- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Hydrophobicity surface]
by Elaine Meng 12 Jun '10

12 Jun '10

Michael Wise brings up an excellent point: several different amino acid hydrophobicity scales have been developed, and although the Kyte-Doolittle scale is one of the earliest and most-used, be aware that the ordering of residue types may be surprising if considered on purely physicochemical grounds. The "hydrophobicity surface" is for qualitative visual interpretation, so we are not highly concerned about the precise values, but users performing detailed or quantitative analyses may want to consider using alternative scales. Below I describe how other scales can be defined in Chimera, and mention that data for two alternative scales are already included with Chimera and merely need to be read in to be used in your own analyses. > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> Elaine Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: June 11, 2010 9:45:28 AM PDT > > On Jun 10, 2010, at 6:48 PM, Michael Wise wrote: > >> Dear Elaine >> Have you ever considered using an alternative hydrophobicity scale >> rather than K&D? I'm attaching a PPT slide from one of my bioinformatics lectures which compares the two scales. You'll note some real oddities in the KD scale. Most notable is Proline (hydrophilic, despite being a cyclised aromatic), but also see W, Y, G, H (which is usually thought of as only slightly basic at physiological pH). KD is by now very well established so I guess you can simply change to an alternative, but it would be a good idea to give users the option. >> Just a thought >> Cheers >> MichaelW > > Hi Michael, > It seemed like the "classical" choice, out of dozens (hundreds?) of published hydrophobicity scales, each with their own strengths and weaknesses. > > However, it is very easy (really!) to use whatever scale you like in Chimera. You would just create an attribute definition file and read it in with command "defattr" or the tool Define Attribute. It's a simple text format, and we include examples that define additional hydrophobicity scales, Wimley-White (as published in Nat Struct Biol 1996) and Hessa-von Heijne (as published in Nature 2005). The files look something like this: > > attribute: wwHydrophobicity > recipient: residues > :asp -1.23 > :glu -2.02 > :asn -0.42 > [ ... etc. ...] > > The three scales are shown in this table: > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> > > Attribute file format: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin…> > > and the complete definition files are linked to both those pages. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco >

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animating "HIDE DUST"
by Dougherty, Matthew T 11 Jun '10

11 Jun '10

Hi, I was trying to generate an animation transition using the HIDE DUST feature. Any suggestions on how to do it (e.g., chimera command, python, etc)? thanks, Matt

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redirecting runCommands output
by Bala subramanian 10 Jun '10

10 Jun '10

Friends, I wrote a small script to calculate the distance between two atoms in a list of pdb files. I would like to know how i can redirect the message that appears in replyobj to a text file. Some chimera commands like findhbon has option to save the result in file. But distance command dosent have the same. import glob from chimera import runCommand as rc filenames=[ fn for fn in glob.glob('*.pdb.*')] for fn in filenames: rc("open " + fn) * rc("distance :1@CA :166@CA") # I have to write this distance to a file.* rc("close all") Thank you, Bala

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User defined h bonds
by snoze pa 10 Jun '10

10 Jun '10

Dear Chimera Users, Manually How can I show hbonds in chimera. Suppose I want to h bonds between residue 65 NH and 80 O. and show them using red or blue color. Is it possible to read this information from a file so that I can read all hbonds information in one run. Thank you S

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Problems for mol2 with H atoms added with REDUCE
by Francesco Pietra 10 Jun '10

10 Jun '10

Hi: With CHIMERA alpha version 1.5 (build 30471 linux 64bit) and protein with H atoms added with program REDUCE: Tools -> Structure editing -> Dock prep (choice: If alternate locations keep only the highest occupancy; Add charges; write mol2) whereby I was asked to confirm residue CL- charge -1 and choose charge method AM1-BCC. getting warning: current charges are unknown for 1 non-standard atom names in otherwise standard residues. Charge 0.0 assigned to unkknown atoms. The log files reports: Charge model: AMBER ff99SB Assigning partial charges to residue CL- (net charge -1) with am1-bcc method Non-standard atom names: CYS H (CYS 55.A H, CYS 134.A H, CYS 141.A H + 39 others) Total charge for #0: -106.4198 The following residues had non-integral charges: CYS 55.A -1.2719 CYS 134.A -1.2719 CYS 141.A -1.2719 CYS 156.A -1.2719 CYS 252.A -1.2719 CYS 272.A -1.2719 CYS 276.A -1.2719 CYS 285.A -1.2719 CYS 287.A -1.2719 CYS 299.A -1.2719 CYS 307.A -1.2719 CYS 323.A -1.2719 CYS 325.A -1.2719 CYS 329.A -1.2719 CYS 55.B -1.2719 CYS 134.B -1.2719 CYS 141.B -1.2719 CYS 156.B -1.2719 CYS 252.B -1.2719 CYS 272.B -1.2719 CYS 276.B -1.2719 CYS 285.B -1.2719 CYS 287.B -1.2719 CYS 299.B -1.2719 CYS 307.B -1.2719 CYS 323.B -1.2719 CYS 325.B -1.2719 CYS 329.B -1.2719 CYS 55.C -1.2719 CYS 134.C -1.2719 CYS 141.C -1.2719 CYS 156.C -1.2719 CYS 252.C -1.2719 CYS 272.C -1.2719 CYS 276.C -1.2719 CYS 285.C -1.2719 CYS 287.C -1.2719 CYS 299.C -1.2719 CYS 307.C -1.2719 CYS 323.C -1.2719 CYS 325.C -1.2719 CYS 329.C -1.2719 As an example, the mol2 file reads for CYS 55: 877 N -27.8300 7.7310 -8.8380 N.am 55 CYS -0.4157 878 CA -28.5410 7.2460 -9.9870 C.3 55 CYS -0.0351 879 CB -27.9030 5.9690 -10.5570 C.3 55 CYS -0.2413 880 SG -26.2400 6.2310 -11.2140 S.3 55 CYS -0.8844 881 C -29.8950 6.7930 -9.5500 C.2 55 CYS 0.5973 882 O -30.0670 6.3000 -8.4370 O.2 55 CYS -0.5679 883 H -27.9010 7.1340 -8.0390 H 55 CYS 0.0000 884 HA -28.5450 8.0610 -10.7260 H 55 CYS 0.0508 885 HB2 -27.8610 5.2050 -9.7670 H 55 CYS 0.1122 886 HB3 -28.5460 5.5710 -11.3560 H 55 CYS 0.1122 ***************************** In the past I encounterd a similar problem, solving it by adding atoms with CHIMERA. This time, however, the complexity of the system suggests to use REDUCE. Thanks for suggestions. francesco pietra

