- Chimera-users - RBVI Mailing Lists

(no subject)
by Hernán Costa 28 Mar '11

28 Mar '11

Hi I need to obtain mutation on differents sites on a protein but i can´t. How can I create a mutual mutation an know if the rotamer selected is Ok? Thanks Hernán Costa

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Energy Minimisation Citation
by Nancy 28 Mar '11

28 Mar '11

Dear All, I used the "Minimize Structure" feature of Chimera to minimize several ligand molecules in preparation for docking (with the "Gasteiger" charges option). I need to cite this in an article that I am to submit for publication, and I need a bibliography of the software, including a description of the minimisation algorithm, force field, etc... Please let me know how I should go about this? Thank you very much, Nancy

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RMSD Calculation
by Nancy 26 Mar '11

26 Mar '11

Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy

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displaying DelPhi results
by Knut Langsetmo 25 Mar '11

25 Mar '11

Hi, I have done a DelPhi calculation on my protein, and when I try to display it, I get the error: "File cam.phi, format delphi Record size 1852798752 > file size 26826676" Any suggestions would be greatly appreciated. Thanks, --Knut

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Automated RMSD Calculations
by Nancy 25 Mar '11

25 Mar '11

Hi All, I would like to calculate RMSDs of a large number of small molecule conformations against a reference conformation, is there a simple software program or method that can be used to perform such calculations? Thanks in advance, Nancy

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Chimera production release candidate (1.5.3)
by Elaine Meng 25 Mar '11

25 Mar '11

A Chimera production release candidate (version 1.5.3) is now available: <http://www.cgl.ucsf.edu/chimera/download.html> Please try it and report any problems. The 1.5 series includes 64-bit versions and will be the last for X11 on Mac (not to worry, the native Mac versions will still be supported). See the release notes for changes relative to previous versions of Chimera: <http://www.cgl.ucsf.edu/chimera/1.5.3/docs/relnotes/1.5.html> Relative to 1.5.2, version 1.5.3: - corrects line width in saved images (affects mesh, silhouette edges, and other lines such as H-bonds) - fixes error on Windows associated with non-Unicode usernames - turns multisampling off by default on Macs (it was associated with bad behaviors on some Mac systems) Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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installation problem
by estrella＠cartuja.csic.es 23 Mar '11

23 Mar '11

Hi, I´ve tried hardly to intall the last Chimera version for Windows (chimera 1.5.3rc), but at the phyton execution time, I have this message: "Unable to execute file: C\Archivos de programa\Chimera 1.5.3rc\phyton.exe Create process failed; code 14001" Ifound this error and it possible solution in internet, without any success. Could you help me? Thanks so much Estrella

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Re: [Chimera-users] chimera help...please...
by Eric Pettersen 23 Mar '11

23 Mar '11

On Mar 23, 2011, at 2:32 AM, Amit Kumar wrote: > > Dear Pettersen, > first of all I like to thanks you as i am getting always nice > graphics from chimera software and hope you still involve in > improving it to compete all over good structure visualizers.... > I am a frequent user of this visualizer and already cited in all my > papers internationally published. I am struggling in getting ... I'm happy you've gotten good results with Chimera, and thanks for the citations -- they help us get our funding renewed! > 1) user guide of UCSF Chimera in pdf version as whole If you go to the Chimera home page and click on the "Documentation" link, there will be a list of links to various documentation. One of those links will be for a PDF of the 1.5 version of the User's Guide. It's about 12.5 MB (828 pages). The Chimera documentation was always designed to be hyperlinked web pages, so the PDF version is not as well organized or concise as it would be if the documentation was PDF-based. I hope you know that the HTML User Guide is bundled with each Chimera download and therefore all the Help buttons in dialogs, the "help" command, and the various functions in the Help menu just access your local copy and don't go over the web. > 2) if i build structure - add atom in structure ----whether we can > plced the atom at my desired place or coordination...if yes > how...and whether i can dragg that atom specifically to some unique > place....how? The atom gets placed in the center of the view, so if you can get the center of the view to be your desired location then you're set. Otherwise, you can use the "Movement Mouse Mode" tool (in the Movement tools category) to move the atom wherever you want it positioned. > 3)whether we can allign the specific atom/residue and accordingly > whole molecule....how? Although i use match maker that allign whole > molecules but my specific residue miss out Use the "match" command to match specific atoms/residues. Open the command line (Favorites->Command Line) and type "help match" for details. As an example if you wanted to match residue 14 in model 0 with residue 20 in model 1 (and they were the same residue type with the same atom names) then "match #0:14 #1:20" will move model 0 so that its residue 14 will be superimposed on model 1's residue 20. > 4)how i can allign heteroatom like in my case i am trying to allign > heme from different hemoglobin molecule with maximum efficiency...as > heme are chemically same for both molecule it should allign > perfectly and accordingly their globin (apoprotein) part... Similarly, if the hemes have the same number of atoms and the same atom names then something like "match #0:HEM #1:HEM" would work (also assuming only one heme per model). If the hemes have differing numbers of atoms or different atom names then you would have to use a more detailed match command where you actually specify the atom names so Chimera knows which atoms to pair up in the match. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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DNA atomic structure fitting with an envelope
by Damien Larivière 22 Mar '11

22 Mar '11

Dear all, James Stroud or Thomas Bishop webservices among others enable to create a portion of DNA in the PDB format. Is it possible in Chimera to import a mesh envelop (see image), the PDB structure of the DNA portion and to force the DNA to fit with the envelope (which has the length and the diameter of the DNA portion)? Many thanks for your help Damien ps: As far I understand, the MDFF tool by Klaus Schulten allows to conform a PDB structure to a mesh (interesting for cryoEM). I have not tested it yet.

