- Chimera-users - RBVI Mailing Lists

fit in map output : coordinate representation of axis, axis point
by Hwang, Youngha,Ph.D. 27 Jan '09

27 Jan '09

Hi, could anyone explain to me what axis points mean in chimera? What unit is used for them? Is it related to the volume dimension? Is the rotation matrix based on Euler-angle representation? Thanks, Youngha. 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.

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3D on Chimera.
by ayassin＠wadsworth.org 27 Jan '09

27 Jan '09

Hello, I am trying to use Chimera to model pdb files into EM maps. When I select the red cyan stereo, the EM map is stereo but the pdb structure is not. -Is there anyway to display pdb in stereo in Chimera, how? -Is there another program that would allow me to do the same thing: fit pdb in EM density map-in stereo(other than "O")? -When I use Chimera on windows VISTA the side view panel does not appear and a message about graphic card appear, anyway to solve this? Thank you all very much. Aymen Yassin. Postdoc Research Affiliate Wadsworth Center, Albany,NY. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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marker coordinates
by Gabor Papai 27 Jan '09

27 Jan '09

Hi, I would like to do the following: I placed markers on density spots. I want to get their coordinates and excise a box around the marked density and save it as a separate file. For this I would like to know how I can retrieve the coordinates of a marker set and possibly how to position exactly a box around a marker to set a subregion (and of course how to set the dimensions of that box). This second feature existed before, but disappeared in the latest releases with the subregion selection tool in the Volume Viewer. Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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Volume information
by vamsee 26 Jan '09

26 Jan '09

Hello All, I am working on a virus and I am trying to figure out its volume. I would want to find out the volume of the nucleic acid and the water inside the virus capsid. That way, if I am thinking right, that should give me the total internal volume of the virus. This volume would be a constant even with the movement of water in and out. Is it possible to use chimera to calculate any of such data, with no prior information about how the nucleic acid is packed inside? Thanks in advance, Vamsee Graduate Student Dept of Chemistry and Biochemistry Montana State University Bozeman, MT - 59715

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suggested feature/model panel
by Matthew Dougherty 26 Jan '09

26 Jan '09

1) ability to create folders in the model panel so models can be grouped 2) ability to have a model in multiple folders 3) ability to show/hide in a folder by a a single checkbox 4) ability to name the folder

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How to display automatically the atoms in Gaussian cube file format
by Hyung Jun Lee 26 Jan '09

26 Jan '09

Gaussian cube file formats include the information about each atom's positions as well as the volumetric data. But, Chimera only displays the volumetric data when importing the cube file format. I want to know how to display automatically the atoms whose positions is included in the cube file, together with the volumetric data.

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Mac 64-bit Chimera version
by Thomas Goddard 26 Jan '09

26 Jan '09

Hi Denis, Conrad Huang in our lab tried building a 64-bit Mac Chimera several months ago. Many of the third-party packages we rely on failed to compile. We decided to pursue this only after Mac OS 10.6 is released. I believe the rationale of that was that Mac OS 10.5 is the oldest Mac OS that supports 64-bit graphical apps. We still support Mac OS 10.4 and our current automated build system targets 10.4. When 10.6 comes out we may target our builds to 10.5. Currently we only provide 64-bit Chimera on Linux. Tom Denis Chrétien wrote: > Dear Thomas, > > We were discussing some time ago about a 64 bit Mac version of Chimera. > Did you progress in this project ? (I'm still very limited for > visualization of large volumes with my mac, although its not a hardware > problem : 16 Gb Ram installed). > > Best regards, > > Denis > > Le 15 mai 08 à 18:41, Thomas Goddard a écrit : > >> Hi Denis, >> >> The Chimera error you reported means there was insufficient memory to >> compute the Fourier transform you wanted. I see from the report that >> your Mac has 18 Gbytes (wow). But our Mac Chimera version is a 32-bit >> program so its memory address space is only 4 Gbytes. In that 4 >> Gbytes has to fit not only data, but all shared libraries, program >> stack and (I think) operating system code. So really you might have >> just 3 Gbytes to work with. Also my Fourier transform code does a >> full complex value FT where it could do a real value FT taking half >> the memory. And the Python library that actually does the FT can only >> use double precision, so 16 bytes per complex value. More memory is >> used when Chimera takes just the magnitude of the FT coefficients. In >> short it is using 20 bytes per grid point. So a 512^3 FT will use 2.5 >> Gb, about the maximum that will fit in the 32-bit address space >> (assuming it isn't already fragmented by other data/libraries since >> you need a 2.5 Gb free block). >> >> We plan on fixing this. We plan on distributing a 64-bit Mac >> Chimera, and have tried compiling it. But some of the ~30 third-party >> libraries Chimera depends on did not compile. So we still need to >> work on that -- maybe within 3 months. Also I plan on making the FT >> code not such a hog, do a real FT and investigate 32-bit float FT >> values for a factor of 4 memory savings. For now your only option >> would be to use one of our 64-bit Chimera versions on Linux or Tru64 >> operating systems. >> >> Tom > > ___________________________ > Université de Rennes 1 > UMR 6026, équipe TIPs > Campus de Beaulieu, Bât. 13 > 35042 Rennes Cedex > France > > Tel. +33 (0)2 23 23 67 64 > http://www.umr6026.univ-rennes1.fr/ > ___________________________ >

