- Chimera-users - RBVI Mailing Lists

rmsd cluster analysis
by Francesco Pietra 18 Dec '07

18 Dec '07

Is it feasible to command a cluster analysis from rmsd? I would like to group for likeliness snapshots from MD with respect to, say, the structure from which MD was started. Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

3 3

Problem with Chimera under Windows XP
by Peter Girard 18 Dec '07

18 Dec '07

I am running release 2304 of Chimera under Windows XP with service pack 2 on a Dell Inspiron 9300 laptop. The image disappears from the screen for no apparent reason. With the structures I am currently working on, this has become frequent and often occurs after just a few seconds when I click anywhere in the Chimera window. I have found that if I use Model Panel, I can get the picture back by clicking the 'Shown' box to remove the tick mark, then clicking it again to re-insert the tick. But the picture soon disappears again. Occasionally, it doesn't disappear completely, but part of it collapses, or spurious long lines appear. I had the same problem with a previous release, 2184, and was disappointed that upgrading didn't fix it. I can find no mention of anything similar in the documentation or email archive. Can anyone suggest a possible cause? Peter Girard (University of Nottingham, UK)

4 4

Regarding getSequence
by Jean-Didier Maréchal 18 Dec '07

18 Dec '07

Hi again, I'd like to return the sequence of the protein I opened in chimera in the python shell. >From what I read through, I thought that chimera.getSequence could be used to do so. I was thinking in a simple script beginning with : import chimera s=chimera.getSequence(0,0) .. However the chimera.getSequence(0,0) comes back with: Traceback (most recent call last): File "<pyshell#50>", line 1, in ? chimera.getSequence(0, 0) File "CHIMERA/share/chimera/Sequence.py", line 614, in getSequence File "CHIMERA/share/chimera/Sequence.py", line 656, in getSequences AttributeError: 'int' object has no attribute 'residues' and chimera.getSequence(0,A) with Traceback (most recent call last): File "<pyshell#48>", line 1, in ? chimera.getSequence(0,A) NameError: name 'A' is not defined Did I understand correctly the role of getSequence? if yes, what would be the correct syntax please? Thanks a lot! All the best, JD -- Dr. Jean-Didier Maréchal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal@uab.es

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 56, Issue 14
by Jonathan Hilmer 17 Dec '07

17 Dec '07

Ryan, Try this as a way to figure out what you can do with an object: dir(chimera.selection.currentResidues()[0]) In the above command I've indexed the list of selections to return just one object, and the dir() function will return a list of names defined by the currentResidues module. It should contain something like the following: ... 'addAtom', 'atomNames', 'atoms', 'atomsMap', 'bondedTo', 'count', 'findAtom', 'findRangeAtoms', 'getDefaultRibbonStyle', 'hasRibbon', 'id', 'isHelix', 'isHet', 'isSheet', 'isStrand', 'isTurn', 'kdHydrophobicity', 'label', 'labelColor', 'labelOffset', 'molecule', 'numAtoms', 'oslChildren', 'oslIdent', 'oslLevel', 'oslParents', 'oslTestAbbr', 'removeAtom', 'ribbonBinormals', 'ribbonCenters', 'ribbonColor', 'ribbonData', 'ribbonDisplay', 'ribbonDrawMode', 'ribbonFindStyle', 'ribbonFindStyleType', 'ribbonFindXSection', 'ribbonNormals', 'ribbonResidueClass', 'ribbonStyle', 'ribbonXSection', 'selLevel', 'type' If you try: chimera.selection.currentResidues()[0].type it will return a string with the 3-letter aa code, and the other options displayed by dir() will output useful things such as more strings, lists, or other objects that can be likewise explored. Try this combination: mySel = chimera.selection.currentResidues()[0] print "%s, %s" % (mySel.oslIdent(), mySel.type) On my test structure it returns '#0:127.A, ARG'. The second line is equivalent to 'print str(mySel.oslIdent() + ", " + mySel.type)', but the formatting I used in the above example helps to keep things clean if you have a complicated output that needs to have a specific format. There are some more advanced features of that approach detailed here: http://www.python.org/doc/1.5/tut/node45.html Jonathan > Date: Fri, 14 Dec 2007 19:55:39 -0500 > From: Ryan <pavlovicz.7(a)osu.edu> > Subject: Re: [Chimera-users] printing "zone" search > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <17bf4817f850.17f85017bf48(a)osu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. > > So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: > > print chimera.selection.currentResidues() > > i get a list like this: > > > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] > > but if i try: > > for x in chimera.selection.currentResidues(): > print x > > i get output that is much closer to what i'm looking for: > > > #0:499 > > #0:496 > > ... > > What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? > > Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, > > ryan

1 0

Re: [Chimera-users] other/5067 (error adding hydrogens)
by Eric Pettersen 17 Dec '07

17 Dec '07

Hi Jean-Francois, I have seen this error reported, but only very rarely (maybe once a year at most). Is there any chance you can tell me how to reproduce it? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

setting pdb path for local mirror
by Moo Cow 17 Dec '07

17 Dec '07

Sorry for an easy question. Chimera has a hook to use a local mirror of the PDB (preferences-PDB) I am too thick to see what path to give it. If you have the PDB, you have the top level /blah/blah/pdb the structure directory /blah/blah/pdb/data/structures/all and the divided directory /blah/blah/pdb/data/structures/divided/pdb When a non-python reader looks at the code (__init__.py), it seems to be trying out the divided directory IDcode = IDcode.lower() subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent" pdbDir = systemPDBdir() if pdbDir is not None: ..... but this does not look correct. The PDB divided path would want subpath IDcode[1:2] to get the subdirectory "pt" from a file like "5pti" Many thanks and sorry for a seemingly daft question. -- Got No Time? Shop Online for Great Gift Ideas! http://mail.shopping.com/?linkin_id=8033174

3 2

Loading .dx maps to chimera
by maya shcushan 17 Dec '07

17 Dec '07

Dear sir, I am trying to load a .dx file (electrostatic potential) onto a molecule in chimera. I successfully loaded the map onto a the molecule's surface. The problem is the potentials I get look differently than the original map. That is, the potentials appear different in the visualization tool of PMV, the program which generated the .dx file I tried to e-load on chimera. Thanks, Maya Schushan, Tel-Aviv university, Israel.

