- Chimera-users - RBVI Mailing Lists

MatchMaker and Find Clash in nogui mode
by Ryan 11 Aug '08

11 Aug '08

Hi. I read in the archive (2004) that someone was looking to use MatchMaker in the nogui mode / command line, but that was not a possibility at the time. I am wondering if this ability has ever been implemented, and if so, how does one go about scripting this. Additionally, i would like to use the 'Find Clashes/Contacts' function in nogui mode. Is this possible? Thanks a lot, ryan

2 1

protonating the protein
by Elaine Meng 11 Aug '08

11 Aug '08

Hi Francesco, > However, if you are using charges assigned in Chimera for something > (Dock Prep with AddH, Add Charge, and write Mol2 for input to DOCK > scoring grid calculations, for example), you would need to add the > protons in Chimera before assigning charges. This could be done by > selecting the carboxylate oxygens you want to get protonated (no more > than one per carboxylate group, of course) and changing their atom > types with the command: > setattr a idatmType O3 sel > prior to running AddH and Add Charge (alone or as steps in Dock > Prep). It is not necessary to rename the residues. Add Charge will > then recognize the neutral forms of ASP and GLU and use the > corresponding partial charges. I just tested this in the Chimera > production release, 1.2540 (July 9). The above is definitely true, you do not need to rename the residues in Chimera, but further tests reveal to get the correct charge distribution on the protonated carboxylic acid, the atom names also need to match the AMBER lib files: the protonated oxygen should be named OE2 (if glutamic acid) or OD2 (if aspartic acid) and the "free" oxygen should be named OE1/OD1. This will already be true sometimes, but not always. If you need to switch the atom names around before adding charges, it can be done by text-editing the PDB file or with commands. For example, you could change the name of an atom by selecting it and then using a command like: setattr a name OE2 sel After assigning charges, you can see the values as labels, for example: labelopt info charge la :6.a Again all this was tested in the production release 1.2540. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Volume planes tool
by Elaine Meng 08 Aug '08

08 Aug '08

Hi Jeff, Here is another idea, still not exactly what you were asking for, but perhaps worth a look. You can use the Per-Model Clipping tool (under Tools... Depiction) to show a thin slab of the data, and you can interactively rotate and translate the slab any way you want relative to the data with the mouse. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ per-model.html Just choose which model to clip, enable clipping, turn on slab mode and adjust clipping with mouse. You may also want to adjust the contour level in Volume Viewer. I tried it on emd_1274.map in the production release (1.2540). You can use it on solid, surface, or mesh volume displays. Below I attach an image of a slab surface display together with an unclipped solid display (a second copy of the same data). There is also a command to control per-model clipping in a script, mclip. It lets you specify location/orientation in the data coordinate system or the viewing coordinate system. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html Best, 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

1 0

Chimera: doubt on axes measurement
by Giovanni Cardone 08 Aug '08

08 Aug '08

Hi everybody, I have a doubt about my proper using the tool Axes for measuring angle between helices. After aligning two model and generating the axes corresponding to the helices of interest, I select them in the 'Structure Measurements' dialog windows. As you can see from a snapshot, they look properly selected. They are almost overlapping, but in the Reply Log I get the following info: col_best_001.pdb helix 10/col_best_005.pdb helix 2 crossing angle: 36.9 degrees, distance: 15.3 angstroms Beside the value of the angle seeming to me too high, shouldn't the distance between the helices be within few angs (at least according to how I interpret the documentation)? Probably I am missing something. Thanks in advance, Giovanni Cardone

2 1

Protonating the protein
by Francesco Pietra 07 Aug '08

07 Aug '08

Hi: I am not saying anything new. I have a (for me) difficult problem of protonating a protein homology model (built with Modeller) where there are several halogen ion ligands. Actually I succeeded in getting a workable model. Chimera loads it and add hydrogens. I could even prepare the model for DOCK6, generating spheres. Now, however (and also because, before docking small ligands with DOCK6, I want to dock polypeptides, probably with DOT2) I would like to assign specific protonation states to certain carboxylic acids. That is, I want to create an overall model where certain facing carboxylic acids actually face as "carboxylate-carboxylic acid" or as "carboxylic acid-carboxylic acid", or, finally, as "carboxylate-carboxylate", the latter also with metal ligand in between or not. Question: to which extent can Chimera aid the task? And which other package (pdb2qr, H++, ...) may aid Chimera? Or no other package, but simply renaming the said residues in the pdb file and let Amber 10 (which is the package I'll use for MD, with ff99B ff for the protein) do the job of eliminating clashes? All that shows that I have no experience in selective protonation, and the halide ions (in the above said work, I have them simply under "ATOM" under the specific chain of the amino acid residues, not "HETATM", as the latter caused a lot or problems) create difficulty to protonating packages. Thanks for giving me a general guideline along with best moving. francesco pietra

2 1

Chimera 1.2540 installer options and unattended installation
by Frank Thommen 07 Aug '08

07 Aug '08

Hi chimera-users, the Chimera installer seems to know some options and modifiers, but I could not find out what they mean: # ./chimera-1.2540-linux.exe -help UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Valid options are -tfupcz and -d <exdir>; modifiers are -abjnoqCLMVX. # Does anybody know what these options and modifiers do or where I can read about them? My motivation is, that I'd like to install Chimera in a non-interactive way (batchscript) in a non-standard location. Is there a way to achieve that? Thanks in advance frank -- Frank Thommen - Structures IT Management and Support - EMBL Heidelberg structures-support(a)embl-heidelberg.de - +49 6221 387 8353

4 4

ConSurf display in Chimera
by Elaine Meng 06 Aug '08

06 Aug '08

Hello everybody, The ConSurf Server <http://consurf.tau.ac.il/> now provides results as Chimera Web data: a single click displays the color-coded query structure and multiple sequence alignment in your locally installed copy of Chimera. For a screenshot and example Web data file, see: http://www.cgl.ucsf.edu/chimera/consurf/consurf.html More about Chimera Web data: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… Special thanks to Elana Erez and the Ben-Tal and Pupko groups at Tel Aviv University, and to Fabian Glaser. Enjoy! Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Re: [Chimera-users] mouse selection problem
by Eric Pettersen 06 Aug '08

06 Aug '08

Meikel Diepholz wrote: > Hi, > just a small problem I hope. > When I am selecting residues with ctrl +left mouse > button, chimera is always replacing the earlier selection, > independent on the selection mode I chose (append, subtract). > > Is it possible to change this? Hi Meikel, This behavior isn't a bug per se, but rather a deliberate design decision. We decided to not have the mouse selection honor the selection mode since it is possible to emulate all the selection modes directly with the mouse (except for intersect). If you hold down the Shift key as you are making a mouse selection then everything chosen with the mouse will have it's selection state toggled (selected items become unselected and vice versa), and other items will not have their selection state changed. So you can "subtract" by shift-control clicking/dragging on selected items, and you can "append" by shift- control clicking/dragging on unselected items. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Text statistics from Matchmaker
by nettles 04 Aug '08

04 Aug '08

I have found MatchMaker in Chimera an incredibly useful alignment tool. Thank you to the UCSF team! Now, I want to do do a mutliple alignment of many structures (~100) off a single reference structure, and output a text record of the residue pairings involved in the individual alignments along with their RMSD. In this particular case, I'll be looking at only small sequence variations of the same protein (with different drugs and cofactors). Accordingly, I would also like to output the RMSD of residue pairs beyond the alignment cut for relatively easy identification of regions having maximal variations. Advise is appreciated, With regard, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine ________________________________________________________

2 1

copy cmd in nogui script
by James A. Cleland 01 Aug '08

01 Aug '08

I was wondering if anyone was able to run chimera 'headless' using -nogui. I would like to be able to run the program from a script and without an X server, or against Xvfb or equivalent if necessary. My command line is /var/lib/chimera/bin/chimera --nogui --silent --script <scriptname> The script that I run sets the window size, element colors, rotates the image, and then does a copy file to save a ray traced PNG file. I have run this without -nogui and accepted the POV Ray license agreement. Adding -nogui results in the following output Error while processing <scriptname>: AttributeError: '_chimera.NoGuiViewer' object has no attribute 'x3dWrite' (see reply log for Python traceback info) Parse error at line 1: no element found My chimera version is "chimera production version 1 build 2540 2008/07/09". This is running on a linux machine, 2.6 kernel. Any suggestions you have would be appreciated. Thanks! James

3 3

problem with the volume display in version 1.2540
by Magali Cottevieille 01 Aug '08

01 Aug '08

Hi, I have just installed version 1.2540 of Chimera (I had before version 1.2470). There is a problem with MRC and SPIDER EM volumes: see attached image: left a volume in the new Chimera; right the same volume with the old Chimera. Is it a bug, or linked to my configuration?? Thanks in advance, -- Magali Cottevieille, Ph.D. Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, 630 W 168th St, P&S Black Building 2-221 New York, NY 10032 Ph: (+1) 212-305-9521 Fax: (+1) 212-305-9500 Email: mc3077(a)columbia.edu magali.cottevieille(a)gmail.com

2 1

import GRID contour map
by Sebastian Kruggel 01 Aug '08

01 Aug '08

Hi All, I try to import a contour map generated with GRID and saved as *.grd or *.cnt file. Trying to open th e*.grd file in chimera I get the error message Opening I:\strukturen\prep_modTemp\1j1b_DRY.grd I:\strukturen\prep_modTemp\1j1b_DRY.grd: UHBD file does not contain integer value 1 at bytes 96-99 using either little or big endian byte order. Found 46146 Done opening I:\strukturen\prep_modTemp\1j1b_DRY.grd With *.cnt I get file not found, because file is supposed to be a *.bmp. Does anybody have an idea, how to open my nice GRID contour map? Greetings Sebastian -- Sebastian Kruggel Institut für Pharmazie Raum 112 Bundesstr.45 D 20146 Hamburg Tel. +49(0)40 42838 3626 Hi All, I try to import a contour map generated with GRID and saved as *.grd or *.cnt file. Trying to open th e*.grd file in chimera I get the error message Opening I:\strukturen\prep_modTemp\1j1b_DRY.grd I:\strukturen\prep_modTemp\1j1b_DRY.grd: UHBD file does not contain integer value 1 at bytes 96-99 using either little or big endian byte order. Found 46146 Done opening I:\strukturen\prep_modTemp\1j1b_DRY.grd With *.cnt I get ‘file not found’, because file is supposed to be a *.bmp. Does anybody have an idea, how to open my nice GRID contour map? Greetings Sebastian -- Sebastian Kruggel Institut für Pharmaz ie Raum 112 Bundesstr.45 D 20146 Hamburg Tel. +49(0)40 42838 3626

3 2

Re: [Chimera-users] question posted in chimera mailing list
by Elaine Meng 01 Aug '08

01 Aug '08

Hi Sebastian, Chimera does not read maps from GRID. Here are the map formats that Chimera knows about: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume Because you used filename extensions we assigned to other formats as shown in that table, Chimera tried to read the file as those formats (which it is not, hence the errors). Also, I do not know what is happening with your chimera-users subscription - maybe try to sign up again? http://www.cgl.ucsf.edu/ mailman/listinfo/chimera-users/index.html Best, 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 On Aug 1, 2008, at 12:54 AM, Sebastian Kruggel wrote: > Dear Elaine, > > I posted a message in the mailing list – and got the answer I > wasn’t member, though I am?! > So I just send it once more, directly to you, because you answered * > very > * helpful last time ;-) > > Message was: > Hi All, > > I try to import a contour map generated with GRID and saved as > *.grd or *.cnt file. > Trying to open th e*.grd file in chimera I get the error message > > Opening I:\strukturen\prep_modTemp\1j1b_DRY.grd > I:\strukturen\prep_modTemp\1j1b_DRY.grd: UHBD file does not contain > integer value 1 at bytes 96-99 > using either little or big endian byte order. Found 46146 > Done opening I:\strukturen\prep_modTemp\1j1b_DRY.grd > > With *.cnt I get ‘file not found’, because file is > supposed to be a *.bmp. > > Does anybody have an idea, how to open my nice GRID contour map? > Greetings > Sebastian > > Thanks in advance > Sebastian > > > > -- > > Sebastian Kruggel > Institut für Pharmazie > Raum 112 > Bundesstr.45 > D 20146 Hamburg > Tel. +49(0)40 42838 3626 >