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Re: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion
by Anindito Sen 26 Jan '09

26 Jan '09

Hi Tom You are correct! The color dialog does appear as you mentioned! In addition - While using Chimera- the display window keeps flickering when I move the density map/pdb files. What can be a possible remedy to solve the problem? Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 --- On Fri, 23/1/09, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: From: Tom Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion To: emailanindito(a)yahoo.co.in Cc: chimera-users(a)cgl.ucsf.edu Date: Friday, 23 January, 2009, 11:35 PM Hi Andy, Sounds like a windowing system problem, not a Chimera problem. If you show the Surface Color dialog (Tools / Volume / Surface Color) and click on one of its color buttons, does the color dialog appear? Tom Anindito Sen wrote: > Dear All > > This may be a bit unusual problem- I am using Chimera (from Daily build) on Ubuntu mounted on my MAC using VMware Fusion (reason- some software packages that run only on LINUX and not on a MAC). The problem is - when I try to get the color panel by clicking on the color tab on the volume viewer- it does not appear. I am not sure if any of you have encountered such problem. > > Thanks > Andy > > > Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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need a script
by Bala subramanian 26 Jan '09

26 Jan '09

Dear Chimerians, Kindly help me If anybody has a script to do the following. Given two pdb files, the script should calculate the vector distance between the atoms, say CA atoms and draw an arrow representing the magnitude and direction of the vector. Do i need to add some plugin to draw arrows through atoms in Chimera. Thanks in advance, Bala

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Chimera on Ubuntu mounted on MAC using VMware Fusion
by Anindito Sen 23 Jan '09

23 Jan '09

Dear All This may be a bit unusual problem- I am using Chimera (from Daily build) on Ubuntu mounted on my MAC using VMware Fusion (reason- some software packages that run only on LINUX and not on a MAC). The problem is - when I try to get the color panel by clicking on the color tab on the volume viewer- it does not appear. I am not sure if any of you have encountered such problem. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Movie Recording
by skmolugu＠miners.utep.edu 22 Jan '09

22 Jan '09

Hi, I am having problems with movie recording. I saved the movie as .avi file and when I upload the movie in to a windows power point slide, it crashes or shows a dark cube. Can you please suggest me a possible solution for this.. Thank you very much for your time. Regards, Sudheer.

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Re: [Chimera-users] Movie Recording
by Sacha De Carlo 22 Jan '09

22 Jan '09

Hi, it sounds lime you're having problems with Windows & Powerpoint, not Chimera... can you play the movie correctly with media player or VLC? Do you have all the video codecs installed correctly? Did you check the Chimera temp directory to see whether the frames have been created? hope this helps. Sacha ------------------------------------------ Sacha De Carlo, Asst. Professor Marshak Building Room 1335 The City College of NY (212) 650-6070 E-mail: sdecarlo(a)ccny.cuny.edu http://www.planetesacha.com/Work.htm ------------------------------------------

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Higher order
by hsosa＠aecom.yu.edu 21 Jan '09

21 Jan '09

Is it possible to assign colors by chain to the surfaces created my the multiscale models tool ? 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 -----------------------------------

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transparency change for a whole model
by Neil Ranson 21 Jan '09

21 Jan '09

Dear All, I am revisiting a movie I made in chimera some time ago with a painfully long script. In this script, I used a command syntax like this: transition transparency #0 0 0.1 1 copy file 'filename' To change the global transparency of model #0 (with lots of different elements all coloured and represented differently) This command seems to have disappeared. Is there an equivalent way now? The only way I can find is to use transparency in the colordef command, but that will be extremely cumbersome. What is the preferred way to fade a model in and out now? Thanks in advance, Neil Ranson Neil Ranson PhD Level 2 Biochemistry Tutor University Research Fellow Astbury Centre for Structural Molecular Biology IMCB University of Leeds, Leeds, LS2 9JT, UK. EM Image Processing Suite - Miall 6.02 Tel: 44 (0) 113 343 7065 email: n.a.ranson(a)leeds.ac.uk

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command files
by Matthew Dougherty 20 Jan '09

20 Jan '09

I have a command file that has a number of reset commands. I would like to 1) interrupt a command file during execution, aborting all further commands, stopping the graphics configuration at the abort (e.g. threshold values, active models, etc) 2) be able to place a hold in a command file, say after the a reset command, and be able to continue the command processing after pressing a key on the keyboard. Does this capability exist? thanks, Matt