3 2

crystallographic symmops and lattice translations in Chimera
by Boaz Shaanan 16 Dec '07

16 Dec '07

Hi, Since the question was raised before, I think I know the answer to my first question about lattice translations but let me verify: 1) Chimera can apply crystallographic symmetry operations to the model as they're listed in the pdb file but it won't apply lattice translations, or in other words, won't display molecules in neighbouring unit cells. Am I correct ? maybe you can surprize me me on this and prove me wrong ? 2) Is it possible to draw the unit cell boundaries after reading in the pdb or should I read in a dummy pdb with coordinates of the unit cell vertices ? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

2 2

Re: [Chimera-users] printing "zone" search
by Ryan 14 Dec '07

14 Dec '07

Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: print chimera.selection.currentResidues() i get a list like this: > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] but if i try: for x in chimera.selection.currentResidues(): print x i get output that is much closer to what i'm looking for: > #0:499 > #0:496 > ... What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, ryan

2 1

Multi-scale models and BIOMT
by Ken Jang 14 Dec '07

14 Dec '07

Hello, I work at Boston University working mostly with pili and helical reconstructions. Recently we have been trying to fit our subunit structures into maps generated from EM data. Because what we work with are helical in nature, we use BIOMT symmetry since it is the easiest to generate using readily available data. We wanted to see just how close our subunits get and wanted to use the MSC or Color Zone commands, but we have run into a problem with the Multi-Scale Models command. Since we are using the same BIOMT data, we assumed that Multi-Scale Models would use the same origin and orientation. This appears to be the case if we don't move the subunit structure after opening it, but after we move the subunit, the generated models don't seem to be in any relavent orientation. I have attached two pictures, both from the same view, and one showing the placement of the subunits using the 'sym' command and the other showing the surface models using Multi-Scale models. Both cases were generated off the same selected subunit. Any advice or clarification on how to use Mult-Scale Models and BIOMT information would be greatly appreciated. Be seeing you- Ken Jang -and all places are alike to me

2 1

Re: [Chimera-users] printing "zone" search
by Ryan 14 Dec '07

14 Dec '07

I am actually currently interested in doing something similar to Francesco's previous question about writing out a list of residue names within a certain zone of a ligand -- however i would like to do this from a Python script. I tried to find the zone selection command to use in a script, but could not. Would it be easiest to just use the runCommand('z<') function to select a zone? Also, when the zone is selected, are the selected residue names stored in a list? If so, how can i access this list to print out the residue names into an output file of my own? Thanks a lot, ryan

2 2

edges
by Vincent Racaniello 14 Dec '07

14 Dec '07

When I display a protein as an edged ribbon, sometimes they have a black line on the edges, other times none. There seems to be no consistency in this behavior. The same also happens with surfaces. Is there a way to regulate this appearance?

2 1

Morphing on small ligand
by Jean Didier Pie Marechal 13 Dec '07

13 Dec '07

Hi everyone, I have a " small" ligand with two substantially different conformations. Just for interest: could we use the morphing module to generate intermediate conformations between those two structures? Cheers, 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

2 1

printing "zone" search
by Francesco Pietra 13 Dec '07

13 Dec '07

I am looking at the protein residues "responsible" for docking a single-residue ligand. select protein & :ligandname z<# works for various values of #. I would like to print the list of residues instead of having to detect them from the screen, which may lead to errors. Also, which section of the manual concerns RMSD? (I would like to calculate RMSD at various stages of DOCK6.1 and Amber9 MD for the above, i..e. how the ligand adapts and the protein follows it, or vice-versa). Thanks francesco pietra ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

2 1

Writing alignment and RMSD out
by shengzhiya＠nibs.ac.cn 10 Dec '07

10 Dec '07

Dear all, I would like to write both the sequence alignment and RMSD out after run “mmaker”, but I do NOT want to do this interactively because I have a batch of structures to deal with. I found Eric’s python script: structAlign.py, which is gui-only, but I do not know how to extract RMSD from the Reply Log in gui mode. Any help would be appreciated. Thanks a lot! Btw, may I know how to run structAlign.py? Is there any command like “chimera structAlign.py” and where should I put the input file structList? I can not run this script right now and here is the error message I got after run “chimera structAlign.py”: Traceback (most recent call last): File "/home/sheng/local/bin/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1253, in open File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython File "/home/sheng/local/bin/chimera/from_mailinglist/structAlign.py", line 18, in ? pdb1, pdb2, output = line.strip().split() ValueError: need more than 2 values to unpack Error while processing structAlign.py: ValueError: need more than 2 values to unpack (see reply log for Python traceback info) Best wishes, Zhiya

3 5

how to export the volume data which is stored in the memory?
by Zhiheng Yu 05 Dec '07

05 Dec '07

Hi, I loaded some volume data (mrc files) into Chimera remotely from a network hard drive. Unfortunately, the network hard drive crashed so I can not access those mrc files anymore. But in Chimera which was started before the drive crash, I still have the volume data and am still able to manipulate them. Apparently, these are stored in the memory. Does anyone know how can I export these data onto a hard drive. I tried "save as" but there is an I/O error since the computer was simply trying to duplicate data from the crashed drive. Any suggestion is appreciated. Thanks, Zhiheng

