- Chimera-users - RBVI Mailing Lists

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

4 3

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

2 1

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

2 1

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

2 1

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

2 1

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

1 0

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

2 1

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

2 1

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

2 1

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

2 2

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

2 1

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

3 3

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

2 1

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.

2 1

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 >

3 3

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 >> >> >> >> > >

1 0

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/

2 4

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

2 1

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

2 1

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

2 1

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

2 2

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

2 1

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

2 1

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

2 1

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

3 2

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

2 1

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

3 2

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

2 1

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

2 1

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.

2 1

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

1 0

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

4 9

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 > >

2 1

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 >>

1 0

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

3 3

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

2 1

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

4 5

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 >>

1 0

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

4 3

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)

2 1

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

2 1

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

2 1

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

2 1

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

3 5

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

3 2

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

1 0

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

2 1

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

2 1

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

3 2

Fwd: presets, python and printing
by Yang, Zheng (YZ) 10 May '10

10 May '10

Begin forwarded message: > From: "Yang, Zheng (YZ)" <yz(a)cgl.ucsf.edu> > Date: May 10, 2010 12:55:03 AM PDT > To: Daniel Gurnon <danielgurnon(a)depauw.edu> > Subject: Re: [Chimera-users] presets, python and printing > > Dear Dan, > > I am using Chimera output STL files, then print out with a uPrintPlus 3D printer. It's pretty handy using the "Export Scene" function to convert models into STL files. Although each single part cannot have mixed color, the printer is capable of printing 8 color APS by changing the cartridge. I have tried various protein representations: surface, ribbons showing the secondary structures, etc. All of them work prefect. > > By going over the Getting Started tutorial (http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html) users can easily get familiar with Chimera. Your students can use either GUI or command line mode. Alternatively, you can prepare them a Chimera commands file (plain text scripts file), containing your preset, bond thickness. (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#c…) They just need to open and load it. > > Chimera has the Undo Move function, allowing backtracking through the most recent model positions. (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove.…) Section saving may solve part of the "Undo" problem. > > Looking forward to collaborating with you on the 3D model printing. > > Best, > YZ > > > > > > > > On May 9, 2010, at 7:51 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...) >> >> 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 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

superimposed 3D structure
by deeba noreen 08 May '10

08 May '10

I am trying to make superimpose two similar proteins. To evalute its structural differences regarding functional aspects, I want to derive a superimposed model. I am using Chimera format... Can you please tell me in terms of commands so i can apply.

2 1

ligand comformation clustering
by Maurice Ho 06 May '10

06 May '10

Hi there, How to cluster the different conformations of a ligand after a docking experiment according to their relative orientations in the binding pocket? Any software can help to do so? I've tried the Ensemble Cluster function in Chimera but it seems clustering the different conformations according to the relative positions of the atoms of the ligand itself. I know that the command rmsd #0.1:UNK #0.2:UNK (UNK is the ligand) could be a way to illustrate how distant in average between different conformations. How could I make use of this command in script so that I could have all the possible comparisons and cluster them in a sensible way? Best regards, Maurice Ho

2 1

Re: [Chimera-users] Sequential stereo
by Greg Couch 05 May '10

05 May '10

(Forgot to cc the list.) Chimera already works with NVidia's 3D Vision, in Windows XP/Vista/7 and Linux, as long as you have a 3D Vision supported Quadro FX card, see <http://www.nvidia.com/object/quadro_pro_graphics_boards.html> for details. Since chimera does stereo within a window, the GeForce cards are not supported. FYI, the latest NVidia drivers, version 197.59, have a bug that affects chimera stereo, so you'll need to use an earlier version of the driver (or presumably a latter version which has the bug fixed). When working with chimera in stereo, you really want a display that shows full resolution left and right eye images, and that generally means that the display refreshes at 120 Hz for 60Hz per-eye (100Hz would work too). If they don't support 120Hz, then the left and right eye images are interlaced when transmitted to the display and adjacent pixels can end up being shown in opposite eyes. And that makes 2D text, like the text in labels or dialogs, very fuzzy until you take the glasses off, but that makes the 3D fuzzy. That is annoying, but if the display is cheap enough, you might be able to live with it :-). For large groups of people, the cost of the active glasses becomes significant (and maintaining the batteries is a chore). So for a large display, I'd recommend considering a technology with passive glasses, like the RealD LP, <http://www.reald.com/Content/proProducts.aspx?pageID=122>, and the DepthQ Polarization Modulator, <http://www.depthq.com/modulator.html>. They are setups for a projector that polarizes the light onto a silver screen (that reflects polarized light coherently) and you use cheap polarized glasses to view the content (same glasses as a movie theater with RealD 3D). And if you use this technology, then you have the option of using a NVidia Quadro FX graphics card or an ATI FirePro graphics card (only the V8700, V8800, and V8750 have stereo DIN connectors). Hope this helps, Greg On 05/05/2010 08:47 AM, Daniel Hitchcock wrote: > Howdy, > > My advisor was interested in setting up a large display (52" screen) > with a computer controlling it for viewing and presentation of > structures in chimera. I have been commissioned to purchase the > hardware, and naturally I want to take it a step further. > > With new "3D Ready" LG and Samsung displays (as opposed to regular > >120Hz displays) they supposedly have an extra chip to properly sync > with an incoming 3D signal from a device, be it a bluray player or > whatever. Nvidia has begun to work on their system and promises a > software update to their 3Dvision line which would allow for the > native signal to be sent to the screen as opposed to just sending a > sequential 2D signal. My questions (if that all made sense), > > 1. Is there or will there be support for nvidia's 3d Vision line? We > will be running windows 7 and the program itself will be run in > windowed mode probably, not always full screen. > > 2. If that does not work, what would be the best recommendation for > some sort of stereoview (prefereably sequential) on a large LCD or > plasma display? > > > Thanks for the help! > -Daniel Hitchcock

1 0

Sequential stereo
by Daniel Hitchcock 05 May '10

05 May '10

Howdy, My advisor was interested in setting up a large display (52" screen) with a computer controlling it for viewing and presentation of structures in chimera. I have been commissioned to purchase the hardware, and naturally I want to take it a step further. With new "3D Ready" LG and Samsung displays (as opposed to regular >120Hz displays) they supposedly have an extra chip to properly sync with an incoming 3D signal from a device, be it a bluray player or whatever. Nvidia has begun to work on their system and promises a software update to their 3Dvision line which would allow for the native signal to be sent to the screen as opposed to just sending a sequential 2D signal. My questions (if that all made sense), 1. Is there or will there be support for nvidia's 3d Vision line? We will be running windows 7 and the program itself will be run in windowed mode probably, not always full screen. 2. If that does not work, what would be the best recommendation for some sort of stereoview (prefereably sequential) on a large LCD or plasma display? Thanks for the help! -Daniel Hitchcock

1 0

Adjust torsion and bump checking
by Kim, Sunghoon 04 May '10

04 May '10

Hi all, I would like to do the bump checking for the various rotameric states of a specific side chain generated by the rotation about dihedral angles. Bumps were detected by chimera command 'rotation' and 'findclash' and at first the script seemed working OK, but I'm not sure if the chi angles were correctly defined. When we look at the 'clashes/contacts' panel in Chimera, there are atom options for "Near" and "Far" positions in the rotating bonds. How can I specifying the 'Near' and 'Far' atoms in my 'rotation' command line in my python script to define my chi angles ? Thanks in advance for any info that you can provide. Thanks, Sunghoon Kim

2 1

place fragment (again)
by Elisabeth Ortega 04 May '10

04 May '10

Dear all, We are trying to place a fragment in an exact position. We created a fragment with tetrahedral symmetry and we are trying to link an atom of other molecule at 2.00 A of the central atom of the new fragment and making a certain angle (120 degrees for example) with one of the substituents to get the correct orientation of the new fragment. Has anybody an idea that how can we do that? Thanks.

3 2

about centroid
by Francesco Pietra 03 May '10

03 May '10

On running movie with centroid - as I was instructed by Eric; sorry I lost the email - I noticed that on long runs a shift is introduced between the protein and the centroid thread. To restore the relative positions between protein and centroid thread, I had to bring back (through the movie) the centroid to its initial position. francesco pietra

2 1

rmsd between two ligands
by Miriam Gochin 01 May '10

01 May '10

Is there a way in chimera to obtain an RMSD between two structures without matching them, ie. just to know the difference between them? Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

2 2

Volume Subtractions
by Murali Ayaluru 30 Apr '10

30 Apr '10

Dear Chimera users/developers, I have two EM density maps (in mrc format) of a complex with different conformations. I want to subtract one density from another. I am wondering if it is possible in Chimera to subtract the densities? Cheers, Murali

3 2

(no subject)
by Hanzhong Liu 28 Apr '10

28 Apr '10

Dear Chimera Developer: I tried to use Chimera to display MD movie. I tried both CHARMM trajectory and single pdb. They all works. When I put "ksdssp" in the per-frame script, it gave me a warning "name ksdssp is not defined". I used the latest version and the OS is windows 7. But when I ran chimera under windows xp, there is no such problem. I'm wondering if there is a bug of chimera. Thanks!-

2 1

DCD format error 1
by Lilian OLIVIERI 28 Apr '10

28 Apr '10

Hello, I'm having trouble using MD/Ensemble analysis tool. When I try to check a MD trajectory generated by CHARMM (version C33b1), I get a "DCD format error 1" message. Here is the Reply Log: MDTools 1.2 Exp (2005-08-20) by James Phillips. Trajectory.DCD.MDToolsMarch97.md.help() for more info. - HomoCoord 1.3 Exp (2005-08-20) - Constants 1.1 Exp (2004-05-17) - AtomGroup 1.4 Exp (2007-02-07) - local 1.1 Exp (2004-05-17) Unknown OSTYPE ??? set. Viewing and plotting are disabled. - Trans 1.2 Exp (2005-08-20) - DCD 1.10 Exp (2007-02-07) - Data 1.2 Exp (2005-08-20) * THIS FILE IS LANGEVINEEF1.INP. * USAGE, CHARMM <LANGEVINEEF1.INP >LANGEVINEEF1.OUT. * RUNS LANGEVIN DYNAMICS WITH EEF1 IMPLICIT WATER. * DATE: 3/22/10 10:32:48 CREATED BY USER: lolivier /labos/lbgm/lolivier/chimera/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py:121: DeprecationWarning: raising a string exception is deprecated raise "DCD format error 1" Traceback (most recent call last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 328, in command File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply File "CHIMERA/share/Trajectory/DCD/__init__.py", line 61, in loadEnsemble File "CHIMERA/share/Trajectory/DCD/__init__.py", line 71, in loadEnsemble File "CHIMERA/share/Trajectory/DCD/DCD.py", line 35, in __init__ File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line 121, in __init__ DCD format error 1 DCD format error 1 File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line 121, in __init__ See reply log for Python traceback. Is there a quick way to fix this problem? Thanks for any reply. -- Lilian Olivieri PhD student INSERM UMR-S 665, DSIMB/LBGM, Faculte des Sciences et Technologies Universite de La Reunion 15 Avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel: +33 262 938 227 (office) Fax: +33 262 938 237 http://lbgm.univ-reunion.fr/ http://www.dsimb.inserm.fr/ **************************************************************************** It has long been an axiom of mine that the little things are infinitely the most important. -- Sir Arthur Conan Doyle, "A Case of Identity" ****************************************************************************

2 2

volume threshold
by Alex Perálvarez Marín 27 Apr '10

27 Apr '10

Hi, there is any command to change the threshold of a density map? I have 100 maps open at the same time, and I want to change the threshold of all of them at the same time. Thanks in advance, best Alex.