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Console window in Chimera
by Varela, Lawrence Rocco 10 Jun '10

10 Jun '10

Is there a console window option available in Chimera similar to that of the single command-line tool? Rocco

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Write Amber/GAFF atom types
by Francesco Pietra 10 Jun '10

10 Jun '10

Hi: With CHIMERA alpha version 1.5 (build 30471 linux 64bit) and protein with H atoms added with program REDUCE: Tools -> Structure editing -> Dock prep (choice: If alternate locations keep only the highest occupancy; Add charges; write mol2) whereby I was asked to confirm residue CL- charge -1 and choose charge method AM1-BCC. getting warning: current charges are unknown for 1 non-standard atom names in otherwise standard residues. Charge 0.0 assigned to unkknown atoms. The log files reports: Charge model: AMBER ff99SB Assigning partial charges to residue CL- (net charge -1) with am1-bcc method Non-standard atom names: CYS H (CYS 55.A H, CYS 134.A H, CYS 141.A H + 39 others) Total charge for #0: -106.4198 The following residues had non-integral charges: CYS 55.A -1.2719 CYS 134.A -1.2719 CYS 141.A -1.2719 CYS 156.A -1.2719 CYS 252.A -1.2719 CYS 272.A -1.2719 CYS 276.A -1.2719 CYS 285.A -1.2719 CYS 287.A -1.2719 CYS 299.A -1.2719 CYS 307.A -1.2719 CYS 323.A -1.2719 CYS 325.A -1.2719 CYS 329.A -1.2719 CYS 55.B -1.2719 CYS 134.B -1.2719 CYS 141.B -1.2719 CYS 156.B -1.2719 CYS 252.B -1.2719 CYS 272.B -1.2719 CYS 276.B -1.2719 CYS 285.B -1.2719 CYS 287.B -1.2719 CYS 299.B -1.2719 CYS 307.B -1.2719 CYS 323.B -1.2719 CYS 325.B -1.2719 CYS 329.B -1.2719 CYS 55.C -1.2719 CYS 134.C -1.2719 CYS 141.C -1.2719 CYS 156.C -1.2719 CYS 252.C -1.2719 CYS 272.C -1.2719 CYS 276.C -1.2719 CYS 285.C -1.2719 CYS 287.C -1.2719 CYS 299.C -1.2719 CYS 307.C -1.2719 CYS 323.C -1.2719 CYS 325.C -1.2719 CYS 329.C -1.2719 As an example, the mol2 file reads for CYS 55: 877 N -27.8300 7.7310 -8.8380 N.am 55 CYS -0.4157 878 CA -28.5410 7.2460 -9.9870 C.3 55 CYS -0.0351 879 CB -27.9030 5.9690 -10.5570 C.3 55 CYS -0.2413 880 SG -26.2400 6.2310 -11.2140 S.3 55 CYS -0.8844 881 C -29.8950 6.7930 -9.5500 C.2 55 CYS 0.5973 882 O -30.0670 6.3000 -8.4370 O.2 55 CYS -0.5679 883 H -27.9010 7.1340 -8.0390 H 55 CYS 0.0000 884 HA -28.5450 8.0610 -10.7260 H 55 CYS 0.0508 885 HB2 -27.8610 5.2050 -9.7670 H 55 CYS 0.1122 886 HB3 -28.5460 5.5710 -11.3560 H 55 CYS 0.1122 ***************************** In the past I encounterd a similar problem, solving it by adding atoms with CHIMERA. This time, however, the complexity of the system suggests to use REDUCE. Thanks for suggestions. francesco pietra

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Hydrophobicity surface
by Beale, John 10 Jun '10

10 Jun '10

I am creating a hydrophobicity surface for a protein using the "Presets -> Hydrophobicity surface" commands. I would like to know what the colors on the surface are telling me. I see a couple of shades of blue, white, and pink to orange. What do these colors mean? Thanks! John M. Beale, Jr., Ph,D. Professor of Medicinal Chemistry and Pharmacognosy St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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Chimera - Surface calculation
by Braker, Jay 09 Jun '10

09 Jun '10

I wanted to contact you about the surface representation of a protein. I used to be able to show the surface of our protein and lately I can't show the surface on most multiple subunit proteins because the calculation fails. However, I noticed that on some previously edited structures (the same one as before, except I deleted some of the subunits/ligands) that the surface calculation would work. So, I started deleting lines in the PDB file to see if I could get the surface to start working. Sure enough, when I got to only 1 subunit left, it worked. So after more investigation, I found that if I insert "End" between each of the subunits/ligands in the PDB file then the surface calculation works for the whole structure. I have seen in the release notes of Chimera that some protein surface calculations fail, so having found a way to get mine to work, I thought I would pass it on in case it could shed some light on this surface calculation issue. Or if you have another idea how to "fix" this issue I am having, I would be glad to hear about it. Finally, I wanted to let you know that I thoroughly enjoy using Chimera, it is a great tool. Thanks. Jay

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superimposing two vrml files ?
by Boaz Shaanan 09 Jun '10