4 7

Re: [Chimera-users] how to export the volume data which is stored in the memory?
by Tom Goddard 05 Dec '07

05 Dec '07

Hi Zhiheng, Here is a script to write out the maps in memory using Chimera 1.2199. You open this script with menu entry File / Open... from the main Chimera window. It will write the files to /tmp. Of course be sure to check those files before closing Chimera. Tom Zhiheng Yu wrote: > Hi Tom, > > I got the following information: > > Beta Version 1 build 2199 2006/01/24 > Platform: linux 2. Windowing system:x11. > > Apparently, it is an older version. > > Thank you very much for your generous help. I really appreciate it. > > Zhiheng > > Tom Goddard wrote: >> Hi Zhiheng, >> >> You must be using an older version of Chimera. Old versions read >> the original file even if the map was in memory when writing out the >> data. Maybe I can give you a script that will write the maps out >> from memory if you tell me what version of Chimera you are running >> (menu entry Help / About UCSF Chimera). >> >> Tom >> # # Write maps to files. For Chimera 1.2199. Only use in-memory copy. # Written for Zhiheng Yu to recover maps lost to failed disk. # from VolumeData import Array_Grid_Data from VolumeData.mrc.writemrc import write_mrc2000_grid_data from VolumeViewer import volume_dialog from os.path import join dir = '/tmp' # Location to write maps. d = volume_dialog() for v in d.data_regions: m = v.full_matrix(read_matrix = False) if not m is None: a = Array_Grid_Data(m, v.data.origin, v.data.step) path = join(dir, v.data.name) write_mrc2000_grid_data(a, path)

1 0

(no subject)
by Julien Orts 04 Dec '07

04 Dec '07

Dear Chimera people, I would like to save a lot of pdb. I have for example 500 pdb. Each saved pdb file should contains 2 pdbs of these 500 pdbs. I can write a script for this but the command write does not work for more than two pdb. Is there any other way? thank you Julien

2 1

question about the model panel
by jean-francois menetret 04 Dec '07

04 Dec '07

Is there is way to reorder the position of the models in the model panel ? (For example putting the mrc files on top and the pdb files at the bottom) Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

2 1

Re: [Chimera-users] Question regarding Chimera usage
by Tom Goddard 03 Dec '07

03 Dec '07

Hi Navya, If you have a 3-button mouse you move the atomic model with the middle button. If that is not working then you probably have the mouse modes assigned differently. You can look at and change what the mouse buttons do with menu entry Features / Preferences category Mouse. Usually button 2 is assigned to translate in x and y (second column of table). It may not be assigned to that operation if you have used other tools like volume path tracer or volume subregion selection that reassign mouse button 2. Tom swetha davuluri wrote: > Hi, > > Thanks for your reply. I am trying to move the atomic model using the > mouse. But I can only rotate the model but not transitionally shift it > i.e. I am not able to move the model either up/down and sideways. Not > sure how to do this. Please let me know. > > Thank you, > Navya. > > ----- Original Message ---- > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > To: swethadn(a)yahoo.com > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Sent: Friday, November 30, 2007 9:27:37 AM > Subject: Re: [Chimera-users] Question regarding Chimera usage > > Hi Navya, > > The first step is to move the atomic model using the mouse close to > the correct location in the EM map. The Fit Model in Map tool will not > move the atomic model if its initial position lies outside the map. > Here are instructions on how to do the fitting. > > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… > > Tom > > > > ------------------------------------------------------------------------ > Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See > how. <http://us.rd.yahoo.com/evt=51732/*http://overview.mail.yahoo.com/>

3 2

Remove steric clashes
by Francesco Pietra 02 Dec '07

02 Dec '07

I would like to delete all water residues that are in steric clash with lipid residues. What I have is a single pdb file that includes both types of residues. Can't have the two as different models. Therefore I can't apply the zone tool that I know how to manage for two different models. The only alternative I can figure out is through the "Find Clashes,Contacts", writing a file for all WAT at a specified distance from the lipid residues and then manually deleting, or inventing a script for that (at <=0.6A there are 386 clashes). Hope to have missed an automatic tool from Chimera. If not, I suggest that as a most useful additional tool for cleaning systems. I dropped into the problem when at the first minimization, in view of MD, the system met segmentation fault after a few steps, with gradient decreasing by eight orders of magnitude along those few steps. Then I recognized not to have been careful enough before making the coordinate files for the MD suite. I should have not relied too much in the membrane builder and I had better spent time in checking for steric clashes. Thanks francesco pietra ____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs

2 1

distance measurement
by sette＠uniroma2.it 30 Nov '07

30 Nov '07

Dear all, I would like to measure the distances between all atoms in a molecule, in particular between all hydrogens. I added the H but it seems to me that is possible to measure only the distance between two selected atoms and not between all atoms in a single command. How is possible to do? Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

2 3

morphing structures
by Elaine Meng 30 Nov '07

30 Nov '07

> Thank you for your help. I did superimpose the structure with pdv > viewer. I did save as a pdb file but when I open the morph > conformations tool and I add the pdb I am not able to create the > interpolation between the structure. > > Do you know why? > Hi Djemel, I would recommend just using Chimera to superimpose the structures. Starting with the two structures in two separate files, open them with File... Open in the Chimera menu, then superimpose them. There are lots of ways to superimpose them but probably this simple command (show command line with Favorites... Command Line) will work fine: matchmaker #0 #1 In Morph Conformations you have to specify more than one structure. There should be more than one line in the Conformations list. My guess (and it's only a guess) is that the way the other program wrote the file it was considered all one structure, not 2 separate structures. 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