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Offsetting residue numbering
by Sumitro Harjanto 22 Mar '11

22 Mar '11

Hi Elaine, Is there a way to introduce a systematic offset to the residue numbering in a model? The numbering in my model is different from the convention. Eg. the methionine that's supposedly in position 5 is labeled as MET 4, alanine in position 6 as ALA 5, and so on. I can't do it manually cos there are many residues. Is there an easy way to resolve this other than using a script to automatically assign the labels? It'll be good if i can resolve this from the root , such that my atom specification is also consistent with the naming convention I use. :) Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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matchmaker output
by Tiziano Tuccinardi 18 Mar '11

18 Mar '11

Dear all, I am using MatchMaker for aligning about 100 structures, and it works very well!! Is it possible to automatically save the pairwise alignment without opening the MultAlignViewer? Due to the large number of structures, I cannot use the Match-Align tool but it would be enough to save the pairwise alignments Thanks in advance Tiziano -- +++++++++++++++++++++++++++++++++++++ Tiziano Tuccinardi, PhD Dip. Scienze Farmaceutiche Via Bonanno 6, 56126 PISA Tel ++39 050 2219595 Fax ++39 050 2219605 E-mail tuccinardi(a)farm.unipi.it <mailto:tuccinardi@farm.unipi.it> http://www.mmvsl.farm.unipi.it/staff/tiziano-tuccinardi/ Adjunct Assistant Professor SbarroInstitute for Cancer Research and Molecular Medicine Centerfor Biotechnology TempleUniversity PhiladelphiaPA 19122 (USA) +++++++++++++++++++++++++++++++++++++

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Movie frames are blank
by Gökhan Tolun 17 Mar '11

17 Mar '11

Dear all, I am trying to create a very simple movie, but my movies turn out blank. I am using the Spin Movie example script on http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html My movie seems to render, and the movie file is created, but when I open the file and play it, its just a blank (all black) video. When I examined the captured frames, theyre also all blank black frames. If I choose Save image, it saves it just fine, so I guess the image capturing algorithm for movies is different the one for saving the images. This is on Windows 7 64-bit, Chimera 1.5.2, Intel Mobile 965 express Chipset GPU (its a TabletPC, hence the GPU). Any suggestions to fix this would be appreciated. Thank you. _______________________________________ Gökhan Tolun, M.S., PhD. Post-doctoral Research Associate Lineberger Comprehensive Cancer Center University of North Carolina 450 West Dr., CB#7295, Room 11-119 Chapel Hill, NC, USA 27599

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Average Backbone B-factor
by Simon Sham 17 Mar '11

17 Mar '11

Hi, I need to read a pdb file and calculate the average backbone (CA, C, & N) B-factor for each residue and compare it with the result some MD. Is there anyway I can do it in Chimera? Thanks, Simon

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Re: [Chimera-users] error: from DockPrep import prep
by wascm 16 Mar '11

16 Mar '11

Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? the exception message as follow: ------------------------------------------------- Executing test.py... Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1537, in open models = func(filename, *args, **kw) File "/home/wascm/chimera/share/chimera/__init__.py", line 972, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 10, in <module> for arg_k, arg_v in opts: NameError: name 'opts' is not defined Error while processing test.py: NameError: name 'opts' is not defined File "test.py", line 10, in <module> for arg_k, arg_v in opts: See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing -t: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing test: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. ---------------------------------------------------------- At 2011-03-15 09:02:09，"Greg Couch" <gregc(a)cgl.ucsf.edu> wrote: (This is really achimera-dev(a)cgl.ucsf.edu mailing list question.) My guess is that your problem is that chimeraInit.init() was never called, so the chimera internals were never set up. So in the beginning of your Python script, add: import chimeraInit chimeraInit.init(nogui=True, silent=True) before using chimera's modules. But, in general, you would be better off running those python scripts with chimera. For example: % chimera --nogui --silent script.py That would set up the the appropriate environment for chimera, execute the python script, and exit. And you would be protected against any future changes in how chimera is initialized. If you want to use other Python modules with chimera, set your CHIMERAPATH environment variable with a list of directories that hold the Python modules (same syntax as PYTHONPATH, but just for chimera). If you want to install other Python packages into chimera's Python that have a setup.py file, use: % chimera --nogui --silent setup.py install It is also possible to make easy_install work with chimera by temporarily putting chimera's bin directory on your path and running the appropriate egg (seehttp://pypi.python.org/pypi/setuptools for details). Right now, chimera is using Python 2.7. HTH, Greg

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radial clipping
by Kelly Dryden 16 Mar '11

16 Mar '11

Hi, I would like to radially clip a density map. There are nice ways to do radial coloring, but I haven't found anything that allows a similar cropping (preferably with capping). Is there an easy way to do this? I do not want to erase the density, but rather be able to see the surface at varying radii, just as you can do with planes. (At the moment, I can only run v1.4). Thank you, Kelly

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Re: [Chimera-users] [chimera-dev] error: from DockPrep import prep
by wascm 15 Mar '11

15 Mar '11

Dear sir: Your suggestions do work well! The problems have been resolved well by your help. Thank you very much! Best Wishes Tao Cui From:Eric Pettersen Date:2011-03-16 05:12 Subject:Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep To:wascm Cc:Greg Couch,chimera-dev BB,UCSF Chimera Mailing List On Mar 15, 2011, at 5:37 AM, wascm wrote: Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) There was an oversight in the code Greg provided: chimeraInit.init takes a mandatory "argv" argument, which is exactly like sys.argv. ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? Yes. Use a --script argument, like this: chimera --nogui --script "test.py -t test" --Eric

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I am having a problem
by Burt Goldberg 15 Mar '11