4 3

something flakey with measure buriedArea?
by Scott Classen 27 Apr '10

27 Apr '10

I'm seeing some very odd results coming from the measure buriedArea command if I use different values for probeRaduis and then grep for WARNINGs I get the following results: probeRadius # of WARNINGs 1.50 = 12 1.40 = 4 1.39 = 14 1.35 = 59 1.30 = 3 1.20 = 0 Here are some examples of the types of warnings I'm seeing: WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 1735 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 2557 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 1836 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 2090 WARNING: class_arete2: warning hole in a reentrant face 1925 WARNING: compute_SES_area: ERROR: Solide angle (-1.972093) for contact face 3142 too large or too small Should I be concerned? Another unusual thing is that for certain calculations I get some crazy answers. For example the following command measure buriedArea '#0:.A,.B & #0:10.Dz<8' #0:10.D probeRadius 1.4 vertexDensity 2 outputs: B1SES = -583.491, B2SES = 51.4762, BaveSES = -266.007 but the same command with the probeRadius changed to 1.37 measure buriedArea '#0:.A,.B & #0:10.Dz<8' #0:10.D probeRadius 1.37 vertexDensity 2 outputs: B1SES = 53.9334, B2SES = 51.7969, BaveSES = 52.8652 Why would B1SES be so radically different for these two measurements? Thanks, Scott ps When doing these calculations Chimera randomly crashes with the following mscalc crash report: Process: mscalc [25532] Path: /Applications/Chimera-1.5b.app/Contents/Resources/bin/mscalc Identifier: mscalc Version: ??? (???) Code Type: X86-64 (Native) Parent Process: python2.6 [25482] Date/Time: 2010-04-27 17:23:08.864 -0700 OS Version: Mac OS X 10.6.3 (10D573) Report Version: 6 Interval Since Last Report: 402 sec Crashes Since Last Report: 1 Per-App Crashes Since Last Report: 1 Anonymous UUID: D0B1026B-AD5E-454C-8E35-49CCF7598339 Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Crashed Thread: 0 Dispatch queue: com.apple.main-thread Application Specific Information: abort() called Thread 0 Crashed: Dispatch queue: com.apple.main-thread 0 libSystem.B.dylib 0x00007fff83cc7886 __kill + 10 1 libSystem.B.dylib 0x00007fff83d67eae abort + 83 2 libSystem.B.dylib 0x00007fff83c7fa75 free + 128 3 mscalc 0x00000001000218e5 MS_delete_SES_face + 920 4 mscalc 0x00000001000361f4 MS_update_ses + 919 5 mscalc 0x0000000100034f68 MS_restart_from_ses + 613 6 mscalc 0x0000000100036963 MS_update_ses + 2822 7 mscalc 0x0000000100037d94 MS_restart_from_triangulation + 591 8 mscalc 0x0000000100046c66 MS_triangulate_SES_component + 925 9 mscalc 0x00000001000066f6 MS_compute_surface + 443 10 mscalc 0x0000000100000ea2 main + 382 11 mscalc 0x0000000100000d1c start + 52 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000000000001 rcx: 0x00007fff5fbfd998 rdx: 0x0000000000000000 rdi: 0x00000000000063bc rsi: 0x0000000000000006 rbp: 0x00007fff5fbfd9b0 rsp: 0x00007fff5fbfd998 r8: 0x0000000000000e03 r9: 0x0000000000000000 r10: 0x00007fff83cc38ca r11: 0x0000000000000206 r12: 0x00000001001e4000 r13: 0x0000000100200000 r14: 0x0000000000000000 r15: 0x00000001004f7c70 rip: 0x00007fff83cc7886 rfl: 0x0000000000000206 cr2: 0x000000010022a000 Binary Images: 0x100000000 - 0x10004eff7 +mscalc ??? (???) <AF86E566-5546-A8C8-DE97-4A16408CB1BC> /Applications/Chimera-1.5b.app/Contents/Resources/bin/mscalc 0x7fff5fc00000 - 0x7fff5fc3bdef dyld 132.1 (???) <B633F790-4DDB-53CD-7ACF-2A3682BCEA9F> /usr/lib/dyld 0x7fff83c78000 - 0x7fff83e37ff7 libSystem.B.dylib 125.0.1 (compatibility 1.0.0) <CB9A4929-61AF-DE71-5635-133E9EC95783> /usr/lib/libSystem.B.dylib 0x7fff885a7000 - 0x7fff885abff7 libmathCommon.A.dylib 315.0.0 (compatibility 1.0.0) <95718673-FEEE-B6ED-B127-BCDBDB60D4E5> /usr/lib/system/libmathCommon.A.dylib 0x7fffffe00000 - 0x7fffffe01fff libSystem.B.dylib ??? (???) <CB9A4929-61AF-DE71-5635-133E9EC95783> /usr/lib/libSystem.B.dylib Model: MacPro1,1, BootROM MP11.005C.B08, 4 processors, Dual-Core Intel Xeon, 2.66 GHz, 14 GB, SMC 1.7f10 Graphics: ATI Radeon X1900 XT, ATY,RadeonX1900, PCIe, 512 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x87), Broadcom BCM43xx 1.0 (5.10.91.27) Bluetooth: Version 2.3.1f4, 2 service, 19 devices, 1 incoming serial ports Network Service: Built-in Ethernet 2, Ethernet, en1 PCI Card: ATY,RadeonX1900, Display, Slot-1 Serial ATA Device: ST3250824AS P, 232.89 GB Serial ATA Device: WDC WD2500JD-00HBC0, 232.89 GB Serial ATA Device: WDC WD1002FBYS-01A6B0, 931.51 GB Serial ATA Device: WDC WD1002FBYS-01A6B0, 931.51 GB Parallel ATA Device: SONY DVD RW DW-D150A USB Device: Hub, 0x05ac (Apple Inc.), 0x9131, 0xfd400000 USB Device: iPhone, 0x05ac (Apple Inc.), 0x1292, 0xfd430000 USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1005, 0xfd410000 USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x021d, 0xfd412000 USB Device: Apple Cinema HD Display, 0x05ac (Apple Inc.), 0x9223, 0xfd420000 USB Device: Hub, 0x05ac (Apple Inc.), 0x9122, 0xfd300000 USB Device: Apple Cinema HD Display, 0x05ac (Apple Inc.), 0x921e, 0xfd320000 USB Device: USB Receiver, 0x046d (Logitech Inc.), 0xc525, 0x1d200000 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8206, 0x5d200000 USB Device: Back-UPS CS 500 FW:806.q5.D USB FW:q5, 0x051d (American Power Conversion), 0x0002, 0x5d100000 FireWire Device: built-in_hub, Up to 800 Mb/sec FireWire Device: unknown_device, Unknown

2 1

help with simple python script
by Scott Classen 27 Apr '10

27 Apr '10

Hi all, I have a number of PDB files that I would like to open, run a buriedArea calculation, save the results to a file, and exit I can put a bunch of commands in a file and launch it from a terminal shell chimera --nogui --nostatus --script calculate_buriedArea.com > results.txt the calculate_buriedArea.com file looks like this: open my.pdb measure buriedArea #0:.A #0:B This works, but is a bit cumbersome. I would like to make a python script so I can call my calculation with the name of the PDB file on the command line like this: chimera --nogui --nostatus --script calculate_buriedArea.py -- my.pdb .... so can someone please get me started here? import chimera myfile = chemera.somefunctiontoopenaPDBfile($1) Thanks, Scott

2 1

ChemGroups
by Mauro Truglio 27 Apr '10

27 Apr '10

Hi, I got to understand the syntax to edit and even create "new" chemical groups for chimera to select (I successfully edited the file __init__.py in ChemGroups). Now I'm facing this problem with aromatic amines: when selecting, for example, primary aromatic amine, *I'd like to include also che C atom in the selection* - not only N,H,H. With other chemical groups this was easy, thanks to the [1,1,1,0,1]-like notation. But these aromatic amines are described in a different way, through the function findAroAmines in miscFind.py, and I'm finding it difficult to edit it. Can you help me? Thanks Mauro Truglio

2 1

Daily Builds
by Jon N. Rumbley 27 Apr '10

27 Apr '10

Why is it that the Windows Daily Builds continue to say March 20, 2010 while the other operating system show the current date? Is the Windows version being built daily? Thank you, Jon Rumbley Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 Life Sciences 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

3 2

saving attribute to file
by Scott Classen 26 Apr '10

26 Apr '10

Hello, When I save attributes to a text file from the "Render/Select by Attribute" dialogue box the values are written to the file apparently in a random order. Is there a way to get the residues or atoms to be written in a sensible way? i.e. by residue/atom number. Thanks, Scott Classen

4 3

POV-Ray setting for movie making
by Paul Brandt 26 Apr '10

26 Apr '10

Hello, I am using chimera alpha version 1.3 (build 2577) running in linux (sled11) to make a movie using POV-Ray. The quality of the first few frames is stunning but thereafter becomes fuzzy around the edges of the molecule. Is there a way to fix this so that the entire movie is as clear and nice as the first few frames? Is there something wrong with my settings? Is what I'm seeing an artifact of mpeg compression? I am using the following POV-Ray settings to make an Mpeg1 movie Quality 11 Antialias: true Antialias method: recursive Antialias depth: 3 Antialias threshold: 0.3 Jitter: True Jitter amount: 1.0 Transparent background: false Wait for POV-Ray to finish false Keep input files: false Thanks for the help!! Paul

4 3

please stop these emails
by Dr. Ahmed Sofy 26 Apr '10

26 Apr '10

Dear chimera organizing Thanks alot for your efforts but i want stop these emails of users Thanks alot again for your efforts

2 1

HELP: I'm wondering about how to access the surface data
by "郑捷凯" 26 Apr '10

26 Apr '10

Hi chimera users, I'm wondering about several question: I installed chimera in my home dir, what's path to import in python? how can I access the data generated by mscalc in python?

7 10

placeFragment
by Elisabeth Ortega 26 Apr '10

26 Apr '10

Dear all, I'm trying to place a fragment in certain position. I did this (on Python IDLE): from BuildStructure import placeFragment placeFragment( fragment, resName, model = 'scratch', position=None) Where fragment = benzene and resName = RING6 but I am not sure about that . Could you give me an example of placeFragment code? Thanks in advance. Elisabeth Ortega , Ph.D Student @ Universitat Autónoma de Barcelona

2 1

"cutoff" parameter in Find clashes/contacts option
by Anna Feldman-Salit 24 Apr '10

24 Apr '10

Dear All, I was unsuccessfully looking for the explanation to what exactly "cutoff" parameter means. I'm using the Find clashes/contacts option to identify the contacts and not clashes, by assigning the default values of -0.4A and 0.0 to "cutoff" and "allowance" parameters. However, I do not understand how it is used. I would very much grateful for the information, since I also want to include it in my dissertation. Best regards, Anna Feldman-Salit

3 2

transform coordinates
by Alex Perálvarez Marín 23 Apr '10

23 Apr '10

Dear all, I would like to change the coordinates (Euler angles) for an EM density map (Tools --> Movements --> Transform molecule coordinates). But in the molecule scroll menu, my map does not appear. Is possible to define the system coordiantes for a EM density map? Thanks in advance, Alex.

2 3

Displacement through vectors
by Elisabeth Ortega 23 Apr '10

23 Apr '10

Dear all, I'm trying to move an atom though a vector but I don't find the correct Python script to do that. The vector starts in the mass center of the molecule and finish in a nitrogen atom. I want to place Helium at 2 angstrom of the nitrogen atom following the mentioned vector. Could you help me with the script? Thanks in advance. Elisabeth Ortega, Ph.D Student @ Universitat Autónoma de Barcelona

2 1

level of detail (vrml)
by Damien Larivière 22 Apr '10

22 Apr '10

Dear all, Chimera is able to display VRML file. Is it able to display VRML file containing level of detail? (My first tentative was not a success but I do not think the file I used respected the format convention). My best reagrds Damien

4 6

Small molecule dimensions
by le monk 21 Apr '10

21 Apr '10

Hello, I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this? Many thanks _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now

3 4

hide dust
by weimin wu 20 Apr '10

20 Apr '10

Sometimes after we remove the dust using the tool of hiding dust, we want to save the map directly instead of using command "mask #0 #0" to generate a maskfile. The reason is that the masked map has minimized map size and different with original one. Even after we recover the map size and origin, it always has half pixel issue, and if we apply this mask to original map, the output will have some masking artifact. The iso-surface of the output will not be as smooth as original map or the map after hiding dust. weimin

3 2

Chimera on Acer Aspire 1410
by Mario J. Borgnia 20 Apr '10

20 Apr '10

Hi, I am running Chimera chimera-1.4.1-linux_x86_64 on my "netbook" style Acer Aspire 1410 with the following specifications: OS: Linux 2.6.31.12-0.2-desktop x86_64 Processor: Intel(R) Celeron(R) CPU 743 @ 1.30GHz Intel Mobile GM45 Express Chipset 1366x768 pixels The program runs well but surfaces disappear upon rotation. This is true for solid surfaces, as soon as I set the opacity to 0.99, the surfaces are no longer affected. Any hints? Thanks Mario Borgnia

2 1

Chimera and Nvidia 3D vision
by Joern Lenz 20 Apr '10

20 Apr '10

Hi there, I am wondering if anyone of you knows if I can use my Nvidia GTX295 together with the 3D vision glasses and a Samsung SyncMaster 120Hz screen to view 3D in Chimera using a Debian Lenny or a Windows 7 OS. About two years ago, Nvidia said they will support Unix systems with their glasses. However, up to now there is no news about that. Do you have any idea or even a way to get 3D on in Chimera using the hardware above ? Many thanks. Cheers, Joern

5 4

Save session for movie
by Francesco Pietra 18 Apr '10

18 Apr '10

Hello: I am carrying out the analysis of MD for a ligand wandering through a protein. Specifically following the pathway through the trace left by the centroid of the ligand. Apparently the "save session" doe not work for movie. I.e., I stopped the movie (with the centroids drawn at the various steps) at a certain step, then "save session" destroyed the graphics and only alpha-numeric appeared on the terminal. Is there a diffent procedure for such a case or only "save image"? This would greatly limit what could be done by reorienting the protein, coloring, labeling, etc. thanks francesco pietra

2 1

Is it possible to make ribbons transparent
by Ajith Harish 17 Apr '10

17 Apr '10

Hi, Please let me know if it is possible to make the ribbon representations transparent like the surfaces? Thanks, Ajith

2 1

Space Navigator on Linux
by Daniel Luque 15 Apr '10

15 Apr '10

Dear all, I am trying to use a 3DConexion SpaceNavigator with chimera in my linux machine. I have installed the SpaceNavigator drivers and they work properly with the manufacturer test tools (xcube and xvalue). Althought I am running the last chimera release, when I open chimera it does not "see" the device. Should I do something special when I start chimera or once it is open in order to use the device? Thanks in advance, Daniel

4 4

why is Chimera so slow?
by Scott Classen 14 Apr '10

14 Apr '10

Hi All, First off, I'm fairly new to Chimera, and so far I'm very impressed with the functionality. Thanks for the great tool. I am embarking on a fairly intensive comparison of a dozen or so structures and I'm running into some serious performance issues. I have an older Mac Pro with dual 2.66GHz Intel Xeon processors, 14GB RAM, ATI RadeonX1900 w/512MB VRAM and Chimera (1.4.1 build 30365). I've got 3 PDBs loaded up and have calculated surfaces for all three with a vertex density of 20 (perhaps too high? but I need accurate values for the solvent-excluded surface for particular residues). With 2 models and 2 surfaces things start to slow down a bit, but are manageable. With 3 models and their associated surfaces I can't even rotate the view at all. Even if I only show one residue and residues with 5A. It's as if Chimera is doing all the behind the scenes calculations to rotate all the surface triangles and atomic coordinates that aren't even being displayed. Is there something I'm missing? Is it it unrealistic to set my surface density to 20? Any advice? Thanks, Scott

2 1

X-server segmentation fault on launching chimera
by Francesco Pietra 14 Apr '10

14 Apr '10

Hello: Having upgraded Debian Linux i386 squeeze release from kernel 2.6.30 to 2.6.32 everything works except X-server segmentation fault on launching CHIMERA, build 30282 of last March 29. I have successfully recompiled CHIMERA, last Apr 14 build, on the updated Linux release, to no avail. I need the experimental builds for features not included in the stable release (centroid trace in movie). To compare, another graphic program, GIMP, can be launched correctly. Below - between *** - the final part of "Xorg.0.log" reporting troubles. Before that, the log is identical to when X-server is working properly. Thanks for suggestions. francesco pietra ********* Backtrace: 0: /usr/bin/X (xorg_backtrace+0x3b) [0x80ada5b] 1: /usr/bin/X (0x8048000+0x5aa75) [0x80a2a75] 2: (vdso) (__kernel_rt_sigreturn+0x0) [0xb78b240c] Segmentation fault at address (nil) Fatal server error: Caught signal 11 (Segmentation fault). Server aborting Please consult the The X.Org Foundation support at http://wiki.x.org for help. Please also check the log file at "/var/log/Xorg.0.log" for additional information. (II) Power Button: Close (II) UnloadModule: "evdev" (II) Power Button: Close (II) UnloadModule: "evdev" (II) AT Translated Set 2 keyboard: Close (II) UnloadModule: "evdev" (II) ImPS/2 Logitech Wheel Mouse: Close (II) UnloadModule: "evdev" ********

