, I opened 2vxi from the PDB and it is only one model, not two. Maybe you opened it two times by mistake? <http://www.rcsb.org/pdb/explore/explore.do?structureId=2VXI> There are a few cases where structures have so many atoms or chains that the PDB has split them into multiple files (e.g. 3bz1 and 3bz2). If those parts collectively have more than 63 chains it won't work to merge them with Chimera because there are only 63 possible different chain ID symbols. Please send Chimera questions to chimera-users(a)cgl.ucsf.edu and not to me directly, and if possible use an informative "subject" line - thanks! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu 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

5 7

Coulombic Surface Coloring
by Francesco Pietra 03 May '09

03 May '09

Hi: I would like to simply color the surface of a protein by the Coulombic Surface Coloring method. I can show the surface, have a file with calculated charges if useful, but i am unable to implement the indications below "There are several ways to start Coulombic Surface Coloring, a tool in the Surface/Binding Analysis category. The molecular surface(s) should first be displayed (using Actions... Surface... show or the command surface) and then chosen from the list of Surfaces to color by ESP. " which tool should be opened from Surface/Binding Analysis? Of those related, I can only see Electrostatic Surface Coloring and that - in my hands - does not bring to the simple Coulombic method. Thanks for clearing francesco pietra

2 1

recording operations
by Fajer 03 May '09

03 May '09

Dear All, Does Chimera record the "menu" selected operations that can be played back in a manner analogous to storing "command" entered operations ? I'd rather avoid having to modify python script of the stored session. Peter Fajer

2 1

My Chimera 1.4 build 27395 is not keeping 2D Labels when saving images except if Pov-Ray tracing is turned on
by Victor Alves 01 May '09

01 May '09

Hi When I save a picture with 2D Labels, they don't show up in the saved image. I tried with different image types (jpg, tiff, png) and even a new image just with some 2D Labels in it. I don't know if this is important but all of them have a white background. The only way I managed to see the labels was to turn on Pov-Ray tracing! Any ideas? Thank you in advance Victor Alves

2 1

Re: [Chimera-users] pivot point
by Elaine Meng 30 Apr '09

30 Apr '09

On Apr 30, 2009, at 10:51 AM, Tatyana Fedotova wrote: > Dear Mrs. Meng, > I have a question about pivot point. > Could you explain howfor example I can rotate part of a helix from a > chosen pivot point. > I fount how I can selet and move atoms. But that's not what I need. > Thanks, > Tanya Dear Tanya, I can think of two ways to move only part of a structure rather than a whole model: (a) by rotating bonds, see Adjust Torsions, where the bonds define the pivots <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > (b) with Movement Mouse Mode, which is probably what you were talking about <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.… > Although method (b) does not include control over the center of rotation (pivot point), you can set the center of rotation before using that tool. You can set the center of rotation to an atom or centroid of a set of atoms by selecting the atom(s) and using "Actions... Set Pivot" in the menu. Or, you can use the "cofr" command to do the same thing, or if you have a fairly recent version of Chimera (1.4, so a daily build), specify particular X,Y,Z coordinates as the center. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html> The center of rotation set as described above also applies when you are rotating whole models. In newer versions of Chimera (1.4), the rotation commands "roll" and "turn" also allow specifying the center to use when executing that command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu rather than my personal address, unless you are describing private data. Even though I answer a lot of those messages, I might be sick, or on vacation, or not know the answer! Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu 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

1 0

creating volume maps
by Nils Becker 29 Apr '09

29 Apr '09

Hi, I would like to use chimera for measuring the steric accessibility of particular atoms in a structure to reactive species in solution. To do that I had the following idea: 1. create a volume map which represents a solid sphere centered on the atom in question (alternatively, a Gaussian blob), with some chosen radius. 2. mask this sphere using the solvent accessible surface of the protein (for example, if the atom is at the surface and the surface is flat, half of the sphere would be cut away) 3. measure the volume of the remaining piece of the sphere. So now my question is: can this work, and how can I generate the sphere in step 1. ? thanks for any advice! Nils