09 Jun '10

Hi, Here is a question raised by a colleague on the ccp4 bulletin board. Since Chimera was mentioned in his post I thought you guys might have an answer to his question (positive or negative), hence I'm posting his message here. Cheers, Boaz Hello, I am working on a protein whose EM model has been built long time ago. The crystal structure has been solved recently and I want to know the difference between the crystal structure and EM model. Unfortunately there is no data in the EM data base, so I can not use Chimera or Phaser to fit the crystal structure into the EM electron density directly. My friend downloaded the VRML file of the EM model ,which can be viewed using Cosmo player. And I can make VRML file from my crystal structure using Pymol or Chimera. My questions is: can I superpose two VRML files which come from EM and crystal models? If so, how can I do that? Thanks in advance! Best wishes leo Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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DCD to PDB file Residue number
by snoze pa 09 Jun '10

09 Jun '10

Dear Chimera Users, I have a simple query related to the residue numbers in chimera. If I will save pdb file in chimera then the residue numbers are not changing but if I will save a pdb file from DCD trajectory file then it set the first residue number to 1 and so on. How to save it to original PDB residue number, which is not starting from residue number 1. Thank you for your help. S

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hbond analysis
by George Tzotzos 09 Jun '10

09 Jun '10

Hi everybody, Is there a way in CHIMERA allowing to detect hbond between ligand and receptor from AMBER trajectory files? Best regards George

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Get xpos and ypos of selected residues automatically
by wei li 07 Jun '10

07 Jun '10

Dear all, Here is my problem: I need to write a cmd script to use 2dlables automatically assign some annotations to some selected residues for many different proteins. However, I did not know the xpos and ypos for these residues and for different proteins there will be different residues which need to be assigned. So, is there any method to get the xpos and ypos via some commands when I only know the residue identifiers? Thanks Wei Li 2010-6-3

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Ramachandran Plots
by James Nettles 07 Jun '10

07 Jun '10

Does Chimera do Ramachandran Plots and I'm missing something obvious? I like doing just about everything else in Chimera :-) Thanks, Jim

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byte order? mac.
by Raymond Wightman 03 Jun '10

03 Jun '10

Hi, I'm trying to open several files that were prepared on imod on a unix system - an imod .rec file, tif stacks and an .mrc file. When I open any of these file formats on my mac the histogram seems to be inverted. Inverting the LUT on the tifs using imagej does not work and using the mrcx command of imod to toggle between big- and little-endian of the .mrc file has no effect - Chimera still displays the same inverted histogram. Is there a way that I can invert everything using Chimera? The mac is intel. Much appreciated, Ray.

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Measuring dimer rotation
by Tom Goddard 03 Jun '10

03 Jun '10

Hi Bobby, The place to send Chimera questions is the Chimera mailing list chimera-users at cgl.ucsf.edu. Here are some ideas about how to measure the rotation of one dimer of your homotetramer on ligand binding. Say the tetramer has chains A,B,C,D and we want to see how dimer CD has moved relative to dimer AB from unbound to bound PDB models. The idea is to use the Chimera "match" command with the showMatrix option. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html First step is that I want to create PDB files for bound and unbound states where the AB dimers are aligned. Suppose model #0 is unbound and model #1 is bound. This command will move the bound model AB to overlap the unbound model AB match #1:.A,.B #0:.A,.B Now align bound CD with unbound CD and report the rotation/translation with the showMatrix option: match showMatrix true #1:.C,.D #0:.C,.D The output in the Reply Log (Favorites menu) looks like the following. I used a dimer example instead of a tetramer to produce this output. Executing match ['#0:.B@CA', '#1:.A@CA'], no iteration Motion from original file coordinates Matrix rotation and translation -0.31727374 -0.31084290 0.89594311 19.18030808 -0.30378517 0.92828353 0.21448604 7.82438547 -0.89836070 -0.20412345 -0.38894945 20.67993251 Axis -0.22719634 0.97384144 0.00383052 Axis point 17.54082727 0.00000000 3.53442960 Rotation angle (degrees) 112.89041450 Shift along axis 3.34122976 Motion from last position Matrix rotation and translation -0.31727374 -0.31084290 0.89594311 19.18030808 -0.30378517 0.92828353 0.21448604 7.82438547 -0.89836070 -0.20412345 -0.38894945 20.67993251 Axis -0.22719634 0.97384144 0.00383052 Axis point 17.54082727 0.00000000 3.53442960 Rotation angle (degrees) 112.89041450 Shift along axis 3.34122976 RMSD between 16 atom pairs is 0.482 angstroms You would look at motion from last position, specifically the rotation angle. For your case (tetramers built from 1pfk and 2pfk) there is a problem that the exact same atoms are not in the two tetramers. The match command requires that you specify an exact pairing of atoms. You can use the Match Maker dialog or mmaker command which will figure out the atom pairing for you. But match maker doesn't report the motion so you would use the "measure rotation" command to do that. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html mmaker #1:.A,.B #0:.A,.B pair ss write relative #0 #1 /tmp/bound-ab-aligned.pdb close #1 open #1 /tmp/bound-ab-aligned.pdb mmaker #1:.C,.D #0:.C,.D pair ss measure rotation #1 #0 showSlabs true Here I aligned the AB dimer then saved the bound version to a file, closed the bound model, and opened the saved file. Did that close/open business because the measure rotation command is going to report values relative to the original file orientations. It doesn't report the motion from the last position because it doesn't remember what the last position was. The match and mmaker commands rotate the coordinate axes for one model and the "measure rotation" command reports the rotation between the coordinate axes of two models. Each model has its own coordinate axes which are initially aligned when the data is opened. I tried this with tetramers built from 1pfk and 2pfk dimers using the Chimera unit cell tool (2x2x2 cells) and the "combine" command and displayed the results with ellipsoids using the "measure intertia" command with the perChain true option. I've attached an image that shows the AB dimer in yellow, the CD dimer in blue and pink, 1pfk in solid and 2pfk in mesh, with separate rotation axes for the C and D rotations which appear quite different and are 2 to 3 degrees. I encountered an unpleasant bug that you saw before with the Chimera morph conformations tools that mmaker did not match chains C with C and D with D, instead matching C with D and D with C. It seems there is currently no way to control this other than modifying the PDB files (renumbering atoms?). Changing the order of the C and D in ":.C,.D" did not help. I've filed (another) bug report for this. http://plato.cgl.ucsf.edu/trac/chimera/ticket/8501 Tom -------- Original Message -------- From: Bobby Laird To: Thomas Goddard Date: 6/2/10 8:38 AM > Hi Tom, > > I was not sure if you would remember me so I attached the previous e-mails that you were kins enough to CC to me a few months ago. I was wondering if you could give me any advice. I am still attempting to compare the quaternary structure of a homotetramer (320 aa's for each monomer). More specifically it appears that when certain ligands are bound there is a rotation about one of the dimer-dimer interfaces. I used the axis function in chimera to approximate angles in order to get a degree of rotation and was wondering if you could give me a basic explanation of how the program calculates these angles? Also, I wanted to create a very simplified cartoon figure of each of the pdb's so that I can superimpose and emphasize the rotation that occurs. Do you have any idea how I could accomplish this? I have tried rendering space filled models and removing the lighting so that the figure appears 2-D but when I overlay the pdb's the textures become very obvious. Sorry for dumping all this on you but I wasn't quite sure where to go with these questions. Thank you very much for for your time. > > Bobby Laird >