1 1

Fwd: Re: install
by Greg Couch 13 Apr '10

13 Apr '10

Forgot to cc the list. -------- Original Message -------- Subject: Re: [Chimera-users] install Date: Tue, 13 Apr 2010 11:25:43 -0700 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: Jay Brown <jcb2g(a)virginia.edu> It may be that you downloaded the 32-bit version but only have the 64-bit runtime libraries installed or vice-versa. If you run "uname -m" in a terminal, it should print x86_64 if you have a 64-bit version of Linux. Please send me the full error message and I may be able to say more. - Greg On 04/12/2010 01:13 PM, Jay Brown wrote: > > Dear Chimera-Users: > > I am trying to install Chimera on a Linux Fedora 12 computer. Download > goes OK, but when I try to install the program I get an error message > saying: bad ELF interpreter: No such file or directory > > Do you know what this means? I can't find anything about ELF interpreter. > > -Jay Brown > > Jay C. Brown > > Department of Microbiology > > University of Virginia School of Medicine > > 1300 Jefferson Park Ave. > > Charlottesville, VA 22908 > > Email: Jcb2g(a)virginia.edu > > Phone: 434-924-1814 > > http://people.virginia.edu/~jcb2g/index.htm > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

xfowarding not working in new chimera
by Kenneth Frankel 13 Apr '10

13 Apr '10

My older version of chimera x forwards with no problem; from the about ucsf chimera window its beta version 1 build 2064 2004/12/15 for linux2 We have upgraded the 32 and 64 bit version which run fine locally. but when we run from another computer with ssh either with -X, -Y, -XY , -o ForwardX11=yes frankel@graphics1 we always get a crashe after trying to do something (e.g fetch a pdb) with the same genral error message frankel@graphics1:/home/frankel 102% /programs/chimera-1.4.1-x86_64/bin/chimera X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 144 (GLX) Minor opcode of failed request: 181 () Serial number of failed request: 5374 Current serial number in output stream: 5379 (serial numbers may differ between runs) Can this be fixed? (We suspect it's a mesa library problem). Also when running nx client, even the old version of chimera from crashes. I'll have to get the error message later, but does anyone have experience running over nx client? we've gotten pymol, and vmd to work. thanks Ken Frankel

2 2

Re: [Chimera-users] Chimera-users Digest, Vol 84, Issue 12
by Chinthaka Silva 13 Apr '10

13 Apr '10

Hi, Is there a way to quantify the electron densities in a unit cell with UCSF? Thanks, Chinthaka. On Tue, Apr 13, 2010 at 2:08 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. install (Jay Brown) > 2. Re: Analysis of dihedral angles (Eric Pettersen) > 3. Re: Analysis of dihedral angles (sette(a)uniroma2.it) > 4. Re: Analysis of dihedral angles (Elaine Meng) > 5. Re: Analysis of dihedral angles (Eric Pettersen) > 6. Re: Display a spider volume data in a specific orientation > (Tom Goddard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Apr 2010 16:13:27 -0400 > From: "Jay Brown" <jcb2g(a)virginia.edu> > To: <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] install > Message-ID: <009501cada7c$9ccfe2b0$d66fa810$@edu> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera-Users: > > I am trying to install Chimera on a Linux Fedora 12 computer. Download goes > OK, but when I try to install the program I get an error message saying: > bad > ELF interpreter: No such file or directory > > Do you know what this means? I can't find anything about ELF interpreter. > > -Jay Brown > > > > Jay C. Brown > > Department of Microbiology > > University of Virginia School of Medicine > > 1300 Jefferson Park Ave. > > Charlottesville, VA 22908 > > > > Email: Jcb2g(a)virginia.edu > > Phone: 434-924-1814 > > http://people.virginia.edu/~jcb2g/index.htm > > > >

2 1

Analysis of dihedral angles
by eduardo.troche＠uvigo.es 13 Apr '10

13 Apr '10

Hi all, I'm a new Chimera user. I'm performing some molecular dynamics with a more or less simple system with Amber,and now that I have them done, I would like to analyze some specific data,like changes in a dihedral angle during the dynamic process, or distances between pairs of atoms. If I select several dihedral angles in Chimera and I play the dynamic movie, I can see these changes, but is it possible to get a table of results that shows the value of this angle for each step of the dynamic process? Thank you every body! Eduardo

4 5

surface holes
by Eric Pettersen 12 Apr '10

12 Apr '10

On Apr 12, 2010, at 5:05 AM, Guy Nimrod wrote: > Hello, > When I load complex structure (e.g., pdb 3mht) and show the surface > of one chain (e.g. selectchainA; action->surface->show), the > generated surface does not cover the interface between the query > protein and the other chains. Consequently, the interface appears as > a hole in the surface (see attached figure). > Is there an easy way to visualize the whole surface (i.e. the > generated surface on a selected chain will disregard chains which > are not selected)? Hi Guy, When you surface some subset of atoms in Chimera, Chimera still considers all atoms in the same "surface category" as the subset for purposes of computing the surface -- it just doesn't show the surface of the atoms not in the subset. So for example if you ask for a surface on a single residue Chimera doesn't make a surface that completely encloses the residue -- the surface is "open" where the residue connects to the rest of the molecule. Similarly, a single chain of a multi-chain molecule may not be completely enclosed if Chimera considers other chains of the molecule to be in the same surface category. That is what has happened here. Chain A (the protein) and the chains C and D (the nucleic acid) have been classified into the same surface category (main). To get the enclosed surface that you want you need to put chain A into a surface category of its own and surface that. These two commands will accomplish that: surfcat prot :.a surf prot The surface actually inter-penetrates the nucleic acid because of the flipped-out base, like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

question about ViewDock
by Miriam Gochin 12 Apr '10

12 Apr '10

I have a question about ViewDock. It works fine for one receptor and several ligands, but if I open a second receptor model and rotate it, then ligands I open with ViewDock for the second receptor are in the original (unrotated) position. Is there a way to correct the ligand positions for the current rotation? Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

2 2

install
by Jay Brown 12 Apr '10

12 Apr '10

Dear Chimera-Users: I am trying to install Chimera on a Linux Fedora 12 computer. Download goes OK, but when I try to install the program I get an error message saying: bad ELF interpreter: No such file or directory Do you know what this means? I can't find anything about ELF interpreter. -Jay Brown Jay C. Brown Department of Microbiology University of Virginia School of Medicine 1300 Jefferson Park Ave. Charlottesville, VA 22908 Email: Jcb2g(a)virginia.edu Phone: 434-924-1814 http://people.virginia.edu/~jcb2g/index.htm

1 0

problem with new Chimera 1.4 and 1.4.1 OSX Aqua
by Miriam Gochin 10 Apr '10

10 Apr '10

Dear Chimera team, I am not sure what I am doing wrong, but the new version does not open correctly on my Mac (OS-X-10.6.2). I get a small black square surrounded by white space that will not enlarge. Is there some setting I should adjust? Best wishes, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

2 2

[Re: Residue exposition cutoff]
by Yasser Almeida Hernández 07 Apr '10

07 Apr '10

Thanks for your answer... About this i have an idea resumed in two question: In principle an solvent-exposed residue must have in average high value of b-factor, so will be very flexible. 1 - Can i say that those residues that have and average b-factor up to a cutoff value AND an areaSAS (or % of that area) superior than a other cutoff value, will be exposed to the solvent??? 2 - There is a cutoff value of b-factor for the residues flexibility? Best regards -------- Forwarded Message -------- From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply-to: Chimera BB <chimera-users(a)cgl.ucsf.edu> To: Yasser Almeida Hernandez <almeida(a)cim.sld.cu> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Residue exposition cutoff Date: Mon, 5 Apr 2010 11:22:37 -0500 Hi Yasser, Actually you don't have to use DMS ... if you show a surface in Chimera it also automatically computes the SES (solvent-excluded surface) and SAS area per atom and per residue, attributes named areaSES and areaSAS. For more details, see these previous posts: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html > Some notes about areaSES and areaSAS: (1) if you don't want to include inside bubbles in the surface area calculations, after creating the surface(s) remove the inside bubbles with the command: setattr s allComponents false (2) the surface that Chimera displays is the SES (also known as Connolly surface or molecular surface), not the SAS, although both sets of areas are calculated Actually Tom Goddard mentioned the areaSAS attribute briefly in an earlier reply to you: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/003995.html> As to what cutoff should be used for classifying atoms or residues as buried or exposed, I'm not aware of any commonly used value. It is a more philosophical issue that depends on your ultimate purpose. You might try coloring by different cutoffs to try to decide what is appropriate for your research (keeping in mind that the SES is what Chimera actually displays), or read publications of similar work to see what other researchers have used. In publications, I have seen residues classified by "fraction" or % of the surface area of a residue in the structure divided by the area of that same type of residue in a hypothetical fully exposed state, but I don't remember the exact cutoffs used, and Chimera does not provide the fully exposed values. An example of a program that does provide such values is GetArea: <http://curie.utmb.edu/getarea.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 3, 2010, at 1:38 PM, Yasser Almeida Hernández wrote: > Hi all.... > I have 2 question, beyond Chimera's issues. > > 1 - There is some cutoff value to consider a residue or more > strictly, an atom exposed to the solvent?. > > 2 - Could i set a this cutoff using the area values and types (SR0, > SC0 and SS0) from the DMS program output? > > 3 - Wich program you recommend to compute SAS? > > Thanks, > best regards ----- Terminar mensaje reenviado ----- -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

2 1

amino acid clashes
by Kirys, Tatsiana 06 Apr '10

06 Apr '10

Dear All, i'm trying to figure out scheme for calculating protein amino acid clashes. I've read in User's Guide that 1) The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs: overlapij = rVDWi + rVDWj dij allowanceij 2) It has an option: Ignore contacts of pairs [ N ] or fewer bonds apart (N=4 by default). i calculated rotamer clashes from "Penultimate rotamer library" according to 1) and there are clashes between N ans C N and CB N and CG CA and CG CA and OD1 etc. i'm sure i do something wrong because "Penultimate rotamer library" was checked for the clashes. I dont understand why 2) option exists, what is the physical meaning of it? and why N can be cosed arbitrary? many thanks Tania

2 1

structural similarity measures in Chimera
by Elaine Meng 05 Apr '10

05 Apr '10

Dear Minming, Dr. Ferrin forwarded your question to me. We recently added calculation of structure similarity measures to Chimera. This capability is not in versions 1.4/1.4.1, but only in 1.5 (recent daily builds, which are also available from our download page). In such recent builds, the "Match -> Align" tool (under Tools... Structure Comparison in the menu) calculates two measures that have been described in previous publications, the SDM and the Q- score. The SDM has been used to construct phylogenetic trees before. I don't know if the Q-score has been used that way. Documentation for Match->Align and details of these measures: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchal… > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchal… > However, there are some issues that may affect whether you decide to use Chimera to calculate these values for your structures: (1) You would need to run Match->Align for each pair. There is no option to do all pairwise comparisons on multiple structures. You would need to script looping through all pairs (with python or shell scripting). (2) There is no Chimera command for Match->Align. Thus Match->Align would also need to be run via python. I don't have scripting expertise, so someone else would have to provide more details if you decide to try this. (3) Before you run Match->Align, the structures need to be superimposed. We purposefully made Match->Align independent of the superposition method. There are several possible ways to superimpose structures in Chimera, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> but probably the easiest in your case would be MatchMaker, which is also available as a Chimera command (matchmaker or mmaker, see that URL and links within). Usually the mmaker defaults work pretty well, for example Chimera commands: open 2mnr open 4enl mmaker #0 #1 (Then you could try running Match->Align interactively. The SDM, Q- score, etc. are reported in the Reply Log, opened with Favorites... Reply Log in the menu.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we recommend sending Chimera questions to chimera-users(a)cgl.ucsf.edu (I CC'd that list here after removing the details from your original mail) > -------- Original Message -------- > Subject: A question about your software(UCSF Chimera) > Date: Tue, 23 Mar 2010 21:55:06 -0400 > > Dear Dr. Ferrin, > > I am very interested in using your software UCSF Chimera, which have > some > commands that can do the job of aligning and measuring a distance > between two > protein structures. > > I am a PhD student at Purdue University working on the evolution of > protein > structure with Professor Peter Waddell. I was hoping to use your > structure > alignment software to obtain a pairwise structure distance matrix. > This > matrix > will then be used in phylogenetic analyses, comparing the trees and > treeness > of that structural distance compared to that produced by other > published > methods. > [...] > Could you please tell me if your structural alignment software can > easily > produce a complete pairwise distance matrix for a list of ~50 > structures? I did > not see a way to do this. If not, is there any easy way to modify it > to > do this? > [...] > > Best Regards and Sincerely, > Minming Li >

3 3

Residue exposition cutoff
by Yasser Almeida Hernández 05 Apr '10

05 Apr '10

Hi all.... I have 2 question, beyond Chimera's issues. 1 - There is some cutoff value to consider a residue or more strictly, an atom exposed to the solvent?. 2 - Could i set a this cutoff using the area values and types (SR0, SC0 and SS0) from the DMS program output? 3 - Wich program you recommend to compute SAS? Thanks, best regards -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

2 1

Possible bug in Chimera RMSD calculation
by Yasser Almeida Hernández 03 Apr '10

03 Apr '10

Hi all.... In Chimera , i selected a single pair of atoms for RMSD calculation with the command rms (rms #1:221.A@NE #0:221.A@NE) and it return the distance between the atoms ???? It would be a bug??? Please check this.... Thanks -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

2 1

Coloring model represented as PipesAndPlanks
by Ibrahim Moustafa 01 Apr '10

01 Apr '10

Dear Chimera team, I have a problem with coloring different regions of the protein presented as PipesAndPlanks. I know I can change the colors of the SS elements from the menu of PipesAndPlanks. But, this is not what I want: I want to color different regions of the protein with different colors and not to be limited with the colors given to the SS. Before, I had no problem in doing so. I think this problem appeared in the recent updates. Something I noticed and could be related is that to change the presentation from the default chimera to PipesAndPlanks the new presentation assigned the same model# as the original model. I think, in previous versions the new presentation used to be given a new model#. Similarly, if I want to create a map for the model using (molmap) it is given the same model # rather than a new model# as used to be. I run Chimera version 1.4.1 (build 30282) on a Mac OSX 10.4 (PPC). Thanks for help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