2 1

color by element
by Eric Pettersen 28 Apr '09

28 Apr '09

On Apr 28, 2009, at 3:31 PM, Thiruvarangan Ramaraj wrote: > Hi Eric, > > I have a question regarding the colouring by element option. > > If I select a surface and I go to colour and choose by element, does > it colour in any order, if so what is the order, how do i find out > what element is given what colour. > > Thanks for your time > > Thiru Hi Thiru, I'm not sure what you mean by "does it colour in any order", but the colors assigned to each element are described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/colortables.html#by… and how you can change them is described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/colordef.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Problem recording raytraced movie
by Tom Goddard 28 Apr '09

28 Apr '09

maya shcushan wrote: > Dear Tom, > Thanks, this was very helpful... > I have a new question: I want to make a simple movie in which the molecule > rotates. Using the commands script I found on the internet, the movie is of > very low quality (attached). Moreover, running it with windows media player > shows the opening in the script, embedded in the movie. This were the > commands: > > "movie record > turn y 3 150 > wait 150 > movie encode mformat avi output spin.avi bitrate 4000" > > I want to record the same movie in good quality, like the pictures I get > with pov-raying. I tried running: > "movie record raytrace true > turn y 3 150 > wait 150 > movie encode mformat avi output spin.avi bitrate 4000" > But it falls all the time. > > I looked in the internet for scripts but didn't find an answer. Can you > please help me to create a simple script in which the molecule rotates and > presented in ray-tracing and high quality? > > Thanksm > Maya > > Hi Maya, In Chimera 1.3 before the movie encode command you need the command "movie stop". movie record raytrace true turn y 3 150 wait 150 movie stop movie encode mformat avi output spin.avi bitrate 4000 Otherwise it keeps on recording frames forever. In Chimera 1.4 (daily builds) this is unnecessary and your original script works correctly because in 1.4 movie encode does a movie stop implicitly. Tom

3 2

measure
by julien(GWDG) 28 Apr '09

28 Apr '09

Dear all, I have the last vesion of chimera 1.4 (27371) under a linux machine. I want to use the measure function. I have two models. The difference between this 2 models is a 5 degree rotation around the x axis. >> matrix rotation #1 #0 >>reply in the log Position of test.pdb (#0) relative to test1.pdb (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 0.00000000 I think the command does not work in this version (if I misunderstood the command please tell me as well). It always give me the same answer for any different models I did try. Since I have to ask my admin each time I want to install something, could you just tell me in which version of chimera this command will work. Many many thanks. best Julien -- European Molecular Biology Laboratory Structural and Computational Biology Unit Meyerhofstraße 1 D-69117 Heidelberg Max-Planck-Institute for Biophysical Chemistry NMR based Structural Biology Am Fassberg 11 D-37077 Göttingen

2 1

noeshow
by Randazzo Antonio 27 Apr '09

27 Apr '09

Hi all, I am new of chimera and I am trying to display the NOEs that I have used in my calculations along with the structured I have obtained. With my big surprise I have discovered that in a previous version of the program (MIDAS) this was possible (by the command NOESHOW), but it seems that this features is not supported in this version of the program. Do you have any clue in how to resolve this? Is there a workaround or I have to use another program? If this is the case, which program (sometimes I need to display an Amber restraint file or a Discover restraint file). Thanks in advance for your help

3 2

Stereo Monitors
by hsosa＠aecom.yu.edu 24 Apr '09

24 Apr '09

Hi, I was wondering if chimera work with one of these stereo monitors that split the image into two opposite circularly polarized images (e.g. MIRACUBE G170S) so that you can use cheap passive glasses, similar to the disposable ones used in some movies. Also I'll be interested If anybody has experience using these monitors. I think they are under $1000 now for a 17' monitor Best Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

3 2

Re: [Chimera-users] Color Key
by YangMingjun 24 Apr '09

24 Apr '09

Dear Professor, Thanks so much. It works well now. Mingjun >Hi Mingjun, >your version is very, very old. For Color Key you need at least the >last production release, version 1.3 from 2008. If you go to the >Chimera home page, > >http://www.cgl.ucsf.edu/chimera/index.html > >there are download links on the left, "production release" for the >most recent production release, and "daily builds" for even newer >ones if you want the things that are described in the "what's new" >link right next to "daily builds." There are release notes for each >version that say what is new in that version. Color Key was a new >feature in the 1.3 release. > >Your version is so old it might not even have those color squares in >the Model Panel that I mentioned before! >Best, >Elaine > > >On Apr 23, 2009, at 6:45 PM, YangMingjun wrote: > >> Dear Professor, >> >> Thanks very much. >> I can't find the Color Key icon in my installed Chimera >> following the step in the link. Is it due to the version I am using? >> I am using Windows os and chimera-1[1].2422-win32.exe >.