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Re: [Chimera-users] a simple question (starting Chimera from R)
by Eric Pettersen 01 Jun '10

01 Jun '10

Hi Amitoj, I think the problem is that you write the PDB file but never tell Chimera about it -- i.e. you need to add it to the command that starts Chimera. So change your cmd<-paste to: cmd <- paste (exepath, "chimera.exe", " ", tovmd, sep="") which will result in the command string: "C:/Senior_Design/Chimera/bin/ chimera.exe random_temp_file_name.pdb". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 28, 2010, at 3:05 PM, Amitoj Chopra wrote: > Eric, > > We got it to work with chimera. Here is our code. > > chimera <- function(pdb, exepath = "C:/Senior_Design/Chimera/bin/") > { > tovmd <- tempfile() > write.pdb(pdb, file = tovmd) > > cmd <- paste(exepath, "chimera.exe", sep="") > cat(cmd) > > system(cmd) > > unlink(tovmd) > } > > > The only problem is that it opens up chimera but doesnt show the PDB > we are trying to view, for this case, 1ly2. Do you know somewhere we > went wrong. pdb should be 1ly2. Thanks. > > On Thu, May 27, 2010 at 3:42 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: > I am in no way an R expert (or even an R newbie), but given what R > documentation I've looked at I see two problems with the below. One > is that you are on Windows, and the code for Windows is commented > out (the "system" call after "if (os1 == "windows")") The other > problem is that you left "vmd -pdb" in the paste() call, so the > command it will try to execute is "/Program Files(x86)/Chimera/bin/ > chimera.exevmd -pdb <pdb-file-name-here>" which obviously won't > work. Changing "vmd -pdb " to just " " will fix that I think. > > --Eric > > On May 27, 2010, at 3:03 PM, Amitoj Chopra wrote: > >> Thank you Eric. Would something like this work. >> >> C:\Program Files\Chimera\bin\chimera.exe >> >> view.chimera<- function(pdb, exepath = "/Program Files(x86)/Chimera/ >> bin/chimera.exe", ...) { >> ## Change exepath to the location of your vmd >> tovmd <- tempfile() >> write.pdb(pdb, file = tovmd, ...) >> >> cmd <- paste(exepath, "vmd -pdb ", tovmd, sep="") >> cat(cmd) >> >> os1 <- .Platform$OS.type >> if (os1 == "windows") { >> ## Insert cmd for calling vmd on windows >> ## system(shQuote(cmd)) >> } >> else { >> system(cmd) >> } >> unlink(tovmd) >> } >> >> pdb <- read.pdb("4q21") >> view.chimera(pdb) >> >> It doesnt seem to be able to run. I am thinking of what to put in >> the "window" because that is what goes to the cmd line. Thanks. >> >> Amitoj >> >> On Thu, May 27, 2010 at 2:53 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> >> wrote: >> On May 27, 2010, at 12:27 AM, Amitoj Chopra wrote: >> >>> Is there any way to use the R script and bio3d package to open a >>> pdb with Chimera using R? Thank you. >> >> Hi Amitoj, >> If R can run external system commands then this is possible. Use >> bio3d to write a PDB file and then use R to start Chimera from the >> command line with the PDB file name as an argument, as documented >> here: >> >> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/startup.html >> >> If you don't know how to run external commands from R, you would >> probably have to ask about that on the R mailing list. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> >> > >

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Reading of charges from PRMTOP file and labeling atoms with charge value ?
by Marek Maly 01 Jun '10

01 Jun '10

Dear all, when using PRMROP/INPCRD(RST,MDCRD) files to load molecule - is Chimera able to read CHARGE information from the PRMTOP file ? If Chimera is able to do it, how is then possible to label atoms with it's charges ? It seems to me that the recommended commands sequence focus labelopt info charge label works only after "Add Charge" procedure which is trying to calculate charges according the residuies in loaded molecule but I do hope that that there is also way how to simply visualize charge values which are already present in the PRMTOP file. Thanks a lot in advance for your comments ! Best wishes, Marek Maly -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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How to hide/show sets of 'named selections' ?
by Ajith Harish 01 Jun '10

01 Jun '10

I have a model with multiple proteins. Each protein chain is split into a separate pdb file (and so separate model). I have selected domains of some proteins or complete chains or others and assigned names to them from the 'namesel' command. I am unable to select multiple named selections at a time to hide certain selections. Could you please let me know how to hide/show groups of named selections. Thank you, Ajith

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Vector artwork
by Mallela, Krishna 01 Jun '10