Detecting residue from command line
by Francesco Pietra 30 Nov '07

30 Nov '07

Sorry for a question that was surely answered many times. How to detect on the screen (from command line) residues from their resSeq number?. I have two different sets of WAT: 522-9999 and 0-4759 and want to check where 0-521 are located in a protein-ligand-POPC membrane. Thanks francesco pietra ____________________________________________________________________________________ Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ

2 3

morphing movie
by Elaine Meng 30 Nov '07

30 Nov '07

> Actually I would like to do some movie with chimera but I never used > before. I have two crystal structure of two different conformation of > the protein that I work with. I would like to see the trajectory from > conformation 1 to 2. I just downloaded the chimera but I don't know > how to start. > > Could you tell me how to make the movie? I would appreciate you help. > Is that possible to load molecule 1 and 2 and see how the trajectory > is ? Begin forwarded message: From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: November 30, 2007 10:29:41 AM PST It sounds like you want to use the Morph Conformations tool (under Tools... Structure Comparison). If you have two structures, it will "make up" a series of in-between structures to create a trajectory. You have to match (superimpose) the two structures yourself first. There are different options of how to make the in-between structures and how many to make. The trajectory-viewing tool, MD Movie, is automatically started to show the trajectory. From MD Movie you can record the trajectory as a movie file (Quicktime or other formats) or just save it as a PDB file for later viewing in Chimera. Probably you will need to learn a little bit about using Chimera so that you can set the display (ribbons, background color, displaying important sidechains) how you want for the movie. Chimera comes with a User's Guide. You can open it directly or search it from the Chimera Help menu. Also clicking the Help buttons on dialogs will automatically open the corresponding man pages. I will give some links to our Web site, but most of the same pages are included with your download. Tutorial on matching structures and making nice images: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html Manual page for Morph Conformations: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html for MD Movie: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (see the "Recording a Movie" section) For basic Chimera use, there is "Getting Started" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html and a more detailed version of that at our web site (not in the User's Guide): http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html but if you get stuck or have trouble finding something, you can ask me about it. 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] Question regarding Chimera usage
by Tom Ferrin 30 Nov '07

30 Nov '07

------- Forwarded Message Date: Thu, 29 Nov 2007 20:06:54 -0800 From: swetha davuluri <swethadn(a)yahoo.com> To: tef(a)cgl.ucsf.edu Subject: Question regarding Chimera usage Dear Dr. Ferrin, I have a question Chimera usage. I am trying to fit a model to an EM map. I cou ld lock the map from moving but I am not able to transitionally shift the model . The translational shift box in "Fit Model in Map" is checked. Please let me k now how to transitionally move the model. Regards, Navya. _________________________________________________________________________ ___________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.ya hoo.com/ ------- End of Forwarded Message

2 1

2D for 3D display
by Gang 'Gary' Ren 29 Nov '07

29 Nov '07

Hi, Chimera, I wonder how to create the 3D display by using the 2D image as below? http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/afm/stmv-afm-large.png best regards Gary ---------------- Gang Ren, Ph.D. Phone: (415) 476-8284; Fax: (415) 514-2550 Email: gren(a)msg.ucsf.edu; Web: 3dem.ucsf.edu Department of Biochemistry & Biophysics 1700, 4th Street, Byers Hall (QB3), room 301C San Francisco, CA 94143-2532

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 55, Issue 29 (heightmaps)
by Jonathan Hilmer 29 Nov '07

29 Nov '07

I would also be interested to learn how to do heightmaps in Chimera, or if it would be possible to add such a feature. Right now we use ImageJ (which doesn't have enough functionality) and Blender (which has too much), while Chimera would be perfect. In response to Gabe's question, it's not terribly convenient but you could use the Zone tool to generate just the 'positive' region and save that as a unique file. The 'combine.py' could then be used to subtract out the positive from the original, leaving the zeroed parent density file. Jonathan > Message: 1 > Date: Wed, 28 Nov 2007 22:12:40 -0800 > From: "Gang 'Gary' Ren" <gren(a)msg.ucsf.edu> > Subject: [Chimera-users] 2D for 3D display > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <web-5552878(a)msg.ucsf.edu> > Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" > > Hi, Chimera, > > I wonder how to create the 3D display by using the 2D > image as below? > > > http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/afm/stmv-afm-large.png > > best regards > > Gary > > ---------------- > Gang Ren, Ph.D. > Phone: (415) 476-8284; Fax: (415) 514-2550 > Email: gren(a)msg.ucsf.edu; Web: 3dem.ucsf.edu > > Department of Biochemistry & Biophysics > 1700, 4th Street, Byers Hall (QB3), room 301C > San Francisco, CA 94143-2532 > > > ------------------------------ > > Message: 2 > Date: Thu, 29 Nov 2007 10:23:49 -0800 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] reverse "zone" tool? > To: Gabriel Lander <glander(a)scripps.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <474F03B5.5060609(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Gabriel Lander wrote: > > Hi Tom, > > is it possible to somehow make the "zone" tool in the volume viewer do > > the reverse of what it does? I have a PDB docked into a density file > > and I want to remove the density surrounding it so that it's easier to > > focus on the rest of the structure. > > By the way, I thoroughly enjoyed your demo of the new Chimera features > > here at the cryo course, I'm sorry I didn't have a chance to chat very > > much afterwards, > > Cheers, > > -gabe > > > > > Hi Gabe, > > One trick would be to use the "Color Zone" tool to color the surface > near the fit model completely transparent (hence invisible). Use menu > entry Actions / Color / From Editor, click the Opacity button and set > opacity to zero. Your molecule will be invisible. Then use Tools / > Volume Data / Color Zone, select all atoms (Select / Select All) and > press the color zone dialog Color button. Then go back and change the > color of the molecule to something visible. > > Three drawbacks of this approach. First, it doesn't allow you to > save the map with the region near the molecule zeroed out -- it is only > coloring the surface. Second, having a partially transparent surface > makes the rendering slower. Third, Chimera only handles one transparent > model correctly. If you try to add a second transparent surface you > will see odd effects, like the invisible patch blocks the second > transparent surface. If these limitations are severe, I can give you a > bit of Python code that actually makes a copy of the map with the part > near the molecule erased. > > Tom > > > ------------------------------