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Coulombic Surface Coloring
by Martin Kampmann 20 Jan '09

20 Jan '09

Hello, I saw on the Chimera online manual that there is a Coulombic Surface Coloring function, which displays an approximate electrostatic potential without having to calculate a file with delphi etc. This sounds great and I would love to use the function. However, in the Tools > Surface/Binding Analysis menu, I don't find it. Is it something to be implemented in future versions of Chimera? Or is there a way of using it in the current release (I have version 1.3 build 2577 from December 9) Thanks a lot! Martin

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marginal issues on installation (linux)
by Francesco Pietra 20 Jan '09

20 Jan '09

hi: replaced hd, installed chimera-1.3.2577-linux.exe on debian i386 lenny ok, though i have to give the full path /usr/local/chimera/bin/./chimera to launch chimera. notice that the directory /chimera is chown to me as user. with previous versions and debian i386 etch (last installation daily built 17 Sept 2008), execution of chimera from anywhere was provided on installation. never mind, are there available env variables for the executable? thanks francesco pietra

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Matchmaker
by hsosa＠aecom.yu.edu 20 Jan '09

20 Jan '09

Is it possible to retrieve the transformation matrix (or angle of rotation and translation) that the Matchmaker tool used to align two atomic models ?. I know that you can get this information when fitting an atomic model into a density map using the tool Fit in Map and then pressing the Results button. Is there anything similar for the MatchMaker tool ?. 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 -----------------------------------

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Re: [Chimera-users] Protskin
by Elaine Meng 15 Jan '09

15 Jan '09

On Jan 15, 2009, at 7:07 AM, Patton, John (NIH/NIAID) wrote: > > Hi Elaine, > Do you have any information concerning using Protskin in conjunction > with > Chimera? The only information I have come across applies to PyMol. > Thanks, > John Hi John, I haven't tried Protskin, but my understanding is that its purpose is to map conservation in a multiple sequence alignment to protein display. (Protskin page: <http://www.mcgnmr.ca/ProtSkin/intro/> ) Chimera itself can (A) read your multiple sequence alignment (many formats, just use File... Open) (B) calculate any of several measures of conservation (entropy, variability, etc.) - in the sequence window menu, choose Preferences... Analysis, set "Conservation style" to "AL2CO" to access further options for calculating conservation, which is shown as a histogram above the alignment <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu… > (C) show them on your structure(s) with any color mapping you desire, or with "worm" thickness - any open structure(s) will associate automatically with sequence(s) in the alignment - in the sequence window menu, choose Structure... Render by Conservation, change attribute to "mavConservation" and show with color or worms <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html… > Example image, 1bzm colored by conservation in PFAM Carb_anhydrase seed alignment: <http://www.cgl.ucsf.edu/chimera/feature_highlights/1bzm-al2co-highlight.png > This tutorial includes coloring by conservation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html> Back to ProtSkin: ----------------- It sounds like ProtSkin emits some file listing the residues and associated values. Certainly you could reformat that into a Chimera "define attribute" file, read it in, and then show the values as in (C) above. Since Chimera already performs the preceding steps quite well and with many powerful options, there hasn't been much impetus to hooking it up to ProtSkin. However, I don't see any barrier other than your needing to convert the output file into the simple "define attribute" format described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Getting a sequence alignment: ----------------------------- Perhaps you didn't already have a sequence alignment, and find ProtSkin to be helpful in generating one. There are many alternative approaches. For example, the ConSurf server does a great job of automatically generating an alignment of a diverse set of sequences related to your single uploaded structure. (ConSurf server: <http://consurf.tau.ac.il/> ) There are more ideas in this page I wrote on "sources of sequence alignments" for use in Chimera: <http://www.cgl.ucsf.edu/home/meng/sources.html> I would be happy provide more detailed help on using Chimera to color by conservation as it applies to your system of interest, i.e. feel free to write back. 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

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Rotating about an axis
by Thomas Goddard 14 Jan '09

14 Jan '09

Hi Kevin, The command "turn x 23" will rotate active models about the screen x axis by 23 degrees. The command "turn 1,1,0 180 center 0,2.5,2.5 coord #1 models #1" rotates just model #1 by 180 degrees about axis 1,1,0 defined in the local coordinates of model #1 about center point 0,2.5,2.5 also in model #1 local coordinates. The fancier forms of the turn command are only in Chimera 1.4 daily builds. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html You align multiple structures by aligning them all to one reference structure. You can align specific residues with the "match" command: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Do do a sequence based structure alignment look at the MatchMaker tool or command: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma… Best to send questions to chimera-users(a)cgl.ucsf.edu. Tom Kevin Koehntop wrote: > Hi Tom, > > In Chimera, how do you rotate a structure along an axis by X degrees? > How is the specific axis selected? Finally, is it possible to align > multiple structures (e.g. their tops, bottoms, centers, etc.)? Thank you > > Kevin