01 Jun '10

Hi, In Chimera, how do I save the image into a vector artwork which can be edited by Adobe Illustrator? Krishna -- Krishna M. G. Mallela, Ph. D. Assistant Professor of Biophysical Chemistry Department of Pharmaceutical Sciences University of Colorado Denver C238-P15, Research 2 12700 E 19th Ave Aurora, CO 80045

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Re: [Chimera-users] Using Chimera to read SMILES string into structure
by Robert Hanson 01 Jun '10

01 Jun '10

Elaine, I picked up this thread off the web archives. I've just implemented reading SMILES into Jmol ( http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm) but I'm pretty dissatisfied with that IU service. Do you know what they are really doing for that? For example, in that one you have there, *C\C=C/C=C/CCCCCCCCCO I note that **C\C=C/C=C\CCCCCCCCCO * gives the same result. Far as I can tell they require C\C=C//C=C\CCCCCCCCCO which as far as I can tell is invalid SMILES. At least, Daylight's DEPICT thinks it is invalid. It has also made several mistakes with relatively simple stereochemistry that I have tried. Is this your experience as well? Bob Hanson principal developer, Jmol -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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attributes
by sette＠uniroma2.it 28 May '10

28 May '10

Hi, I created my attribute file (attached) and defined by I cannot see it in the Render (by residues) attributes. I missed something? Since it was defined I don't think it has to be put in some particolar directory, or not? Thanks, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Virus Capsid Reconstruction--Slow Performance
by Carlos Lopez 27 May '10

27 May '10

Hello, I am currently trying to make a pseudo-atomic resolution model of a virus capsid, but I've run into memory problems whenever I try to combine all the asymmetric units together into one large PDB file composed of 60 copies of the asymmetric unit arranged using icosahedral symmetry. My problem is that I keep running out of memory, and I was wondering whether this is normal for the dataset I'm working on. The method I use has worked fine for smaller models, so I'm sure I'm running into the memory problems because this model is particularly large, but I still wanted to check with you guys to see what else I could try. I first start out with an asymmetric unit composed of 52 copies of protein gp24 (PDB ID: 1YUE [monomer] and 1Z1U [hexamer]). That is, I use 8 hexamers and 4 monomers. The individual chains in the unit are stripped to their alpha-carbon backbone by removing all their residues (including the solvent) to minimize how much memory they take up. The monomer weights 47.274 kDa (with residues), so that gives about 22,347 total residues for the asymmetric unit. After stripping off everything except the backbone, I ended up with a 6.4 MB PDB file. After positioning the model, I then run the command sym #1 group i,222r. This creates the 59 other copies in the expected locations. The problem arises when I try to combine all the units together into one model. Having all the models open takes up about 10 GB (out of my machines 16 GB) worth of memory, though there is still some inactive and free memory left. When I then use the copy/combine command, the memory required rises steadily until it starts to page out to the swap space and bring the machine to a grinding halt. I tried leaving it to run overnight (+18 hours), but even then it still wasn't finished. To recap: I'm trying to do a memory intensive reconstruction. I've already: 1) closed all the other models I'm not working on 2) closed all other programs on the machine 3) removed all the side chains so I'm only working with the alpha-carbon backbone 4) tried the chimera --nogui option to send the commands without having to render the graphics It's still having issues, so I was wondering if you had any additional ways I can cut down on the memory usage enough to combine the units into one map. Here are some of the things I'm still thinking of checking on: 1) Running the job on a computer with no graphics card but more RAM than my desktop station. I am able to SSH to the machine and send instructions through the console and the chimera --nogui option. Is it a problem that it doesn't have a graphics card? 2) Checking for a memory leak in Chimera--I've noticed that sometimes not all the memory is given back when I manually close models in the model panel. How can I check for sure/fix it from within a session? I've been able to deal with this by closing my session and opening it again, but it'd be best to be able to do it from within a session. 3) My system keeps saying I still have 4 GB of inactive RAM, though it's never used. I don't know if this is an issue with Chimera or with my machine, but I'll try to find out. If you need any more info, please let me know. Thank you for your help! ~Carlos Lopez My system specs: Mac Pro 4,1 Mac OS X 10.6.3 Quad-Core Intel Xeon, 2.66 GHz 1 proc, 4 cores 16 GB memory Graphics Card NVIDIA GeForce GTX 285, VRAM total: 1024 MB Chimera: Alpha version 1.5 build 30286 2010-03-23 platform: darwin 64bit, windowing system: aqua

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a simple question
by Amitoj Chopra 27 May '10

27 May '10

Is there any way to use the R script and bio3d package to open a pdb with Chimera using R? Thank you. Amitoj

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locking docking
by Alex Perálvarez Marín 27 May '10

27 May '10

Dear all, after running a Docking, I want to build a covalent bond between the receptor and the ligand and then run MD simulations. Is it done with the "build structure" menu? There is another way of doing it? Probably this has been discussed earlier, can you direct me to that topic? Thanks a lot! Alex

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creating virus capsid
by Elaine Meng 27 May '10

27 May '10

On May 25, 2010, at 10:39 PM, 江一波 wrote: > hello meng! > how can i construct a virus by chimera? > i have get a nucleocapsid protein about a virus from > http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtosh… > such as ,i get ID :2I9F structure...one of a nucleocapsid for a virus ...this is symmetrical structure! > i want construct a virus ...how can i do? is there somethings paper about how to construct ? > thank you!!! Sometimes the PDB file will include matrix information needed to build the capsid. If it does, you can use the Chimera tool "Multiscale Models" to show the whole thing. However, the authors of this structure (2I9F) did not include the necessary information in the PDB file. Next I tried to see if that structure is in VIPERdb, which would also allow showing the whole thing in Chimera. However, when I tried "File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was not found. Sorry, I don't have any ideas about how to make a whole capsid from this structure. A different structure that does include the information is 1POV. If you open that one, then start Multiscale Models (under Tools... Higher-Order Structure) and click the "Make models" button near the bottom, it will show the whole capsid. Please send Chimera questions to the chimera-users(a)cgl.ucsf.edu address. Thanks, Elaine ------------------------------ Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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translation of proteins with added pseudobonds
by Joern Lenz 26 May '10

