- Chimera-users - RBVI Mailing Lists

surface view of large file in chimera
by G.-Q. Hu 17 Feb '09

17 Feb '09

Hello, I am trying to show a large file by surface view in chimera. But I found that the structure lost the detail and the surface was smoothed. I guess there is a sampling problem for large file. Is there any way to view the large file at the original resolution? Thanks. Guiqing

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Volume->Fit in Map question
by Keren Lasker 17 Feb '09

17 Feb '09

hello, Is there a way to fit a density map to a pdb rather than a pdb to a density map ? Or in other words, that in the end of the fitting procedure the map would move to best fit the model rather than the other way around. thank you, Keren Lasker.

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configuration file for chimera
by Bala subramanian 17 Feb '09

17 Feb '09

Dear chimerians, Sorry if this question has been asked before. Where can i fix the default parameters for chimera. I explored the preferences option in favourites menu and set chose some preferences. In addition to that I want to the following like setting the color of carbon atoms as green as default setting the color of hydrogen atoms as white as default setting some macros setting the command line option when the chimera starts up (every time i go to favourites and click command line to invoke it) and other settings something like the configuration file used for vmd (.vmdrc ). Thanks in advance, Bala

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stereo view
by Francesco Pietra 17 Feb '09

17 Feb '09

Hi: I would greatly appreciate advice about the following requests (between "".."") by the referees (interaction between two proteins; graphics by chimera): 1) "there is way too much wasted black space in figures". As the complex of proteins is elongated along one axis, I found it unavoidable to have wasted space around. Perhaps using a white background in the hope that white is less offending than black? Or is it a way to tailor the background according to the shape of the object? 2) "a stereoview might be helpful for better understanding". How to fulfill this request with chimera I have no idea. 3) "a molecular surface representation of the docking site would be useful". I read on passing about molecular surfaces on this forum. Is that feasible for the highly complex situation of 3D perspective with so many atoms at different "layers"? Thanks indeed for answering francesco pietra

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Consurf .chimerax file under linux
by Boaz Shaanan 16 Feb '09

16 Feb '09

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Re: [Chimera-users] Chimera 3D labels
by Elaine Meng 16 Feb '09

16 Feb '09

On Feb 16, 2009, at 6:53 AM, nettles wrote: > > Dear Elaine, > I'm thinking this should be possible, but don't know how to do it. > Can the labeling function in Chimera could be made more spacially > flexible? > > An example is below. The residue label coordinates are anchored to > a fixed 3D point that may, or may not be desirable for a given > view. Can this be adjusted? > > It looks like these references may be set at centroids. Maybe one > could have a toggle switch that sets the anchor projected a certain > distance from a C-alpha along the viewing vector. That might give > quick access unified text float-over > > Thanks again for such a great tool. > Jim [attachment removed by Elaine] Dear Jim, I am frequently irked by the same issue. Currently residue labels are anchored at the centroid of the displayed atoms, whereas sometimes it would look better if they were anchored at the alpha- carbon. I've previously created a bug report about this. Longer term we would also like them to be movable with the mouse, but that also can't be done currently. Here is the bug/request tracking info: http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/6866 http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/167 One current workaround is that you can label some particular atom in the residue with residue information. However, currently that atom must be explicitly displayed (won't work to label some backbone atom if ribbon is shown and suppresses that atom... which I've also complained about!). Commands to do that: labelopt info residue la @ca [or if ribbon is shown, "la @cb" instead if you can live without the glycine residue labels] I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Animating a C-alpha chain trace
by Tom Goddard 13 Feb '09