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Docking crystal structure in density map
by Anindito Sen 14 Jan '09

14 Jan '09

Dear All I have docked the crystal structure of a protein monomer manually in the density map ( of a filament) and with some movements done with a long alpha helix(part of the crystal structure) to make a decent fit. However when I generated multiple copies of the docked structure- regions where manual adjustments on the alpha helix were made- came out like thin wires instead of being a ribbon. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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chimera on fedora10
by Bala subramanian 14 Jan '09

14 Jan '09

Hello, I installed chimera on fedor10. The installation was done but when I try to open, it gives me the following error. How should i resolve the problem python2.5: can't open file '/usr/local/share/checkOpenGL.py': [Errno 2] No such file or directory Thanks, Bala

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Saving a Morph movie
by R. Andrew Byrd 14 Jan '09

14 Jan '09

Greetings, I have been trying to use the Morph tool in the production release from summer 2008. The tool works very well and allows playing the trajectory in the graphics window. However, when I try to save the file as a movie, it consistently crashes. I am running Win XP SP3, on a Dell M1330 laptop. It has also crashed on a Dell desktop running XP SP3. Are there special tricks to saving the movie for use in a Powerpoint presentation? Thanks for any help/suggestions! Andy -------------------------------------------------

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Coloring bonds/sticks independent of the atom color
by David Chenoweth 13 Jan '09

13 Jan '09

Dear Chimera team, Is it possible to color bonds / sticks independent of the atoms so that I could have colored balls corresponding to atom types but have all the sticks connecting the balls/atoms to be a different color or colors. Thanks again, Dave

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precise overlay of ligands
by David Chenoweth 13 Jan '09

13 Jan '09

Dear Chimera team, Hi! I have two ligands in two different PDB files which have a very similar core structure. I have constructed a framework of dummy atoms based on the centroids of several aromatic rings to use as a positioning system for the two ligands. I have three points/dummy atoms for each ligand in space in their respective pdb files and I would like to overlay or map the three points of one onto the three points of the other so I can make measurements in chimera. Is there a simple way to open the two pdb files, select the three points that belong to each ligand and overlay them (maybe even minimize the rms deviation between them with some kind of fit to the plane defined by the three points). I can do this by hand and get them close but not exact. I would also like to be able to calculate the rms deviation between similar atoms in the core structure if possible. Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu **********************************************

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Re: [Chimera-users] Generating symmetry-related molecule
by Elaine Meng 12 Jan '09

12 Jan '09

Hi Virginia, I definitely tried it myself before sending the message, but in a much newer version (daily build Jan 9, 2009!). However, I just now tried it in both 1.2540 and the most recent production release 1.3 (Dec 2008), and in both of those versions the command works either with or without the pound signs (#). The error message sounds like you have additional models besides the DNA structure with model number 0. If so, I think the command would work if you close those, use sym, and then reopen or regenerate them as possible. You may want to update to a newer version to get other new features, but my experiments suggest it will not affect this particular problem. 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 Jan 12, 2009, at 1:41 PM, Virginia Pett wrote: > Elaine, > Thanks for the fast reply! > > I had tried what you suggested. > sym #0 #0 > and just now I tried > sym 0 0 > and generated error message: > Multiple models with id: 0 > > I am using Chimera ver 1.2540 and perhaps the problem is that I need > to update the software? > > Virginia

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Generating symmetry-related molecule
by Virginia Pett 12 Jan '09

12 Jan '09

I am trying to display PDB file 2O1I, which is a DNA structure. I would like to generate the biological macromolecule with 2 strands of DNA, but I'm having a hard time figuring out how to do this. The PDB file has BIOMT records in it and I thought I could use the sym command to generate the other strand of DNA. What do I use for the refmol? Is there a tutorial on this topic? Virginia _______________________________ Virginia B. Pett Professor of Chemistry The College of Wooster 943 College Mall Wooster, OH 44691-2363 voice: 330-263-2114 fax: 330-263-2386

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"Extra" hydrogens in Dockprep and addH steps
by CHIU,YEUNG 12 Jan '09

12 Jan '09

Dear colleagues and friends, I notice that during "Tools -> Dockprep" and "Tools -> addH" steps Chimera sometimes will automatically add hydrogens to the positions considered necessary by the program itself. However, these positions do not always really have these hydrogens imposed on them. One situation is when I added hydrogen to the molecule containing nitrogen with lone-pair electrons, Chimera added hydrogen to the position of this lone-pair. One other situation is in the disulfide bond. It seems that Chimera can not recognize the disulfide bond, so hydrogen is added to each of the thiol group, which is obviously inappropriate. I'm wondering what causes these situations and how users can prevent them happening. Any help is appreciated. If you coincidently encountered with similar situation, I'm glad to hear your story as well~ Happy new year and best wishes to your research! Sincerely yours CHIU,YEUNG