1 0

Re: [Chimera-users] reverse "zone" tool?
by Thomas Goddard 29 Nov '07

29 Nov '07

Gabriel Lander wrote: > Hi Tom, > is it possible to somehow make the "zone" tool in the volume viewer do > the reverse of what it does? I have a PDB docked into a density file > and I want to remove the density surrounding it so that it's easier to > focus on the rest of the structure. > By the way, I thoroughly enjoyed your demo of the new Chimera features > here at the cryo course, I'm sorry I didn't have a chance to chat very > much afterwards, > Cheers, > -gabe > Hi Gabe, One trick would be to use the "Color Zone" tool to color the surface near the fit model completely transparent (hence invisible). Use menu entry Actions / Color / From Editor, click the Opacity button and set opacity to zero. Your molecule will be invisible. Then use Tools / Volume Data / Color Zone, select all atoms (Select / Select All) and press the color zone dialog Color button. Then go back and change the color of the molecule to something visible. Three drawbacks of this approach. First, it doesn't allow you to save the map with the region near the molecule zeroed out -- it is only coloring the surface. Second, having a partially transparent surface makes the rendering slower. Third, Chimera only handles one transparent model correctly. If you try to add a second transparent surface you will see odd effects, like the invisible patch blocks the second transparent surface. If these limitations are severe, I can give you a bit of Python code that actually makes a copy of the map with the part near the molecule erased. Tom

1 0

Server and Client machines with different OS
by Isabelle Vergely 28 Nov '07

28 Nov '07

Hello, I know that it is possible to open one or several pdb files on a linux machine using a system command line like "> chimera [options] [input1 input2 ...]". My question is: Is it possible to use this command on a linux server to display chimera on a Windows client machine? Thank you very much in advance for your help. Best Regards. Isabelle

5 4

ppt and movies
by Markus Voehler 27 Nov '07

27 Nov '07

I have recorded a movie of a pdb in chimera with the following command: movie record supersample 3 . . movie stop movie encode bitrate 6000 mformat avi output ./pol_b_movie.avi I can import it into ppt (2004, V 11.3.5) on my Mac (OS X 10.4.11) and it plays fine in the editing mode, but when I go to the slideshow and start the movie, there is a blank screen for the duration of the movie. When it is done, it shows the standing slide again. Any idea what might be going on? Also, is there a better way to improve the resolution then setting the bitrate to 6000, 30 f/s? I have tried the supersample 3 option, but this does not seem to make much of a difference in the final movie. Any input is appreciated. Markus

5 4

Re: [Chimera-users] [Fwd: Re: Chimera hide all models button]
by Eric Pettersen 27 Nov '07

27 Nov '07

I guess I do have some tips to offer here. You can use the "Configure..." button of the Model Panel to change what happens when you double click on a model. By default, double clicking shows the attributes of a model. You can have double click do any combination of button actions, so you could instead have double click both "show only" the model and "activate only" the model. With that configuration, if you wanted to show and activate two specific models you would click on one model and then control-double- click on the other one. If you want to show and activate all models you would click on the first model listed in the Model Panel and then shift-double-click the last model. --Eric On Nov 27, 2007, at 8:57 AM, Tom Goddard wrote: > Eduardo thinks we need better controls for showing just one or two > models and activating just one model when many are present. > > -------- Original Message -------- > Subject: Re: Chimera hide all models button > Date: Tue, 27 Nov 2007 08:34:07 -0700 > From: Eduardo Sanz-Garcia > To: Tom Goddard > > > Tom Goddard wrote: >> Hi Eduardo, >> >> Perhaps clicking on the "Shown" heading in the Model Panel could >> hide all models if all are shown, or show all if all are hidden. >> If some are hidden and some are shown maybe it would show all, >> then a second click would permit you to hide all. I don't really >> like this idea because very few people would know to try it. >> Usually clicking on list headings sorts using that column. > That is true. I didn't realize about this. >> Although sorting may seem not too useful for the "Shown" column I >> can imagine if you have 50 models open with just a few shown you >> might want to sort to bring those to the top. >> >> A slightly harder way to show just one model is to select its >> line in the Model Panel and press the "Show only" button in the >> right column of buttons. Unfortunately that button is way down on >> that scrolled list of buttons. You can hide many of those buttons >> using the "Configure..." button on the Model Panel and it will >> remember the hidden ones in your preferences file. But there is >> no way to reorder the buttons as far as I know. >> >> The oval next to the step size above volume histograms allows you >> to show/hide that map. Maybe I could enhance that so if you use >> the right mouse button instead of the left then it shows that map >> and hides all others. Cryptic but not unexpected behavior. > Yes, this is a little cryptic but a fast method. >> Still there are only 3 histograms shown by default. Perhaps if I >> added the scrollbar for the histograms as you suggest that would >> further improve switching display between individual maps. > I believe that the scrollbar is a very good idea! > > I believe that Chimera should improve the way to show or activate > all the models faster from the GUI. I spend a lot of time > activating two models, deactivating the rest, and showing only > these two models. The command line is fast but there are some, like > me, that always forget the commands. >> >> Let me know what ideas you think are best. It is quite difficult >> to make the user interface simple to use and powerful. Thanks for >> your ideas. >> >> Tom >> >> Eduardo Sanz Garcia wrote: >>> Do you mind if I share a very personal suggestion? >>> I always open 5 or more maps at the same time (chimera >>> directories*/*100.map) . I normally want to examine each >>> individually, and then compare them. I would like to undisplay >>> all of them at the same time. I know that this is possible from >>> the command line (~modeldisplay), but I always forget it. It >>> would be nice to have the same function from the GUI. I am >>> suggestion to be able to click in the black circle (bottom image) >>> and un/display all the models at once. >>> >>> Anyway, thanks for the volume viewer capabilities of chimera. >> >> >