1 0

Re: [Chimera-users] suggestion for superimposig
by Elaine Meng 01 Aug '08

01 Aug '08

On Aug 1, 2008, at 7:35 AM, Srinath Thiruneelakantan wrote: > Hi, > I am microbiologist and wanted to know the strucutre of a protein > of M. tuberculosis, whose crystal structure has not been solved, > but its homologue in Bacillus has been. So by Swiss-modeller > generated a MODEL and downloaded it in PDB format. Now I wanted to > superimpose the generated model with of bacillus and with PDB of > truncated protein of E. coli. As I am not of bioinformatic > bakground, please suggest me how to get the FINAL output in PDB > format so can have a comarison of domains between these three > proteins. > Thank you, > Srinath Hi Srinath, Just open all of the PDB files in Chimera (for example, with File... Open). You can change the display if you want, for example with Presets... Interactive 1 (ribbons). Then you can use the MatchMaker tool (under Tools... Structure Comparison) to superimpose the proteins. Choose the "reference" structure on the left and one or more structures to match onto it on the right. It usually does not matter which one you use as the "reference" - try using the first one listed. In most cases, the default settings work well, so it is very easy: turn off "Show alignment(s)..." if you don't want to see the sequence alignments, but otherwise just click "Apply" to match the structures. It will take a few seconds to compute the alignments and then match the structures. Then you can compare the structures in Chimera, or write out PDB as mentioned below. If that does not give a good enough superposition, then you can try changing parameters. For details see the MatchMaker manual page (simply clicking "Help" on the dialog will open your local copy): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html These tutorials have examples of superimposing and comparing structures: "Superpositions and Alignments" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ alignments.html "Structure Analysis and Comparison" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html Additional discussions about superimposing structures: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html#superimposing http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ images.html#matching After the proteins are superimposed, you can write out the structures as one or more PDB files with "File... Save PDB" in the Chimera menu. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb 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

1 0

Distance Lines
by hsosa＠aecom.yu.edu 31 Jul '08

31 Jul '08

Hi , I want to make a solid line (with chosen color) between two atoms. Kind of like the line that appears when measuring distances between atoms, but without the distance legend. Is there an easy way to do that ? Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

2 1

PDB morphing
by Dougherty, Matthew T. 28 Jul '08

28 Jul '08

I have a complex structure in two conformations: resting and active. Each structure consists of 24 monomers, corresponding to 24 pdb files. Each monomer file between conformations matches in terms of atom numbers, chain ID, etc. I can morph a single monomer between conformations. I am having no success morphing all the monomers simultaneously between the conformations. Any suggestions on how to organize my data to overcome this? thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

2 3

Distance between helices
by Thomas Goddard 28 Jul '08

28 Jul '08

HI Tom How do I compute and show the distance between 2 regions (2 alpha helixes) of 2 crystal structures (docked in the density maps), similar portions of each is already highlighted/selected to show the DNA binding region (without showing the atoms). THanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

3 3

Re: [Chimera-users] BIOMT matrix in Chimera?
by Elaine Meng 28 Jul '08

28 Jul '08

On Jul 27, 2008, at 10:38 AM, Francesco Pietra wrote: > > Hi Elaine: > After a brief playing with Multiscale Models, I was considering your > last suggestion below. I modeled each chain separately, also because > the X-ray diffr data show some conformational differences. Modeling > gave very good DOPE score. Now the problem is appending Chain B to > chain A, etc (each chain opens correctly in Chimera). I have a Python > script (not tried yet) to insert the Chain identifier (which Modeller > did not print), update the Atom serial number, and then append the > files. May I ask, in view of Chimera, if the "Atom number + 1" printed > in Modeller pdb files at column 80 can be left at it is, i.e. not > updated on appending the files? I forgot about that and I have already > problems enough with the script at my minimal level with Python. I > assumed that Python identifies the columns one unity less than PDB > numbering. Finally, do you know what means "1SG" at columns 74-76 of > Modeller pdb files? Hi Francesco, I don't know what MODELLER puts in those columns after "B- factor" (61-66, which may actually contain the "modeller error profile," since a homology model doesn't really have B-factors). Maybe you could ask the modeller people. However, for Chimera purposes they could be omitted (changed to blank). According to the description of ATOM lines: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html 67-76 is supposed to be blank, 77-78 element symbol, 79-80 charge. I believe Chimera tolerates lines without the last few columns, as long as the X,Y,Z coords are still there. If your files have stuff in the later columns, it might still be OK, just try opening them in Chimera to see. My suggestion of modeling the multimer from a template multimer would still incorporate the chain differences - you would still use A as the template for A, B for B, etc. However, I don't know how to make modeller do that. > Following the "appending" plan below, is it correct to > append pdb files lacking all hydrogens (as provided by Modeller) and > then rely on Amber's LEAP to complete the multimer? > francesco I don't know what you mean by "complete the multimer" - if just adding hydrogens, you can do that with AddH in Chimera (or addh command). That does not use leap/amber. Best, Elaine

2 1

How to print molecular structures?
by �� 28 Jul '08

28 Jul '08

Hi all, I want to print 1000 molecular structures one by one. I am wondering if it is possible to print molecular structures by Chimera. If it is not, are there some other software can do this? Please kindly advice. Any answer would be appreciated! Best regards, Yolanda Guo Northeast Normal University

2 1

Pointers to writing extensions in chimera
by Mario J. Borgnia 26 Jul '08

26 Jul '08

Hi all, I would like to try and write an extension to chimera. Could anyone give me some pointers on where to find the tools necessary to do so. Thanks Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

3 2

BIOMT matrix in Chimera?
by Francesco Pietra 25 Jul '08

25 Jul '08

>From a homotrimer pdb template I have created (with Modeler) a homology model, with very good score, using a single subunit. Is it possible with Chimera to create the homology homotrimer, as this is what I need? To this concern, the original pdb for the template includes the BIOMT transformation matrix for both crystallographic and non-crystallographic operation. That is, the pdb includes as many identical chains to open directly the homotrimer for the crystallographic pose. Is that BIOMT matrix usable by Chimera for the homology model? Or the way ti take is another one? I used much technical language, well above - however - my expertise in these affairs. That in view of any help, for which I'll be most grateful. Thanks francesco pietra

2 1

nogui vrml export?
by Paul 25 Jul '08

25 Jul '08

Hello, Is there any way to export .vrml or .wrl in the nogui mode? The idea would be to run a script that would load a .pdb file and transform it into a few different representations and then export them. I saw in previous posts that there is no support for exporting images in this mode. Thanks, Paul

2 1

superimposing active sites
by Elaine Meng 24 Jul '08

24 Jul '08

On Jul 23, 2008, at 6:18 PM, Maria wrote: > Elaine, > I have created active sites by using the zone in > chimera for 72 proteins. Is there a way I can > do structural superimposition of the active > sites using chimera? > Thanks, > Maria Hi Maria, Sure, there are many, many ways to superimpose structures in Chimera. If the structures are homologous (have the same fold, usually also some sequence similarity), probably the easiest are these two methods: (A) MatchMaker tool (or the "matchmaker" command, which acts exactly the same way) - it creates a sequence alignment and then uses those alignment columns to superimpose the structures (B) if you already have a sequence alignment, you can open that in Chimera and use it to superimpose the structures With both (A) and (B) you would use the whole structures - it is OK if you are only displaying a zone as long as the other atoms are still there (are merely hidden, not deleted). Some other approaches can be used for either homologous or nonhomologous proteins: (C) "match" command - you specifically name the atoms you want to use for fitting in the command; for example, atoms from a few active site residues and/or from the ligand (D) interactive fitting "by hand" Links to more detailed information... Discussion and examples of more than one method: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#s… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#com… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#match… MatchMaker man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma… "matchmaker" command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html "match" command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Using a pre-existing sequence alignment: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/fr… (see "Structural Superposition" section) Best, 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

1 0

making MD movie
by bala 24 Jul '08

24 Jul '08

Hello freinds, While recording a MD movie or saving an image, chimera considers full screen ares. Is there any way that i can select a particular area in the screen and ouput the image or the MD movie accordingly. Thanks, Bala

2 1

Movie recording does not stop
by Tom Goddard 23 Jul '08

23 Jul '08

Hi Jean-Paul, The script you sent works for me with Mac X11 Chimera 1.2540 on Mac OS 10.4.11. I open two maps and the resulting movie is correct. You don't have any motion going on like a "roll" do you? Because the first line of this script "wait" with no frame count means that subsequent lines of the script will not be executed until all motion ceases. Likewise you have wait command with no frame count on the first two transparency setting lines. Tom Jean-Paul Armache wrote: > Thank you for the reply. It seems that I have today a lot of questions. > There is one more: > I have a script. When not in movie recording mode, it works fine. > However, if I input movie record and at the end movie stop and encode, > then at some point the script stops. Once it stopped with the labels, > so at the end I removed the labels. Now I have one map visible and I want > it to slowly get transparent to a point when it is no longer visible. > And here lies the problem. The script is fairly easy: > > wait; > movie record directory /Users/jean-paularmache/tmp-chimera; > > volume #1 transparency 0.0; wait; > volume #0 transparency 0.0; wait; > > > volume #0 transparency 0.05; wait 3; > volume #0 transparency 0.1; wait 3; > volume #0 transparency 0.15; wait 3; > volume #0 transparency 0.2; wait 3; > volume #0 transparency 0.25; wait 3; > volume #0 transparency 0.3; wait 3; > volume #0 transparency 0.35; wait 3; > volume #0 transparency 0.4; wait 3; > volume #0 transparency 0.45; wait 3; > volume #0 transparency 0.5; wait 3; > volume #0 transparency 0.55; wait 3; > volume #0 transparency 0.6; wait 3; > volume #0 transparency 0.65; wait 3; > volume #0 transparency 0.7; wait 3; > volume #0 transparency 0.75; wait 3; > volume #0 transparency 0.8; wait 3; > volume #0 transparency 0.85; wait 3; > volume #0 transparency 0.9; wait 3; > volume #0 transparency 0.95; wait 3; > volume #0 transparency 1.0; wait 3; > > > #movie finished > movie stop; > movie encode bitrate 12000 mformat avi output > /Users/jean-paularmache/Desktop/firstmovie.avi > > > > Ok, what happens is that Chimera generates endless amount of images. > Really, without cease. Now, if I do "movie stop;" from the command > line, it generates the avi file. However, the whole avi file consists > of one frame movie (meaning that even though it has the right amount of > frames, all are just one frame). > What is more surprising is that with other scripts this transparency > works. It is just right here that it doesn't want to cooperate. Could you > think of any reasons it might be behaving like that? > > > Best regards, > > Jean-Paul Armache