15 Mar '11

Dear, Chimera, as I opened the program it prompted me to re-register. I tried 3 time but got a Error message PKCS7. HELP!!!! Burt -- Burt Goldberg, PhD Professor of Chemistry & Biochemistry Chemistry Department Affiliated Research Professor Medical Parasitology New York University School of Medicine New York University

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Re: [Chimera-users] Selection through bond and fragment naming
by Jean Didier Pie Marechal 14 Mar '11

14 Mar '11

Dear all, thanks a lot for your answers. I seem to have a problem though. When running the script, one way or another I always ends up with something like: a.residue.removeAtom(a) AttributeError: 'NoneType' object has no attribute 'removeAtom' AttributeError: 'NoneType' object has no attribute 'removeAtom' File "M:\REUNIONS\dibuixos\Manipulate_structure\newres.py", line 20, in <module> a.residue.removeAtom(a) See reply log for Python traceback. I think I got the origin of the problem but can't figure out how to solve it. What I observed is that, before running the script if I do the following after selecting my atoms: >>> for a in at: print a.residue I have the following list printed UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 but doing the same AFTER having run the script gives : None UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 ... It seems like the residue type of the first atom disappeared. Any clue? all the best, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Divendres, Març 11, 2011 8:29 pm Assumpte: Re: [Chimera-users] Selection through bond and fragment naming > On Mar 11, 2011, at 7:42 AM, Jean Didier Pie Marechal wrote: > > > Hi, > > > > I have a system from which I only have xyz coordinates. What I > would > > like to do is to define myself residue attribute on different > > fragments of the molecules. Could you tell me how (or if there is > a > > way to ): > > > > 1. expand a selection to bonding atoms (i.e. I click on one atom > and > > expand selection through one bond after each actions) This would > be > > of the easiest way for me to select the fragments I want to. > > Hi JD, > My only idea as to how to do this is with a short Python script: > > from chimera.selection import currentAtoms, addCurrent > addAtoms = set() > for a in currentAtoms(): > addAtoms.update(a.neighbors) > addCurrent(addAtoms) > > You could then use the open command to run it: > > open <script folder location (e.g. ~marechal/scripts)>/expand.py > > which you could short to "xp" with the alias command: > > alias ^xp open blah-blah/expand.py > > > > > 2. set a residue attribute to the given selected fragment. I > think I > > remember how to do so in scripting, but what is the command line > to > > do so? > > So, do you really want to set a residue-level attribute, or do you > want to organize the selected atoms into a residue? Setting a > residue- > level attribute for the atoms is easy: > > setattr r myAttrName my-attr-val sel > > Organizing the atoms into a residue again requires Python, and not > as > simple a script as for your first question, e.g.: > > # script designed to run under "runscript" command, therefore has > an > "arguments" variable available... > try: > rname, rnum = arguments > except ValueError: > raise chimera.UserError("must supply residue name and number > arguments") > > try: > rnum = int(rnum) > except ValueError: > raise chimera.UserError("residue number (second arg) must be an > integer") > > atoms = chimera.selection.currentAtoms() > if not atoms: > raise chimera.UserError("No atoms selected") > > # make a new residue > newRes = atoms[0].molecule.newResidue(rname, "A", rnum, ' ') > > # withdraw atoms from their current residues > for a in atoms: > a.residue.removeAtom(a) > if len(a.residue.atoms) == 0: > a.molecule.deleteResidue(a.residue) > > # add atoms to new residue > for a in atoms: > newRes.addAtom(a) > > So you would run this script with the command "runscript blah- > blah/ > newres.py TYR 1", which could again be shorted using aliasing: > > alias ^nr runscript blah-blah/newres.py $1 $2 > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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registration and user group
by SteffenVfx 14 Mar '11

14 Mar '11

Hi there. I've been trying to register with you all for some time, but it always comes back with a registration error. I'd like to enroll in your mailing list and user group forum. can you pass along my information? thanks casey *Steffen VFX ~the science of storytelling~* *| Casey Steffen M.S. | President/Chief Creative Officer | 211 6th Ave. #2a | Brooklyn, NY 11215 | **Web:**www.steffenvfx.com | **Twitter:**SteffenVfx<http://twitter.com/steffenvfx> | **Blog:**http://blog.steffenvfx.com | **Phone:347-875-0423 |*

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bond selection
by Elisabeth Ortega 11 Mar '11

11 Mar '11

Dear Chimera Dev. Team, I have a little question for you. How can I select a bond using the Command Line (or the IDLE)? Thanks in advance. Elisabeth Ortega-Carrasco Universitat Autònoma de Barcelona

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Selection through bond and fragment naming
by Jean Didier Pie Marechal 11 Mar '11

11 Mar '11

Hi, I have a system from which I only have xyz coordinates. What I would like to do is to define myself residue attribute on different fragments of the molecules. Could you tell me how (or if there is a way to ): 1. expand a selection to bonding atoms (i.e. I click on one atom and expand selection through one bond after each actions) This would be of the easiest way for me to select the fragments I want to. 2. set a residue attribute to the given selected fragment. I think I remember how to do so in scripting, but what is the command line to do so? Kind regards, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es

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error: from DockPrep import prep
by wascm 10 Mar '11