1 0

How do I
by Eduardo Sanz Garcia 26 Nov '07

26 Nov '07

I am using Chimera alpha version 1 build 2467 2007/10/31 I liked how each volume map opened has a different color. That's a great idea!! But I have a problem, I am displaying 4 volume maps at the same time. The volume viewer window only shows 3 histograms, therefore to modify the threshold of the fourth I have to close one of the volumes. Is there a way to modify the fourth histogram in the volume viewer window without close another? I also found a different behavior if you close the upper, middle and bottom histogram. Thanks.

2 1

saving color palette
by William Jeffrey Triffo 26 Nov '07

26 Nov '07

is there a way I can save the color palette to a file? I realize it seems to be saved as a user setting somewhere because it always pops up again in the same configuration as the previous session, but I would like to be able to back it up intentionally if possible. Also, is it possible to save/load various palettes? thanks, -Jeff --

4 5

Chimera vs Amber, which one digresses from the average pdb rules?
by Francesco Pietra 26 Nov '07

26 Nov '07

A lipid/water pdb file that was good for Leap (Amber9) to get top/crd, once passed through Chimera 2470 to remove residues is no more good for Leap. All TER were removed by Chimera, ATOM renamed HETATM, while CONECT records were added. As such, Leap said: In file [chirality.c], line 142 Atom named C217 from POP did not match Aborting I knew such type of message. There is no C217 atom. On previous (different) occasions, insertion of TER records put the house in order. I inserted all TERs between POPC residues and between WAT residues (thanks to Python!). Now Leap said: In file [atom.c], line 444 bond AtomProblem found Aborting As I did not know this type of message, I tried to investigate that line 444. Following vim's command :n,444 that line, indicated at bottom of terminal as "444,1", reads HETATM 441 O31 POPC 5 -44.082 -12.831 14.685 1.00 0.00 O A carbon atom (if "[atom.c]" means carbon, is at line 447,1, which reads HETATM 444 C32 POPC 5 -46.343 -12.925 15.140 1.00 0.00 C In the original (good for Leap) pdb those lines read: ATOM 441 O31 POPC 4 -37.722 -19.453 18.019 1.00 0.00 L11 O ATOM 444 C32 POPC 4 -39.844 -19.273 18.941 1.00 0.00 L11 C Chimera also changed atom names, such as in the final part of the POPC residue (Sybyl naming?, if so, there is an alternative in Chimera not to follow Sybyl rules?) HETATM 528 XH14 POPC 5 -47.646 -9.424 -0.112 1.00 0.00 H HETATM 529 YH14 POPC 5 -46.217 -10.553 -0.172 1.00 0.00 H HETATM 530 5C31 POPC 5 -47.890 -11.168 -1.419 1.00 0.00 C HETATM 531 XH15 POPC 5 -47.763 -12.309 -1.296 1.00 0.00 H HETATM 532 YH15 POPC 5 -48.986 -11.063 -1.417 1.00 0.00 H HETATM 533 6C31 POPC 5 -47.242 -10.566 -2.756 1.00 0.00 C HETATM 534 XH16 POPC 5 -46.135 -10.759 -2.831 1.00 0.00 H HETATM 535 YH16 POPC 5 -47.802 -11.112 -3.597 1.00 0.00 H HETATM 536 ZH16 POPC 5 -47.451 -9.454 -2.737 1.00 0.00 H TER which, in the original (good) pdb was: ATOM 528 H14X POPC 4 -38.665 -14.879 4.398 1.00 0.00 L11 H ATOM 529 H14Y POPC 4 -39.080 -16.603 3.952 1.00 0.00 L11 H ATOM 530 C315 POPC 4 -40.370 -15.221 2.996 1.00 0.00 L11 C ATOM 531 H15X POPC 4 -41.330 -15.752 3.099 1.00 0.00 L11 H ATOM 532 H15Y POPC 4 -40.694 -14.148 3.019 1.00 0.00 L11 H ATOM 533 C316 POPC 4 -39.787 -15.573 1.664 1.00 0.00 L11 C ATOM 534 H16X POPC 4 -39.553 -16.661 1.544 1.00 0.00 L11 H ATOM 535 H16Y POPC 4 -40.534 -15.211 0.948 1.00 0.00 L11 H ATOM 536 H16Z POPC 4 -38.782 -15.094 1.533 1.00 0.00 L11 H TER Although it is not clear to me yet where really Leap crashed (nor am I placing Leap as the standard; simply I have to get top/crd from it, if I want to carry out MD with Amber). Elaine already kindly clarified the ATOM/HETATM issue. I hope now to get help about the atom names , ie a table of conversion to get Leap working or a not-Sybyl choice in Chimera. Once again, I regret very much to pose so many problems of language. Thanks francesco pietra ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

3 6

<< Rendering proteins with Chimera >>
by Hatuey Hack 23 Nov '07

23 Nov '07

Hi all, As a Chimera new users, I notice that the proteins are rendering different depending on the program they where prepared. I used the preset to render them. I have a protein with all residues in different color and the other protein is rendered in a single color. My question is: this is a problem of Chimera or it is a problem with the protein file? Regards, Hatuey