4 6

StrucMeasure and distance
by Jean Didier Pie Marechal 23 Jul '08

23 Jul '08

Dear all, a small question. I know how to calculate the distance between two atoms calling the "distance" command and I generally use it embedded in the scripts I write. However, this time, I'd like to have access through my script only to the values of the distances (nothing related to the display) in order to stock them. I thought I would find my way through by using the StructMeasure module, but I am not able to do so. How could I just have a return of the distances between two atoms in the shell? Thanks a lot, JD Dr. Jean-Didier Maréchal Professor Lector 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: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Agost 8, 2007 9:00 pm Assumpte: Chimera-users Digest, Vol 52, Issue 6 > 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. writing translation/rotation (Thomas C. Marlovits) > 2. Re: writing translation/rotation (Elaine Meng) > 3. Re: writing translation/rotation (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 8 Aug 2007 14:19:43 +0200 > From: "Thomas C. Marlovits" <marlovits(a)imp.univie.ac.at> > Subject: [Chimera-users] writing translation/rotation > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <BAFCFCAA-D911-4E0C-8F5E-B41430E8E1B6(a)imp.univie.ac.at> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > am looking for an analysis tool in Chimera that would write out - > let's say a matrix for translation/rotation of a pdb-file in > respect > to another one. > > Usage: would like to align chain A and chain B present in a pdb- > file > and want to know which translation/rotation matrix has to be > applied > in order to convert the non-aligned pdb-coordinates of chain B to > the 'new" aligned pdb-coordinates. > > Thanx for your help, > -Thomas > > > > -------------------------------------------------------------------- > ---- > ------- > > Thomas C. Marlovits, PhD, M.A.S. > > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences > (IMBA) > > Dr. Bohr-Gasse 3 > Room IMBA/6.02 > A-1030 Vienna > Austria, Europe > > fone: (++43-1) 79044-4630 > fax: (++43-1) 79044-4401 > email: marlovits(a)imp.univie.ac.at > > > >

3 2

Making a spin movie
by Tom Goddard 23 Jul '08

23 Jul '08

Hi Andy, Here is a Chimera command script to make a movie that rotates the displayed models 360 degrees in 3 degree increments (120 frames) and writes the movie in Quicktime format (*.mov). movie record turn y 3 120 wait 120 movie stop movie encode output /tmp/movie.mov mformat mov bitrate 6000 Put this in a file with suffix *.cmd (e.g. spin.cmd) and open it with Chimera File / Open... or the open command to create the movie. Tom Anindito Sen wrote: > Hi Tom > Thanks for the reply. > > in the crystal structure- the region of interest (selected and > highlighted) lies in the interior. The idea is to make a movie of the > crystal structure rotating around the Y axis and one can visualize the > region of interest in a better manner. > > Therefore how can I generate a movie of this kind. > > Thanks > Andy

1 0

Electron density map around selected residues
by Miles Pufall 23 Jul '08

23 Jul '08

Hello - I have a couple of structures depicting a complex where the function of a loop appears to be important, depending on conditions. An overlay of structures solved under these two conditions shows subtle differences, but an examination of omit maps for this loop overlap where the model is built, but show quite different extra density, suggesting different alternate conformations. I am trying to make a figure of this loop with the 2fofc and omit maps overlaid on this loop under the two conditions. The figure, with a model and two electron density maps, can get messy. I would like to show just the electron density surrounding just the loop. Can you recommend a way to do this in chimera? Thanks - Miles Miles Pufall UC San Francisco

3 2

vista chimera 1.2540 R6025-pure virtual function call error when opening pdb or mrc file
by Nils Woetzel 23 Jul '08

23 Jul '08

Hi, I have problems with chimera 1.2540 win32 and 1.2539 win32. it is working in version: 1.2524 win32 I installed it an windows vista business sp1. I have also installed visual studio 2008 (9.0). When I try to open either pdb or an mrc file I get the same error window: Title: Microsoft visual c++ runtime library text: Runtimje Error! Program: C:\Program Files\chimera\bin\pythonw.exe R6025-pure virtual function call. the debug command line option just brings: initializing graphics create application loading Tix loading Pmw creating main window creating menus creating toolbar creating lenses initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: 255 Press return or enter to to exit i try to open the pdb file (different files) before the return code: 255 I am not sure if the error actually comes from python.exe - but i could not find anything when searching for it. http://support.microsoft.com/kb/125749 explains the error, but i am not sure how to debug python code Is there a problem with that version of python or chimera with a visual studio installation or this runtime library error appearing independently of having visual studio installed or not. But the older release is working just fine: 1.2524 win32 so some new feature in chimera probably causes the error and might only show up in my environment?! Thanks Nils Woetzel Vanderbilt University

3 2

surface rendering
by Peter Lewis 22 Jul '08

22 Jul '08

Dear Chimera-Users I've recently changed my computer to a quad core system which runs Red Hat and virtual Windows. I've installed chimera (32 bit) on both linux and windows. I have tried using chimera downloads posted in both June and July this year but cannot get surface rendering to work for either operating system. Is this a bug with recent versions of chimera, and if so, how do I fix it, or is it a bug with my new system? Any help gratefully appreciated. Peter A/Prof Peter Lewis Molecular Microbiology Group School of Environmental and Life Sciences University of Newcastle Callaghan NSW 2308 Australia Ph: +612 4921 5701 Fx: +612 4921 5472

2 1

Movie contains overlapping windows
by Tom Goddard 22 Jul '08

22 Jul '08

Hi Jean-Paul, Yes movie recording will include windows that overlap the Chimera graphics window. This is an unfortunate limitation of the Chimera image saving caused by it capturing images directly from the screen. On some platforms an overlapped window may not appear because the contents of the graphics window are saved even when another window overlaps. But that is not the case on most platforms. So in most cases the machine cannot be used for other purposes when a movie rendering is in progress. We have been interested in eliminating this limitation for some years but Greg Couch who handles image capture has not had time to get to it, If you use raytracing for the movie capture then it does not matter if the Chimera window is covered. But raytracing takes much longer to render. Tom Jean-Paul Armache wrote: > Hello again, > > I re-checked the spider loading, and now it seems to work. I don't > know why it did not previously. > > I have another question though. I have two versions of Chimera on my > computer now. I am using Chimera X Window to generate movies, > because in respect to the Aqua version, if I start another application > (like Keynote, web browser etc), the movie does not contain any parts of > the screen on top of it. > If I use the Aqua version (and on Linux is the same), it includes the > currently on-top graphics into the movie. Is there a way to not do so in > Aqua? > > Best regards, > > Jean-Paul Armache >

1 0

10.5 mac Chimera hangs on resize
by Eric Pettersen 22 Jul '08

22 Jul '08

On Jul 21, 2008, at 4:32 PM, Jean-Paul Armache wrote: > Submitter Name: Jean-Paul Armache > Platform: (X11) Darwin 9.4.0 i386 > Chimera Version: production version 1 build 2540 2008/07/09 > Description > well, the X window tends to hang just after manually resizing the > window. Hi Jean-Paul, I was able to reproduce this and was able to come up with two solutions. One is to resize carefully. In particular, do not release the mouse button until you have stopped the mouse. I find that this always avoids the hang. The other solution is to upgrade your X11.app to the 2.3.0 version (as a prerequisite you need to be at OS X 10.5.4. or later). You can download 2.3.0 from here: http://xquartz.macosforge.org/trac/wiki/X112.3.0 --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Problems saving eps files on Windows
by Julianne Chung 21 Jul '08

21 Jul '08

Hi, I am having trouble saving images in Chimera and was hoping that you may be able to help me out. I am running the latest version of Chimera on Windows. I have a molecule that I want to save as an eps file. I got to File --> Save Image --> Save As -->change the file type to eps and click Save, but no eps file appears in the directory I specified. Jpeg, png and tiff all work fine, but I can't get eps and ps to work. I've installed Ghostscript too, but that doesn't seem to help. Any suggestions are appreciated, Thanks, Julianne Chung Emory University

2 1

Re: [Chimera-users] Possible image saving bug
by Walter Novak 21 Jul '08

21 Jul '08

Hi Elaine, I agree that some colors are shinier than others. Also, my brightness was not zero, but was the default of 1. I think however, I have tracked the issue down to the position of my lights. I had them pretty straight on and resetting this position gives the pov-ray shininess I was expecting. Thank you, Wally On Jul 17, 2008, at 9:29 PM, Elaine Meng wrote: > Hi Wally, > on to problem #2. > > I was unable to reproduce this problem. Are you sure that the > "brightness" is >0? If brightness is zero, there are no > highlights. Below are two images, the top with shininess 128 and > brightness 10, the bottom with shininess 128 and brightness 0. > Actually now that I look at it carefully, the bottom one confuses me > because the cyan things are still shiny, so I'm cc-ing the others > (Greg, any explanation??). The other colors in the bottom image are > non-shiny as expected, however! > > Best, > Elaine > > <imagebright10.png> > > > <imagebright0.png> > > > Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

2 1

<< two questions about Chimera >>
by Hatuey Hack 21 Jul '08

21 Jul '08

Hi all, I have to questions about Chimera: 1st.- Is it possible to search the mailing list to avoid doing questions that were already answered? 2nd.- As I do not know the answer to the first question, I would like to know how I can visualize double and triple bound as well as aromatic rings explicitly within Chimera. Regards, Hatuey

3 2

Morphing aligned maps
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Haixin, The morph map tool just linearly interpolates the two volume 3-d arrays at each grid point. So it does not work correctly if you have moved one map relative to the other since it ignores their relative positioning. To use it in this case you need both maps to use the same grid so you have to "resample" one map. That is you recompute that map on the same grid as the other map using interpolation. The command to do that is "vop", for example, vop #1 resample onGrid #0 modelId #2 Now use morph map between model #0 and the resampled volume #2. Morph map doesn't provide a way to morph between more than 2 maps. That would be useful. You can use it to morph the separate pairs of maps 0 -> 1, then 1 -> 2. You can almost record a movie of this using the following trick. First record 0 -> 1 but when it asks you to save the movie leave that dialog alone (don't cancel since that will erase the saved image frames). Then record 1 -> 2 and then save the movie. Frames from both morphs will be included in the movie. The problem is that each morph plays both forward and backward so you get 0 ->1 -> 0 jumps to 1 -> 2 -> 1. You could avoid the looping with a small modification to the Morph Map code. You would edit chimera/share/MorphMap/gui.py adding a few lines in the next_frame_cb() routine. if next_f >= fmax: next_f = fmax self.step_direction = -1 would become if next_f >= fmax: next_f = fmax self.step_direction = -1 if self.recording: self.finish_recording() Keep indentation as shown since that is important in Chimera. Tom Haixin Sui wrote: > Hi, Tom > > ... > I have a map morphing question. I manually aligned two maps in Chimera > in order to do a map morphing for my presentation. However, the map > morphing does not happen at the aligned positions but shifted the > second map back to the position before the alignment. I wonder how > should I get arroudn this problem. Saving the second maps relatie to > the first and read it in again? > > Meanwhile, I have several maps I want to do map morphing and show > changing in between them. It will be great if chimera can work with > more than one maps and show the changed from map#1 to map#2, and then > #3 ... This feature can be helpful when people want to show several > conformational changes. > > Haixin

1 0

selection of a specific region from different chains
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Andy, Use a command like "select :100-200 to select residues 100 through 200 in all chains. Tom Anindito Sen wrote: > HI Tom > I have a 5 separate chains (of the same crystal structure) docked > along my filament reconstruction. How do I select and highlight a > certain length of amino acids from each and every chain. Problem > happens when I try to select a region of the second or 3rd chain, > which "deselects" the pervious selection. > > Best Andy

2 1

3 volume histograms
by Tom Goddard 18 Jul '08

18 Jul '08

Hi Haixin, Chimera can display any number of volume data sets. But it only shows 3 histograms in the volume dialog, the 3 whose settings were most recently changed. You can use the Data menu on the volume dialog to show the histogram for a different volume (replacing the least recently used of the current 3 histograms). If you want a different maximum number of histograms (like 1 or 5) there is a setting in the volume dialog Data Display Options panel for "Maximum number of histograms". To make this new value the default use the Features menu Save Default Dialog Settings. Tom > >> *From: *Haixin Sui >> *Date: *July 17, 2008 6:12:29 PM PDT >> >> Installed the newest version and found a problem. This version can >> only work with at most three density maps. When you have four or more >> density maps read in, the volume viewer window will only display the >> control for the last three maps. >>