2 2

Daily build requirements
by sherden＠caltech.edu 31 Mar '10

31 Mar '10

So to get thermal ellipsoids to display from a .cif file (as opposed to a .pdb) it looks like I need version 1.50 or greater of Chimera, but it looks like versions of Chimera above 1.4x don't seem to run on my Mac (I have system 10.4.11). What OSX system version do I need so that I can run a version of chimera that I can get thermal ellipsoids to display from a .cif file? Or, conversely is there a way I can get one of the more recent daily builds to run on OSX system 10.4.11? --Nat (Nathaniel Sherden) California Institute of Technology

2 2

Problem in Surface depiction
by Kshatresh Dutta Dubey 31 Mar '10

31 Mar '10

Dear All, I am using chimera 1.41 and 1.4 on a 3 GB Core 2 duo machine. When i draw surface for any ligand or residue then suddenly it get closed. This problem occurs in both versions 1.4 and 1.4.1. Kindly suggest me to fix this problem. Regards Kshatresh Dutta Dubey

3 3

Re: [Chimera-users] named selections
by Elaine Meng 30 Mar '10

30 Mar '10

Hi Ajith, We are very happy to hear you will be the "Chimera guy" for your group, and that the tutorials are useful! But sometimes it is hard to find certain things, which is why we have the chimera- users(a)cgl.ucsf.edu list (recommended rather than sending mail to me individually). It sounds like you really want to use aliases rather than named selections. See the "alias" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> and also how to specify particular models, residues, chains, etc: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierar… > For example, to alias residues 10-42 and 55 in chain A and 80-100 in chain B: alias myresidues :10-42.a,55.a,80-100.b color red myresidues These would be the residue numbers in the structure, which are not always the same as in a sequence file. Session files are not friendly/intended for viewing as text. Aliases are saved in sessions, but you would just use the alias command without arguments to list the definitions of the existing aliases. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 30, 2010, at 8:05 PM, Ajith Harish wrote: > Hi Elaine, > I will not bother you with too many questions after this last one > (at least for a while ;-)). There are a lot of features to explore > and I am playing with it and have learnt quite bit today. Also the > tutorials on the website are very helpful. I am soon going to be the > "Chimera Guy" of our group ;-) > > But there was one feature I could not figure out. Is it possible to > name sections without actually selecting the sequence from the GUI. > I need color different parts of large ensembles. Different domains > in multiple chains of a single pdb file. For now I open the sequence > of one chain at a time form the "Tools > sequence > sequence" and > then pick the residues (amino/nucleotide) based on the numbering > from the corresponding Fasta file from PDB and then name it from > "Select > Name Selection". Is it possible to assign names on a FASTA > file? > > I also looked into the session.py file. I could not relate the > numbers corresponding to my names in the session file to the residue > numbers or the residues. It would be great if I could assign names > in a file and then acess the names to color. Even better would be > assign colors to those named selections. > > Thanks much for your help. > Best wishes, > Ajith >

2 1

Matching RGB color code from Adobe Illustrator
by Ajith Harish 30 Mar '10

30 Mar '10

Hello, I would like to color different regions of a molecule corresponding to RGB colors from Adobe Illustrator. Chimera RGB ranges from 0.000 to 1.000 where as the Illustrator RGB ranges from 0 to 255. Could you please let me know how these two scales are related? Thank you very much, Ajith

2 3

Trouble with thermal ellipsoids
by sherden＠caltech.edu 30 Mar '10

30 Mar '10

I can't seem to get the thermal ellipsoids to work. I have a number of .cif files that are all perfectly good files (have been cif-checked) and all of which I know for a fact have anisotropic data as I can get thermal ellipsoids to display from these files in other programs like Diamond (which we are trying to move away from). But any time I select an atom or group of atoms and use either the "aniso" command or the "Show Thermal Ellipsoids" dialogue box I just get: "No atoms chosen had anisotropic information." This is just not true though, I can open up the .cif files in question and see the anisotropic data listed for the given atoms with my own two eyes. Any thoughts? I am probably doing something immensely stupid, that is usually the case with such situations. --Nat (Nathaniel Sherden) California Institute of Technology Department of Chemistry

2 2

RMSD
by Beale, John 29 Mar '10

29 Mar '10

What is the best way to use Chimera to compute the RMSd value of an MD trajectory snapshot relative to the crystal structure of the protein? 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

2 1

zones and residue name/number
by Francesco Pietra 29 Mar '10

29 Mar '10

Hi: I was trying to detect all residues (or atoms) within a given distance from a single-atom ligand in model #0 (PDB file). There are several such single-atom ligand atoms in model #0 (practically invisible in chimera as they are not shown at their relative vdw size), each specified by different residue and atom numbers. I want to carry out the task for each single-atom residue. Therefore I can't use the standard command select #0:single-atom-ligand z(or za)<given.distance because that applies to all those single-atom-ligands. Unless the residue can be specified differently (the residue number in place of residue name did not work), the only way that I found to come out was to set different names for the different single-atom ligands. Is anything better? Secondary question: is there any plan to support psf/dcd format (which I am now using for MD with namd) beyond reading movies? Thanks francesco pietra

3 3

Converting SDF files to Mol2 Format
by Nancy 29 Mar '10

29 Mar '10

Hi Elaine, I need to convert a large number of PubChem SDF files into Mol2 format. When I convert an SDF file into Mol2 format, I add partial charges and run energy minimisation on the molecule, as this is necessary for the program I am inputting the files into. So far, I have only used Chimera in this method to convert individual files. Is there a way to convert a large number of SDF files to Mol2 format at once, and also preserve the filenames? Thanks in advance, Nancy

3 2

Question related to chimera H-bond constraints
by snoze pa 26 Mar '10

26 Mar '10

Dear Chimera Users, I have a question related to number of hydrogen bonds. 1. When I am using the Relax H-bond constraints then chimera is showing 76 H-bonds as shown below figure (h bonds are shown in cyan color) http://img260.imageshack.us/img260/6467/screenshotau.png 2. If I will select the option color H bonds not meeting precise criteria differently, then still it shows 76 H bonds with some bonds that do not meet the criteria in red color http://img690.imageshack.us/img690/5607/screenshot1ks.png In 2, Why the red H bonds are different from 1 though H bonds are relaxed. If it is true then why chimera is showing these bonds in Relax H-bond constraints in 1. 3. However, if I will not choose the option to relax H bonds constraints then it is showing 50 H bonds as shown below http://img153.imageshack.us/img153/3822/screenshot2kr.png Thank you very much for your time and help. S

3 6

Binding Pocket Internal Volume Calculation
by ppwanjari 24 Mar '10

24 Mar '10

Hello Everyone, I want to determine the inside volume of a pocket shaped molecule. Does anyone know how can I do it with Chimera? I am only able to measure volume of pocket-making atoms with Chimera, but not the inside volume. Thanks. Piyush

2 4

Chimera crashes on my mac even after a reinstall
by David Chenoweth 23 Mar '10

23 Mar '10

Hi! I recently downloaded a new version of Chimera (Mac OS X (Cocoa, Intel, 64-bit)MD5: e54f53e4313817e26dbc68450bd5312d) and it's been running great until today. After using the program all day it finally crashed just as I was trying to save a session and I didn't get the crash message. I restarted the program and as soon as I tried to open a file the program crashed. I tried shutting my computer down and this didn't help so I deleted that version of chimera from my computer and downloaded it again. After reinstalling the program I still have the same problem and now I'm a bit stumped! I have a lot of work saved in session files from today and I can't seem to get the program to run at all. I am using a new 15 inch Macbook pro (OSX 10.6.2). Any suggestions? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

2 3

Dimer construction from a monomer generated using Modeller
by akshita kumar 23 Mar '10

23 Mar '10

Dear Members, Using 1T3D as template, we have generated a homology model via Modeller. As the biological unit is a trimeric structure we need to generate trimer of the model too. Therefore we undertook structural alignment of the model and individual template 1T3D chains ("a, b , c"). However in our model the loop region that falls at the interface between two dimers is much longer and as a result the loops between dimer overlap each other. Can anybody please suggest a solution for generating a dimer/trimer from the monomer built using homology modelling. Thanks Akshita

6 8

Re: [Chimera-users] Scripting to write / save multiple models into single pdf file
by Eric Pettersen 23 Mar '10

23 Mar '10

Hmm, it seems that you have the Model Panel set to autostart in your preferences. Now, Chimera probably should ignore autostarting tools when it is in nogui mode, but currently it doesn't. So what you will have to do for now (until we fix this) is to start Chimera normally, turn off the autostart of the Model Panel (and any other graphical tools probably), save the new preferences, and then run your script. If you look in the "Preferences" preference category, it will show the location of the preferences file. You could squirrel away your original preferences file somewhere, make the version with no autostarting, copy that somewhere, and then put your original version back. You would then be able to use the no-autostarting preferences by specifying it's location with the --preferences startup option. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 8, 2010, at 7:32 PM, Sumitro Harjanto wrote: > Hi Eric, > > Thanks for the suggestion. I don’t really script, I usually use a c+ > + code / excel to generate the command (.cmd) files. Should be okay > for the automation for now, if I run into any problem then I will > post it up here again. =] > > Mean while I try running the command “chimera.exe –nogui” in PATH/ > chimera/bin but got the following error message. I followed the > instruction and copy over the debug message (below). any advise? I’m > on a win7 X86 platform btw. > > Thanks, > Sumitro > > ----------------------------------------------------------------------------------------------------- > > Chimera failed abnormally; the exit code was: 1 > Use –debug command line option for the full error message. > > -------------------------------------------------------------------------------------------------- > Cannot execute 'gzip': no automatic decompression of .Z files > Traceback (most recent call last): > File "E:\Chimera\share\__main__.py", line 65, in <module> > value = chimeraInit.init(sys.argv) > File "E:\Chimera\share\chimeraInit.py", line 401, in init > extension.startup(startExtensions) > File "E:\Chimera\share\chimera\extension\base.py", line 1056, in > startup > manager.autostartTools(extNames) > File "E:\Chimera\share\chimera\extension\base.py", line 959, in > autostartTools > > emo.activate() > File "E:\Chimera\share\ModelPanel\ChimeraExtension.py", line 23, > in activate > display(self.module('base').ModelPanel.name) > File "E:\Chimera\share\chimera\dialogs.py", line 77, in display > dialog = find(name, create=1) > File "E:\Chimera\share\chimera\dialogs.py", line 62, in find > return d() > File "E:\Chimera\share\chimera\baseDialog.py", line 523, in __init__ > BaseDialog.__init__(self, master, *args, **kw) > File "E:\Chimera\share\chimera\baseDialog.py", line 244, in __init__ > self.fillInUI(self.__top) > File "E:\Chimera\share\ModelPanel\base.py", line 217, in fillInUI > self._addColumns() > File "E:\Chimera\share\ModelPanel\base.py", line 436, in _addColumns > self._buildTable() > File "E:\Chimera\share\ModelPanel\base.py", line 454, in _buildTable > % len(filter(lambda s: s == 1, self.shownColumns))) > File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 1306, in __init__ > cnf, kw) > File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 307, in __init__ > self.tk.call(widgetName, self._w, *extra) > _tkinter.TclError: invalid command name "tixScrolledHList" > Return code: 1 > Press return or enter to to exit >

3 15

question concerning volumetric data
by Eric Pettersen 22 Mar '10

22 Mar '10

Hi, I have a EM map, spider file and the data are scaled by a factor of 3.6. I need to expand the map by this factor. How can I do this with chimera? Thank you very much for your help Best Regards Stefan

2 1

Regarding backbone images for protein structures
by Saurabh Gupte 17 Mar '10

17 Mar '10

Hello, I have been using Chimera for observing the 3D model of protein structures. For viewing the backbone structure, I used the following commands: show backbone or show minimal But in the latest production version 1.4, I am not able to view the backbone/minimal structure. The 3D structure is rendered properly but the above command do not seem to work. Have there been any changes in the format for above commands or have they been substituted by some other commands? Thanks, Saurabh

4 4

Step size in MD Movie
by Francesco Pietra 16 Mar '10

16 Mar '10

Hi: In my hands, with "chimera alpha version 1.5 (build 30193) 2010-03-06 09:27:34 GMT" linux 64bit (Debian lenny) the step size in MD Movie is always "1", no matter how higher it is set. I did not check if the stable version has the same problem. Could please users verify what happens on changing the step size? thanks francesco pietra

2 2

Volume surface colors
by Will Moore 15 Mar '10

15 Mar '10

Hi, I'm trying to write a script to change the surface colors of volumes in Chimera: This is what I have so far. for m in chimera.openModels.list(): print m.surface_colors m.surface_colors = [(1.0, 0.0, 0.0, 1.0)] print m.surface_colors This seems to alter the surface colors, but has no effect on what the maps look like in the UI. Do I need to call something else for the UI to be updated, or am I using the wrong approach entirely? Also, I would like to only select the volumes in the first line but I don't know what modelTypes this is: for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): Many thanks, Will. William Moore Wellcome Trust Centre for Gene Regulation & Expression College of Life Sciences MSI/WTB/JBC Complex University of Dundee Dow Street Dundee DD1 5EH United Kingdom Phone 01382 386364 http://openmicroscopy.org.uk

2 3

file format conversion using chimera
by snoze pa 12 Mar '10

12 Mar '10

Dear Chimera Users, I want to save/convert a pdb file into .mrc or .ccp4 format using chimera I think I did it before using chimera but don't remember exactly how! I will highly appreciate your help. Thank you S

2 1

Re: [Chimera-users] Chimera: Display map around atoms
by Elaine Meng 12 Mar '10

12 Mar '10

Hi Greg, That "bv" shortcut creates a new, larger map (periodically extended as needed to cover the atoms), which sounds like the opposite of what you want. You can limit the density display to a zone around selected atoms. Choose "Zone" from the "Features" menu in the Volume Viewer dialog to add the relevant controls to the dialog. The zone feature is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… > For future questions, it's better to send Chimera questions to the chimera-users(a)cgl.ucsf.edu list rather than to me directly. That way it won't fall through the cracks if I'm on vacation, or sick, or don't know the answer. I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 12, 2010, at 1:24 PM, Greg Friedland wrote: > Hi Elaine, > Thanks for your earlier help with Chimera. I'm currently have > difficulty displaying a density map. I'd like to only display the > density around protein atoms, not the full symmetry density. I tried > the shortcut 'bv' according to http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/003002.html > but the new map still contains lots of the symmetric molecule > density. Is there another way? > Thanks, > Greg > > Greg Friedland > Postdoc > Sandia National Lab > Joint BioEnergy Institute