2 1

Aligning a protein into a membrane
by Francesco Pietra 22 Nov '07

22 Nov '07

Elaine: Relating to your instructions of last 19 Nov (I printed your mail, then unfortunately I deleted it) how to align a protein into a membrane (for both I have valid pdb and valid Amber parameters) I am probably made elusive mistakes at the stage of saving new pdbs. I aligned the protein into the membrane, then (with protein selected and membrane not active) I saved the new pdb, getting two files, "0" for the membrane and "1" for the protein. In Amber LEaP both these pdb file could be loaded and combined, however save top/crd failed because something was wrong with the membrane file. In fact, if the original pdb for the membrane is used, top/crd can be saved, though the protein is not accurately aligned. Clearly, my plan is to remove superimpositions among molecules for the "whole" obtained from Amber. Thanks francesco pietra ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/

2 7

Re: [Chimera-users] ppt and movies
by Elaine Meng 22 Nov '07

22 Nov '07

Hi Markus, I can answer this one: > Why does the command movie record supersample 3 give virtually the > same file size then just movie record? Supersampling in Chimera initially saves a larger image for each frame but then samples it down to the requested size. This reduces "stairstepping" along edges without changing the pixel dimensions of the image that is ultimately saved for each frame. It increases calculation time rather than file size. Supersampling is also an option for saving individual images (File... Save Image) when you are not raytracing. You can see the difference provided by this feature independent of the movie-encoding process by comparing images saved with and without (1x1) supersampling. 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] chimera help - surface exposed sides
by Elaine Meng 22 Nov '07

22 Nov '07

On Nov 22, 2007, at 1:07 AM, Thomas C. Marlovits wrote: > Hi Elaine, > I am trying to find an easy way to determine solvent > accessible/surface exposed side chains but also buried side chains > from atomic structures. > The idea would be to: > - display the surface > - have a command that would highlight (color) surface exposed side > chains/amino acids > Optional: color the identified aa by physical property, etc > - show all the identified amino acids on a primary sequence > - write out the amino acids into a text file. > > Would be great if you can let me know, how to do this most efficiently. > Thanks, > -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, - First assign atoms (or residues) an attribute with values equal to their solvent-accessible surface areas (more details below). - Then you can use Select... By Attribute Value to select any subset of those based on some cutoff, for example all atoms with surface area > 0. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#select The selection can be written as a list of atoms (or residues) with Actions... Write List, and the Sequence tool will show the current selection on the protein sequence (it would also be shown on a multiple sequence alignment associated with the structure, if you have such an alignment). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html - Of course you could also color the selection, but now that numerical attributes are assigned, you can map values to colors that will gradually shade from one to another with "Render by Attribute" or the command "rangecolor" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html Now, back to how to get the attribute values assigned. Currently it is necessary to use the "Area/Volume from Web" tool (under Tools... Surface/Binding Analysis). It sends coordinates to the NIH StrucTools server. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html We are in the process of generating our own surface-calculation code that will provide these values within Chimera, but it is not done yet. The main inconvenience of this server approach is that you should first delete things like water and ligands if you don't want them lumped with the protein during the calculation. "Area/Volume from Web" has a few different options of what is calculated. You can use its MSMS method to calculate both molecular surface and solvent-accessible surface (this will generate two attributes) or the Gerstein method to calculate solvent-accessible surface. Atom attribute values will automatically be assigned by this tool. If you want them summed to residue attribute values, you must also use "Attribute Calculator". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html There are examples of using Area/Volume from Web, Attribute Calculator, and Render by Attribute in the Attributes tutorial, part 2: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ attributes.html#part2 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

Coloring a surface according to distance from a selection
by Paul.Pillot＠ac-nice.fr 21 Nov '07

21 Nov '07

Hello, I can color a surface according to the distance from a single point or a plane, but is it possible to do it according to the distance from a selection (eg an other chain or molecule) ? My aim is to show the contacts between an antibody and an antigen. I tried the tool intersurf for doing it, but the result is pretty crude (low definition of the surface compared to the usual surfaces available). Thanks in advance, Paul

3 2

spaceball 5000
by Jean-Paul Armache 20 Nov '07

20 Nov '07

hello, i have a question regarding usage of a 3d manipulation device. i have a spaceball 5000 device, which i would like to use under linux (or windows). is there a way of using this device in chimera? best regards, Jean-Paul Armache AG Beckmann LMU Gene Center

3 2

move a structure into another one
by Francesco Pietra 18 Nov '07

18 Nov '07

I have installed chimera-1.2470 on Debian Linux i386. Thank you. I want to insert a protein into a lipid membrane in a precise opientation, then save the protein pdb in this configuration. I used VMD in the last few days to this redard. I wonder whether I can stick to Chimera for this purpose too. I tried by selecting "protein", though it was difficult to proceed. Thanks francesco pietra ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/