26 May '10

Dear all, here is my problem: I have a protein and added pseudobonds that make up a triangle in order to highlight a pharmacophore. However, as soon as I loaded in the pseudobonds and translate my protein afterwards, the triangle made of pseudobonds does not do the same translation but kept being at its original position. Is this a bug or am I doing something wrong ? Any answer is much appreaciated. Cheers, Joern

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problems reading .rec file
by Shawkey,Matthew D 25 May '10

25 May '10

Hi, I have a .rec density map 2000x2000x1000 (xyz) but when i open it in Chimera it only shows the first image of the series (i.e. the dimensions are 2000x2000x1). do i need to convert it to a different format? thanks Matt ***************************** Matthew D. Shawkey, Ph.D. Assistant Professor Department of Biology Integrated Bioscience Program University of Akron Akron, OH 44325-3908 (office) +1 330-972-8192 (lab) +1 330-526-3225 http://gozips.uakron.edu/~shawkey

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measure rotation rod
by le monk 25 May '10

25 May '10

Hi all, I have used measure rotation to draw a rod down an axis of symmetry. Does anyone know a way of altering the diameter, length and color of the rod? Many thanks _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now

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prmtop
by richardbonnet 24 May '10

24 May '10

Dear, Is there a way to use writeprmtop with the command line? Is it a way to use chimera to write prmtop amd inpcrd files for a ligand (gaff type + am1-bcc charge) + the corresponding protein (Gasteiger charges + ff99sb) with the command line? I have lot of problems with input format for antechmaber. It can intersting to use chimera with the command line to solve this type of stuff. Thank a lot per avance, Richard Bonnet

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Amino acid substitution with Chimera
by Hayeon Kwak 19 May '10

19 May '10

Hi, I am currently working on a homology-modelled protein. How do I mutate a certain amino acid with Chimera? For example, if I wanted to mutate 55N into 55K to look at how the structure changes, what would I do? Any help would be appreciated. Thank you.

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Re: [Chimera-users] weighted distance
by Greg Couch 19 May '10

19 May '10

On 05/19/2010 02:07 PM, Eric Pettersen wrote: > Hi Bala, > > On May 18, 2010, at 2:04 AM, Bala subramanian wrote: > >> 1) When i type help(object) in chimera's python shell, it shows the >> help message, is there any to way to make the help information to be >> displayed in a separate window. I tried in config setting but i >> couldnt make it. > > I don't know of any way to make help() output go elsewhere. > Here's a technique to bring up the help() documention in your web brower: (1) start the IDLE tool in chimera (2) type into the IDLE dialog: import pydoc pydoc.gui() At that point, pydoc brings up a dialog where it says it started up a web server on your computer and you can "open browser" to browse all of the builtin chimera and Python documentation. There are a couple downsides: (1) chimera becomes unresponsive until you press the "quit serving" button and then chimera exits -- so browse the documentation with one chimera and program in another, (2) pydoc fails for some chimera modules, e.g., the important chimera module -- that's a pydoc bug unfortunately. - Greg

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weighted distance
by Bala subramanian 19 May '10

19 May '10

Dear Friends, Is there any way to display weighted distance in chimera. For example, in the attached data file, we have distance in column 1 and its corresponding importance in column 2. What i would like to do is to load the structure, display the distance between two group of residues and adjust the width of the line (created by distance monitor) according to the importance of the distance in the data file. Thank you, Baa

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Re: [Chimera-users] Grouping models
by Thomas Goddard 19 May '10

19 May '10

Hi Thomas, I don't understand well enough what you are doing. You can move several models at once with commands like turn y 30 models #15-25 coord #1 which will rotate models 15 through 25 about the y axis of model 1 by 30 degrees. I'm not sure if a Chimea command can save multiple PDB models in a single file. It looks like the "write" command can't do that. I'm not sure why it would be limited since the Chimera Save PDB... dialog can save multiple models. Probably Elaine or Eric can explain that. You could use the "combine" command to make one molecule from several molecules using multiple chains, but PDB format is limited to 62 chains (single letter upper/lowercase/number chain identifier). The combined molecule could then be saved with the "write" command. Tom > Hi Tom, > > we are working at the interphase of EM and atomic structures and would > like to do some interactive docking/prediction/validations etc . So our > wish would be if we can use chimera in an automatic fashion to load > atomic coordinates and simulate the structures by positioning them at > various positions within a volumetric box (such as applying a rotation, > turn around x, etc). The problem that we have is that we have to load > many structures (>60 !) at the same time as we are working with a highly > oligomeric complex. It would be great, if we can use a chimera > command-line based option to do the modifications of coordinates on a > sub-group of the loaded structures (Q: can we group several models > easily ?) and save the new coos in a single file. For now, we would need > to do it by hand, as we couldn't find a command line based saving > options into a single pdb-file .... but this can be quite tedious, if > one would like to test hundreds of possibilities. Do you have a > procedure that you would recommend for generating such simulations (for > now, we treat the structures as rigid bodies) ? > > Best, > -Thomas > >

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Saving BRIX volume file, missing data
by Thomas Goddard 18 May '10