1 0

Recording trajectory
by Francesco Pietra 11 Mar '10

11 Mar '10

Hi: I am interested in following the pathway of a ligand forced to leave a protein. I can follow that path with the movie (NAMD format) but I would be interested to also have a trace of the pathway recorded. I would like to show around the protein the various traces for different pathways of exit of the same ligand. thanks francesco pietra

3 5

Re: [Chimera-users] Recording trajectory
by Eric Pettersen 09 Mar '10

09 Mar '10

On Mar 9, 2010, at 2:17 PM, Francesco Pietra wrote: > Hello Eric: > I have seen your later correction mail. > > I had a bad day, that is little time for chimera and with little > success. Please try to guess were I was faulty. > > francesco@tya64:~$ chimera --version > chimera alpha version 1.5 (build 30193) 2010-03-06 09:27:34 GMT > francesco@tya64:~$ > This is amd64, at the moment I have no 32bit computer. > > <select ligand> selects too much. > > <select :residue.number> > <select :residue.name> > do select exactly what I want (which is a small ligand of HEME ligand > of the protein. > > The problem was with <define> command > > MD-movie...Per-Frame "define centroid :residue.number" ... Apply > > then activating the movie gave the same view as not going through the > Per_Frame, i.e., the small ligand does not leave any sphere on the > path. I did not investigate if the sphere are too small to be seen at > the magnification I used, ore have the same color as the background > (black). Very likely, I did some other major mistake. Not sure what to say. Works for me. I've appended an image of centroids tracing the motion of a small ligand in an RNA binding site. I used a step size of 10 and this 'define' command: define centroid raiseTool false radius 1.0 color goldenrod sel "raiseTool false" prevents 'define' from trying to bring up the Axes/ Planes/Centroids tool (and update that tool's table) for every centroid created. The other options control the size and color of the centroid. I had the small ligand selected so 'sel' is my atom spec. I tried it a second time with ":35" (which also selects the small ligand) and that worked too. FYI, "~define" will get rid of all the centroids. I hope this helps somehow. Are you sure you had the "Interpret script as" part of the per-frame dialog set to "Chimera commands"? I can't imagine that you didn't, since you would have gotten some kind of error if it had been interpreted as Python. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

2 1

Re: [Chimera-users] Scripting to write / save multiple models into single pdf file
by Elaine Meng 08 Mar '10

08 Mar '10

On Mar 7, 2010, at 5:12 AM, Sumitro Harjanto wrote: > Hi Meng, > I would like to use chimera to help me with a process of combining > receptors and ligands that were modelled separately (in separate > files) > > So here is my intended framework: > > For each iteration: > • open “template.pdb” template file (which contains the receptor/ > ligand complex) I used to model the receptor and ligand > • open the receptor_model.pdb > • open the ligand_model.pdb > • match receptor to template > • match ligand to template > • close template.pdb > • save the models in their current position into a single new pdb > file. > > I was exploring the feasibility of using the command “write” but I > am not too sure if it will allow me to save the complex as a single > pdb file..? > > On a side note, if it’s possible, any suggestion on how to optimise > the run time since I might be running this for a large number of > iterations ..? I read somewhere about switching off the GUI to save > time, does it help..? > > Thanks! > Cheers, > Sumitro Hi Sumitro, You can't save multiple models in one file with the "write" command, but you can use "write" multiple times, one for each model you want to save. If you make sure to save each model "relative" to the same model, they will be in the correct positions with respect to each other when you reopen the files. See the "relative" keyword: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> Or, if you really need to have them in a single file, you can use the "combine" command to create a new single model from multiple models. You would do that after the matching, but before saving the PDB file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> I can't answer about how to script for multiple models, or how much faster it might be to use noGUI, so I'm sending this to the chimera- users list. In the future, please send Chimera questions to the chimera-users(a)cgl.ucsf.edu list, because I might be away from work or (like now) others may be better able to answer the question. I hope this helps, ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

2 1

Problem with energy minimization
by Bill McIntire 05 Mar '10

05 Mar '10

I used Dock Prep for my modeled structure, and get no error comments. However, when I try to energy-minimize, I get the following message: No MMTK name for atom "HN1" in standard residue "PRO" PRO is at the N-terminus. I cannot find any help in manual. Please help with this problem. Thanks Bill McIntire

2 2

cap color from command line
by Jean-Paul Armache 05 Mar '10

05 Mar '10

Hello, Thank you for all your previous answers. I would like to ask you whether there is a way to change the cap color not only from the Surface capping tool, but the command line as well and declare it maybe in a script (like for example coloring of the maps and models). Thanks, Jean-Paul

2 1

make one chain from two chains ID in PDB
by Dong, Jianbo 04 Mar '10

04 Mar '10

Hello, I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way. May I get some help for this? Is there a easier way to do this? Many thanks, Jianbo

4 5

positive and negative overlaps
by Kshatresh Dutta Dubey 03 Mar '10

03 Mar '10

Dear all, Can anyone tell me the significance of positive and negative overlaps results in structure analysis module of chimera, as i got 140 contacts that contains both positive and negative overlap values? Any help is appreciated. Thanks in advance Kshatresh Dutta Dubey

2 2

show axis ?
by Stefan Bäckström 03 Mar '10

03 Mar '10

Hi. It is possible to show the box of a volume, and I wonder if it is possible to show the X, Y and Z axis as lines ? Best, Stefan Bäckström Medical Biochemistry Göteborg University Sweden

2 1

groups
by Jean-Paul Armache 03 Mar '10

03 Mar '10

Hello, I am often juggling between different sets that are to be turned on/off together. Is there a way of grouping maps/pdbs so that instead of turning 20 pdbs on, i could just click on a group to which they belong ? If there is something like that, could you point me to it ? And if not, would it be possible to have it in the Model Panel? Best regards, Jean-Paul Armache

3 2

chimera-users@cgl.ucsf.edu
by Jozef Lewandowski 03 Mar '10

03 Mar '10

Hi everybody, I am trying to get a list of all hydrogen atoms within certain distance from a specific atom. I found an old thread suggesting using findclash for that. When I use: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 everything works fine and I get the list of all the atoms within the desired distance limits. However, I get all types of atoms. To select only for contacts to hydrogens, I have tried to add the "test" option but when I type: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 test @H the procedure does not report on any contacts. Am I misunderstanding the syntax? What is the way to get only the distances between :4@c and all hydrogens within ~10A? Moreover, I am ultimately interested in the sum of all reported distances (or more specifically sum of (1/r)6 where r is the distance). Is there simple way to get this value calculated in Chimera (e.g. simple script)? Unfortunately, I have no idea about Python coding, so right now I have to import the list to Excel and calculate what I need in there (which is fine for a few atoms but slightly tedious when you have to check several hundred of them...). Any help would be appreciated. Thanks, Józef

3 5

Sum of distances
by Jozef Lewandowski 03 Mar '10

03 Mar '10

Hi everybody, I am trying to get a list of all hydrogen atoms within certain distance from a specific atom. I found an old thread suggesting using findclash for that. When I use: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 everything works fine and I get the list of all the atoms within the desired distance limits. However, I get all types of atoms. To select only for contacts to hydrogens, I have tried to add the "test" option but when I type: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 test @H the procedure does not report on any contacts. Am I misunderstanding the syntax? What is the way to get only the distances between :4@c and all hydrogens within ~10A? Moreover, I am ultimately interested in the sum of all reported distances (or more specifically sum of (1/r)^6 where r is the distance). Is there simple way to get this value calculated in Chimera (e.g. simple script)? Unfortunately, I have no idea about Python coding, so right now I have to import the list to Excel and calculate what I need in there (which is fine for a few atoms but slightly tedious when you have to check several hundred of them...). Any help would be appreciated. Thanks, Józef

1 0

constraints and restraints
by Elaine Meng 02 Mar '10

02 Mar '10

Hello, The Chimera release notes describe what is new or changed in a release: <http://www.cgl.ucsf.edu/chimera/docs/relnotes.html> ... clicking the "1.4" link: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html> The meaning of "constraint" "restraint" and "tether" may change based on which program you are using. Each program should explain it in its own documentation. In programs I've used, "constraints" meant atoms are completely fixed in place (frozen, cannot move) whereas "restraints" use a force constant like a spring, and allowed some movement. I don't have any opinion on the technical definition of "tethering." Again, don't rely on my descriptions as final because different programs may use the words to mean different things. Chimera minimization only allows "fixing" some of the atoms so they can't move at all. It does not allow holding atoms in place with force constants. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html > nice to give you a letter! > is there a new one ,really? > what is the new feature in the least software? > > I want constraint ,restraint and tether some atoms and backbone. > how can I do constraiting ,restrainting and tethering in > software.how can i set value for constraiting ,restrainting and > tethering. > what is the difference between them? > > thank you! > >

1 0

NAMD trajectory and AMBER topology
by Francesco Musiani 02 Mar '10

02 Mar '10

Hi all, I would like to visualize in Chimera a trajectory obtained with the program NAMD, but I have a .prmtop topology file generated using AMBER instead of a .psf topology file. I have these files beacuse in NAMD is possible to use AMBER format topology. Is it possible to implement an additional feature in Chimera which allows to visualize NAMD trajectory using AMBER topology? Thanks in advance, Francesco -- Francesco Musiani -- Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin 40, I-40127 Bologna, Italy Phone: +39-051-2096236 - Fax: +39-051-2096203 E-mail: francesco.musiani(a)unibo.it Web: http://bioinorg.agrsci.unibo.it

2 1

load pdb files from local PDB mirror
by Mark Moll 02 Mar '10

02 Mar '10

I have a local mirror of all PDB structures (as pdb files). It’d be nice if Chimera could use this, but it seems that Chimera expects a “flat” directory structure rather than the hierarchical directory structure of the PDB. For example, on my machine the pdb file for 1ady is stored in ${HOME}/pdb/ad/pdb1ady.ent.gz, but when I fetch by ID, the file will not be found. Instead, Chimera will download the file and save it in ${HOME}/pdb/PDB/1ADY.pdb. Is there some way to handle both cases (flat & hierarchical directory structure)? -- Mark

3 4

multi-threading
by Jean-Paul Armache 02 Mar '10

02 Mar '10

Hello, I know that this topic might've emerged earlier, but I was curious whether there were any plans to implement multi-threading into Chimera ? Best regards, Jean-Paul Armache

2 1

Re: [Chimera-users] How are chains paired in morphing?
by Eric Pettersen 01 Mar '10

01 Mar '10

The sequences are in input order unless you ask for the return value to be a dictionary (with the 'asDict' keyword). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 22, 2010, at 11:25 AM, Conrad Huang wrote: > There's a comment in Segment.py: > > # Get the chains from each model. If they do not have the > # same number of chains, we give up. Otherwise, we assume > # that the chains should be matched in the same order > > It uses molecule.sequences() to get the chains. Eric, does > sequences() return the chains in input order, or is it random (eg > hash order)? > > Conrad > > On 2/22/2010 10:26 AM, Thomas Goddard wrote: >> Bobby Laird showed me a homo-tetramer with chains A, B, C, D that >> when >> morphed between two states with the Chimera morph conformations tool >> swapped two of the monomers. In other words the 4 chains from one >> state >> weren't correctly paired with the 4 chains from the other state so >> two >> monomers exchanged positions during the morph. The tetramers were >> built >> from dimers 1pfk and 2pfk by using the symmetry of the unit cell with >> other software (coot?). >> >> How does morph conformations decide which chains to pair? >> >> >> Tom >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

2 1

saving moved maps
by Erika Mancini 26 Feb '10

26 Feb '10

Dear Chimera users, is it possible, after moving maps around, to save them into their new positions? I tried save map from volume viewer, but maps are saved in their original positions. Thanks! erika

2 1

question
by Huang, Xinlei 25 Feb '10

25 Feb '10

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help. Thanks xinlei

2 1

variable surface visualization
by Zambonelli, Carlo 25 Feb '10

25 Feb '10

Dear All, I am working with a glycoprotein structure and I want to visualize the protein surface as a continuum with the glycans sticking out as sticks. If I visualize the surface of the whole molecule (including sugars), and then I select the sugars only and visualize them as sticks, the surface of the amino acids immediately connected to the sugar (Asn) appear to be clipped. One solution could be to the following: 1. save the model with a different name 2. load the 2 identical structures and align them 3. remove the sugars from one structure only and use it to visualize the protein 4. the second structure is used for visualizing the sugars and not the protein. I used to do something similar with Pymol, and it should work with Chimera as well, but I am sure there is a better/simpler solution. Any suggestion? Thank you for your help. Carlo

2 2

quesitons
by Xinlei Huang 25 Feb '10

25 Feb '10

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help. Thanks xinlei Chemistry Department Indiana University-Bloomington

1 0

Re: [Chimera-users] [chimera-dev] run chimera's IDLE in terminal on mac os x
by Eric Pettersen 24 Feb '10

24 Feb '10

On Feb 24, 2010, at 5:34 PM, Yang wrote: > Hi Eric > > I want to manipulate with electron density maps, and just use > chimera functions for reading pdb files and density maps. However, > for high-resolution maps, it takes too long to run the my program on > my mac book. So I want to remotely use the server of our department, > which has much larger memory, to complete this task by typing > commands in terminal. Before that, I had everything done in > chimera's IDLE. So I prefer using chimera functions somehow in > terminal assuming chimera is installed first. > > Thanks for your advice. I think you just want to take whatever commands you were using in IDLE and put them in a Python script (file ending: .py). You can then execute them with "chimera --nogui myscript.py". If you need to supply arguments to the script then instead run it like this: "chimera --nogui --script myscript.py -- arg1 arg2 ...". This is described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

version 1.3
by n.prahl＠freenet.de 24 Feb '10

24 Feb '10

Hi everybody, I don`t find a link on your homepage to download the chimera version 1.3. I only find version before or after chimera 1.3. How can I download the version 1.3? I need this version for my studies. Thank you, Nicole Heute schon ge"freeMail"t? Jetzt kostenlose E-Mail-Adresse sichern! http://email.freenet.de/dienste/emailoffice/produktuebersicht/basic/mail/in…