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Changes after 1.3
by Jon Rumbley 12 Jan '09

12 Jan '09

I noticed you were going to remove the DelPhi interface after Chimera ver 1.3. I have used this interface to generate electrostatic surfaces in Chimera for both teaching and research, will there be something replacing it? Thank you, Jon Rumbley Dr. Jon N. Rumbley Assistant Professor Dept. of Chemistry and Biochemistry/ Dept. of Pharmaceutical Sciences University of Minnesota-Duluth 253C SSB 1035 Kirby Dr. Duluth, MN 55812 Phone: 218-726-7423 email: jrumbley(a)d.umn.edu

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Higher Order
by hsosa＠aecom.yu.edu 11 Jan '09

11 Jan '09

I have another related question: If I were to deposit a PDB coordinates file of a helical structure, what would be the best place to put helical symmetry information (the file includes the full coordinates for only one asymmetric unit) so that chimera can generate a model with more than one asymmetric unit ?. The idea being to be able to see the contacts between asymmetric units and the symmetry of the complex. Should I use the the SMTRY, or the MTRIX entries ?. Does it make any difference in chimera ?. 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 -----------------------------------

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Higher order
by hsosa＠aecom.yu.edu 11 Jan '09

11 Jan '09

Hi, Is it possible to use the tools in: Higher Order Structures > Multiscale Models to generate full atomic models (with atoms and all the display capabilities of chimera) from the symmetry entries in the PDB file (SMTRY entries) ? So far I been able to produce only a rough surface representation of the symmetry related molecules. 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 -----------------------------------

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Re: [Chimera-users] delphi
by Elaine Meng 08 Jan '09

08 Jan '09

Hi everybody, I'm happy to report that Chimera (version 1.4 builds Jan 8, 2009 and later) can now read electrostatic potential maps from the Intel Mac version of DelPhi provided by the Honig lab as of mid-2008: <http://wiki.c2b2.columbia.edu/honiglab_public/index.php/ Software:DelPhi_System_Requirements> The problem was that part of the potential file was written in double precision. Their group may be updating that executable so that it does not write double precision, but either way, the newer builds of Chimera will be able to read the maps. This does not solve the problem Darren was having, I assume using a PPC Mac rather than an Intel Mac. The PPC Mac version of DelPhi from the Honig lab still requires certain library files that I don't think are freely available. The Honig web site (URL above) does mention this issue. 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 Dec 30, 2008, at 4:55 PM, Elaine Meng wrote: > Hi Darren, > Unfortunately it is an unsolved problem getting a pre-made delphi > executable for Mac OSX that gives results that can be shown in > Chimera. Just to clarify for everybody, DelPhi is a program freely > provided by another group, but without official support. > > I went through several weeks of trying to get an older executable from > the Honig site to work, installing various files myself just as you > have. Here is the chimera-users message where I describe running up > against this wall: > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-November/ > 001113.html >> > > I reported these problems to the Honig group, and some months later > (July 2008) they updated their Mac OSX Intel executable so it does not > require these additional libraries. Maybe you downloaded an > executable before that time or have a PPC Mac rather than Intel. > Honig group DelPhi download page: > <http://wiki.c2b2.columbia.edu/honiglab_public/index.php/ > Software:DelPhi_System_Requirements >> > > However, although the Intel executable runs nicely and can be > controlled by DelPhiController, something about the map format changed > and Chimera cannot read the result. We were unable to get information > from the Honig lab on how the format changed, or even reverse-engineer > the changes given our example maps. There is nothing else we can do - > it is a limitation recorded in our database as problem report #6228.

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question about measuring volume via command line and the nogui option
by Bruno Villoutreix 07 Jan '09

07 Jan '09

Dear Chimera Users i am new to chimera, is it possible using something like: chimera --nogui open myfile.mol2 and then i would like to measure the area and volume...but i am not sure which command to use. I can get the surface with this command but to get the volume, i have to use the graphic interface, i do not see either the name of the command in the command history list... thanks if you can give me some advices Bruno

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problem with new release
by Lionel Nauton 06 Jan '09

06 Jan '09

hi all, I don't know if everyone else have this problem, but i 'm not able to use the last release of chimera (chimera-1.3.2577-linux.exe <https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=linux/chimera-1.3.2577…>) installation script works well, but when I try to start the program, i have a black screen , and my session shutdown and restart, it seems that chimera fall down my Xorg. I'm working on PC linux ( X86_64), but i used the 32 bits version of chimera, ( test with X86_64 version give the same result), my pc linux work with fedora 10 , i have no problem with chimera-1.3.2540-linux.exe thanks per advance for your answer ================================================= NAUTON Lionel Ingénieur d'études. Laboratoire de Synthèse Et Etude de Systèmes à Intérêt Biologique UMR6504 : université Blaise Pascal – CNRS 24, avenue des Landais – Campus des Cézeaux 63177 AUBIERE Cedex France Tel : 04 73 40 55 06 mèl : lionel.nauton(a)univ-bpclermont.fr <mailto:lionel.nauton@univ-bpclermont.fr> site web : http://seesib.univ-bpclermont.fr/site_web/pageaccueil.htm <http://seesib.univ-bpclermont.fr/site_web/pageaccueil.html> =================================================