13 Feb '09

Hi Matt, A Python script can make a chain trace movie with density display that adds one residue at a time. I've attached an example script and movie. I used the today's Chimera daily build that has a nice 1-layer transparency option. That won't work in earlier Chimera versions. Tom Matthew Dougherty wrote: > Hi Tom, > > Over the last couple years I have moved my animation off the > SGI/IrisExplorer to Chimera/Amira. > > I have one piece of code on Explorer that I have not moved; attached > is a typical animation. > > what is being accomplished is a demonstration of the folding of a > protein based on c-alpha backbone and related density. > starting at the first residue, it proceeds by adding one residue at a > time. > > How would you suggest to move this to chimera? > > Matt > > > > > > > > > > > > > > > # ----------------------------------------------------------------------------- # Trace C-alpha backbone adding one residue at a time and show simulated map. # pdb_path = '/usr/local/src/staff/goddard/pdb/pdb1fav.ent' resolution = 5.0 # Simulated density resolution, Angstroms map_color = (.6,.7,.8,.3) # red,green,blue,opacity. from chimera import runCommand # Open model from chimera import openModels as om m = om.open(pdb_path, 'PDB')[0] # Orient molecule runCommand('turn y 90') runCommand('turn x 30') # Color molecule and background runCommand('rainbow') runCommand('set bg_color white') # Create residue number label runCommand('2dlabel create rlab xpos 0.1 ypos 0.9') # Set display style. runCommand('repr stick #%d' % m.id) m.stickScale = 5.0 # Fatter sticks # Order residues by number and chain id. rlist = m.residues rlist.sort(key = lambda r: (r.id.position, r.id.chainId)) # Hide all atoms. for a in m.atoms: a.display = False # Show density adding one residue at a time. from MoleculeMap import molecule_map atoms = [] map = None for r in rlist: # Accumulate atoms from residue. atoms.extend(r.atoms) # Close previous map. if map: om.close([map]) # Make map. map = molecule_map(atoms, resolution, gridSpacing = .2*resolution, showDialog = False) map.set_parameters(surface_colors = [map_color], one_transparent_layer = True) map.show() # Display backbone atoms. for a in r.atoms: if a.name == 'CA': a.display = True # Update residue label text = 'chain %s residue %d' % (r.id.chainId, r.id.position) if r.isHelix: text += ' helix' elif r.isSheet: text += ' sheet' runCommand('2dlabel change rlab text "%s" color black' % text) # Draw one frame. runCommand('wait 1')

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Re: [Chimera-users] Command Line - Slecting Zone Parameters
by Elaine Meng 11 Feb '09

11 Feb '09

On Feb 11, 2009, at 2:54 PM, Thiruvarangan Ramaraj wrote: > Hi all, > I am trying to find all the atoms that lie within a certain > distance from a selected chains. I am able to do this by going to > select -> zone and giving the distance I want and selecting all the > atoms that met my criteria. I would like to do this on command > line. I am unable to figure it out. > Any help would be greatly appreciated. > Thank You > Thiru Ramaraj Hi Thiru, The following command would select all residues with any atom within 4.5 angstroms of your current selection: select sel z<4.5 You could use "za" instead of "z" if you want an atom-based cutoff instead of whole residues, > instead of < to get the atoms farther away, and of course, a different distance. Also, you don't have to use selections. For example, this would color all atoms within 5 angstroms of chain A red: color red :.a za<5 Description of command-line zone specification: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ atom_spec.html#zones> More examples appear in various tutorials: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ attributes.html#part2> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ squalene.html#surfaces> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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maps handling
by Benoit Zuber 11 Feb '09

11 Feb '09

Hi, I want to handle a large number of small density maps (around 1000 maps of approx 50x50x50 pixels). I need to group them (in around 5 groups). Then I need to treat all the maps of each group in a certain way. For example, I would like to change the level threshold for display, or the display style for every maps in a group at once. Also I would like to show or hide all maps of a group at once. The maps are not opened in an order related to their group. I remember someone recently suggested model 'folders' as a new functionality. Has this been incorporated in the latest versions of chimera? Even if it is the case, It would be too tedious to have to click on each individual model to assign it to a group. Similarly a simple command passed at the command line wouldn't be very elegant: I would have to write each volume number since they are unsorted. I suppose a python script would be much more appropriate. The script would have some functions to do tasks like those described above on each members of a group and a function to read group composition from a text file. I looked in chimera's programmer guide for a section on volume handling but I couldn't find much material on that. Did I miss it? What approach would you recommend? I guess I could use runCommand() but there are maybe better ways. Also the script would have to run in interactive mode. I suppose that IDLE would work for that purpose. How should I do that? Open IDLE and import my module? Where can you define the paths that chimera uses to look for packages? Thanks in advance! Ben -- Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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examples of python scripts
by Bala subramanian 11 Feb '09

11 Feb '09

Dear Chimerians, Can someone help me by providing examples of python scripts written for analyzing structures inside chimera. I have seen the chimera programmers guide but i need some more scripts written for different tasks to understand the way of accessing certain residues or atoms in a structure and extracting its attributes etc. Cheers, Bala

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making movies with CMM files
by Keren Lasker 06 Feb '09

06 Feb '09

hello, Is there a way to generate a movie out of a set of CMM files ( similar to MD Movie with PDB files)? thank you very much, Keren.