18 May '10

Hi Miguel, I just tested saving volume data in BRIX file format on Chimera 1.4 and also with the current daily build and both worked correctly, nothing left out. Could you send me an MRC map that when I open it and save it as BRIX does not work correctly? Also please give me the exact Chimera version and operating system (Help / About Chimera...). BRIX format saves only 8-bit values. So if you have a large range of values -- say most map values are 0-10 and then one is 10000, then all the 0-10 values will be reduced to the same value (0) when it is forced into the 8-bit BRIX value range by a linear scaling. Thanks, Tom > Hi Tom, > > Thank you! This way I can extend the number of total torsions at least ten times, though I'm not sure I'm gaining much with that. I will see better once I start filling VdW volumens. > > Just a remark: I have noticed something wrong with brix format maps: they are not saved properly, a part of them is left out. I haven't found out whether this is a problem with a certain count threshold, or a number of grid points, the fact is that a good part of the map is lost. This happens whether I save it from the script as you say or from the GUI using the File menu of the Volume Viewer. So I am using MRC format for the time being, which works fine in all cases. > > Best regards, > > > Miguel > > Le 17 mai 2010 à 19:40, Thomas Goddard a écrit : > >> Hi Miguel, >> >> The Python call to save your volume data model v in a file is >> >> v.write_file('/tmp/myfile.brix', format = 'dsn6') >> >> If you do not want to create the volume model you can instead directly write out the grid object. >> >> from VolumeData import save_grid_data >> save_grid_data(grid, path, format) >> >> I figured this out by looking at the write_file() Python code in >> >> chimera/share/VolumeViewer/volume.py >> >> The allowed formats are listed in the file_writers variable in >> >> chimera/share/VolumeData/fileformats.py >> >> Tom >>

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Re: [Chimera-users] Save session for movie
by Eric Pettersen 18 May '10

18 May '10

Hi Francesco, On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote: > If at all, I did not understand if a continuous trace of the centroid > (instead of a series of balls) can be obtained in the context of the > protein. That would improve the presentation further. Otherwise, the > series of balls for the centroid, with appropriate choice of radius > and step size, shows the pathway of the ligand through the protein > adequately. Nothing simple comes to mind. One way that's a bit of work would be to save the centroid information to a file (the 'Save' button on the Axes/Planes/Centroids interface) and the use a text editor to create a BILD file (BILD format) showing lines/cylinders connecting the centroid centers. > As a minor point, I was unable to render helices transparent. > Transparency would help to to see the centroid trajectory in between > helices. Should be possible unless there's something wrong with your graphics cards. Try this: Select->Structure->secondary structure->helix Actions->Color->from editor This will bring up a color editor. Try making a transparent red. For me, the editor looks like this when I do that: (note the "Opacity" box is checked) and the structure looks like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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accessing atom information
by Bala subramanian 17 May '10

17 May '10

Friends, I have just begun to explore the chimera-python linkage. I loaded a pdb file using chimera.openModels function. Then i tried to loop through the residues and display atom information based on a condition. >>>for r in mymodel.residues: *#this works for me* if r.type=='ARG': print r.atoms >>>for r in mymodel.residues: *#this dose not work. I know there is a ARG residue with id 151.* if r.id=='151': print r.atoms I dnt understand how atom attributes are packaged within a residue. Kindly write me few examples of accessing atom information from a residue. Thanks, Bala

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clip planes in vrml
by Daniel Gurnon 17 May '10

17 May '10

Hi all, I'm thinking of the 3D printing of physical models, and how informative clipping planes can be....would it be feasible to add capped-clip planes to vrml output? I also ran into a problem when I exported a surface to vrml and tried to view it with Adobe 3D reviewer. The color information didn't transfer. This isn't a problem when saving ribbons or bonds as vrml. Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Creating movies
by Tom Goddard 15 May '10

15 May '10

Hi Matthew, The movie images including the command-line is very weird -- never heard of that happening before. It is almost certainly a graphics driver problem. You can try a Chimera daily build which uses a different image capture method. Also you can report the bug with the version you are using Chimera menu entry Help / Report a Bug.... That will give us information about your graphics card and driver that may help us advise you further. Tom > Tom, > > Thanks for the note -- regarding "all my commands show during the > movie" -- > > When I use the command line interface, the entire chimera window gets > recorded, not the viewing window with the protein. When I play back > the movie, I see the tool bar complete with the command line. I > even get to watch the text appear in the command line as it was > entered. I am using the linux version and will take the opportunity > to try the daily build. > Thanks for the help. I'll keep you updated. > > Cheers, > Matthew > > > > > Tom Goddard wrote: >> Hi Matt, >> >> Not sure what you mean by "all my commands show during the movie". >> Your second problem sounds like part of the image is corrupted and >> that is most likely a graphics driver problem causing the saved >> images to be wrong. You might want to try a Chimera daily build >> instead of the Chimera 1.4.1 production release because the daily >> builds use a different image capture method that may work better on >> your machine. >> >> You might also look at the 2009 movie course material which is more >> up-to-date than the 2008 material. >> >> http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html >> >> Both 2008 and 2009 materials primarily use command scripts and that >> is the recommended approach. >> >> Tom >> >> >>> Hello, >>> >>> I am fairly new to using chimera and created my first movie using >>> command line syntax. I am mostly pleased with the results, except >>> for two things: >>> (1) I used the 'movie record' option and all my commands show during >>> the movie. >>> (2) the right hand side of the image looks like 'snow'. >>> >>> I followed similar instructions to the tutorial for ligand flying >>> into unbound conformation from: >>> http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html >>> >>> Should I be using a script instead? Is there a better way to do this? >>> >>> Thanks for any help. >>> Matt Skeels >>

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Creating movies
by Matthew Skeels 15 May '10

15 May '10

Hello, I am fairly new to using chimera and created my first movie using command line syntax. I am mostly pleased with the results, except for two things: (1) I used the 'movie record' option and all my commands show during the movie. (2) the right hand side of the image looks like 'snow'. I followed similar instructions to the tutorial for ligand flying into unbound conformation from: http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html Should I be using a script instead? Is there a better way to do this? Thanks for any help. Matt Skeels

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Energy Minimization
by Eric Pettersen 13 May '10

13 May '10

Dear All, Using Minimize command, I can minimize the the energy of the protein. But is there a way by which I can check the energy the protein before I perform the minimization and after minimization or least after minimization. Thanks and Regards Monisha (originally sent to chimera-bugs)

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Solvate RNA-protein Complex
by Andrew Tran 12 May '10