2 1

Re: [Chimera-users] [chimera-dev] run chimera in terminal on mac os x
by Elaine Meng 24 Feb '10

24 Feb '10

On Feb 24, 2010, at 11:45 AM, ylei(a)ecs.umass.edu wrote: > Dear all > Could somebody tell me how to run Chimera in terminal on the system > of mac? > Thanks. > Yang Hi Yang, It is described in the User's Guide page on Chimera startup: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecore.html> See the part about Mac OS X. To summarize, if Chimera is installed as /Applications/Chimera , to start it from Terminal you would type: /Applications/Chimera.app/Contents/MacOS/chimera (or if it is in a different place or you gave it a different name, substitute those instead). Since that is kind of a long thing to type, you may want to make an alias. My aliases are in the file named .tcshrc in my home directory on the mac, but the filename could be different depending on what shell you are using (maybe .bashrc or .cshrc or something like that). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Chemical groups
by Mauro Truglio 23 Feb '10

23 Feb '10

Hi, I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g.. It could be useful to add some sort of identifier, like: FG1: atom atom atom FG2: atom atom atom How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.: Group number 1 : [<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>] Group number 2 : [<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>] Thank you Mauro Truglio (Bioinformatics Lab - University of Rome Tor Vergata)

2 1

Rendering a vector/axis
by Richard Stanton 23 Feb '10

23 Feb '10

Hi, Is there a way to render a vector after defining it as an axis in the "Axes/Planes" tab under "Structure Measurements"? I am able to define an axis using the selected atoms in my structure but I am not sure how to visually render and alter its appearance, as there is no visual representation on the graphics screen. I was hoping that after using my selected atoms to define the axis I would then have an arrow or line showing me the axis/vector and I could then create different vectors/axis and view them simultaneously to show the difference between their angles. Is there a way to do this? Thanks in advance for the help! Thanks, Rich

3 3

Chemical groups
by Mauro Truglio 23 Feb '10

23 Feb '10

Hi, I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g.. It could be useful to add some sort of identifier, like: FG1: atom atom atom FG2: atom atom atom How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.: Group number 1 : [<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>] Group number 2 : [<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>] Thank you Mauro Truglio (Bioinformatics Lab - University of Rome Tor Vergata)

1 0

Defining planes & Thermal ellipsoids
by David Chenoweth 22 Feb '10

22 Feb '10

Hi! Thanks so much for adding the define plane and define centroid features. Is there any way to add the option of defining the border of the plane as a polygon where the selected atoms define the polygon vertices? This would allow a plane in the shape of a hexagon or any other heterocycle to be inset inside of an aromatic ring for example without the edges of the plane being visible outside the bond enclosed area. Also, the thermal ellipsoid feature looks fantastic, however the probability setting doesn't seem to be functioning. Thanks again for adding all these features, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

2 3

How are chains paired in morphing?
by Thomas Goddard 22 Feb '10

22 Feb '10

Bobby Laird showed me a homo-tetramer with chains A, B, C, D that when morphed between two states with the Chimera morph conformations tool swapped two of the monomers. In other words the 4 chains from one state weren't correctly paired with the 4 chains from the other state so two monomers exchanged positions during the morph. The tetramers were built from dimers 1pfk and 2pfk by using the symmetry of the unit cell with other software (coot?). How does morph conformations decide which chains to pair? Tom

1 0

Which Mac daily build to use
by Thomas Goddard 21 Feb '10

21 Feb '10

> on another note: which of the daily builds should I be using? aqua, > aqua-intel, intel-cocoa, intel-cocoa-64. > > not sure on the + & -'s > > do not mind taking some crash risks to push sw dev objectives and reporting. > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine/Houston Texas USA Hi Matt, The Mac Chimera builds are far too numerous now. I recommend the 64-bit Cocoa build. That is what I use. It has one very serious issue right now that pressing Option-e or Option plus many other other characters will immediately crash Chimera. It is a Tk Cocoa bug that I reported but I need to put a fix into Chimera while I wait for the Tk developers to fix it. If that sounds too dangerous use the Chimera Aqua build (32-bit only). That uses the Mac Carbon API which is the older Mac API that Apple says they will not provide 64-bit support for. So we will replace that with Cocoa in the Chimera 1.5 release in a few months. My least favorite choice is Mac X11 which is not the native Mac windowing system and is the least well supported. That Chimera version will also be eliminated in the future. For the 32-bit versus 64-bit Chimera Cocoa you should use 64-bit if you have Mac OS 10.6 (Snow Leopard) or 32-bit for older Mac OS versions. We don't offer 64-bit Mac Chimera on Mac OS 10.5 or older Mac OS versions. Mac OS 10.6 is the first version of Mac OS that uses 64-bit by default. I've measured performance of 64-bit Mac Cocoa Chimera and it is as good as 32-bit. For the Chimera 1.5 release we hope to only be offering two production Mac Chimera versions 32-bit and 64-bit Cocoa. The X11 version will be in the unsupported category and the Aqua (= Carbon) will be gone. Tom

4 4

centroid measurements typo
by David Chenoweth 20 Feb '10

20 Feb '10

Hi, Sorry there was a typo in the last message! The centroid feature is great, but I would like to select two centroids or a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

2 3

Centroid measurements
by David Chenoweth 20 Feb '10

20 Feb '10

Hi, The centroid feature is great, but I would like to select two centroids of a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

1 0

command line writing PDB files
by Matthew Dougherty 19 Feb '10

19 Feb '10

Is there a command line string for writing out selected atoms as a PDB file? thanks, matt Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================== ==================================

4 3

distance measurements
by Bala subramanian 19 Feb '10

19 Feb '10

Friends, Greetings. I have 5Aromatic residues and 4 aliphatic residues in a loop. I want to calculate the CA distance between between each of Aromatic with the CA of each of the aliphatic residues in a single command. Can i do it in some fancy way. I have tried distance command but it takes exactly two atoms. Any example script would be of great help to me. Thank you, Bala

3 2

Density map in Chimera
by Pancera, Marie (NIH/VRC) [C] 17 Feb '10

17 Feb '10

Hi, I opened an electron density map in chimera. For some reason it is forming a box and I am not quite sure how to get the density outside of the box (to cover symmetry molecules etc...) Thanks for helping me with that. Best regards, Marie

2 1

copyright permission
by M P Williamson 17 Feb '10

17 Feb '10

Hi folks. I am getting near to the end of writing a book called How Proteins Work (to be published by Garland, hopefully this fall). I would like to include a figure showing anisotropic B factors for a protein, and the best image I have come across is of heme on your website, http://www.cgl.ucsf.edu/chimera/feature_highlights/ellipsoids.png I would like to include this image in the book. Could you let me know if there are copyright restrictions on the image, and how you would like me to refer to it? Thanks Mike Williamson

2 1

help
by Giuseppe Falini 17 Feb '10

17 Feb '10

Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe

4 5

writing a trajectory to multiple pdbs
by Dan Gurnon 16 Feb '10

16 Feb '10

Hi everyone, How would one write a trajectory read into MD Movie to a series of pdb files instead of one large file? I don't see a suitable option specified for the "write" command, and for "Save PDB" it seems the option of multiple files is only available when multiple models are selected. Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

2 1

Re: [Chimera-users] Hydrogen Atoms
by Elaine Meng 16 Feb '10

16 Feb '10

On Feb 14, 2010, at 11:31 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am working on calculating the Solvent accessible Surface Area on > the antigen interaction region. I am confused about adding/removing > hydrogen's, my question is will there be a change in SASA if you > have or not have hydrogen's atoms added. > Thank You. > -Thiru > Hi Thiru, Yes, it will be different with and without hydrogen, because the molecule is treated as a set of spheres where each atom is a sphere. There will be more small bumps on the surface when there are hydrogens. Also, the radii of the other atoms may change because there are different defaults for structures with and without hydrogens, as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> I think surface area calculations are usually done on structures without hydrogens. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html P.S. you may want to use "measure buriedArea" (or maybe you are already doing that): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedAr… >

5 6

reference for saving pdb
by Samuel Coulbourn Flores 12 Feb '10

12 Feb '10

Hi Guys, I'm having what I am sure is a trivial problem. When I save my PDB coordinates, I am asked what the reference is, and choose a density map. But when I read those coordinates back in, they are translated/rotated from where they should be and no longer match the density map. Can you tell me what is the correct procedure for setting the reference? Thanks Sam

2 2

Row interleaved stereo and Zalman monitors under Linux
by David Bhella 12 Feb '10

12 Feb '10

Hello again! I have just installed a Zalman M220W monitor on one of our workstations under OpenSuse 11.1, after a small amount of fiddling to get it working with dual head mode it seems to be behaving. In Amira it gives beautiful 3D, although the assignment of left and right eye views seems fairly random, as Amira has the option to reverse left and right eye views this is not a problem. In Chimera however with row interleaved stereo I seem to always get the views the wrong way around. It took me a while to work out why it didnt seem to be giving good depth and it was quite disconcerting to look at while viewing cryoEM 3D reconstructions, however with a pdb file it was quite obvious that my right eye was getting the left eye view. There only seems to be the option of reversing the views for sequential stereo however.... I would be grateful if anyone could advise me on how I can fix this. Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Skype: d.bhella Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html

3 2

Shadows
by David Bhella 12 Feb '10

12 Feb '10

Hi, I just updated my Chimera installation to 1.4.1 (Mac OSX aqua), and I noticed that for some reason shadows are not so nicely rendered in standard 3x3 super-sampled output. They look very blocky, much as they always have done in the viewer. In version 1.4 I always got very nice shadows when I saved an image. I am trying to save images of an isosurface view of a 3D reconstruction. Is there a setting I need to adjust to get high quality shadows back again? Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Skype: d.bhella Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html

4 3

session writing
by Jean-Paul Armache 11 Feb '10

11 Feb '10

hello, i would like to ask whether it would be possible to save sessions with relative path, instead of absolute one ? it is a bit complicated to move the sessions between different platforms with the absolute one. thank you, best, jp armache

2 1

Re: [Chimera-users] 64-bit version of Chimera for windows
by Tom Goddard 11 Feb '10

11 Feb '10

Hi Pu, Greg Couch in our lab is working on a 64-bit version of Chimera for Windows 7. It should be available in a month or two if we don't run into overwhelming difficulties. Tom > Hi Tom, > > Do you have 64-bit version chimera for windows. Our computer manager asked me > this question. > > Happy Chinese New Year. > > Best regards > > > Pu Qian > > >

1 0

Peptide Builder in 1.4x
by nettles 10 Feb '10

10 Feb '10

Hi All, I was very excited to download the 1.4 version of Chimera with it many improved features yesterday. However, I was surprised today when I tried to build an anti parallel beta sheet and it came out looking like an alpha helix. After experimenting around i realized all option give alpha helix. This is true for 1.4 (build 26788) and 1.4.1 (build 29977)and . The old version 1 build 2540 works fine. (It worked with a newer version I had too, but silly me overwrote that with the 1.4.x) Thought you would like to know. I appreciate your excellent software. Thanks, Jim Nettles

4 5

measure crossing angles for axes
by Tom Duncan 09 Feb '10

09 Feb '10

I have used the "measure rotation" command to create several axes. In each case, a marker set (to show the axis) is generated that consists of 2 pseudoatoms and 1 bond. Is there a simple way to measure the crossing angle between 2 such axes? If the marker set had 3 atoms, I could probably use the Axes/Planes tools to do this. Thanks, Tom

3 2

BCC CHARGES
by emrys.fslife.co.uk 08 Feb '10

08 Feb '10

Hi folks Is it possible(within Chimera) to get the dipole moment of low-molecular weight ligands alongside their calculated BCC atomic charges? Best wishes E.Thomas

3 2

Chimera/VMD visualization difference
by Keith Battle 08 Feb '10

08 Feb '10

Hello Chimera team, I recently conducted a MD simulation of a 12-mer peptide adjacent to a hydroxyapatite crystal using NAMD 2.6. When I viewed the output coordinates from the simulation in pdb format using Chimera 1.4, the protein ribbon was broken and the hydrogens of certain residues were not bonded but in close proximity. All of the non-bonded hydrogens were colored purple by default. The waters of the system and the crystal looked normal. Overall, the protein looked distorted. I decided to visualize the peptide using VMD 1.8.7 and to my surprise the protein ribbon was intact with all hydrogens bonded to their respective residues. Any insight into why this difference occurred would be greatly appreciated. Best, Keith Battle Research Technician University of South Alabama

3 2

Align the molecule
by snoze pa 08 Feb '10

08 Feb '10

Dear Chimera Users, I am wondering if it is possible to align the molecule along the X-Y or Z axis. I want to place the molecule, along a line joining N to C terminal line. Idea is to place a molecule along this line(N to C line) which is X or Y or Z axis. Thank you, S

2 3

display comsia contour maps
by Joern Lenz 08 Feb '10

08 Feb '10

hi there, i am wondering if it is possible to display contour plots for 3d qsar (comsia) made by sybyl in chimera. any help is much appreciated, cheers, jorn

2 1

Aligning planes with principal planes
by Dipl.-Ing. Thomas Mitterfellner 05 Feb '10

05 Feb '10

Hello! Is there a command in Chimera that turns a molecule in a way that a plane (explicitly created or just the selected atoms defining the plane) is parallel to the xy or the other principal planes? Thank you, Thomas

2 1

SDF partial charges
by Elaine Meng 04 Feb '10

04 Feb '10

Hello, An additional follow-up to Nancy's question from Jan 31. <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004754.html > Daily builds (version 1.5) dated Feb 4 or newer will now automatically read the partial charges in 3D SDF files obtained directly from the PubChem database. <http://pubchem.ncbi.nlm.nih.gov/release3d.html> However, I wanted to caution everybody that the protonation states of the resulting molecules are not what you would expect at physiological pH. The functional groups that would generally be charged near pH 7 are neutralized, at least from the few examples that I've examined: carboxylic and other acids fully protonated rather than formally negative, aliphatic amines neutral rather than formally positive. For example, alanine is given as H2N-CH(CH3)-COOH rather than + H3N- CH(CH3)-COO - If that is the case for all of the 3D SDFs obtained directly from PubChem (Nancy, you may want to take a closer look at a sample of your structures), I would not recommend them for docking. Instead, you may want to get small molecule structures from some place that has attempted to put them in reasonable charge states, such as the ZINC database. <http://zinc.docking.org/> 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