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delphi
by Darren Thompson 05 Jan '09

05 Jan '09

I installed the ibm compiler libraries on Mac OSX tiger, but delphi still does not see them Applications System Folder mach.sym Applications (Mac OS 9) TheVolumeSettingsFolder mach_kernel Desktop (Mac OS 9) Trash opt Desktop DB Users private Desktop DF Volumes sbin Desktop Folder automount sw Developer bin tmp Documents cores usr Library dev var Network etc System mach the opt folder (ibm) is there. I did a symbolic link to the Mac OSX executable in the /usr/local/ release1.1/exe directory to /usr/bin/delphi, downloaded the example files from delphi's website, [psb-232-45:release1.1/examples/example_1] darren% delphi param_1 dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib Referenced from: /usr/bin/delphi Reason: image not found Trace/BPT trap when I try directly [psb-232-45:local/release1.1/exe] darren% ./delphiMacOSX dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib Referenced from: /usr/local/release1.1/exe/./delphiMacOSX Reason: image not found Trace/BPT trap Does it matter that it's looking for /libxlf90.dylib and I have / libxlf90.A.dylib? Have some xmas charity Help a newb Darren Thompson Graduate Student UCSC 1156 High St. Santa Cruz, CA 95064 831-459-3390 voice 831-459-2395 fax http://people.ucsc.edu/~ministry

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Motivational Posters, Demotivators
by Breann Crenshaw 02 Jan '09

02 Jan '09

Rofl Motivational Posters http://www.roflposters.com

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Re: [Chimera-users] Chimera - calculating surface area?
by Elaine Meng 29 Dec '08

29 Dec '08

On Dec 29, 2008, at 8:54 AM, Uli Strych wrote: > Hi Dr. Meng, > I would like to calculate the surface exposed area of only the > hydrophobic amino acid residues for my protein of interest. > I saw your email (at > http://www.ccl.net/cgi-bin/ccl/message-new?2008+03+07+013+raw ) where > you explain how to do so using Chimera. > My problem is the "Attribute Calculator" step, where I don't seem to > be able to find the correct format of entering the formula to > calculate the surface area of the residues that I have previously > selected in the Render/Select menu. Hi Uli, Another necessary step is to show the surface (which creates the surface area values): command "surface" or menu "Actions... Surface... show". You could do that for the whole protein before selecting the residues, or just for the selected residues, either way is fine. That will assign values for the residue attributes named areaSES (solvent-excluded surface area) and areaSAS (solvent- accessible surface area). Then in "Attribute Calculator" you would Calculate attribute [some name, doesn't matter] for [models] Formula: sum(residue.areaSES) with these options checked on: "Restrict formula domain to current selection, if any" (only sum over the selected residues, not all residues) "Open Render/Select by Attribute" (because this dialog will show the answer, the sum value) You want a "models" attribute because you want only one number, the sum over the selected residues. Click Apply (or OK, which would also dismiss the calculator dialog) to calculate the value and show it in the Render/Select by Attribute dialog. Of course, you could use areaSAS instead of areaSES as you prefer. The SES is probe contact and re-entrant surface, and is shown in Chimera. The SAS is where the probe center goes, about 1.4 Angstrom farther out from the molecule, not shown in Chimera. Attribute Calculator manual page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcula… > This tool is also used in the Attributes tutorial, part 2: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#p… > I hope this helps! Best regards, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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transparent background error
by odonnell＠chem.fsu.edu 23 Dec '08

23 Dec '08

Hi, I can't find a previous entry in the archives for an error message i receive when i impose a transparent background. As soon as i read in a map i receive this: Runtime error! ProgramC:\Program Files (x86)\Chimera\bin\pythonw.ese R6025 -pure virutal function call Hitting OK I receive... Chimera failed abnormally; the exit code was:255. Thanks in advance for any advice!!!! -Jason ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Still having connection problems with Internet...
by Kenward Vaughan 23 Dec '08

23 Dec '08

Hi all, I wrote in once about this, and have only slowly paid attention to it due to busy schedules, kids, etc. I have build # 2576, and the darned thing pesters me for registration ;-) and still cannot connect for DL'ing PDB's from the data bank. I have no proxy server, and this issue did not exist in earlier versions (I'm uncertain how long ago, to be honest... within a year, I believe). The usual error notice shows up on attempted registration, and fetch attempts give a socket error about a service being unknown: Error reading 1d66: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') All other Internet apps I have work well. What else can I try to clear this up? Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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ubuntu graphics problem
by Elaine Meng 23 Dec '08