2 3

Puzzle with WAT
by Francesco Pietra 17 Nov '07

17 Nov '07

I am faced by a recurring puzzle with WAT (standard TIP3). In Amber9 xleap I loaded a pore protein_noH.pdb model getting top and crd files In both Chimera and VMD these showed that the WAT oxygen atom (natural, inside the pore) had been added of two hydrogens with intramolecular bonding between the two hydrogens. Otherwise, the geometry was correct for water. Correspondingly. in Chimera dockprep complained that one hydrogen of that WAT had incorrect valency, and refused to proceed. The protein.pdb created with ambpdb from such top and crd files showed the WAT correctly, without intramolecular H-H bonding. The geometry was exactly the same as for the above "wrong" WAT. With this protein.pdb, Chimera's dockprep was happy. That allowed docking with various (big) ligands, including amber re-score. I posted to dock-fans that the issue was solved, and how. Now I wanted to carry out Amber9 MD of that protein-ligand complex, inserting it into a lipid bilayer. I first tried the above protein.pdb alone into a membrane. A new venture for me. I posted separately a question how to create a hole around the protein. However, even when that is solved, I am faced again by the problem of viewing WAT into the pore as a triangle. Also, the many WAT mixed to the POPC of the membrane are also viewed as triangles. Actually, when that protein.pdb is loaded to xleap (as before leaprc.ff99SB and leaprc.gaff), the WAT into the pore is seen as a triangle. Thus, the protein.pdb, created with amdpdb is good for viewers and dockprep and docking, not back for LEaP. Although, it may seem as a loop, these are the facts (that so far I am unable to understand). I did not try yet if that allows MD, just because going on with such triangulated water seems unsafe. The protein.pdb ends as follows: TER ATOM 6885 O WAT 445 -0.036 0.094 -2.262 ATOM 6886 H1 WAT 445 0.921 0.094 -2.262 ATOM 6887 H2 WAT 445 -0.276 1.021 -2.262 TER END The membrane.pdb ends as follows: ATOM 50316 O WAT 3357 47.120 46.103 -26.069 1.00 0.00 W45 O ATOM 50317 H1 WAT 3357 46.727 45.819 -26.895 1.00 0.00 W45 H ATOM 50318 H2 WAT 3357 47.214 47.052 -26.153 1.00 0.00 W45 H END as a representative of the many WAT present. Thanks francesco pietra (the membrane was created with VMD and the file rearranged to be understood by Amber9) ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

1 0

1.2470 production release available
by Eric Pettersen 16 Nov '07

16 Nov '07

Hi all, The production release, version 1.2470, is out now. A list of changes from the previous production release (1.2422) can be found here: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2470.html I think that page is pretty easy to scan through, but for those of us who are really time-challenged, the important changes, I think, are: 1) Incorporation of what were previously "experimental features", such as morphing between volume data sets 2) Volume Viewer improvements: a) Multi-data set interface b) Distinct initial map colors c) Resampling of rotated maps d) Improved large-file handling e) Single-plane display f) Scriptability 3) Display of dendrograms in Multalign Viewer 4) Use of rotamer libraries in swapping residue side chains with the ability to evaluate possible swaps based on clashing, fit into density maps, or hydrogen-bond formation Mac users with the new Leopard OS should note that it seems that 3- button mouse emulation is off by default in Leopard's X11. So, if you have a one-button mouse and want to be able to scale/translate using the mouse + alt/command, do the following: 1) click on the X11 icon (it should show up in the dock when you start Chimera) 2) open the X11 menu from the menubar at the top of the screen 3) choose the Preferences... entry 4) in the resulting dialog choose the Input tab 5) enable the Emulate three button mouse option --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Ramachandran Plots
by Quinton Dowling 16 Nov '07

16 Nov '07

Hi, I am interested in creating a ramachandran plot from an md trajectory. Particularly I would like to track the change in phi/psi angles over time for specific amino acids throughout the md in a fashion that is easily presentable. Is there a way to do this with Chimera? Or any way at all? Thanks a bunch. Quinton Dowling Research Computing Center The College of Idaho Caldwell ID 83605

3 2

Re: [Chimera-users] Z-slice transparency
by Tom Goddard 15 Nov '07

15 Nov '07

I met Lu in San Diego and found out he was showing a volume slice and a second model which was also a volume using solid rendering style. The trouble is that Chimera cannot correctly display two transparent models -- at most one can be transparent. If two are transparent, the last one drawn (higher model id number) always appears on top of the other transparent models. This is a (serious) limitation of the Chimera graphics architecture. Technically Lu has the single plane set to be completely opaque, but all solid rendered volumes are rendered as if they have transparency even if the coloring is set for complete opacity. (The OpenGL z-buffer which records the depth of visible objects and prevents obscured surfaces from being shown is not used with "transparent" rendering). We tried using the TomoPlane Chimera extension from Karin Gross and Christoph Best and that draws truly opaque volume planes, but it is much slower. Tom Lu wrote: > Hi Tom, > > I tried everything that you mentioned, including adding multiple > points to the histogram, but I can still see stuff through the > Z-slice. Anyway, I noticed that you're going to be at the Scripps EM > workshop next week. If you have time at the workshop, I'd be happy to > show you the type of Amira movie that we'd ultimately like to make > using Chimera. > > Cheers, > -Lu

1 0

mutation of residue
by hjoseph＠brandeis.edu 15 Nov '07

15 Nov '07

Hi everyone, I want to model my mutated residue into crystal structure and see its interactions. If anyone knows and easy way of doing it in Chimera please let me know. Thanks everyone, Helen Josephine

2 2

how to make a bond
by dominique matt 15 Nov '07

15 Nov '07

I want to draw a bond between two atoms which appear linked by a dotted line. This is often the case when one atom is a metal. How can I draw the bond ? Thank you for your help Kind regards Dominique MATT Strasbourg

3 2

Ribbackbone spec?
by Jean Didier Pie Marechal 14 Nov '07

14 Nov '07

2 2

Z-slice transparency
by Lu 13 Nov '07

13 Nov '07

Dear Chimera Crew, Is there a way to adjust the transparency of a Z-slice using the Volume Viewer's "planes" feature? Right now, it looks like the Z-slice has transparency and lets you see the isosurfaces/segmentations below it. We would like to turn off the Z-slice transparency so that it blocks everything that is behind it. Such a feature would allow us to use Chimera to make a movie that we've been using Amira for, i.e., a movie in which the isosurface (or segmentation) is "revealed" as the map's Z-slice drops down. If the effect that I'm describing isn't clear, I'd be happy to forward a link to such a movie. Thanks! -Lu -- Lu Gan Postdoc, Jensen Lab Caltech Broad Center, MC 114-96 1200 E. California Blvd. Pasadena, CA 91125 Tel: 626-395-8848 Fax: 626-395-5730

4 3