1 0

Calculating sigma level for EM map
by Thomas Goddard 04 Feb '10

04 Feb '10

Hi Andy, I don't know any convention defining the sigma value for an EM map. For x-ray maps there is a convention because the density is periodic you can just take the root-mean square density value across a whole unit cell. Note that that isn't a measure of noise level -- it's just a reproducible value describing the typical density levels across the unit cell. That isn't useful in EM maps because the value depends on how big the box is that contains the non-periodic structure. A bigger box contains more grid points outside the structure (values near zero) that make the root-mean square value (RMS) smaller. So such an RMS value isn't a reproducible measure of density values since it depends on the box size. I think when sigma is mentioned in EM papers they tend to mean the noise level. I don't know of any standard protocol for determining the noise level. If you knew the sigma level you wished to use, Chimera is still not able to display density values in sigma units. That is on our feature request list. Currently you have to take the values Chimera displays and divide by the sigma value yourself. I haven't added this capability yet because the notion of sigma does not seem to be well defined in EM work. Since Chimera map analysis is primarily used for EM, not x-ray, showing sigma units has not been a high priority. Tom -------- Original Message -------- Subject: Re: Threshold From: Anindito Sen To: Tom Goddard Date: 2/4/10 1:09 AM > Hi Tom > > I should have been more specific- my reconstruction is a EM density map > of a helical biopolymer. In that case what should be the correct > approach to calculate the threshold. Can you site any reference which > may be useful in this regard? > > Do we have the option of directly obtaining sigma value for the > threshold in Chimera ? > > Dr. Anindito Sen (Ph.D) > > --- On *Thu, 4/2/10, Tom Goddard* wrote: > > > From: Tom Goddard > Subject: Re: Threshold > To: "Anindito Sen" > Date: Thursday, 4 February, 2010, 9:29 > > Hi Andy, > > That may be right. But there are many issues. If your map is for > a crystal unit cell then that seems reasonable. In other cases > where the map is not a crystal unit cell then the RMS of the whole > map will depend on what the boundaries are of the map. For > instance, for an EM single particle reconstruction the RMS will > depend on how much padding of zeros there is, ie how big the box > is. If it is an x-ray map but not a unit cell again the RMS will > vary depending on what part of the map is taken. > > Tom > > > -------- Original Message -------- > Subject: Threshold > From: Anindito Sen > To: Tom Goddard > Date: 2/3/10 7:23 PM >> * >> >> Hi Tom >> >> I am "cropping" out high electron dense region from my >> density map to determine the volume of that region. The value of >> the Level in my Volume viewer is 438 (Range -618- 1024). The other >> factors are : >> >> f15_volume035.brix: mean = 23.123, SD = 137.14, RMS = 139.07 >> >> Therefore following your email, can I say, threshold is 438/139.07 >> = 3.1s >> >> Thanks for your help. >> >> Best Wishes >> >> Andy >> >> >> >> Tom Goddard* >> /Tue May 20 15:54:10 PDT 2008/ >> ------------------------------------------------------------------------ >> Hi Dave, >> >> Chimera can report the mean, standard deviation and root mean square >> map value using menu entry >> >> Tools / Volume Data / Volume Mean, SD, RMS >> >> The values using whatever normalization the map file has. If you divide >> the threshold level you set in the volume dialog by the RMS value you >> will get a sigma value. Actually I'm not sure if that is correct -- >> depends on the definition of sigma. Maybe you have to take the volume >> dialog number, subtract the mean and divide by the SD. The reported SD >> and RMS differ only in that the SD is the standard deviation of the map >> about the mean while the RMS is the standard deviation about 0. >> >> Allowing the volume dialog to show the sigma values directly is on our >> requested features list (item 88) but has not yet been implemented. >> >> http://www.cgl.ucsf.edu/chimera/plans.html >> >> Tom >> >> >> David Chenoweth wrote: >> >/ Hi! >> />/ >> />/ Can you please let me know if there is a way to report or set the >> />/ sigma value for an electron density map from a high resolution crystal >> />/ structure. I am using a ccp4 FWT.map and DELFWT.map file for >> />/ structures <1.2 angstrom resolution. Can I somehow find the sigma >> />/ value that corresponds to the Level setting in the Volume viewer? >> />/ >> />/ Thanks, >> />/ Dave Chenoweth >> />/ >> / >> >> ------------------------------------------------------------------------

1 0

Smooth Surface
by sudheer molugu 03 Feb '10

03 Feb '10

Hi, I've installed the latest chimera version. I wanted take pov-ray pictures of a cryo-EM map. I would greatly appreciate if you can help me in make the map surface smooth. I couldn't find the option for smooth surface. Thank you, Sudheer.

2 1

Mac 64-bit Chimera for large data sets
by Tom Goddard 02 Feb '10

02 Feb '10

A 64-bit Mac Chimera daily build is now available for Mac OS 10.6. It will not run on Mac OS 10.5. http://www.cgl.ucsf.edu/chimera/download.html#daily If you work with EM maps larger than 1 Gbyte or molecular models of several hundred thousand atoms the larger addressable memory in the 64-bit version will help avoid out-of-memory errors and crashes. The 32-bit Mac Chimera versions can only address 4 Gbytes of memory and because libraries, stack and other uses of memory the practical working data size limit for 32-bit versions of Chimera is about 1 Gbyte. You should have more than 4 Gbytes of memory installed in order to benefit from the 64-bit version. The 64-bit Mac Chimera is in early testing so will have more bugs than usual. I've tested the 64-bit Mac Chimera running Gaussian filtering on a 2048 by 2048 by 800 map requiring about 3.2 Gbytes for the floating point result and 0.8 Gbytes for the original map. This worked correctly (took about 3 minutes on a machine with 6 Gbytes of memory) but failed with 32-bit Mac Chimera. We are also working on a 64-bit Windows Chimera that will work with Windows 7. This may be available within a month if no serious obstacles are encountered. A 64-bit Linux Chimera has been available for a few years. Tom

1 0

alter volume data with python
by Michael Zimmermann 02 Feb '10

02 Feb '10

Dear Chimera users, I cannot find a way to search the chimera-users archive, so I appologize if this has been asked already. I wish to alter some volume data in specific ways; delete (zero out) all volume values that do not meet certain density criteria. The following code modifies the matrix values, but I can't figure out how to update the map that is being displayed in the volume viewer. I would like to be able to do something like: opened[0].full_matrix = H Then I would only see the swath that I "selected" with the following code. # ------------------------------------------------------------------------ source = '1R0A_antigen_6A_8s_0.425f_inv.mrc' opened = chimera.openModels.open(source) em = opened[0] H = em.full_matrix() s = H.shape for k in range(0,s[2]-1): for i in range(0,s[0]-1): for j in range(0,s[1]-1): if(H[i,j,k] >= -.28) and (H[i,j,k] <= -0.001): H[i,j,k] = H[i,j,k]+1 else: H[i,j,k] = 0 # ------------------------------------------------------------------------ Thank you, -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University

3 2

SDF Partial Charges
by Nancy 01 Feb '10

01 Feb '10

Hello, I am performing protein-ligand docking simulations, and the preferred ligand input file format is Mol2. I obtained some of my ligand structures from PubChem in SDF format, and I noticed that the SDF files contain partial charges ("PUBCHEM_MMFF94_PARTIAL_CHARGES"). Is there a way to preserve the charges in Chimera when converting to Mol2 file format? Thanks in advance. Nancy

2 1

Converting SDF to Mol2: Errors
by Nancy 01 Feb '10

01 Feb '10

Hi All, When I convert an SDF file to Mol2 format using UCSF Chimera, I noticed that some valence errors were introduced. I can correct these errors for individual molecules, but doing so for large sets becomes cumbersome; is there any solution to this problem? Thanks in advance. Nancy

2 1

Re: [Chimera-users] [Chimera] #8137: undesirable window placement (was: Chimera bug report submission)
by Eric Pettersen 01 Feb '10

01 Feb '10

Guy Nimrod wrote: > When I do an action that opens a new window (e.g. ‘file’ -> ‘save > session as’ or ‘file’-> ‘fetch by ID’), it seems that the new window > is located in a random position. Sometimes it is out of the borders > of the screen which is very problematic. Hi Guy, I think the new window-placement behavior is an improvement for most people. Nonetheless, it seems to be a problem for you so I've changed it into a preference (with the new behavior as the default). Starting with tomorrow's daily build there will be a preference in the General category called "Try to avoid placing dialogs over main window" which you can change to "false". Unfortunately the daily build for Windows hasn't been working lately, so it may be a few days before you can get a version with this preference available... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Re: [Chimera-users] holle,sir!
by Elaine Meng 30 Jan '10

30 Jan '10

On Jan 29, 2010, at 10:14 PM, gytjyb wrote: > holle,sir! nice to send a letter to you! > (1) about FindHBond .I can find out some HBond between ligand and > receptor,by chimera. I also use Accelrys Discovery Studio to find > out some HBond . but Accelrys Discovery Studio find out HBond to be > more than chimera. why?which one result is ture? > (2)what is meaning about Clashes/Contacts?what is useful for Finding > Clashes/Contacts > (3)how can i find out interaction between ligand and receptor and > classify displaying. > (4)can i use this software to publicate my paper ,directly? > best wishes for you ! (1) FindHBond vs. other programs. Different programs use different methods and cutoffs, and there is no reason to expect exactly the same results. The world of science does not agree on one exact definition of H-bond. Each program should explain its own method, as we have in the FindHBond documentation. Click "Help" on the FindHBond dialog or go here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon… > Also, this same question was discussed 2 days ago on the chimera-users list, see: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004746.html > (2) What are clashes and contacts? This is explained in the Find Clashes/Contacts documentation. Click "Help" on the Find Clashes/Contacts dialog or go here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas… > (3) use FindHBond and Find Clashes/Contacts. The "Structure Analysis and Comparison" tutorial is one example of using these tools: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> (4) yes, you can use images and calculation results from Chimera in your paper, but please remember to credit Chimera as described here: <http://www.cgl.ucsf.edu/chimera/docs/credits.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

H Bonds in MD simulation
by snoze pa 29 Jan '10

29 Jan '10

Dear Chimera Users, I am analyzing a MD trajectory in chimera. After selecting H binds when I am playing the trajectory, then it always shows the hydrogen bond. Though some of the bonds are broken during the simulation but it always connect the step 1 h bonds connected.. How can I show the h bonds which breaks during the simulation. Thank you very much for your help. S

3 11

Re: [Chimera-users] Rename atoms...and chains, residue numbers
by Jonathan Sheehan 28 Jan '10

28 Jan '10

On Mon, Jan 25, 2010 at 4:25 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > This is actually a little trickier than it really should be in the current > builds. As of tomorrow's daily build the following will work without any > issues to set the name of selected atoms to 'X1': > from chimera import runCommand > runCommand("setattr a name X1 sel") > --or-- > from chimera import selection > for a in selection.currentAtoms(): > a.name = "X1" Hi- Following up on this, I'd like to offer a feature request regarding structure editing. Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection. I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode. :-) Would this be difficult to implement? Thanks for considering it, -Jonathan -- Jonathan Sheehan, Ph.D. Comput. Biol. Educ. and Outreach Vanderbilt Univ. Ctr. for Struct. Biol. 5138 MRB3, 465 21st Avenue S. Nashville, TN 37232-8755

3 3

Re: [Chimera-users] Chimera-users Digest, Vol 81, Issue 21 - chopped ccp4 maps in chimera
by Boaz Shaanan 28 Jan '10

28 Jan '10

Hi, The possible reason for the chopped ccp4 maps when they are displayed in Chimera (whereas they're fine Coot) may have to do with the fact that as far as I know Chimera does not apply the crystallographic symmetry operations to the ccp4 map (at least that's how it used to be in v1.3), whereas Coot does. So if the map is defined for the asymmetric unit only, it has to be expanded in order to cover all the region which one wants to display before being read into Chimera. There could of course be other reasons for the chopped maps. Cheers, Boaz ----- Original Message ----- From: chimera-users-request(a)cgl.ucsf.edu Date: Thursday, January 28, 2010 21:11 Subject: Chimera-users Digest, Vol 81, Issue 21 To: chimera-users(a)cgl.ucsf.edu > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Chimera movie question (Tom Goddard) > 2. Contouring ED Map: Sigma versus Chimera > thresholds (Veer Bhatt) > 3. Re: Contouring ED Map: Sigma versus Chimera thresholds > (Elaine Meng) > 4. Contouring ED Maps (Hector Viadiu) > 5. Re: Contouring ED Maps (Tom Goddard) > 6. H Bonds in MD simulation (snoze pa) > 7. Re: H Bonds in MD simulation (Elaine Meng) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Wed, 27 Jan 2010 12:51:19 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > To: Bridget Carragher <bcarr(a)scripps.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Chimera movie question > Message-ID: <4B60A747.5030705(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Bridget, > > I put an example animation on the Chimera web site in the > animation > gallery called "Herpes virus slices". There is also a link > to a command > script which makes this movie. You just use File/Open... > in Chimera to > run the command script. > > > http://www.cgl.ucsf.edu/chimera/animations/animations.html > Tom > > > > > > OK, thanks Tom. Any tips on how to do all three planes > at once - or > > > rather keep the others constant while eating though the side > plane. I > > > have sen movies like this but can;t seem to figure out how > to do it in > > > Chimera. > > > Bridget > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 27 Jan 2010 19:12:31 -0500 > From: Veer Bhatt <veer82(a)gmail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Contouring ED Map: Sigma versus Chimera > thresholds > Message-ID: <C41C6E8E-343B-4FA1-BB71-49BAADB32DF2(a)gmail.com> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > Hi, > This in context of using Chimera to view *ccp4 format > electron > density maps. How does Chimera 'Threshold Level' ('Level' in > Volume > viewer) equate or relate to sigma level reported by some > other > programs. For example a 'Level' of 0.4 seems like a map > contoured at > 1.5 sigma or so. > I was wondering if someone could point out how these two are > related, > more precisely. > > Thanks > > Veer Sandeep Bhatt > >