23 Dec '08

Fabian reports a Chimera/ubuntu problem and a solution: Begin forwarded message: > > Hi Elaine, > > To save people painful dealing with the newest version of ubuntu, > 8.10, if everybody asks you, chimera has an incompatibility with the > "desktop effects" and "compiz" effects of this version. The only > solution I found (after two days of trials) is to remove compiz (apt- > get remove compiz) and completely disallow the desktop effects > (through system settings). > > Best regards, > Fabian > >> Something more urgent, I have recently updated my kubuntu system to >> 8.10, and the nvidia graphics card to nvidia-glx-177 (177.80 to be >> precise) which should be the correct one. The problem is that after >> a few seconds of working with some molecule in the chimera window >> (which opens fine), it gets stuck and works very very slowly if at >> all. That is a problem since I use chimera very heavily. Any hint >> you could give me of how to solve the problem would be invaluable. >> Just to mention that I have heard of problems with this version of >> kubuntu, but surely there is a workaround. >>

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anti-aliasing in mac version
by Grigore Pintilie 22 Dec '08

22 Dec '08

If I'm not mistaken it looks like anti-aliasing is not used in the mac build of chimera... is there a way to enable this? I'm using a Macbook pro with the nvidia card and Mac os X. Greg

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NMR-Style structures
by Eric Pettersen 18 Dec '08

18 Dec '08

On Dec 18, 2008, at 2:28 PM, Huang, Shengyou wrote: > Is any way for Viewdock in Chimera to open a pdb file with NMR-style > structures so that I can view those NMR-style structures one by one? Yes, you can use ViewDock for that. When ViewDock asks you what the file type is, choose either "Dock 3 or 3.5", "Dock 3.5.x single", or "Dock 4, 5 or 6". Then the normal ViewDock interface will come up. There won't be much information in the various fields because an NMR PDB file doesn't have the embedded information that a DOCK output file does, but nonetheless you can click through the list of structures like normal. Another possibility is to open the NMR file as a trajectory (MD/ Ensemble Analysis->MD Movie) and play through the conformations that way. You could also use other analysis capabilities of the MD Movie tool, such as the RMSD map function. You might also want to try out the Ensemble Cluster tool, which will cluster your NMR ensemble and let you look at representative structures from each cluster. It sounds like you have a lot of conformations, so the Ensemble Match (compare your N structures in an NxN table) and Tile Structures (show all the conformations at once tiled in a grid on the screen) are probably not as useful as they would be for smaller ensembles. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Stereo view
by Eric Pettersen 18 Dec '08

18 Dec '08

On Dec 18, 2008, at 2:28 PM, Huang, Shengyou wrote: > Another question is how to see a stereo view of a structure in > Chimera. Do I need a pair of special glasses for that? You can use the Camera tool (Stereo) to make Chimera show either a cross- or wall-eyed stereo view. You don't need special glasses to use those modes, but you do need to be able to cross or unfocus your eyes (respectively) to get the two images to merge. Some people have difficulty doing that. The other stereo modes mentioned on the page I linked to do require special glasses, and are described in detail on that page. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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info about energy in the minimize module
by Bruno Villoutreix 18 Dec '08

18 Dec '08

Hello not sure this is the right place to ask... when running minimization in Chimera, do you have a window that show the energy values before and after the process ? or should this be done via a terminal window using the nogui option ? maybe the info is here around but could not find it so far many thanks Bruno

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possibilities to save parts of models (selection)?
by Sebastian Kruggel 17 Dec '08

17 Dec '08

Hi all, is there a simple way to save incomplete models (eg the current selection)? The write command seems to work only with complete models and not with atomic specifications and the split command does only give me the possibility to split complete chains. Probabaly I just don't see something *very* easy... Thanks for help! Sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 D 20146 Hamburg Tel +49(0) 40 42838 3626

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Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids
by Eric Pettersen 16 Dec '08

16 Dec '08

On Dec 11, 2008, at 3:43 PM, David Chenoweth wrote: > Hi Eric, > Thank you very much for the ellipsoid script! I really appreciate > your help and I think this will do the trick for now. I have been > learning some python on my own and I was wondering if you have some > good beginner examples of scripts for making geometrical shapes, > changing size and color, orientation, etc. that work in chimera. Hi David, You can show cones, arrows, boxes, and a variety of simple geometric shapes by opening a BILD format file in Chimera: BILD format. It may be a little awkward having a script write a temporary file, so instead you can use a StringIO object, as described here: [Chimera-users] BILD object question You can also use the 'shape' command to draw spheres, cylinders, and icosahedrons. You can run any Chimera command from Python by using Chimera's 'runCommand' function, e.g.: from chimera import runCommand runCommand("shape sphere center ligand color dodger blue radius 25") Feel free to ask more questions! --Eric