10 Mar '11

Dir sir I try to write a indenpendent python script and run it from command line some global variables was first set: export LD_LIBRARY_PATH=/home/wascm/chimera/lib:$LD_LIBRARY_PATH export PYTHONPATH=/home/wascm/chimera/share:/home/wascm/chimera/lib:$PYTHONPATH export CHIMERA=/home/wascm/chimera the script work well when import following module import chimera from chimera import runCommand, openModels, MSMSModel from WriteMol2 import writeMol2 from WriteDMS import writeDMS however, when add the code: from DockPrep import prep the error information as follows: ####################################### Traceback (most recent call last): File "./xx.py", line 12, in <module> from DockPrep import prep File "/home/wascm/chimera/share/DockPrep/__init__.py", line 15, in <module> from prefs import prefs, defaults, INCOMPLETE_SC, MEMORIZED_SETTINGS File "/home/wascm/chimera/share/DockPrep/prefs.py", line 13, in <module> from Rotamers.prefs import defaults as rotamerDefaults File "/home/wascm/chimera/share/Rotamers/__init__.py", line 574, in <module> from prefs import defaults, CLASH_METHOD, CLASH_THRESHOLD, HBOND_ALLOWANCE File "/home/wascm/chimera/share/Rotamers/prefs.py", line 13, in <module> from DetectClash.prefs import CLASH_THRESHOLD, HBOND_ALLOWANCE, PB_COLOR, \ File "/home/wascm/chimera/share/DetectClash/__init__.py", line 157, in <module> val = getColorByName(val) File "/home/wascm/chimera/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material ################################################# how can i solve this problem? best wishes Tao Cui

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error: from DockPrep import prep
by wascm 10 Mar '11

10 Mar '11

Dir sir I try to write a indenpendent python script and run it from command line some global variables was first set: export LD_LIBRARY_PATH=/home/wascm/chimera/lib:$LD_LIBRARY_PATH export PYTHONPATH=/home/wascm/chimera/share:/home/wascm/chimera/lib:$PYTHONPATH export CHIMERA=/home/wascm/chimera the script work well when import following module import chimera from chimera import runCommand, openModels, MSMSModel from WriteMol2 import writeMol2 from WriteDMS import writeDMS however, when add the code: from DockPrep import prep the error information as follows: ----------------------------------- Traceback (most recent call last): File "./xx.py", line 12, in <module> from DockPrep import prep File "/home/wascm/chimera/share/DockPrep/__init__.py", line 15, in <module> from prefs import prefs, defaults, INCOMPLETE_SC, MEMORIZED_SETTINGS File "/home/wascm/chimera/share/DockPrep/prefs.py", line 13, in <module> from Rotamers.prefs import defaults as rotamerDefaults File "/home/wascm/chimera/share/Rotamers/__init__.py", line 574, in <module> from prefs import defaults, CLASH_METHOD, CLASH_THRESHOLD, HBOND_ALLOWANCE File "/home/wascm/chimera/share/Rotamers/prefs.py", line 13, in <module> from DetectClash.prefs import CLASH_THRESHOLD, HBOND_ALLOWANCE, PB_COLOR, \ File "/home/wascm/chimera/share/DetectClash/__init__.py", line 157, in <module> val = getColorByName(val) File "/home/wascm/chimera/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material ---------------------- how can i solve this problem? best wishes Tao Cui

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Re: [Chimera-users] using chimera command in batch mode
by cuitao＠webmail.hzau.edu.cn 10 Mar '11

10 Mar '11

Dear sir I am so grateful to you for your detailed answer. Thanks a million. best wishes Tao Cui ------------------ 原始邮件 ------------------ >From: Eric Pettersen <pett(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: "cuitao(a)webmail.hzau.edu.cn" <cuitao(a)webmail.hzau.edu.cn> >Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >Subject: Re: using chimera command in batch mode >Date: Wed, 9 Mar 2011 13:11:31 -0800 > On Mar 8, 2011, at 5:30 PM, Tao Cui wrote: Dear sir: I have seen one message you posted in dock-fans mail list. http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html The batch mode solution you privided is really helpful to me. I wnat to know if I can complete similar batch mode works for other applation? for example, delete all H atoms, save molecule to pdb format and writedms. Thank you very much! Hi Tao, You can use the same approach outlined in the dock-fans post to write scripts for other purposes. The script in that post uses Python since that is the only way to call DockPrep from a script, but if the things you want to do are available as Chimera commands you can just write a Chimera command script and use it the same way (the script would need to end in .com or .cmd instead of .py though). So deleting all H atoms would just be the command "del H". You would save a file in PDB format with the "write" command (type "help write" in Chimera to see what arguments you would want). Writing a DMS file isn't available as a command, so you would need to use Python scripting for that, along the lines of: from chimera import runCommand, openModels, MSMSModel # generate surface using 'surf' command runCommand("surf") # get the surf object surf = openModels.list(modelTypes=[MSMSModel])[0] # write DMS from WriteDMS import writeDMS writeDMS(surf, "output.dms") You would need to keep in mind that Chimera's surface generation will fail for some structures, more so on Windows than other platforms, so you might want to check that the output file actually has some surface points in it. Alternately, in Chimera, the surface attribute "calculationFailed" will tell you if the surface calculation succeeded or not, so you could do something other than try to write the DMS file if that attribute is False. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Internal water molecules
by Tom Goddard 10 Mar '11

10 Mar '11

Hi John, Here's an idea about how to define internal water molecules and identify them in Chimera. Make a density map of the molecule at some resolution, say 5 Angstroms, using the Chimera "molmap" command, then define internal waters to be the ones that are located at a point above a certain density threshold. You can use the Chimera "Values at Atom Positions" dialog (menu Tools / Volume Data) to get the interpolated density map value at each atom position. It assigns the density value to each atom. Then you can use the Render by Attribute dialog (menu Tools / Structure Analysis) to select just those atoms with values above the threshold density. Then you can intersect that list of atoms with waters since it will also include protein atoms. All this is easy to do but since you want to do it for many frames of a molecular dynamics simulation you need a script that can be run for each MD frame. Unfortunately the values at atom positions and the render by attribute selection capability don't have Chimera command equivalents. But those capabilities (like all Chimera capabilities) can be used with a Python script. I could provide you a script if this sounds useful. Also I'll add to our feature request list the need for Chimera commands that would allow you to do it without resorting to Python. Tom > Hello, > > Is it possible, in Chimera, to select only the internal water > molecules of a protein structure? I need to find out how many water > molecules enter the protein structure from the outside during a > molecular dynamics simulation. > > Thanks! > > John

