- Chimera-users - RBVI Mailing Lists

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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