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Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids
by Tom Goddard 16 Dec '08

16 Dec '08

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. Tom David Chenoweth wrote: > Hi Tom, > > Here is the description of the thermal ellipsoids and option to change > the probability lavel from the Raster3D page. > > -prob Plevel > By default, isosurfaces are drawn to enclose the 50% probability > level in the probability density function described by the Uij values > in the ANISOU record. The -prob option allows you to select a > different probability level instead. If 0<Plevel<1 this value is > interpreted as a fraction; if Plevel > 1 this value is interpreted as > a percent. > > http://skuld.bmsc.washington.edu/raster3d/html/rastep.html > > -Dave > > > On Dec 12, 2008, at 10:27 AM, Tom Goddard wrote: > >> Hi David, >> >> By probability level do you mean occupancy? You could change the >> script to show only atoms with > 50% occupancy by changing: >> >> for a in atoms: >> perMol.setdefault(a.molecule, []).append(a) >> >> to >> >> for a in atoms: >> if a.occupancy > 0.5: >> perMol.setdefault(a.molecule, []).append(a) >> >> Tom >> >> >> David Chenoweth wrote: >>> Hi Tom, >>> >>> Thanks for the script and all the help. The script works great, but >>> I was just wondering if there is a way to set a probability level >>> (50%)? >>> >>> Thanks again, >>> Dave >>> >>> On Dec 12, 2008, at 9:58 AM, Tom Goddard wrote: >>> >>>> The script for drawing aniosotropic b-factor ellipsoids makes uses >>>> 1280 triangles per ellipsoid surface which slows down your graphics >>>> for cases with more than 1000 ellipsoids. You can reduce the >>>> "subdivision_levels = 3" in the script to "subdivision_levels = 1" >>>> to use just 80 triangles, or to a value of 2 for 320 triangles. >>>> The number of triangles controls how smooth the ellipsoid looks (T >>>> = 20 * 4^S, S = subdivision_levels). >>>> >>>> Tom >>>> >>>> >>>> Eric Pettersen wrote: >>>>> On Dec 10, 2008, at 3:41 PM, David Chenoweth wrote: >>>>> >>>>>> Dear Chimera team, >>>>>> >>>>>> It looks like preserving PDB ANISOU in Chimera is now a solved >>>>>> problem and I was just wondering if the ability to display >>>>>> anisotropic temperature factor ellipsoids would be added soon. >>>>>> Our small molecule lab and molecular observatory at Caltech is >>>>>> starting to use Chimera and I think small molecule >>>>>> crystallography labs in general would use Chimera more if this >>>>>> feature were available. I do have to admit that I am interested >>>>>> in this feature for selfish reasons. I am using Chimera for >>>>>> several publications and for the graphics in my thesis which, has >>>>>> to be finished in the next couple of weeks, and I would really >>>>>> like to use this feature. >>>>> >>>>> Hi Dave, >>>>> Yes, reading/preserving the ANISOU info lays the groundwork for >>>>> eventually showing anisotropic ellipsoids. There's still a lot of >>>>> work to go before showing the ellipsoids becomes a usable feature >>>>> of Chimera. It might make it into our next release (middle of >>>>> next year) and it might not. As a stopgap, I've attached a script >>>>> that will show ellipsoids for any currently selected atoms. You >>>>> can run it by simply using File->Open or the "open" command. The >>>>> first two lines of the script control the size and color of the >>>>> ellipsoids, so change them if you like. The script leverages some >>>>> code that Tom Goddard wrote for showing principal axes of inertia >>>>> as an ellipsoid. >>>>> Good luck with the thesis! >>>>> >>>>> --Eric >>>>> >>>>> Eric Pettersen >>>>> UCSF Computer Graphics Lab >>>>> http://www.cgl.ucsf.edu >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu >>>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >

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making ribbon representaiton
by Bala subramanian 13 Dec '08

13 Dec '08

Hello all, I have a pdb file of a RNA duplex containing only the Phosphate atoms. How to make chimera to draw the ribbon representation. This is possible in vmd by using Tube as graphic style but i want to know if i can make it in Chimera too. Bala

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length of a curved alpha helix
by Anindito Sen 12 Dec '08

12 Dec '08

Dear All I was wondering as how can I measure the length of "curved" alpha helix. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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problems before even getting to the plate...
by Jon Kenniston 12 Dec '08

12 Dec '08

Howdy, Trying to run latest Chimera release version 1.3.2577 on my OSX 10.4.11 with X11 version 1.1.3 and while the chimera program opens, I cannot open a PDB (or at least I can't see the opened PDB - no error message, and bottom left of chimera screen states "Opened XXX.pdb" for about a minute until it goes to blank). Should I try installing an older version of chimera? Any help would be much appreciated. Thanks, Jon

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