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Re: [Chimera-users] castp visualization
by Elaine Meng 09 Mar '11

09 Mar '11

On Mar 9, 2011, at 9:06 AM, Irene Newhouse wrote: > Remember a few days ago, I sent you an image from a Chimera castp visualization & it looked really weird, with strips connecting two apparently disconnected regions? Well, I put up PyMol & its castp viewer & it manages to plot the surface understandably - blackish represents the 'outside' of the cavity... I think my protein is nonetheless somewhat pathological, because if I try to render the same surface in mesh, it swells to occupy nearly the whole molecule, which is not right - mesh & solid should enclose the same volume. However, the solid rendering does reproduce where the substrate goes, and how on earth it gets in there is now my problem:-) > > I just tried something else -- I have the new Chimera on my linux station, & that's where I was seeing the odd renderings. On my PC, I have the previous version of Chimera & it shows the same surfaces as PyMol! The image chasurfs.png shows the odd effects [from the current release on my linux station], for only one of the dimer units [I thought maybe the dimer was the issue. No.] Possibly the surface rendering of cavities in the current release of Chimera is correct most of the time, but it looks as if it's not for a protein as odd as this one. For debugging purposes, the PDB is 1X09 [I used Chimera to generate the other dimer unit]. > Hi Irene, Given your observations, it may be a graphics driver problem on your linux machine. I.e. the salient difference may be the platform, not the Chimera version. However, wasn't what you sent before from Surfnet, not CASTp? In any case, my understanding is that the same Chimera code is used on the different platforms, and I don't think these tools have been changed for months. I just tried "open castp:1x09" in the 1.5 release and a recent daily build (v1.6 Feb 24) and looked at a few pockets, and the surfaces seemed fine. Since I deal with the user interface and not programming or hardware issues, I included the list in case others have suggestions or comments. Best, Elaine

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Re: [Chimera-users] using chimera command in batch mode
by Eric Pettersen 09 Mar '11

09 Mar '11

On Mar 8, 2011, at 5:30 PM, Tao Cui wrote: > Dear sir: > > I have seen one message you posted in dock-fans mail list. > > http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html > > The batch mode solution you privided is really helpful to me. I > wnat to know if I can complete similar batch mode works for other > applation? for example, delete all H atoms, save molecule to pdb > format and writedms. > > Thank you very much! Hi Tao, You can use the same approach outlined in the dock-fans post to write scripts for other purposes. The script in that post uses Python since that is the only way to call DockPrep from a script, but if the things you want to do are available as Chimera commands you can just write a Chimera command script and use it the same way (the script would need to end in .com or .cmd instead of .py though). So deleting all H atoms would just be the command "del H". You would save a file in PDB format with the "write" command (type "help write" in Chimera to see what arguments you would want). Writing a DMS file isn't available as a command, so you would need to use Python scripting for that, along the lines of: from chimera import runCommand, openModels, MSMSModel # generate surface using 'surf' command runCommand("surf") # get the surf object surf = openModels.list(modelTypes=[MSMSModel])[0] # write DMS from WriteDMS import writeDMS writeDMS(surf, "output.dms") You would need to keep in mind that Chimera's surface generation will fail for some structures, more so on Windows than other platforms, so you might want to check that the output file actually has some surface points in it. Alternately, in Chimera, the surface attribute "calculationFailed" will tell you if the surface calculation succeeded or not, so you could do something other than try to write the DMS file if that attribute is False. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

select by atom number
by Francesco Pietra 09 Mar '11

09 Mar '11

Hello: Is any trick to select by atom number? Having NAMD files with CHARMM FF, i.e., SEGID and no chain ID, I find now difficult to use CHIMERA the way I used it. Thanks francesco pietra

3 2

color bond distance, angle and so on
by Jean-Didier Maréchal 08 Mar '11

08 Mar '11

Hi guys, How can I change the color of the labels associated to distance between atoms, angles etc (both the for the text and the dashes). Thanks a lot JD **************************** Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es

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Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues
by Elaine Meng 08 Mar '11