1 0

Distance between atoms using Python
by Tom Goddard 18 Jul '08

18 Jul '08

Hi Ed, Attached is some Python code for controlling ligand display based on distance between two atoms. Tom Edward Brignole wrote: > > Tom, > > Thanks again for your help with that atom display. Got another > MDtrajectory issue for you. I've got a ligand in each of 10 domains > in the structure and I only want to display the ligands in the frames > that have less than a certain distance between a particular atom in > the ligand and a particular atom in a neighboring domain. > > The distance command won't work for me because all it does is add a > distance to the distance dialog when I need it as a variable in the > script to evaluate with "if distance < 10: display atomspecs" > > Sorry to keep bugging you with these things but I assure you it isn't > without trying for several hours to no avail before finally resorting > to asking. > > Ed > def atom_distance(spec1, spec2): from chimera.specifier import evalSpec atom1 = evalSpec(spec1).atoms()[0] atom2 = evalSpec(spec2).atoms()[0] d = atom1.xformCoord().distance(atom2.xformCoord()) return d from chimera import runCommand if atom_distance('#0:15.B@C4', '#0:7.A@N3') >= 10: runCommand('display #0:SPM') else: runCommand('~display #0:SPM')

1 0

center of mass for multiple models.
by Jean Didier Pie Marechal 18 Jul '08

18 Jul '08

Hi everyone, I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem. In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently. import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point #Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i) #Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i] The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064 Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem? Thanks a lot for any answer, All the best JD Dr. Jean-Didier Maréchal Professor Lector 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: chimera-users-request(a)cgl.ucsf.edu Data: Dijous, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17 > 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: Possible image saving bug (Greg Couch) > 2. Possible image saving bug (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Possible image saving bug > To: Walter Novak <wnovak(a)brandeis.edu> > Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.OSF.4.63.0807171001010.1939086(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Thu, 17 Jul 2008, Walter Novak wrote: > > > Hi All, > > > > I submitted a bug report on this, but the behavior is both odd > and > > reproducible for me. Using the latest production release and > trying to save > > an image using supersampling, the image is not stitched back > together > > appropriately. It is odd, because it always happens for a certain > session > > file I have. It doesn't seem to happen if I open a new molecule > and make a > > picture. I can provide the session file if needed. First image is > using 3x3 > > and second is 6x6. > > I see from the bug report that you're using Mac OS X 10.5. We are > having > "issues" with the new X11 application in 10.5. And we have seen > that > slightly different X11 applications are installed on otherwise > identical > Macs and that reinstalling from the Mac OS X Install Disk fixed a > non-chimera bug. > > Also, I have read on the web that if you install the 10.4 X11 > application > on 10.5, then OpenGL applications will work better. Since that is > not an > option for everyone, we are spending more time to improve the Aqua > version > that is available as a Snapshot release on the chimera download > page. It > has different bugs, but the graphics is better. So you should try > it out > and see how well it works for you. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2008 10:40:13 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [Chimera-users] Possible image saving bug > To: wnovak(a)brandeis.edu > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Wally, > I also had this tiling problem. We think it may be something about > > X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not > been > observed with 10.4/X11. > > Two workarounds that were successful in my case (I don't know if > they > will fix all instances of the problem): > > (A) simply show the Command Line before saving the image. I tried > hiding it again after that, but then the problem reoccurred, albeit > in > a more subtle fashion. > > (B) save the session, restore it in the aqua version of Chimera > (still > on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) > is > easier, but I didn't discover that one until this morning, after > receiving your mail. > > I hope these solutions are general! Sorry about the inconvenience, > 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 > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 63, Issue 17 > ********************************************* >

2 1

center of mass for multiple models
by Jean Didier Pie Marechal 18 Jul '08

18 Jul '08

Hi everyone, I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem. In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently. import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point #Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i) #Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i] The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064 Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem? Thanks a lot for any answer, All the best JD Dr. Jean-Didier Maréchal Professor Lector 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: chimera-users-request(a)cgl.ucsf.edu Data: Dijous, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17 > 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: Possible image saving bug (Greg Couch) > 2. Possible image saving bug (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Possible image saving bug > To: Walter Novak <wnovak(a)brandeis.edu> > Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.OSF.4.63.0807171001010.1939086(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Thu, 17 Jul 2008, Walter Novak wrote: > > > Hi All, > > > > I submitted a bug report on this, but the behavior is both odd > and > > reproducible for me. Using the latest production release and > trying to save > > an image using supersampling, the image is not stitched back > together > > appropriately. It is odd, because it always happens for a certain > session > > file I have. It doesn't seem to happen if I open a new molecule > and make a > > picture. I can provide the session file if needed. First image is > using 3x3 > > and second is 6x6. > > I see from the bug report that you're using Mac OS X 10.5. We are > having > "issues" with the new X11 application in 10.5. And we have seen > that > slightly different X11 applications are installed on otherwise > identical > Macs and that reinstalling from the Mac OS X Install Disk fixed a > non-chimera bug. > > Also, I have read on the web that if you install the 10.4 X11 > application > on 10.5, then OpenGL applications will work better. Since that is > not an > option for everyone, we are spending more time to improve the Aqua > version > that is available as a Snapshot release on the chimera download > page. It > has different bugs, but the graphics is better. So you should try > it out > and see how well it works for you. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2008 10:40:13 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [Chimera-users] Possible image saving bug > To: wnovak(a)brandeis.edu > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Wally, > I also had this tiling problem. We think it may be something about > > X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not > been > observed with 10.4/X11. > > Two workarounds that were successful in my case (I don't know if > they > will fix all instances of the problem): > > (A) simply show the Command Line before saving the image. I tried > hiding it again after that, but then the problem reoccurred, albeit > in > a more subtle fashion. > > (B) save the session, restore it in the aqua version of Chimera > (still > on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) > is > easier, but I didn't discover that one until this morning, after > receiving your mail. > > I hope these solutions are general! Sorry about the inconvenience, > 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 > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 63, Issue 17 > ********************************************* >

1 0

Possible image saving bug
by Elaine Meng 17 Jul '08

17 Jul '08

Hi Wally, I also had this tiling problem. We think it may be something about X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not been observed with 10.4/X11. Two workarounds that were successful in my case (I don't know if they will fix all instances of the problem): (A) simply show the Command Line before saving the image. I tried hiding it again after that, but then the problem reoccurred, albeit in a more subtle fashion. (B) save the session, restore it in the aqua version of Chimera (still on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) is easier, but I didn't discover that one until this morning, after receiving your mail. I hope these solutions are general! Sorry about the inconvenience, 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

1 0

Possible image saving bug
by Walter Novak 17 Jul '08

17 Jul '08

Hi All, I submitted a bug report on this, but the behavior is both odd and reproducible for me. Using the latest production release and trying to save an image using supersampling, the image is not stitched back together appropriately. It is odd, because it always happens for a certain session file I have. It doesn't seem to happen if I open a new molecule and make a picture. I can provide the session file if needed. First image is using 3x3 and second is 6x6. Also, when using pov-ray, the balls are completely devoid of shininess, regardless of my shininess settings (I set it to 128). That is the last image. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

2 1

Coloring a binding site
by Tom Goddard 17 Jul '08

17 Jul '08

Hi Andy, To color a binding site I would select the ligand (DNA in your case) then select all the nearby atoms using Select / Zone..., then use Actions / Color to color those atoms. Tom Anindito Sen wrote: > Another question - I need to color a portion of the crystal structure > differently (ribbon diagram) in order to indicate the binding sites of > the DNA with the protein molecule and how do I do that. > > Thanks and Best Wishes > Andy

2 2

possible bug
by Ben Keshet 16 Jul '08

16 Jul '08

Hi, when I un-select atoms, I had some weird long lines crossing my structures across (picture attached). I restarted the program how ever the same exact thing happened again. The two files that were opened worked perfectly in the past and before I un-selected the atom (ctrl+left click in the "air"). Other wise - great software. Thank you. Ben

2 1

Re: [Chimera-users] History feature for command line between sessions
by Eric Pettersen 15 Jul '08

15 Jul '08

> On Apr 17, 2008, at 8:52 AM, Boaz Shaanan wrote: > > > The history of commands in the command line mode is retained > > within a session and is very convenient but I was wondering whether > > there is a feature that will allow you to recall commands from > > previous sessions (such as in O for example - it generates an .o- > > history file which is being constantly updated and is very > > convenient). If not, is it possible to request the addition of such > > a feature ? There are many ways to implement this of course and I'm > > sure you'll find the best way, if it's not already there lurking in > > Chimera. > > Hi Boaz, > Good idea -- and shouldn't be too hard to implement. I was thinking > of remembering the last 100 commands. Will that be enough you think? > > --Eric This is implemented now. It should show up in the next daily build that works. Only remembers 60 by default, but that number is changeable in Preferences. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Can't type in Chimera
by Thomas Goddard 15 Jul '08

15 Jul '08

Hi Andy, I don't know how Chimera could get in a state where it will not accept any typed input. Do you recall the last thing you did in Chimera before it stopped accepting key input? If I were stuck in this situation and could not type a file name to save the Chimera session I would create an empty file with the session file name I wanted using a text editor. Then choose that file with the mouse in the Chimera session saving dialog. Desperate measures. If you can reproduce the problem please tell me how and I will fix Chimera. Tom Anindito Sen wrote: > HI Tom > > I have installed the latest version of Chimera on my LINUX box Fedora > Core 6.0. I faced a strange problem- while carrying out a docking of a > crystal structure in a density map I was using the command line for the > differnt movements and controls. After some time I am unable to type > anything on the command line. Infact I am even unable to save the > session as I cannot type the "NAME" of the session. I checked my keyboad > and typed on the terminal and on text editiors and it worked normally. > > Waiting for your response. > > Best Wishes > Andy > > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908

1 0

Re: [Chimera-users] reg. ribbon reprsentation
by Elaine Meng 15 Jul '08

15 Jul '08

>> >> Greetings. I have already posted a similar question on the forum >> previously and hence i am writing to your email. My problem is when >> i open a protein pdb, i get wonderful ribbon representation when i >> opt for it. But when i give a protein pdb with only a CA atoms/ >> CA,C,N atoms, i dnt get the ribbon representation. I understand >> that ribbon is constructed by considering CA,C,N,O and OXT atoms. >> What i did was that i simply removed O and OXT atoms by going >> through Tools--> Depiction --> Ribbon style Editor. It may be a >> wrong idea to do that. But i would appreciate if you could write me >> some way to draw the ribbon for protein having only CA or CA,C,N >> atoms IF POSSIBLE. >> >> Regards, >> Bala >> Hi Bala, If you have N-CA-C atoms, it actually works pretty well if you open Ribbon Style Editor, go to the "Residue Class" tab, choose "amino acid" but then change the "Orientation atom" to C instead of O, and Apply. (You still need to show ribbon if you didn't already do that.) You can save and name the new residue class for re-use in some later Chimera session if you want. The resulting ribbon looks the same to me as the standard ribbon made from N,CA,C,O (I tested this by writing a PDB of only the N,CA,C atoms from a complete structure, reading it back in, and experimenting with Ribbon Style Editor). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon… If you have CA atoms only, then there is no way to figure out the plane of the ribbon - it does not work to set both the "Guide atom" and "Orientation atom" to CA. Unfortunately this prevents you from displaying "licorice" ribbons even though they don't use an orientation plane. My only solution in this case is to use some program to build the additional atoms from the CA trace, for example this web server: http://www.ebi.ac.uk/Tools/maxsprout/index.html 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