1 0

Re: [Chimera-users] Color Key
by YangMingjun 23 Apr '09

23 Apr '09

Dear Professor, Thanks very much. I can't find the Color Key icon in my installed Chimera following the step in the link. Is it due to the version I am using? I am using Windows os and chimera-1[1].2422-win32.exe Mingjun >I forgot to mention that you can drag colors from the squares in the >Model Panel to the squares in the Color Key dialog. That is probably >the easiest way to make the intermediate colors match. >Best, >Elaine > >On Apr 23, 2009, at 9:32 AM, Elaine Meng wrote: > >> Dear Mingjun, >> Oh, now I see -- you want a color key! Yes, you can do that in >> Chimera: choose Tools... Utilities... Color Key. In that dialog you >> can set the colors and the value labels. You can click and drag with >> the mouse to draw the key in the Chimera window. If you need more >> text, you can add it with 2D Labels, which is another tab on the same >> dialog as Color Key. >> >> Here is the full description: >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ >> 2dlabels.html#colorkey> >> >> and here is an example image with both Color Key and 2D Labels: >> <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> >> >> You would add that stuff while you are still in Chimera, and then >> when you save the image, it will be included. You might also be >> interested in this page on "tips" for making images: >> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >> 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 Apr 23, 2009, at 12:18 AM, YangMingjun wrote: >> >>> Dear Professor, >>> Thanks so much. I am the first time to use Chimera so I am sorry >>> that if my questions seem to be too simple... Sorry that I didn't >>> describe my question clearly in last post. >>> I had got the figure of 20 frames which are colored by using the >>> command "rainbow models red, blue". Then I saved the figure with >>> the file name a.png. Now I'd like to use the color range to denote >>> each frame in the paper, e.g. color range from red to blue gradual >>> changes corresponds to colors used by model 1 to 20 in the saved >>> figure. Since I don't know what is the name it is should be called >>> in English language, I send you an example in the attachment. >>> Many thanks. >>> Mingjun >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >.

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 72, Issue 26
by YangMingjun 23 Apr '09