08 Mar '11

On Mar 8, 2011, at 1:03 PM, Ingmar Buerstel wrote: > Dear Elaine, > thanx a lot for your quick answer. In fact I have already a modelled structure (made with swiss model) of the protein. > I was looking for a possiblitiy to fit a 4Fe4S-cluster in the position of the original cluster. The cysteines are conserved, thus, I just need to copy/paste the 4Fe4S-cluster into my structure. I would be glad, if you could help me concerning this problem. Dear Ingmar, You could superimpose your model and the related structure that does contain this cluster (residue SF4) and then merge the SF4 residue into your model. However, the result may be rough, depending on how well the structures match in 3D. It might be better to start over and use Modeller as described in my previous message, because it can make a model that already includes the cluster. However, if you want to try the superimposing approach, here are more details. (a) In Chimera, open your model and then open the known related structure that contains the cluster. (b) Superimpose the two structures, for example with the Matchmaker tool. Here is some discussion of different ways to superimpose structures in Chimera. You will want to make sure that the structures match well at the four cysteines. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (c) Delete everything in the known structure except for the part you want to paste into your homology model, and then combine the two models into one. For example, if your model is open as #0 in Chimera and the known structure is open as #1, you could use commands delete #1 & ~:sf4 combine #0,1 The delete command gets rid of all atoms in #1 except the SF4 residue. The combine command creates a new model, #2, by merging the SF4 residue in #1 with the homology model in #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> You can save the new model #2 to a file (for example, with File... Save PDB). However, you would hope that the cysteine sidechains in your model are pointing in the correct orientations to bind the cluster. If not, you might have to paste in those residues from the known structure too, and delete them from your homology model, before merging. Then you might have to manually text-edit the PDB to add bonds between the merged cysteines and the rest of the homology model. Again, it might be better just to start over and use a modelling method that can include the cluster in the first place. 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 > > > > Subject: Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues > > From: meng(a)cgl.ucsf.edu > > Date: Mon, 7 Mar 2011 09:38:45 -0800 > > CC: chimera-users(a)cgl.ucsf.edu > > To: ingmar_b(a)hotmail.com > > > > Dear Ingmar, > > It sounds like you want to model your whole protein including the 4Fe4S cluster, am I right? Or is there a structure of your protein but that does not include the cluster? > > > > I would not recommend modeling this "from scratch" (building one atom by one atom) in Chimera but instead, homology-modeling your protein and cluster from the structure of a related protein that contains the cluster. Of course, this all depends on the existence of a known structure for a related protein. > > > > Chimera includes an interface to the Modeller program for homology-modeling. To use it, you would have to first go to the Modeller website > > <http://www.salilab.org/modeller/registration.html> > > and register to get a license key (free for academic use). In Chimera, you could choose "Tools... Sequence... Blast Protein," paste in the sequence of your protein, and then blast it against the PDB to see if there are any structures related to your protein. If there is a hit that seems good enough to you, you could use the Blast results dialog to open the structure and also the alignment of the two sequences. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/blast.html> > > Then, in the sequence alignment window, choose "Structure... Modeller Tools" to show the interface to Modeller. Use "Advanced Option" to "Include non-water HETATM residues from template" so that the FeS cluster will be included in the model. > > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> > > > > Or, you could simply see if there is already a model of your protein available in ModBase by using "File... Fetch by ID" in the Chimera menu. However, those models probably wouldn't contain the FeS cluster. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html> > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html> > > > > Some related references I just saw but didn't read in detail: > > > > Fee, J. A.; Castagnetto, J.M.; Case, David A.; Noodleman, L.; Stout, C.D.; Torres, R.A.; "The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters". J. Biol. Inorg. Chem. 2003, 8: 519-526. > > <http://dx.doi.org/10.1007/s00775-003-0445-8> > > > > Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein. > > (2002) J.Mol.Biol. 315: 1155-1166 > > <http://dx.doi.org/10.1006/jmbi.2001.5292> > > (goes with PDB entries 1iqz, 1ir0 ... I see that the residue name of the cluster is SF4, so you could also use the searching tools at the PDB website to find structures that have this cluster) > > > > I hope this helps, > > Elaine > > > On Mar 6, 2011, at 6:44 AM, Ingmar Buerstel wrote: > > > Dear users, > > > i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. > > > > > > So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster > > > Thanx in advance, > > > Ingmar > >

1 0

Searching chimera-users archive
by Tom Goddard 08 Mar '11

08 Mar '11

Hi Conrad, Searching the Chimera mail archives from the Chimera documentation web page does not work at all well. http://www.cgl.ucsf.edu/chimera/docindex.html I tried searching for "Beale" and it produced no results. > Your search - *Beale site:www.cgl.ucsf.edu/pipermail/chimera-users > -filetype:gz* - did not match any documents. > > Suggestions: > > * Make sure all words are spelled correctly. > * Try different keywords. > * Try more general keywords. > * Try fewer keywords. > There is a message in August 2010 from John Beale. If I search for that message using www.google.com (chimera "startup options" John Beale) I do get the message. So it has been indexed. Some other revealing problems. Searching the Chimera archives from the documentation page for "chimera" produces only 20 hits, all but 5 are attachments. Likewise a search for "windows" produces just 4 hits (one from 2005, one 2006, one 2007, one 2010). Obviously this isn't working. Maybe we should remove the search field from the documentation until we have time to fix it because users (even ones who should know better like me) sometimes believe the search results that there are no archived messages on the topic. Tom > On Mar 8, 2011, at 10:58 AM, Tom Goddard wrote: > >> Hi Eric, >> >> How do I reply to an old chimera-users message and keep my reply in >> the same mailing list thread? I guess there is some mail header line >> that allows the mailing list to recognize which messages belong to >> the same thread. But I don't have the old chimera-users email I want >> to reply to. The web interface to the archive doesn't appear to >> provide a way to reply. > > Well, I don't know for sure, but I assume it is threaded based on the > In-Reply-To header and/or the References header. Now, the archive > doesn't show you either of those so I assume they're buried in some > internal location, so you're stuck. Besides, threading is broken > across month boundaries anyway, so isn't the point moot really? > > --Eric >

2 1

saving charmm layout
by Francesco Pietra 07 Mar '11

07 Mar '11

Hello: Is it possible to save pdb conserving as much as possible charmm layout (in particular the segments (P1, P2, etc)? I find speedy to edit graphically with Chimera but, afterward, much time is required to restore charmm layout. thanks francesco pietra

2 1

How to model a 4Fe4S cluster on conserved Cys residues
by Ingmar Buerstel 07 Mar '11

07 Mar '11

Dear users, i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster Thanx in advance, Ingmar