1 0

Re: [Chimera-users] email address
by Khanei Mkumeni 15 Jul '08

15 Jul '08

khmlukundo(a)gmail.com

1 0

SpaceNavigator with Linux
by D. Greening 14 Jul '08

14 Jul '08

Hi, I just downloaded Chimera 1.2540 and was pleased to see that the SpaceNavigator 3-D mouse is now supported for Windows and Mac. Will those of us who use Linux be able to use our SpaceNavigators with Chimera any time soon? Thanks. D. Greening Memorial University of Newfoundland

2 1

drawing molecules
by Kathleen.Zocher＠ernaehrung.uni-giessen.de 14 Jul '08

14 Jul '08

Dear Sir or Madam, I`ve just one question concerning some special tools of Chimera. Is it possible to draw small molecules (ligands) within chimera? I can not find some information for this problem in the manual. For further docking experiments I just need a 3D-structure which is minimized (in a mol2 file). Many thanks in advance! Sincerely yours Kathleen Zocher ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

2 1

Question about bond length modification
by Benjamin G.S. Horsman 14 Jul '08

14 Jul '08

Hello, I have what appears to be simple problem but is I can't find the solution in previous mailing list queries. My problem is that I am unable to modify the lengths of any bonds in a PDB molecule. I am rather frustrated with myself over such a stupid problem, having tried dozens of times over dozens molecules to get it right but to no avail. Any possible solutions from the community? I am using MacpyMol to generate PDB structures and Chimera v1 build 1470. Thanks for any help, Ben

2 1

Re: [Chimera-users] [Chimera-announce] Chimera production release
by Elaine Meng 13 Jul '08

13 Jul '08

Hello Yao, Don't worry, the new versions still include the ability to fit map in map. It is simply that two tools were combined into a new tool with a slightly different name. Changes in this production release relative to the previous one include: "Fit Model in Map" and "Fit Map in Map" (Volume Data) — * merged into new "Fit in Map" tool * can update fit values continuously * can simulate map from atomic coordinates, report map-map correlation current documentation: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ fitmaps/fitmaps.html Best, 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 On Jul 12, 2008, at 11:49 PM, Yao Cong wrote: > Hello Chimera developer, > > Appreciate your great efforts to make Chimera an perfect tool for > Cryo-EM study. > > I and many of my colleges notice that in your latest versions, you > omit the "fit map into map" module, which is very convenient in > many cases. Is there a specific reason for that? And we all > consider it will be very helpful if you could add this function > back in your next version, maybe daily release? Otherwise, we still > keep the old version to have that function and meanwhile install > your newer version to enjoy the newer functions. > > Thanks, > Yao > ----------------------- > Yao Cong, Ph.D. >

1 0

Creating abridged multimer
by Francesco Pietra 12 Jul '08

12 Jul '08

I am posting again after having once again subscribed In order to create an abridged multimer made of non covalently bound subunits (from available pdb of subunit) which is the preferable route? (1) Load the monomer, delete substructures, and then assemble an abridged multimer? Are the headers furnished with the monomer OK for the abridged subunit? (2) Build the unabridged multimer and proceed to simplify each subunit the same way? Thanks francesco pietra

2 1

distance measurements on surfaces
by Daniel Hautzinger 11 Jul '08

11 Jul '08

Dear all, from the Volume Visualization Tour, I discovered the topography command that now allows me to dsiplay atomic force microscopy data (basically bitmap images with grey scales representing height). In that way I got some very nice images. I also found out how to scale the voxel size, so the scale of the structures should be correct. To test this, and to be able to add some length markers, I wanted to measure distances on the surface generated by the topography command. But while that seems possible for volume data (by setting markers), I had no success with the surface representation of my data nor the original image (which is handled as kind of a volume, but a single slice) when it came to setting markers or measuring distances in another way. Did I miss anything, or is that just not possible? I am using build number 2509, because of the topography feature. Setting markers is described as working by setting the marker in the first maximum in the line of sight at the click position. For surfaces, you could just take the position of the visible pixel clicked. Or maybe it is possible to convert surfaces to volumes? Thank you for your help Daniel Hautzinger

2 1

changing selection color
by Michael DiMattia 10 Jul '08

10 Jul '08

Hi all, I have a quick question regarding a figure I am trying to make. I have a multi-chain protein loaded with each subunit surface-rendered individually. We wanted to find a way to highlight the outline of one of the subunits in the 3d surface rendering and selecting the surface of the chain works really well for this in Chimera. The familiar green outline highlights the subunit well, even though I realize this is probably not the primary purpose for such highlighting. I imagine it is just to let the user know what is selected. But if i were to use the selection highlighting to show such an outline in a figure, i was wondering if it is possible to change the color of the selection outline from green to any other color or if it is possible to change the width of the outline. I realize it's a long shot, but thought I'd ask anyway in case anyone has tried this before. Many thanks Mike DiMattia

2 1

Chimera production release
by Elaine Meng 10 Jul '08

10 Jul '08

Hi everybody, A new production release, version 1.2540, is now available from: http://www.cgl.ucsf.edu/chimera/download.html#production Many improvements and new features have been added since the previous production release (Nov 2007), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html For the time-challenged, here are just a few of the reasons you may want to use the new version: 1) new fetch types: - comparative models from ModBase - protein pocket data from CASTp database - small molecule structures from Pub3D - small molecule structures built from SMILES strings 2) surface improvements: - increased reliability - surface areas automatically calculated - Actions menu, other tools work on more types of surfaces 3) appearance: - default lighting changed to improve POV-Ray results - larger default scale - helix ribbon insides can be colored separately - 2D labels can include Greek letters and other symbols 4) new tools: Axes, EnsembleCluster, Solvate, Structure Diagram 5) new commands: export, mclip, molmap, perframe, ribinsidecolor, shape, solvate, topography, vop See the release notes for details. The production release includes versions for Windows, Mac/X11, Linux, SGI IRIX, and HP Tru64. The Mac Aqua version has been improved significantly, but for now remains a snapshot download: http://www.cgl.ucsf.edu/chimera/download.html#snapshots Enjoy! The Chimera Team

1 0

Multiscale models and surface coloring
by David Sept 10 Jul '08

10 Jul '08

I need to create a series of images of large protein complexes, and since it is tedious to do this through the menus, I am trying to script this for Chimera. I want to create low-res, EM looking surfaces and color the individual protein chains different colors. So far, I can read in multiple structures and create the surfaces, but I can't figure out how to change the coloring. Here's what I have: ---- test.py ------- from chimera import openModels m = openModels.open('model-1.pdb')[0] import MultiScale d = MultiScale.show_multiscale_model_dialog() d.make_multimers([m]) chimera.viewer.viewAll() ---- test.py ------- The above python script work and makes very nice blobs. I can color the entire structure (say red) by adding something like: d.select_all_chains_cb() d.change_color_cb((1, 0, 0, 1)) but I can't figure out how to select individual chains and color them (not sure how to use select_chains). This also gets more complicated when I load in two structures at the same time and they have common chain letters. Since I found a way to get this (almost) working in python, I've been sticking with it, but if this can easily be done directly using a chimera command file, I'm happy to do that. Any help is appreciated. Thanks, Dave ---------------------------------------------------- David Sept, Ph.D. Associate Professor Biomedical Engineering and Center for Computational Biology Washington University, Campus Box 1097, St. Louis, MO 63130 Phone: (314) 935-8837 Fax: (314) 935-7448 dsept(a)biomed.wustl.edu http://habanero.ibme.wustl.edu

3 3

Coloring different set of marker with different radius
by Bui Khanh Huy 08 Jul '08

08 Jul '08

Hi, I tried to color my EM electron density and thought that if I can color different maker sets with different radii, that would make thing much easierMy idea is to color one set using radius a, then select another set, color with radius b. But then the color from the first set disappeared. . Is there any way to do that? Best regards, Huy

2 1

Mac Chimera in-window menu bars
by Thomas Goddard 08 Jul '08

08 Jul '08

Hi Kevin, The Chimera Aqua version has a menu bar at the top of the screen as normal Mac applications do and also at the top of the graphics window. I agree there should be a preference setting to eliminate the in-window menu bar. Here's the reason for this weirdness. There are 13 Chimera dialogs that have their own menu bars and menus. Use of these involves switching between actions in the main window and the dialog repeatedly. With menus for the active window only shown at the top of the screen this interaction becomes very tedious. For this reason I added menu bars within each Chimera window that has its own set of menus. Those in-window menus don't work very well. If you post one menu then put the pointer over an adjacent menu it will not pop up. An even worse atrocity in Aqua Chimera is that it implements "focus follows mouse". As the pointer is moved over the various Chimera windows the one underneath becomes active. This again was added because common Chimera usage involves switching frequently between windows and the normal Mac "click to focus" behavior is inconvenient for this. We would like instead to use "click through" where the first mouse click on a window both activates that window and presses the button or activates the entry field that was clicked on. I have not been able to do this in Aqua Tk, the windowing toolkit we use. The problem we're facing is that the Chimera user interface with its many windows and frequent switching between windows is poorly suited to the Mac GUI conventions. The in-window menus and focus-follows-mouse mode are a first stab at a compromise solution -- still much to be desired. Tom Kevin Walzer wrote: The latest build of Chimera from 7/3/08 on OS X/Aqua (10.5.4) includes menubars at the top of the screen (the standard OS X behavior) *and* on the main toplevel window itself, as on Windows and X11. This behavior is simply weird--two menus? It can only b e regarded as a bug, not a feature. What purpose does it serve? The correct Mac behavior can be restored by commenting out lines 1470-1476 of tkgui.py. If some of your Mac users are requesting this kind of behavior in menubars, at the very least the non- standard window-based menubar should be a preferences item that can be toggled off.

1 0

Tile Structure default view
by Eduardo Sanz Garcia 07 Jul '08

07 Jul '08

I would like to request an extra feature for chimera, if it is not there already. I normally open multiple structures in chimera and then I use the "Tile Structure" button to visualize them in an array. This is nice, for example, to visualize the evolution of a cryo-EM 3D reconstruction. I would like that chimera could open multiple structures in an array view by default. Could a "Default view" button be added to the Tile Structure window, so that the "Border scale" value setting is saved and then the next time I open several structures they would be displayed in array view? Thank you very much.

3 2

renumbering pdb
by bustik＠gmx.net 05 Jul '08

05 Jul '08

dear chimera-users, i am just starting to use chimera, so this will be a really simple question to you (although i didn't find anything about this in the manual...): is there a simple command to change residue numbers in a pdb file (i built up a homology model and want to elevate all residue numbers in the model the same amount)? thanks in advance sebastian -- Sebastian Kruggel Eppendorfer Weg 17d D 20259 Hamburg fon: +49 (0)40 4192 9579 mobil: +49 (0)151 1789 2232 e-mail: bustik(a)gmx.net

2 2

graphics performance: amira v. chimera
by Matthew Dougherty 03 Jul '08

03 Jul '08

I loaded a MRC file, isosurfaced it, gave it a transparency around 0.48, and generated a vrml in chimera. I loaded the vrml into amira. initial comparison: I reloaded the vrml into chimera, I turned off the fog on chimera, moving the object around the refresh rate seems to be around 8 fps. On amira it seems to be around 24fps. results: The graphics on Chimera seems to be better during the rotation of transparent objects: full rotation in chimera is flawless, full rotation in amira results in flipping of the object (vertices in back quantum-ly jump to the front, front vertices go to back, looks like a z buffer error) periodically at 180 degrees, making it useless for many camera positions. Any comments or suggestions?