2 1

Contouring ED Map: Sigma versus Chimera thresholds
by Veer Bhatt 27 Jan '10

27 Jan '10

Hi, This in context of using Chimera to view *ccp4 format electron density maps. How does Chimera 'Threshold Level' ('Level' in Volume viewer) equate or relate to sigma level reported by some other programs. For example a 'Level' of 0.4 seems like a map contoured at 1.5 sigma or so. I was wondering if someone could point out how these two are related, more precisely. Thanks Veer Sandeep Bhatt

4 3

lighting in Chimera
by Dan Gurnon 27 Jan '10

27 Jan '10

I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

5 6

running command scripts
by Michael Zimmermann 27 Jan '10

27 Jan '10

Dear Chimera users, I am getting to know Chimera a bit more and was just going through the scripting tutorial here: http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Scr… For the command line script 1gfl.com, the tutorial just says "run it" but does not say how. I just typed "run 1gfl.com" in the chimera command line, but I get a syntax error in the script. I can't seem to copy the error text, so a screenshot is attached. Is this an issue with the script or how I am running it? I use chimera v. 1.4 on win XP - 64bit. Thank you, Mike Z

3 2

Rename atoms...
by Yasser Almeida Hernández 25 Jan '10

25 Jan '10

Hi.. How can i rename atoms? How would be the script python syntax? Thanks Best regards -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI

2 1

Fitting a structure to a DAMMIN/SAXS model/volume
by Byrd, Robert A. (NIH/NCI) [E] 25 Jan '10

25 Jan '10

Chimera Team & users, We have been using SAXS data and the DAMMIN software from the Svergun group. The bead model that DAMMIN produces approximates the shape and volume of the molecule. If one has a three dimensional structure of the molecule, then it becomes valuable to do a best superposition of the structure into the bead-model shape. Chimera is our preferred molecular display & analysis software, and we would like to perform this fitting in Chimera. Do you have any experience in how to display the bead-model output of DAMMIN and to fit or superimpose the bead model with a known structure? Thanks Andy Byrd

2 1

Re: [Chimera-users] Failed surface calculation
by Elaine Meng 25 Jan '10

25 Jan '10

Hi Ibrahim, First, make sure you set the New Surfaces preference value before showing the surface for the first time -- it would not affect a surface that already exists (even if it is hidden when you set the preference). If the surface already exists, you could change it to single-component by changing its attributes, such as with the command given in my previous message. However, if the Reply Log says there is only one component of the surface in both sets of parameters, I think it is still possible for a surface area to decrease when the VDW radii increase. I'm imagining a case where there is a lot of concavity. Similar to the situation of an inside bubble shrinking or disappearing, a concave part of the surface could become shallower or much less extensive as the VDW radii are increased. This is just a case I'm imagining. If you feel there is an error, please use "Help... Report a Bug" in the Chimera menu and be sure to describe exactly what you did to get the two area measurements, what two values you are comparing, and attach the PDB file of the structure (or just include the PDB ID in your description if it is taken directly from the Protein Databank). Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Failed surface calculation
by Ibrahim Moustafa 23 Jan '10

23 Jan '10

Dear Chimera, I¹m trying to calculate the surface for a protein but I get an error ²Surface calculation failed, mscalc returned code 5². I tried to change the probe size from 1.4 to 1.5 or 1.7 but still getting the same error. I know there is some issue with The code that calculates the surface (if I¹m not wrong) but I wonder if there is a way to get around this. For some smaller pdb files I don¹t have this problem. I¹m not sure if the size of the protein is a factor here. The protein having the problem is a single chain protein with 880 amino acids. Any advice? Thanks for help. Ibrahim

2 4

Compatibility of Chimera with MacOS 10.4.11. PPC
by Arwid.Bierbach 22 Jan '10

22 Jan '10

Ldies and Gentlemen, The Chimera version Mac OS X (Aqua, PowerPC) chimera-alpha-osx_ppc_aqua.dmg Size: 73241868 bytes MD5: 39623fa9e0d9f4a869a4c985d45223bb Jan 22, 2010 is not compatible with G4 PPC Mac OS 10.4.11. Do you plan to quit the G4 PPC OS 10.4.11. - Compatibility ???? With best regards, Dr. Arwid Biebach, Germany

2 1

Massive superposing...
by Yasser Almeida Hernández 22 Jan '10

22 Jan '10

Hi... I'm performing a massive superposing of aminoacids in different conformations. The first model is a arginine "template" reference structure that is the fixed model in all matching iterations. I've loaded 236 models and i want to match the arginine guanidine group on the template guanidine. In each iteration i execute two matching, with different atoms selections. The first selection is the "right" selection: CD,NE,CZ,NH1,NH2 and the second is the "inverse" selection: CD,NE,CZ,NH2,NH1. I run the two superpositions, and i want to show that with the minimal RMSD between the guanidine groups. This is the code: import chimera from chimera import runCommand right = "@CD,NE,CZ,NH1,NH2" inverse = "@CD,NE,CZ,NH2,NH1" for i in range(2,328): print "Superposing..." runCommand("match #"+str(i)+right+" #0"+right+"; close 1") right_rmsd = runCommand("rmsd #"+str(i)+right+" #0"+right+"; close 1") runCommand("match #"+str(i)+right+" #0"+right+"; close 1") inverse = runCommand("rmsd #"+str(i)+inverse+" #0"+right+"; close 1") if right < inverse: print "Minimum RMSD =",right,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") elif right > inverse: print "Minimum RMSD =",inverse_rmsd,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") In principle this script should show the matching with the minimum RMSD, but it doesn't work. Please, help... Thanks -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI

2 1

Measuring Distances in Chimera
by Beale, John 21 Jan '10

21 Jan '10

Hello, I am trying to measure distances between atoms using the Tools -> Structure Analysis -> Distances routine. Chimera is requesting that two atoms must be selected in the main graphics window for this to work. I can't figure out how to select the atoms. Can someone help me? John

3 4

Ligand Binding to Homodimeric Proteins
by Nancy 17 Jan '10

17 Jan '10

Hi All, I am performing molecular docking simulations of a ligand binding to a homodimeric protein, to determine a potential binding site(s). Due to the symmetrical nature of a homodimer, I would expect that the binding site(s) on one protomer would be identical on the other protomer. Therefore, a ligand should bind with equal probability and affinity to both sides of the protein. However, when I perform a molecular docking simulation (using an X-Ray crystal structure), the ligand preferentially binds to one side of the homodimer. Is this outcome likely the result of errors inherent in the X-Ray crystal structure, as one would expect identical binding to both sides? Thank you very much. Nancy

2 2

adding hydrogens and charges
by Elaine Meng 17 Jan '10

17 Jan '10

> 1 how can i calculate the charges for molecular. > to calculate the charges both for ligand and receptor > individually. > if i want to do docking,if i must calculate charges. > 2 how can i add hydrogen for HIS. Maybe , no exact position for HIS. > how can i add hydrogen directly? > thank you very much! > Hello, Use the Dock Prep tool (in menu, Tools... Structure Editing... Dock Prep). It can do several things to prepare a structure, including adding hydrogens and charges. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Re: [Chimera-users] [chimera-dev] Calculating RMSD
by Elaine Meng 15 Jan '10

15 Jan '10

Hi Victor, I'll CC the chimera-users(a)cgl.ucsf.edu list -- that address is better for general Chimera "user" questions, while chimera-dev is more for "programmer" questions, i.e. involving python or other code. The "rmsd" command does not automatically use serial number to pair the atoms. You can control the order by specifying the residues and their atoms in the command. Of course, that can be painful if you want to include very many atoms in the calculation. If the order is not given in the command, "the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number" as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> You can see command manual pages using the "help" command, e.g.: help rmsd What approach is best depends on your particular case -- whether these are multi-residue macromolecules or single-residue small molecules, and how many atoms you want to include in the calculation. If they are single-residue small molecules, you might just modify the mol2 files so that the atoms you want to pair have the same names in the two structures (but unique within a structure). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 15, 2010, at 2:11 AM, Victor Muñoz wrote: > Hi, > I want to calculate the RMSD between two mol2 structures in place. > The two structures are different forms of the same structure. I > haver modified the mol2 so that the two of them have the same > serialNumber in their respective atoms. The problem is that when I > use the command rmsd #model1 #model2, it return an incorrect value > of the rmsd, as the value showed is too high, about 5, when it > should be about 1 (the two structures are very similar). Is there > any way to calculate the RMSD value in place correctly or I am > doing anything wrong? > Thanks for your help. >

1 0

Re: [Chimera-users] [chimera-dev] adding an atom at the centroid of a blob
by Jean Didier Pie Marechal 14 Jan '10

14 Jan '10

Thanks a lot Elaine for answering me, I was indeed interested in both user interfase ...as well as the python shell one... best, jd Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dimecres, Gener 13, 2010 11:26 pm Assumpte: Re: [chimera-dev] adding an atom at the centroid of a blob > > On Jan 13, 2010, at 8:01 AM, Jean Didier Pie Marechal wrote: > > > Hi everyone, > > I have obtained cavities for a given atom selection using surfnet > > > and I want to put an atom at the centroid of the main blob. I > know > > how to do this for a selected set of atom but I am struggling > with > > the surfaces. > > > > At this point, I splitted it (accelator Sc) and then I can select > > > the blob I am interested in. But how could I create a particular > > object for this blob? From there, how could I add an atom (i.e. > > helium) and the centroid of the blob? > > Thanks for any help, > > JD > > Hi JD, > > Now that you have your one surface piece selected (and nothing > else), > you could use the command "focus sel" or menu item "Actions.. > Focus" > to center the view on it, then add the atom at the center of view > with the Build Structure tool (under Tools... Structure Editing). > You would go to the "Add Atoms" tab in that tool, choose "atom" and > > click "Add." > > It may not be the centroid of the blob as calculated from its > vertices, but the center of its bounding box. You may want to try > it > and see if the result is sufficient. > > That's the user interface way. Maybe you meant in python -- if so, > > somebody else will have to answer! > > Best, > > Elaine >

1 0

importing colored VRML file into cinema 4d
by odonnell＠chem.fsu.edu 14 Jan '10

14 Jan '10

Hello, I'm curious if anyone has had difficulty importing a colored VRML 3D object into Cinema 4D. I have exported a colored VRML file from chimera but the color is lost when opening it in the 3D graphics program Cinema 4d. Reopening the VRML file in chimera shows the color is there. Thanks in advance for your time. -Odie ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 1

Re: [Chimera-users] [chimera-dev] adding an atom at the centroid of a blob
by Elaine Meng 13 Jan '10

13 Jan '10

On Jan 13, 2010, at 8:01 AM, Jean Didier Pie Marechal wrote: > Hi everyone, > I have obtained cavities for a given atom selection using surfnet > and I want to put an atom at the centroid of the main blob. I know > how to do this for a selected set of atom but I am struggling with > the surfaces. > > At this point, I splitted it (accelator Sc) and then I can select > the blob I am interested in. But how could I create a particular > object for this blob? From there, how could I add an atom (i.e. > helium) and the centroid of the blob? > Thanks for any help, > JD Hi JD, Now that you have your one surface piece selected (and nothing else), you could use the command "focus sel" or menu item "Actions.. Focus" to center the view on it, then add the atom at the center of view with the Build Structure tool (under Tools... Structure Editing). You would go to the "Add Atoms" tab in that tool, choose "atom" and click "Add." It may not be the centroid of the blob as calculated from its vertices, but the center of its bounding box. You may want to try it and see if the result is sufficient. That's the user interface way. Maybe you meant in python -- if so, somebody else will have to answer! Best, Elaine

1 0

Looping with Chimera commands
by Yasser Almeida Hernández 12 Jan '10

12 Jan '10

Hi... It's possible run a Chimera's command iteratively? I have loaded several structures (more than 300) and i want to superimposed them to a reference structure. How i perform the matching command for every structure iteratively? Thanks -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

3 2

movie
by Alex Perálvarez Marín 12 Jan '10

12 Jan '10

Hi, I have the output files for an MD movie from Gromacs, an xtc and a tpr file. When trying to build the movie, Chimera ask for a tpr and trr files for the Gromacs input. I try anyway with my files but naturally Chimera crashes. Any help for this? Thank you in advance. Alex.

4 3

problem to download chimera
by Gabriele Gucciardo 12 Jan '10

12 Jan '10

Dear Chimera developers, I have some problem to download Chimera. I'm trying to download the Chimera software. Once I clicked on the "download link" in the home web page of chimera, a new blank page was opened but nothing happened. I'm currently using Mac os X 10.4.11. I used browser safari 4.0.4 and Firefox 3.5.7, both gave same results. Kind regards, Gabriele Gucciardo School of Chemistry & Chemical Biology College of Life Sciences UCD, Belfield, Dublin 4 Ireland 00353 1 7162972 gabriele.gucciardo(a)ucd.ie

2 2

showing conservation
by Elaine Meng 07 Jan '10

07 Jan '10

On Jan 7, 2010, at 6:30 PM, gytjyb wrote: > hello, > 1 how can i use this software to do molecular dynasty? > 2 can you tell me how to asure conservation sequence through > protein alignment. > maybe this is just for basic knowledge,but i am a freshman. > Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of just to me. (1) maybe you mean molecular dynamics - sorry, Chimera does not do molecular dynamics. (2) I recommend going through some of the Chimera tutorials. There are some beginner tutorials and others that include showing conservation and aligning protein structures. You can see the tutorials by choosing "Help... Tutorials" from the Chimera menu, or by going to our web site: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html> Also, I have my own page on where you can get sequence alignments for viewing in Chimera: <http://www.cgl.ucsf.edu/home/meng/sources.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Permission to use image in educational textbook
by Carolyn Arcabascio 07 Jan '10

07 Jan '10

To Whom It May Concern: I am writing to you from the Photo Research department of Jones and Bartlett Publishers. I am currently working on the second edition of an educational textbook by Dr. Lynne Cassimeris and colleagues titled, "Lewin's Cells." The authors of this project have requested to use the image shown here: http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/actin/actin.html A hi-res version of the image has been downloaded from the website. I'd like to inquire how best to proceed with obtaining permission to use this figure. WE do have our own standard permission letter, and if this would be acceptable, I'd be happy to follow up and address the letter to the appropriate contact. Thank you very much for your time. I look forward to hearing from you. Kind regards, Carolyn -- Carolyn Arcabascio Assistant Photo Researcher Jones and Bartlett Publishers LLC 40 Tall Pine Drive Sudbury, MA 01776 Phone: 978-579-8284 Fax: 978-579-8331 www.jbpub.com

2 1