2 1

question on volume viewer usage
by Bala subramanian 04 Mar '11

04 Mar '11

Friends, I am using chimera version 1.5 (build 31401 downloaded on 2010-09-16). I have three pdb files (of same protein) and for each pdb file, i have an electro static potential file (.dx file). I opened the three pdb files and then the .dx potential files successively through volume viewer. Each time i open the .dx file, the isosurfaces are mapped on to the first pdb file. Why is it so ?. 1) Precisely 1.dx should be mapped on 1.pdb, 2.dx on 2.pdb...etc. How can i do this ? 2) Is there any way to have a universal setting of volume display options. Like in isosurface threhold (+2 and -2 in my case), color for +ve and -ve surface, transparency etc. Because presently i am doing these settings individually for each .dx file. Thanks, Bala

2 1

1 out of many helices shown as pipe
by odonnell＠chem.fsu.edu 03 Mar '11

03 Mar '11

Hi all, I have a pdb with many alpha helices but I only want one or two to stand out as a pipe. I tried highlighting that particular sequence(s) and going to Depiction => pipesAndPlanks but it will change all of them. Many thanks for a push in the right direction. -Jason ------------------------------------------------------------------------- Sent via webmail for Chemistry & Biochemistry @ Florida State University https://webmail.chem.fsu.edu -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 1

ambient lighting mode for simple drawing style missing
by Benda, Christian 03 Mar '11

03 Mar '11

Hi possibly a simple question but it has kept me buffled for two weeks now, so I decided to ask: how can I set lighting mode to ambient? I am trying to create images using a simple drawing style like exemplified in http://www.cgl.ucsf.edu/chimera/ImageGallery/ p53 simple drawing or Clathrin but I don't find ambient lighting mode in the viewing tools - lighting menu. The only options given are lights (head light, 1, 2) or quality (normal, glossy). I am using Chimera 1.5 build 30417 fir darwin 64bit, aqua on a MacBook Pro with Mac OS X 10.6.6. Many thanks in advance Christian ________________________________ Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: benda(a)biochem.mpg.de

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Re: [Chimera-users] Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 02 Mar '11

02 Mar '11

Thank you, I had missed the settings on that other place. Now it works quite well. (barring some issues with external monitor) I also noticed that overlay setting in same menu should be on or whole desktop would get blurry (with or without stereo glasses on). -vpk On 3/1/11 10:36 PM, Greg Couch wrote: > If both Chimera and PyMol are complaining, then you've haven't > configured OpenGL stereo correctly. The NVidia Quadro driver > configuration has two places to setup stereo. There are the > "Stereoscopic 3D" settings that are not helpful for chimera (except for > making NVIDIA's stereo image viewer work). So in addition to that, you > want to setup stereo in the "3D Settings / Manage 3D Settings" dialog. > In there, turn on "Stereo - Enable" and select the appropriate kind of > stereo in "Stereo - Display mode". > > Good luck, > > Greg > > On 02/28/2011 09:11 PM, Veli-Pekka Kestilä wrote: >> >> I have done all of these and as I said in my original e-mail I got the >> full screen tests nvidia provides working. Problem is that when I try to >> start Chimera or PyMol it fails complaining that 3d vision mode isn't >> available. So question still basically is if it's possible to get it >> working with Quadro 880M >> >> On 2/23/11 4:40 PM, Sabuj Pattanayek wrote: >>> also see : >>> http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#NVidia_NVision… >>> >>> . It has some instructions on how to setup 3d vision on windows. >>> >>> On Wed, Feb 23, 2011 at 8:36 AM, Sabuj Pattanayek<sabujp(a)gmail.com> >>> wrote: >>>> IIRC there's an option in the windows nvidia configuration utility >>>> that enables and disables nvidia 3d vision. I assume that's the setup >>>> you're trying to use, so check that to see if it's enabled or >>>> disabled. >>>> >>>> 2011/2/23 Veli-Pekka Kestilä<veli-pekka.kestila(a)helsinki.fi>: >>>>> Hi Tom, >>>>> >>>>> On 2/22/11 8:12 PM, Tom Goddard wrote: >>>>>> Hi Veli-Pekka, >>>>>> >>>>>> This is either a driver configuration problem or driver limitation or >>>>>> driver bug. Your driver is from Oct 2010 and there are newer ones. >>>>>> The >>>>>> following 266.58 driver was released Jan 18, 2011 and the notes >>>>>> say it >>>>>> adds support for various "3d vision notebooks". Maybe the new >>>>>> driver is >>>>>> needed. >>>>>> >>>>>> http://www.nvidia.com/object/notebook-win7-winvista-64bit-266.58-whql-drive… >>>>>> >>>>> I installed back the newest driver and problem still persist. So it's >>>>> problem either with driver or the card. >>>>> 880M isn't very high end on the Quadro Cards. >>>>> >>>>>> If it is a driver configuration problem, I don't know about that. Our >>>>>> expert on stereo and Windows is on vacation this week but can >>>>>> advise you >>>>>> next week. >>>>> Seems that I will be waiting for that. Thank you for your reply. And >>>>> hope to hear from you next week. >>>>> >>>>> -vpk >>>>> >>>>>> Tom >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I have problem with Nvidia Quadro FX 880M and Stereoscopic view. >>>>>>> When I >>>>>>> switch the stereoscopic view on in Chimera it gives me following >>>>>>> error: >>>>>>> >>>>>>> stereo viewing (Unable to find hardware stereo support >>>>>>> (couldn't choose pixel format >>>>>>> Couldn't configure togl widget)). >>>>>>> >>>>>>> I have installed the Quadro drivers version 259.57 in Windows 7 >>>>>>> 64bit. >>>>>>> And separate 3D driver for Quadro. >>>>>>> >>>>>>> Greetings, >>>>>>> Veli-Pekka Kestilä >>>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> University of Helsinki / Institute of Biotechnology / >>>>> veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, >>>>> Biocenter 3 >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