4 3

OS X Chimera
by Christopher Vavricka 02 Jul '08

02 Jul '08

I have OS X 10.4.11 and I am trying to run Chimera. When I start Chimera.app it tells me to start X windowing system (Apple X server). X11 is not located in my applications/utlilties folder. How do I get this application? Is it on my installation disc for OS X? Regards, Chris Vavricka

3 2

(no subject)
by Levy, Hazel C. 02 Jul '08

02 Jul '08

Hi, I am a postdoctoral researcher and an enthusiastic Chimera user. We are trying to finish up a manuscript to submit tomorrow to JSB and we have been frantically trying to figure out how to convert from Chimera's "contour level" to the more conventional "sigma level" for density map viewing at different noise levels. We understand that the higher the contour level the smaller the map volume displayed (less noisy), but we are not quit sure how to report this as a sigma level. Each map that we are comparing has a different contour range assigned, I am wondering if sigma level corresponds to some proportion of the maximum volume. Please let us know how to do this conversion or please point us in the direction toward the person that can help us. Thanks you so much...this information will settle a long-standing mystery for us. Hazel Levy

2 1

Mutate by D- res...
by Yasser Almeida Hernández 30 Jun '08

30 Jun '08

Can Chimera mutate by D-residues? If this is possible, how i can do it? Thanks... -- Yasser Almeida Hernández Estudiante, 4to Año Bioquímica Facultad de Biología Universidad de la Habana

3 2

Dummy atoms
by Jean Didier Pie Marechal 30 Jun '08

30 Jun '08

Dear all, I think the question was already posted but I can't find it. I would like to make an atom I placed as an helium to a Dummy: What is the corresponding atom type in Chimera? All the best JD Dr. Jean-Didier Maréchal Professor Lector 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: chimera-users-request(a)cgl.ucsf.edu Data: Dimarts, Juny 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 21 > 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: how could u know the order of atoms? (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 23 Jun 2008 14:22:31 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] how could u know the order of atoms? > To: Kamal Al Nasr <k_alnasr(a)yahoo.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <8901DE4E-D117-4B18-968B-D3095AD735D4(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote: > > > Dear Sir/Madam, > > > > I am using Chimera viewer..and it is a great viewer ever... > > Thanks! I'm glad you like it. > > > I kindly have a question... how could you know (from PDB file) > the > > coorect bonding between atoms? I mean that how could you know > that > > this atom is connected with CA not N nor C.....do u have all > these > > bonds stored already in a database? or you use atom positions to > > determine that? > > For standard amino and nucleic acids, Chimera has templates > containing the correct connectivity. For non-standard residues it > bases the connectivity on inter-atomic distances, with a few added > heuristics (e.g. hydrogens can only have one bond). > > The templates are accessible in the Python layer with the > chimera.restmplFindResidue() function. You can look in the > Rotamers > extension for examples of its use. The distance-based connectivity > > function is also available for an entire molecule as > chimera.connectMolecule(). It takes the molecule as its only > argument and adds bonds to it. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

2 1

"Floating exception" error message
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

3 3

"Floating exception" error message
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

2 1

(no subject)
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

1 0

hydrophobic pocket
by bala 27 Jun '08

27 Jun '08

Dear Chimerian's, How do i detect hydrophobic pockets in a protein using chimera ?. Thanks in advance, Bala

3 2

Re: [Chimera-users] Question about avi files in chimera
by Tom Goddard 27 Jun '08

27 Jun '08

Hi Jaap, The AVI files produced by Chimera movie recorder use the MSMPEG-4v2 (Microsoft MPEG4 version 2) video codec and the encoding is done by the open source ffmpeg program. The file size depends on the movie recorder "bit rate" setting (default 2000 Kbits/sec = 250 Kbytes/sec = 15 Mbytes/min). Changing this setting allows you to trade off file size versus image quality. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… Tom Jaap Brink wrote: > > Hi Tom, > > > > I was wondering given the size difference in avi files that chimera > generates versus other program (Video Edit Magic for instance), which > video codec is being used? I searched the list of embedded software > packages in chimera and found the library of libavcodecs. > > > > Thanks in advance, > > > > Jaap >

1 0

upcoming production release
by Greg Couch 26 Jun '08

26 Jun '08

Hello, We are currently getting ready to put out another chimera production release. At this point, we consider the daily builds to be release candidates, so please download one and try it out. Not all of the daily builds will be production releases, in particular, the Mac OS X Aqua version is not quite ready, and will be a snapshot release. And the Linux off-screen OpenGL version is experimental and will probably stay as a daily build. Greg Couch UCSF Computer Graphics Lab Daily builds: <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html> New features: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>

1 0

Re: [Chimera-users] how to draw lines in Chimera
by Elaine Meng 25 Jun '08

25 Jun '08

On Jun 24, 2008, at 4:24 PM, Qing Xie wrote: > Hi, > I'm trying to draw a bunch of axes from center (0,0,0). I could do > this > in 'O' by calling this macro: > > begin_object symax > colour blue > stick_xyz 139.05, -0.00, -16.25, -139.05, 0.00, 16.25, 0.25 > stick_xyz -111.40, 43.12, 73.02, 111.40, -43.12, -73.02, 0.25 > stick_xyz -107.48, 80.74, 39.10, 107.48, -80.74, -39.10, 0.25 > stick_xyz -66.72, 119.11, -31.00, 66.72, -119.11, 31.00, 0.25 > stick_xyz 50.41, 73.78, -107.77, -50.41, -73.78, 107.77, 0.25 > stick_xyz 100.65, 0.20, -97.31, -100.65, -0.20, 97.31, 0.25 > stick_xyz -68.88, 113.16, 45.26, 68.88, -113.16, -45.26, 0.25 > stick_xyz -39.02, 80.98, -107.34, 39.02, -80.98, 107.34, 0.25 > stick_xyz 10.15, 0.20, -139.64, -10.15, -0.20, 139.64, 0.25 > stick_xyz 50.47, -73.42, -108.00, -50.47, 73.42, 108.00, 0.25 > end_object symax > > Since I had to use some features in Chimera, do you know what > commands I > should combine to do similar things above? > Thank you! > Sincerely, > Qing Hi Qing, You can make a BILD file defining the objects, for example containing the following: .color medium blue .cylinder 139.05 -0.00 -16.25 -139.05 0.00 16.25 1 .cylinder -111.40 43.12 73.02 111.40 -43.12 -73.02 1 .cylinder -107.48 80.74 39.10 107.48 -80.74 -39.10 1 .cylinder -66.72 119.11 -31.00 66.72 -119.11 31.00 1 .cylinder 50.41 73.78 -107.77 -50.41 -73.78 107.77 1 .cylinder 100.65 0.20 -97.31 -100.65 -0.20 97.31 1 .cylinder -68.88 113.16 45.26 68.88 -113.16 -45.26 1 .cylinder -39.02 80.98 -107.34 39.02 -80.98 107.34 1 .cylinder 10.15 0.20 -139.64 -10.15 -0.20 139.64 1 .cylinder 50.47 -73.42 -108.00 -50.47 73.42 108.00 1 and open it in Chimera to create the objects. I also attached this below as the file sticks.bild to be opened directly in Chimera. I didn't think 0.25 looked that good, but you can edit the file to whatever radius (and color, etc.) that you want. The BILD language also includes many other objects: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Best, 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

1 0

Re: [Chimera-users] find levels and morph conformations
by Thomas Goddard 24 Jun '08

24 Jun '08

Hi Ed, The Morph Conformations tool works with submodels. It will not work between two models or submodels that have different numbers of chains. The error message you get means that you are giving it models with different numbers of chains. Tom Edward Brignole wrote: > Tom, > > ... I'd like to use morph conformations between two pdbs each > composed of the same submodels/chains. I've tried to do this through the > dialog but it displays an error telling me "cannot interpolate the > models have different numbers of chains". The only way I can see to do > this is to write the pdb as a mol2 so that all atoms are in a single > model without submodels, open the mol2, and run morph conformations. > Is there another method or is this the simplest? > > Thanks, > Ed

3 2

selecting/displaying zones
by Elaine Meng 24 Jun '08

24 Jun '08

On Jun 24, 2008, at 11:56 AM, Thomas C. Marlovits wrote: > > Am using Chimera and would like to do the following: > - would first like to focus on specific side chain residues (for > example lysines) > - at a specific atom of either one or all lysines present in my > sample, I would like to draw a region of interest (which should be > a sphere with a given distance ... then make it rather transparent > like soap bobbles ...) ... the idea of this is to highlight areas > within a given distance away from this atom > - then I would like to read out all other side chains that are > within such an area ( in a table or so) ... and eventually > highlight them with specific colors ... > > Elaine, is there an easy way to do this ? > Tx, > -Thomas > ---------------------------------------------------------------------- > --------- > > Thomas C. Marlovits, PhD, M.A.S. > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences (IMBA) Hi Thomas, You can definitely (1) select the atoms or residues within a specified cutoff of some other atoms and write a list of what is selected to the Reply Log or to a file. Slightly trickier is (2) displaying a "bubble." (1) The following command selects all atoms within 4.5 angstroms of atom NZ in lysine 92, chain A (example structure 2gbp): select :92.a@nz za<4.5 to select the whole residues with any atom in the zone, use "z" or "zr" instead of "za", and to use all the atoms of that lysine, just omit "@nz" from the command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#zones This selection process can also be done by Ctrl-clicking to select the atom and then using Select... Zone. You can write out a list of the selection with Actions... Write List (click Log if you want to send it to the Reply Log instead). The default is a list of all the atoms individually, but you can set it to "residues" instead to just get one line of output per residue. The command to do that same thing is "writesel" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html (2) The "bubble." I imagine something like Volume Eraser would be nice (check it out: Tools... Volume Data... Volume Eraser). However, that does not let you specify particular coordinates for the center. You have to move it around by hand. Volume Eraser really just makes a big atom and gives it a transparent color. You could add an atom in Build Structure (under Tools... Structure Editing), color it a transparent color, and change its radius with "vdwdefine" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html#build http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html It doesn't let you enter specific coordinates for the atom. However, if you add the atom as a "new model" you can match it to different locations on the first. For example, if the new atom is model 1 and the structure of interest (say 2gbp) is model 0: rep sphere #1 colordef tpink 1 .6 .6 .6 color tpink #1 vdwdef 3.0 #1 vdwdef +1 #1 vdwdef +1 #1 match #1 #0:147.a@nz select #1 za<5 & #0 [... etc. ...] The radius would just be for display purposes. You'd still have to specify the zone distance when selecting. A couple of failed ideas: (a) You can make a spherical surface of specified radius with the command "shape" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html but you cannot directly specify coordinates for the center or easily modify radius after it has been created. (b) Create a spherical object in BILD format. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Disadvantages are inability to make it transparent and having to delete/recreate the object just to change its radius. Best, 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 > >

1 0

how could u know the order of atoms?
by Kamal Al Nasr 23 Jun '08

23 Jun '08

Dear Sir/Madam, I am using Chimera viewer..and it is a great viewer ever... I kindly have a question... how could you know (from PDB file) the coorect bonding between atoms? I mean that how could you know that this atom is connected with CA not N nor C.....do u have all these bonds stored already in a database? or you use atom positions to determine that? I appreciate your time.... Kamal