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Re: [Chimera-users] [chimera-dev] alias menu
by Eric Pettersen 06 Feb '09

06 Feb '09

On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote: > Dear Chimera Developers, > > Perhaps I have missed it, but I would find a menu for selected > aliases very useful. Having returned to Chimera from PyMol recently, > it would be great to have an option for the alias command that > allowed the particular alias to be listed in a separate window and > ran the alias by clicking on the alias name listed there. > > Best regards, > > Tim Hi Tim, As Elaine pointed out in her reply, aliases are frequently used as shorthands for long atom specs rather than as replacements for complete commands. However, the form of the alias command that uses '^' (so that matching only occurs at the start of the line) typically is used to define full command aliases. So my thinking is this: aliases defined with the '^' character would be placed in an 'Aliases' top-level menu (created on the fly as needed). Such aliases would automatically be remembered across Chimera invocations (and populate an Aliases menu). The menu could be torn-off (except on Aqua) to make a stand-alone window. Those aliases could be deleted as normal with the ~alias command (which would remove them from the menu and no longer remember then in subsequent Chimeras). Would this be good enough? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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script command for writing out areaSAS attribute?
by Julius Su 05 Feb '09

05 Feb '09

Hello, Does anyone know what script command could be used to output an "attribute assignment file" in Chimera, specifically for the areaSAS attribute? I am trying to show how the solvent accessible surface area on various residues changes over the frames of a multitrajectory PDB file. To do this I am trying to write a small script in "MD movie" that computes the solvent accessible surface for each frame, then outputs the areaSAS values. I was previously able to do this by loading in all the PDB geometries at once, then using the "Render attributes by ..." dialog, but this method does not scale well to very large proteins (the program runs out of memory trying to compute all the surfaces at once). Thus I am trying to do this task sequentially with a script. Thanks much! Julius

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Is it possible?
by Ahir Utsav Pushpanath 04 Feb '09

04 Feb '09

Hello Dear Sir/Madam, I am very fond of chimera, and everytime I have looked at scripts for doign things, I find that chimera has them already inbuilt as features. There is one particular problem that I am sure chimera has the capability of doing but I am struggling to do it. 1) I want to use structural superposition servers such as Mammoth etc to produce a structural alignment of two proteins, 2nadA and 1ybaB. However, some of these servers do not produce a sequence alignment output in a format compatible with chimera (i.e such as .aln or aligned fasta). But they do produce a .pdb file showing the superposition. 2) If I load the .pdb onto chimera, sometimes in "model list" window, i see the two proteins, wheras in others I only see 1 model(yet there is clearly 2 models there) 3) I was wondering whether you can load the superposition onto chimera, and see the sequence alignment that gives rise to that structural superposition, so that I may save it as a .aln format using multialign viewer. How do I do this? Apologies if this is a very straightforward scenario. Thanks Ahir

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roll command:
by Bui Khanh Huy 02 Feb '09

02 Feb '09

Dear all, I tried the roll command with my model (EM map) open: roll z 30 1 center 50,50,50 Chimera showed msg "wait_frames argument not implemented". Just wonder how to implement that command without the error? Huy

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Calc buried surface area between 2 chains
by Tom Duncan 30 Jan '09

30 Jan '09

I saw an earlier post (Dec. 29, 2008; Digest vol. 68, issue 28) in which Elaine Meng described a procedure for calculating surface area for selected atoms. I did this for atoms on chain A that were selected as contacting atoms on neighboring chain B, but the sum(atom.areaSES) probably includes area buried within the chain A, not just between the 2 chains. I tried checking this by calculating the sum(atom.areaSES) for chain A (all atoms in A) in the whole model, then again for a model from which chain B was deleted before calculating the surface. However, the results indicated a larger areaSES for chain A in the absence of chain B! There were some errors reported in calculating the surfaces; perhaps this contributed. Is there a better way to calculate the buried surface on 1 chain due to contacts with a 2nd chain? Thanks, Tom Duncan

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error message
by Katherine Parra 28 Jan '09

28 Jan '09

Hello! I'm trying to get the hydrogen bonds between some selected residues during a trajectory, using per frame commands from tools. But when I get the possible hydrogen bonds formed between the selected residues I also get the following error message in the Reply Log: *Skipping possible acceptor with bad geometry: #0:2108@O Wrong number of grandchild atoms for phi/psi acceptor #0:2108@O *What could be happening? Thank you in advance. KP

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color zone on command line
by Giulia Zanetti 28 Jan '09

28 Jan '09

Hi all, I would like to make a movie in which areas of my map are coloured while the surface is rotating. Any idea how to use color zone from the command line? thanks Giulia

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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 27 Jan '09

27 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 15 Jan '09

15 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 12 Jan '09

12 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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