1 0

odd output from surfnet
by Irene Newhouse 02 Mar '11

02 Mar '11

I'm trying to get an image of channels in the attached protein. It's actually a dimer, & the surfaces looked bizarre for the dimer, so I thought maybe surfnet was choking on the repeated residue numbers when you use chain ID, so I clipped it down to the monomer. That' still odd. I've attached a png of the result, using the defaults, & the pdb file of the monomer. What am I doing wrong? Is there a way to get the n largest channels, instead of all of them? Thanks! Irene Newhouse

2 5

morph problem
by Andres Palencia 02 Mar '11

02 Mar '11

Dear Chimera Users, I am trying to morph the complex1 and complex2 from the same system (protein-RNA) to make a video monitoring the conformational changes. As complex 1 is missing one domain and a helix (not visible in the crystal structure), I need to remove these parts in complex 2 to have an equal number of atoms in both complex and could morph it. The resulting video is not so nice because shows the gaps corresponding to the missing part. So, to avoid that, I have modelled the missing part in the complex 1 to have the same atoms, and afer morph it again to make the video, but this is not working. In the transition between complex 1 and complex 2, the RNA encounter one helix on the way that needs to move out to let the RNA to get the position observed in complex 2. If I take out this helix, the video can perfectly be done, but still is not perfect because show gaps. Anybody could give an idea in how to solve the problem? We need the video to include in a publication,. Thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: palencia(a)embl.fr phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/

2 1

3-D
by Jason Bouvier 02 Mar '11

02 Mar '11

Hi, how do I view proteins in 3-D in Chimera? And would I use standard 3-D glasses or are special ones required? I viewing in stereo with some old 3-D glasses that I had around but to no avail. Thank you. Cordially, Jason Bouvier Jason Bouvier | Graduate Student, <http://mcb.illinois.edu/departments/biochemistry/> Biochemistry | <http://www.life.illinois.edu/gerltlab/research.html> Gerlt Lab | <http://www.igb.illinois.edu/> Institute for Genomic Biology | Rm 3200 | <http://illinois.edu/> University of Illinois at Urbana-Champaign | 1206 W. Gregory Dr. | MC-195 | Urbana, IL 61801 | office 217.333.2673 | lab 217.333.2699 | <mailto:jbouvier@illinois.edu> jbouvier(a)illinois.edu

2 2

Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 01 Mar '11

01 Mar '11

Hello, I have problem with Nvidia Quadro FX 880M and Stereoscopic view. When I switch the stereoscopic view on in Chimera it gives me following error: stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I have installed the Quadro drivers version 259.57 in Windows 7 64bit. And separate 3D driver for Quadro. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

4 6

chimera ?
by Alexander Spyros Maris 01 Mar '11

01 Mar '11

Hi, I was attempting to start part of the tutorial by fetching "1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this? Thanks! -- Alex Maris

4 4

Internal water molecules
by Beale, John 28 Feb '11

28 Feb '11

Hello, Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation. Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

2 1

hem group
by "dr. R�szer Tam�s" 28 Feb '11

28 Feb '11

Hello, I would like to add HAEM group to a protein reconstructed from pdb data. I am working on Windows platform. Could you please help me how can I do that? many thanks Tamas

3 2

How to
by M. Amin Arnaout 28 Feb '11

28 Feb '11

I am running Cimera 1.5.2 on Mac. I am now unable to show a cabonyl O, N or CA of a residue while ribbon is also displayed. Could do that in the earlier version. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 4

Re: [Chimera-users] [chimera-dev] clashes and contacts with hidden models
by Elaine Meng 28 Feb '11

28 Feb '11

On Feb 28, 2011, at 5:28 AM, Elisabeth Ortega wrote: > > I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? > Hi Elisabeth, With either the graphical interface of Find Clashes/Contacts or the command findclash, you can specify which two groups of atoms to examine for clashes. The remaining atoms will be ignored. I believe it doesn't matter whether the atoms are displayed or active. With the command, it would be something like findclash #1 test #2 [other options] Another example: findclash ligand overlap -0.4 hb 0 test aromatic Use command "help findclash" to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> With the GUI, the procedure is slightly different: you would select one group (say #1), click Designate, choose option "second set of designated atoms", select the second group (say #2), click "Designate selection as second set", Apply. Click the Help button to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas…> This is more of a chimera-users(a)cgl.ucsf.edu question (how to use Chimera) than chimera-dev (programming related to Chimera), so I'm also CC-ing the former list. 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

1 0

suggestion: sym option
by Dougherty, Matthew T 25 Feb '11

25 Feb '11

add an SYM command option to specify the model number of the resulting model Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

2 1

morph shape/bild objects
by Do-Nyun Kim 25 Feb '11

25 Feb '11

Hello, I'm using shapes in bild format to make spheres and cylinders in Chimera. Is there a way of morphing these shapes, spheres in one conformation to spheres in another conformation? Thanks you. Best regards, Do-Nyun Kim.

2 1

Chain/Structure ID as label
by Berhane Temelso 25 Feb '11

25 Feb '11

Hi, I often read in 1-30 hydrogen-bonded molecular clusters from XYZ files and tile them for analysis. It would be great to label each cluster/model with its chain ID or file name. Labeling them using the 2Dlabel command is inconvenient especially when I have a large number of models. Is there an easy way of doing this? Thanks in advance. Berhane

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Inter-helical angle?
by Brian Cannon 24 Feb '11

24 Feb '11

I need to calculate the angle between two helices in a protein. Do you have any instruction about how I could go about doing this? Any help would be greatly appreciated. Thanks! Brian

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