2 1

connectivity
by Jean Didier Pie Marechal 19 Jun '08

19 Jun '08

Dear all, I would like to use chimera to generate inputs for gaussian QM/MM calculations (ONIOM). One of the element I need is the connectivity of the atoms. I looked around the programmer's guide but couldn't find the right module that takes this in charge. what is the way to have access the connectivity of a given molecule? All the best, JD Dr. Jean-Didier Maréchal Professor Lector 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: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Juny 18, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 18 > 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. Find contour level to enclose a specified volume (Thomas > Goddard) 2. Re: Find contour level to enclose a specified volume > (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 17 Jun 2008 15:44:57 -0700 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: [Chimera-users] Find contour level to enclose a specified > volume > To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <48583E69.5090608(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Ed Brignole asked about setting a volume contouring level so that > the > resulting surface encloses a desired volume (cubic Angstroms). > Attached > is a Python script that does this in two ways. The first way is > fast > but approximate finding the level such that the number of enclosed > grid > points times the voxel volume equals the requested volume. > Estimating > the enclosed volume of the surface this way can give a much > different > result than actually computing analytically the volume within the > surface. The second approach computes surfaces at different > contour > levels and calculates analytically the volume. It uses bisection > to > find the correct contour level. This approach can be slow, about > 30 > seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface > triangles. Most of that time (80%) is actually computing the > enclosed > volume. That should be very fast but the code is checking for > holes in > the surface in a rather slow way. Both methods use the step size > (subsampling) set in the volume dialog. > > Tom >

2 1

Find contour level to enclose a specified volume
by Thomas Goddard 18 Jun '08

18 Jun '08

Ed Brignole asked about setting a volume contouring level so that the resulting surface encloses a desired volume (cubic Angstroms). Attached is a Python script that does this in two ways. The first way is fast but approximate finding the level such that the number of enclosed grid points times the voxel volume equals the requested volume. Estimating the enclosed volume of the surface this way can give a much different result than actually computing analytically the volume within the surface. The second approach computes surfaces at different contour levels and calculates analytically the volume. It uses bisection to find the correct contour level. This approach can be slow, about 30 seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface triangles. Most of that time (80%) is actually computing the enclosed volume. That should be very fast but the code is checking for holes in the surface in a rather slow way. Both methods use the step size (subsampling) set in the volume dialog. Tom # ----------------------------------------------------------------------------- # Find threshold level so that a contour surface encloses a specified volume. # # Method: Estimates how many grid points should lie within # surface then finds the level having that many grid points with higher values. # This method can produce a level where the enclosed volume is very # different from the requested volume. # def level_enclosing_grid_points(v, vol): (x0,y0,z0), (x1,y1,z1) = v.xyz_bounds() tvol = (x1-x0)*(y1-y0)*(z1-z0) r = 1.0 - vol/tvol s = v.matrix_value_statistics() level = s.rank_data_value(r) return level # ----------------------------------------------------------------------------- # Find threshold level so that a contour surface encloses a specified volume. # # Method: Computes surfaces for different levels and resulting volumes # using bisection to determine the correct level. # def level_by_bisection(v, vol, iterations = 10): m = v.matrix() l0, l1 = m.min(), m.max() ijk_step = v.region[2] from numpy import product voxel_volume = product(ijk_step) * product(v.data.step) mvol = vol / voxel_volume return find_level(m, l0, l1, mvol, iterations) # ----------------------------------------------------------------------------- # def find_level(m, l0, l1, mvol, iterations): l = 0.5*(l0+l1) if iterations <= 1: return l from _contour import surface varray, tarray = surface(m, l, cap_faces = True) from _surface import enclosed_volume vl, hole_count = enclosed_volume(varray, tarray) varray = tarray = None if vl == mvol: return l if vl > mvol: l0 = l else: l1 = l return find_level(m, l0, l1, mvol, iterations - 1) # ----------------------------------------------------------------------------- # vol = 3.227e6 # sfv.mrc, threshold level 1000. from chimera import openModels from VolumeViewer import volume_list for v in volume_list(): level1 = level_enclosing_grid_points(v, vol) level2 = level_by_bisection(v, vol) print v.name, level1, level2

2 1

3D surfaces from MacMolPlt or Gamess
by David Chenoweth 13 Jun '08

13 Jun '08

Dear Chimera team, I am having a bit of trouble reading a file into Chimera. Currently I am using Gamess to run DFT calculations and I can open these files in MacMolPlt which allows me to display orbitals or plot electrostatic potential surfaces. I can export the 3D surface data however I can't get Chimera to read the 3D grid files. Can you help me? I attached the file format info below and I can send you example files if you need. I am really trying to use Chimera for all my graphics needs wether it be viewing surfaces or orbitals from DFT calculations or looking at electron density maps from crystal structure data. If I could convert the 3D surface data files below into ccp4 or cns formated files that should also work for Chimera I just haven't found a way to do this yet. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu ********************************************** File format data info: http://www.scl.ameslab.gov/~brett/MacMolPlt 2D and 3D Surfaces (Import and Export) MacMolPlt implements a simple format for importing and exporting 2D and 3D surface data. To export a surface first create a surface and make sure that the surface is updated so that the grid data is available for export. Then choose the Export menu command and the Surface export format. MacMolPlt will then export the surface grid data to the file you specify (this is useful to check the input format as well). To import a 2D or 3D surface create a new General 2D or 3D surface. From the surface dialog you can then choose the file containing the grid data. The format for the 2D and 3D files are similar but there are a couple of differences. Floating point numbers may be given in a variety of formats and the grid data may contain any number of values per line. The units for the coordinate system should normally be angstroms. For 2D planes the format is: 1Line Label 30 # grid points -4.165882 -4.306789 0.839681 //Origin of the 2D grid 0.297019 0.000000 0.000000 //X inc vector 0.000000 0.297019 0.000000 //Y inc vector -0.000018 -0.000021... (# of grid points squared grid values) For 3D surfaces: 1 Line label 35 12 41 //nx ny nz -4.687880 -1.587537 -5.059790 //Origin of the 3D grid 0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z))) 0.000000 0.000000... (nx*ny*nz grid values)

2 2

3D surfaces from MacMolPlt or Gamess
by David Chenoweth 13 Jun '08

13 Jun '08

Dear Chimera team, I am having a bit of trouble reading a file into Chimera. Currently I am using Gamess to run DFT calculations and I can open these files in MacMolPlt which allows me to display orbitals or plot electrostatic potential surfaces. I can export the 3D surface data however I can't get Chimera to read the 3D grid files. Can you help me? I attached the file format info below with an exported density file and electrostatic potential map. I am really trying to use Chimera for all my graphics needs wether it be viewing surfaces or orbitals from DFT calculations or looking at electron density maps from crystal structure data. If I could convert the 3D surface data files below into ccp4 or cns formated files that should also work for Chimera I just haven't found a way to do this yet. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu ********************************************** File format data info: http://www.scl.ameslab.gov/~brett/MacMolPlt 2D and 3D Surfaces (Import and Export) MacMolPlt implements a simple format for importing and exporting 2D and 3D surface data. To export a surface first create a surface and make sure that the surface is updated so that the grid data is available for export. Then choose the Export menu command and the Surface export format. MacMolPlt will then export the surface grid data to the file you specify (this is useful to check the input format as well). To import a 2D or 3D surface create a new General 2D or 3D surface. From the surface dialog you can then choose the file containing the grid data. The format for the 2D and 3D files are similar but there are a couple of differences. Floating point numbers may be given in a variety of formats and the grid data may contain any number of values per line. The units for the coordinate system should normally be angstroms. For 2D planes the format is: 1Line Label 30 # grid points -4.165882 -4.306789 0.839681 //Origin of the 2D grid 0.297019 0.000000 0.000000 //X inc vector 0.000000 0.297019 0.000000 //Y inc vector -0.000018 -0.000021... (# of grid points squared grid values) For 3D surfaces: 1 Line label 35 12 41 //nx ny nz -4.687880 -1.587537 -5.059790 //Origin of the 3D grid 0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z))) 0.000000 0.000000... (nx*ny*nz grid values)

1 0

Swapaa from Java Runtime.exec
by ProtEUS 11 Jun '08

11 Jun '08

Hello all! I am sorry if this is a dump question, but is it possible for swapaa to run fromJava server with Runtime.exec()? Thank you very much!! Andreas, Greece.

2 3

translation + rotation of a whole scene
by Nils Becker 11 Jun '08

11 Jun '08

Hi list, I have a question about rotating and translating a bunch of models together while preserving their spatial relations. In particular, I would like to apply a matrix almost as in the matrixset command. THe difference is that I do not want to apply it individually to each model, but to one chosen models, while having the rest move together with the chosen model. Is that feasible in chimera? cheers, Nils

3 4

saving 2 maps for difference
by Gabriel Lander 09 Jun '08

09 Jun '08

I have 2 density maps, and use the "fit in map" function to best align the 2 of them. I'd like to use this fitting to create a difference map, but the original maps are not the same size. Does anyone know how to save both maps to the same grid in Chimera? For now I've been using the "subregion selection" tool in combination with "resampling voxel size", but if someone has a more direct method it'd be much appreciated. Thanks, -gabe

2 1

<< Plotting Gaussian MO >>
by Hatuey Hack 09 Jun '08

09 Jun '08

Hi all, I have a cube file with the Molecular Orbitals calculated with Gaussian. When I load the cub file into Chimera, I am only seen half of the orbital surface. I would like to know what should I do to get the whole molecular orbital surface colored (as usually) with only to colors (each on for one half). Regards, Hatuey

3 3

gaussian orbitals, Chimera-users Digest, Vol 62, Issue 11
by Jonathan Hilmer 09 Jun '08

09 Jun '08

Hatuey, If I remember correctly, you need to open the density map twice, then contour at the same level for both maps: one at the positive value and the other negative. Each map is colored independently, so they can be depicted however you want. Jonathan On Mon, Jun 9, 2008 at 1:00 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. << Plotting Gaussian MO >> (Hatuey Hack) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Jun 2008 10:24:29 -0300 > From: "Hatuey Hack" <hatuey.hack(a)gmail.com> > Subject: [Chimera-users] << Plotting Gaussian MO >> > To: chimera-users(a)cgl.ucsf.edu > Message-ID: > <612c95fa0806090624l5395ab11k6c9b235379e1a4fe(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I have a cube file with the Molecular Orbitals calculated with Gaussian. > > When I load the cub file into Chimera, I am only seen half of the > orbital surface. > > I would like to know what should I do to get the whole molecular > orbital surface colored (as usually) with only to colors (each on for > one half). > > Regards, > > Hatuey > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 62, Issue 11 > ********************************************* >

1 0

Molecular voodoo
by Tom Goddard 06 Jun '08

06 Jun '08

While debugging a bit of Chimera code I stumbled upon molecular voodoo. Stick pins in any evil molecule. Ask your doctor if this treatment may be right for you. A snake toxin (PDB 1a0m) has been fully cursed in the attached image. I attach the voodoo doll Chimera script for your amusement. You open voodoodoll.py in Chimera and then ctrl-right-mouse-button lets you place pins. Works in Chimera production release 1.2470 and newer. Tom def mouse_down_cb(viewer, event): from VolumeViewer import slice xyz_in, xyz_out = slice.clip_plane_points(event.x, event.y) from chimera import selection selection.clearCurrent() from VolumePath import place_marker place_marker(xyz_in) place_marker(xyz_out) from chimera import mousemodes as m m.addFunction('hide triangle', (mouse_down_cb, None, None)) m.setButtonFunction('3', ['Ctrl'], 'hide triangle')

1 0

smoothening the edge of molecular surface
by Maurice Ho 06 Jun '08

06 Jun '08

Is there any way to smoothen the edge of molecular surface when only part of it would be displayed? It's quite often that a couple of triangles sticking out from the edges which makes the image a bit absurd. Please kindly advice. rgds, Maurice Ho