12 May '10

Hi Chimera support, I am trying to analyze a protein-RNA complex and would like to neutralize the phosphate backbone with ions and solvate the complex. When I try to do this using Chimera (through AMBERtools?), the complex dissociates. Is there a way to add ions and solvate without dissociation of the complex? Andrew Tran Brown University Biochemistry and Molecular Biology

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error
by zxd 11 May '10

11 May '10

Hi, I'm helping Chinese Academy of Sciences test 3D Stereo display with your Chimera-1.4.1. We are using the Samsung Syncmaster 2233 monitor, Nvidia 3D Vision kit (transmitter plus glasses). I'm able to open the software. When I select, tools->camera->sequential stereo, the application will enounter an error and exit. Attached are the snapshots of the error message and details of our computer. Xiaodong Zhao 2010-05-11 zxd

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Chimera failed abnormally
by emirate14 10 May '10

10 May '10

Hi, I've downloaded the chimera-1.4.1-win32.I am succeeded to run it for several times. However, the program had a error named as "Chimera failed abnormally; the exit code was: 1. use the --debug command line option for the full error message." and I can not start it anymore (same as Johan Börjesson, http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-November/000578.html) I notice there is a note in debug box "Type=screen distance must be positive", does it cause the problem? I am looking forward to your reply. Thank you very much. Best regards . Qian Wang Zhejiang University, Hangzhou, China

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ksdssp assignments
by Tom Duncan 10 May '10

10 May '10

I noticed that the secondary structure assignments for a specific protein by ksdssp (default parameters) show a few significant differences versus the DSSP assignments shown at the PDB (file = 1aqt). Any idea why? Thanks, Tom

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output data from findclash
by Kim, Sunghoon 10 May '10

10 May '10

I'm trying to see clashes of a specific sidechain with its rotating chi angles using 'findclash' command in python script. At this point, because I 'm just looking for a set of rotamers that doesn't have any contacts or clashes, I just want to see the number of contacts from a set of specific rotameric states, rather than a detailed information. But I don't know how to print 'the number of contacts' together with its corresponding chi angles. Is there any way to write a output file from findclash calculation? Or can I modify reply log as I want ? Thanks, Sunghoon

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Re: [Chimera-users] presets, python and printing
by Greg Couch 10 May '10

10 May '10

On 05/09/2010 07:51 AM, Daniel Gurnon wrote: > Hello everyone, > My colleague and I are planning to incorporate 3D physical models into > the introductory biochemistry course at our university, and I want > students to use Chimera in the design of models. I've seen the > technotes on 3D models made by the uPrint printer > (http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html) We'll > hopefully be collaborating with the folks at MSOE on this, using their > Z-corporation printer. They use RasMol to design models, but the file > read by the printer is in .stl format. > > Here are my questions: > 1) Has anyone used Chimera to create models to be printed on a Z-corp > printer? (if yes, I'll have many more questions for you...) If you are using a Z-corp printer, you should look into sending it chimera's VRML output. That is because chimera's STL output works well when you limit it to surfaces and ribbons, but the triangles generated for bonds and atoms (interpenetrating cylinders and spheres) confuse some printer's software. The Z-corp printers come with their ZPrint software that accepts VRML and should do the proper triangulation for their printers (I say "should" because we've never tested it, but from everything I've read, I expect it to work). - Greg

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Volume covered by a group of atoms
by Miguel Ortiz Lombardia 10 May '10

10 May '10

Dear all, I would like to represent as a volume the space that would be covered by a set of atoms that are bound by "torsionable" bonds when one systematically modifies those torsion angles. An example would be the side-chain of an amino acid; imagine I would like to have a glimpse of what part of the space could be occupied by that side-chain. As a first approximation I wouldn't care about clashes. I would appreciate if someone can point me to an existing way of obtaining such representation or to an algorithm that could be implemented within chimera (which I would be happy to share with other interested people; if I manage to code it, that's it!) Cheers, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

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Ensemble Cluster via command line
by Jan H. Löhr 10 May '10

10 May '10

Dear Chimera users, I have been using the Ensemble Cluster tool to cluster a set of PDB-files. Now I would like to do this via command line or python script without GUI in order to run it multiple times. However, it seems the Ensemble Cluster tool cannot be used via command line. The only thing I have been able to is to load it up with 'start Ensemble Cluster'. Is there a way to access the tool via command line? Or is there a way to record my mouse actions and translate them to commandline-style? Here are the steps I am trying to do: Load PDB-file (multiple models in it) Start Ensemble Cluster Parts to Match: :xxx-yyy (optional) OK Write List of modelnames/cluster End This can be done by mouse, but apparently not by commandline, can it? Thank You Jan Univ. Hamburg, Germany

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presets, python and printing
by Daniel Gurnon 10 May '10

10 May '10

Hello everyone, My colleague and I are planning to incorporate 3D physical models into the introductory biochemistry course at our university, and I want students to use Chimera in the design of models. I've seen the technotes on 3D models made by the uPrint printer ( http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html) We'll hopefully be collaborating with the folks at MSOE on this, using their Z-corporation printer. They use RasMol to design models, but the file read by the printer is in .stl format. Here are my questions: 1) Has anyone used Chimera to create models to be printed on a Z-corp printer? (if yes, I'll have many more questions for you...) 2) Is it possible to define a user preset in Chimera with Python? I know this isn't currently possible with chimera commands, and I am *just* getting into Python now. Because students have difficulty jumping in to a project like this if they first have to learn to enter commands at a prompt, I want to make some presets that apply settings compatible with a 3D model; bond thickness, colors, etc. 3)If one knew Python, would it be possible to design a simplified user interface for Chimera? Even as simple as a pop-up window that contained the key features I want students to have access to right away? 4) Probably the biggest drawback to using Chimera with undergrads is the lack of an "Undo" button. I'm guessing this is extremely difficult to implement because of all 3rd party extensions incorporated into Chimera? What about an option to autosave every five or ten minutes? Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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