23 Apr '09

Sorry that I send my question to you directly by replying your last response in the mailing list. I have sent one to the chimera-users(a)cgl.ucsf.edu Mingjun >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. Color Key (Elaine Meng) > 2. Re: Color Key (Elaine Meng) > 3. Re. Volume squeeze (Priyaranjan.Bhakat(a)csiro.au) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 23 Apr 2009 09:32:05 -0700 >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Subject: [Chimera-users] Color Key >To: YangMingjun <mjyang(a)dicp.ac.cn> >Cc: Chimera-users <Chimera-users(a)cgl.ucsf.edu> >Message-ID: <68DDED9E-E816-42B3-AEF3-6138C60F2BDA(a)cgl.ucsf.edu> >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > >Dear Mingjun, >Oh, now I see -- you want a color key! Yes, you can do that in >Chimera: choose Tools... Utilities... Color Key. In that dialog you >can set the colors and the value labels. You can click and drag with >the mouse to draw the key in the Chimera window. If you need more >text, you can add it with 2D Labels, which is another tab on the same >dialog as Color Key. > >Here is the full description: ><http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ >2dlabels.html#colorkey> > >and here is an example image with both Color Key and 2D Labels: ><http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> > >You would add that stuff while you are still in Chimera, and then >when you save the image, it will be included. You might also be >interested in this page on "tips" for making images: ><http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> > >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >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 Apr 23, 2009, at 12:18 AM, YangMingjun wrote: > >> Dear Professor, >> Thanks so much. I am the first time to use Chimera so I am sorry >> that if my questions seem to be too simple... Sorry that I didn't >> describe my question clearly in last post. >> I had got the figure of 20 frames which are colored by using the >> command "rainbow models red, blue". Then I saved the figure with >> the file name a.png. Now I'd like to use the color range to denote >> each frame in the paper, e.g. color range from red to blue gradual >> changes corresponds to colors used by model 1 to 20 in the saved >> figure. Since I don't know what is the name it is should be called >> in English language, I send you an example in the attachment. >> Many thanks. >> Mingjun > > >------------------------------ > >Message: 2 >Date: Thu, 23 Apr 2009 10:34:06 -0700 >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Subject: Re: [Chimera-users] Color Key >To: YangMingjun <mjyang(a)dicp.ac.cn> >Cc: Chimera-users BB <Chimera-users(a)cgl.ucsf.edu> >Message-ID: <02C7876C-10D1-4B2D-B6C4-0619D6EC2065(a)cgl.ucsf.edu> >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > >I forgot to mention that you can drag colors from the squares in the >Model Panel to the squares in the Color Key dialog. That is probably >the easiest way to make the intermediate colors match. >Best, >Elaine > >On Apr 23, 2009, at 9:32 AM, Elaine Meng wrote: > >> Dear Mingjun, >> Oh, now I see -- you want a color key! Yes, you can do that in >> Chimera: choose Tools... Utilities... Color Key. In that dialog you >> can set the colors and the value labels. You can click and drag with >> the mouse to draw the key in the Chimera window. If you need more >> text, you can add it with 2D Labels, which is another tab on the same >> dialog as Color Key. >> >> Here is the full description: >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ >> 2dlabels.html#colorkey> >> >> and here is an example image with both Color Key and 2D Labels: >> <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> >> >> You would add that stuff while you are still in Chimera, and then >> when you save the image, it will be included. You might also be >> interested in this page on "tips" for making images: >> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >> 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 Apr 23, 2009, at 12:18 AM, YangMingjun wrote: >> >>> Dear Professor, >>> Thanks so much. I am the first time to use Chimera so I am sorry >>> that if my questions seem to be too simple... Sorry that I didn't >>> describe my question clearly in last post. >>> I had got the figure of 20 frames which are colored by using the >>> command "rainbow models red, blue". Then I saved the figure with >>> the file name a.png. Now I'd like to use the color range to denote >>> each frame in the paper, e.g. color range from red to blue gradual >>> changes corresponds to colors used by model 1 to 20 in the saved >>> figure. Since I don't know what is the name it is should be called >>> in English language, I send you an example in the attachment. >>> Many thanks. >>> Mingjun >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >------------------------------ > >Message: 3 >Date: Thu, 23 Apr 2009 12:07:33 +1000 >From: <Priyaranjan.Bhakat(a)csiro.au> >Subject: [Chimera-users] Re. Volume squeeze >To: <chimera-users(a)cgl.ucsf.edu> >Message-ID: > <DB072BAE3B16E3488CEF9F65E6D35B3F2E3CF42A(a)exvic-mbx01.nexus.csiro.au> >Content-Type: text/plain; charset="us-ascii" > >Hi, >I was trying to overlay two volumes one from PDB and other from single particle reconstruction software EMAN (*.mrc). When I open EMAN generated 3D volume and then PDB file, EMAN 3D volume got reduce. However, when EMAN generated 3D volume is only in the 'volume viewer' screen, there is no change. Furthermore, if I press 'center' tab of 'volume viewer' volume became squeeze again. >Alternatively, what the best way to overlay and compare two volumes. >Thanks in advance for any clue, >Priya >

1 0

Re. Volume squeeze
by Priyaranjan.Bhakat＠csiro.au 23 Apr '09

23 Apr '09

Hi, I was trying to overlay two volumes one from PDB and other from single particle reconstruction software EMAN (*.mrc). When I open EMAN generated 3D volume and then PDB file, EMAN 3D volume got reduce. However, when EMAN generated 3D volume is only in the 'volume viewer' screen, there is no change. Furthermore, if I press 'center' tab of 'volume viewer' volume became squeeze again. Alternatively, what the best way to overlay and compare two volumes. Thanks in advance for any clue, Priya

2 1

transition command
by Eaazhisai Kandiah 23 Apr '09

23 Apr '09

Hi, I found the answer for the transition command. Actually It has been discussed in the forum before. It is in the Experimental features site and under Animation commands. Will try that. Sorry about repeating the question. Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe(a)mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629

1 0