3 2

Installing Chimera in Ubunty Hardy
by David 05 Jun '08

05 Jun '08

Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu for 6 gb of ram that couldn't be used in XP 32 bits. I need help installing Linux version of Chimera, I have read and goggled web for instructions, and none of them seems to work, I run .exe in terminal (knowing linux doesn't use .exe i find this confusing) and nothing happens, I try that Chmod command and running again and nothing too... Im a really beginner here in linux, also browsed Ubuntu forums for help and at least till today have got no answer. All help would be greatly appreciated. sincerely, David Bulnes Abundis

2 1

Chimera - quantitative possibilities using surfnet?
by mgochin＠touro.edu 05 Jun '08

05 Jun '08

I am wondering if it is possible to get numerical values for areas / volumes of molecular cavities and indentations drawn by surfnet in either the Interface or Selected Atoms mode. Any help is appreciated. - Miriam Gochin

3 2

coloring residues according to electrostatic force
by Maurice Ho 05 Jun '08

05 Jun '08

How to color residues of a protein according to the electrostatic potential map generated by APBS? I could only color the molecular surface by loading the potential map. Please kindly advice. Thanks and regards, Maurice Ho

2 1

OS X aqua version
by Glenn Millhauser 04 Jun '08

04 Jun '08

Hi Folks, I just saw the mac aqua version at the download site and decided to give it a try. Layout looks terrific. However, it seems to move molecules much more slowly than the X windows version. I'm running on a macbook (intel) with inherent limited graphics capabilities, so perhaps that's the problem. Any comments? thanks, g Glenn Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 459 2935 fax 831 566 3337 cell glennm(a)chemistry.ucsc.edu http://chemistry.ucsc.edu/~glennm

6 12

making a plane through the atoms of a ring and Distance measurements
by David Chenoweth 04 Jun '08

04 Jun '08

Dear Chimera team, I would like to make a plane through the atoms of an aromatic ring and then measure a distance from an atom to the ring centroid. I would also like to measure the angle between the normal to the ring plane and the line joining the centroid and the atom I am measuring from. It would also be nice if I could specify the dimensions, color, and transparency of the plane. In addition it would be great to be able to make multiple planes through atoms, select and color them separately, and measure the angles at the intersection of the planes. Just wondering if there is a way to do this with Chimera. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu **********************************************

3 2

fit correlation
by Elena Orlova 03 Jun '08

03 Jun '08

Dear Chimera team, I have some troubles in getting numbers of the quality of the atomic structure fit into EM map. I wonder if you can give me directions where I can find the quantitative assessment of such fit? Do you have something like Cross Correlation Coeficient or R factor, or any other statistical test ? many thanks in advance. Elena -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Elena Orlova Dept. of Crystallography Tel: (+44) (0)20 7631 6845 Birkbeck College Fax: (+44) (0)20 7631 6803 University of London Malet Street London WC1E 7HX UK e-mail: e.orlova(a)mail.cryst.bbk.ac.uk

4 3

Re: [Chimera-users] Chimera-users Digest, Vol 61, Issue 29
by Ibrahim Moustafa 02 Jun '08

02 Jun '08

Dear Chimera developers, Many many thanks for your great help. The script provided by Eric Peterson did the job very easily. Many thanks, Ibrahim On 5/31/08 12:54 PM, "chimera-users-request(a)cgl.ucsf.edu" <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. Re: Plotting modes from PCA onto the structure (Eric Pettersen) > 2. Re: add atom type in MMTK (Elaine Meng) > 3. Import error with chimera-1.2509-osx_x11.dmg, May 01, 2008 > (Bruce D. Ray) > 4. Re: Import error with chimera-1.2509-osx_x11.dmg, May 01, > 2008 (Randy Heiland) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 May 2008 15:15:02 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Plotting modes from PCA onto the > structure > To: Ibrahim Moustafa <I.moustafa(a)psu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <476E9F7A-2FDD-4558-8053-5345D9995A02(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Ibrahim, > As Bala pointed out, IED in VMD may well be the way to go for now. > Also, the "porcupine needles" can be accomplished with BILD, as > Elaine mentioned. I've attached a script that reads a file of > displacements and applies them to the CAs of a structure. Obviously, > there should be as many lines in the file as there are CAs in the > structure. Each line should consist of 3 numbers, the X, Y, and Z > displacements. Since the script only modifies the CAs, you should > probably only be displaying the CAs -- the rest of the structure will > be out of position. You may need to edit the script to put in the > name of the file with the displacements, otherwise it will use a file > named "displacements" in the same directory as the script. You run > the script by simply opening it with File...Open or the "open" command. > We are working on closer coordination between Amber and Chimera, > with the help of Wei Zhang. He has already contributed one tool, > Solvate, which uses sleap to solvate a system. Solvate is available > in daily builds. In the short term he hopes to write tools to add > ions and write parmtop files. Longer term goals are to include the > minimization and MD functionality of NAB, and ptraj trajectory analysis. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > ? > On May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote: > >> Dear Chimera support, >> >> I hope Chimera (with supporting scripts) can be used to make the >> figures described below: >> >> I want to make a figure to display the different modes >> obtained from PCA analysis (on MD trajectory obtained from AMBER) >> as different snapshots of the structure under study. >> >> To explain it more, I have a file containing the displacement in >> X, Y, Z for each C-alpha in a column format. Is there a simple >> script that can add the displacement vectors to the x, y, z >> coordinates of the original structure? So the new structure with >> modified C-alpha can be plotted representing a particular mode in >> Chimera. >> >> Also, related to the same point, is it possible to represent the >> vectors at each C-alpha as arrows/porcupine needle in Chimera? >> >> P.S. It would be great if Chimera can add features to represent >> these kind of figures from PTRAJ output or similar analysis >> programs used in MD simulation. Especially, Chimera support >> analysis of AMBER trajectory. >> >> Thanks in advance for your great support, >> 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 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

1 0

How to define a center of rotation when applying a symmetry
by Giovanni Cardone 02 Jun '08

02 Jun '08

Hi, I would like to apply a rotation to a pdb model, in order to place copies of it in equivalent symmetry points (icosahedral symmetry). I am not sure I understand all the different coordinate systems in chimera, but digging into the program code, I was able to write the following script. I am not sure it is the best way to do it, and obviously at the moment it does not work properly, because I am not specifying the center of rotation. With respect to the coordinates of the pdb model, I know the center of symmetry, let's say (161,161,161), but I don't know how to impose it. I tried to assign these coordinates to the parameter 'cofr', but the result does not change. Does anyone know how to apply, inside a script, a rotation matrix around a given point? Any other feedback on the correctness of the script is very welcome. Thank you. Giovanni ############################################### from chimera import openModels, Point from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') for rmat in icomats: xf = chimera_xform(rmat) m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = xf # set rotation ############################################### ============================================= Giovanni Cardone Laboratory of Structural Biology Research National Institutes of Health 50 South Drive (Building 50), Room 1511 Bethesda, MD 20892-8025 USA Tel: (301) 451-8247 FAX: (301) 480-7629 Giovanni_Cardone(a)nih.gov =============================================

2 1

rotation matrices around a given center (Chimera-users Digest, Vol 62, Issue 3)
by Jonathan Hilmer 02 Jun '08

02 Jun '08

I haven't tried it out, but it looks like all you have to do is apply a transformation to your model before you apply the set of rotations. You could create a set of matrices to do it all in one step, but that's more trouble than it's worth. Something like this should work: Jonathan ############################################### from chimera import openModels from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') centerRot = (161.,161.,161.) tMat = ((1.0,0.0,0.0,-centerRot[0]), (0.0,1.0,0.0,-centerRot[1]), (0.0,0.0,1.0,-centerRot[2])) for rmat in icomats: m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = chimera_xform(tMat) # set translation to for center of rotation offset m.openState.xform = chimera_xform(rmat) # set rotation ############################################### On Mon, Jun 2, 2008 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > 1. How to define a center of rotation when applying a symmetry > (Giovanni Cardone) > 2. Re: Volume viewer negative isosurface (Elaine Meng) > 3. problem with opengl glx kubuntu (Fabian Glaser) > 4. Re: OS X aqua version (Thomas Goddard) > 5. Re: OS X aqua version (Eric Pettersen) > 6. Re: problem with opengl glx kubuntu (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Jun 2008 12:18:25 -0400 > From: Giovanni Cardone <cardoneg(a)mail.nih.gov> > Subject: [Chimera-users] How to define a center of rotation when > applying a symmetry > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <919BC0E8-98BD-4F1A-97DD-13F048B71C13(a)mail.nih.gov> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I would like to apply a rotation to a pdb model, in order to place > copies of it in equivalent symmetry points (icosahedral symmetry). > I am not sure I understand all the different coordinate systems in > chimera, but digging into the program code, I was able to write the > following script. > I am not sure it is the best way to do it, and obviously at the > moment it does not work properly, because I am not specifying the > center of rotation. > With respect to the coordinates of the pdb model, I know the center > of symmetry, let's say (161,161,161), but I don't know how to impose it. > I tried to assign these coordinates to the parameter 'cofr', but the > result does not change. > Does anyone know how to apply, inside a script, a rotation matrix > around a given point? > Any other feedback on the correctness of the script is very welcome. > > Thank you. > > Giovanni > > > > ############################################### > > from chimera import openModels, Point > > from PDBmatrices import chimera_xform > > from Icosahedron import icosahedral_symmetry_matrices > > > icomats = icosahedral_symmetry_matrices(orientation = '222r') > > > for rmat in icomats: > > xf = chimera_xform(rmat) > > m, = openModels.open('/dummy/dummy.pdb') # open a copy of the > model > > m.openState.xform = xf # set rotation > > ############################################### > > > > > ============================================= > Giovanni Cardone > Laboratory of Structural Biology Research > National Institutes of Health > 50 South Drive (Building 50), Room 1511 > Bethesda, MD 20892-8025 USA > > Tel: (301) 451-8247 > FAX: (301) 480-7629 > Giovanni_Cardone(a)nih.gov > =============================================

1 0

problem with opengl glx kubuntu
by Fabian Glaser 02 Jun '08

02 Jun '08

Hi, I installed a new version of chimera in kubuntu,and after a while, I started to get the following error when I click chimera: "Missing opengl windowing protocol (glx)" I am using kubuntu version: Linux 2.6.24-16-generic #1 SMP UTC 2008 i686 GNU/Linux nvidia and nvidia-glx are updated and installed. Any help will be highly appreciated. Best, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

2 1

Volume viewer negative isosurface
by Miguel Ortiz-Lombardía 02 Jun '08

02 Jun '08

Hi, I'm using Chimera 1.2509 for X11 on a G4 iBook running OSX.4.11 I have a problem with Volume Viewer to visualize an electrostatic potential map calculated with APBS. The same potential map can be used without trouble to color a molecular surface. The problem is that when I try to set a negative isosurface to a negative value, the box that contains map also gets colored, making the scene unclear. I'm attaching a picture to illustrate this effect. I have tried to change several settings but so far unsuccessfully... Thanking you in advance for your help, Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

2 1

Import error with chimera-1.2509-osx_x11.dmg, May 01, 2008
by Bruce D. Ray 31 May '08

31 May '08

I have a Mac G4 PPC running OS X 10.3.9 on which previous versions of chimera have run without incident. I installed chimera-1.2509 of May 01, 2008 after removing the chimera-1.2492 of Feb 11, 2008 I had been using. However, when I attempted to run chimera-1.2509 it did not start and the following error messages were written to the console.log file accessible by console.app rather than to the X-terminal: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 279, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 15, in <module> from _chimera import * ImportError: dynamic module does not define init function (init_chimera) This appears to be specific to the Mac OS X version as the Windows version of chimera-1.2509 works. Obviously, I removed chimera-1.2509 from the Mac and reinstalled chimera-1.2492 of Feb 11, 2008 which does work on this Mac. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273

3 4