- Chimera-users - RBVI Mailing Lists

volumetric filling
by jayant_jacques 04 Oct '06

04 Oct '06

hi! I am striving to perform voluertric filling of a crystal structure into an EM reconstruction. I have down loaded and complited the Linux_64 bit version. I first load my crystal structure and then the EM reconstruction on the same screen and set the EM reconstruction as DATa. I am not able to figure out where the FIT buttons is located in the pop up menus!!! I would be very grateful if you could help me sort out this issue! Thanks Jayant NB I am using the online manual to help me in this endeavour http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodel… Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

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Slicing a 3d model
by Thomas Goddard 04 Oct '06

04 Oct '06

Hi Pu Qian, Use clip planes to cut a model in half in Chimera. There are two types of clip planes. The front and back clip planes are always parallel to the screen. The per-model clip planes can be oriented at any angle. Both can clip away the back as well as the front. The following web page describes how to use both for EM density maps. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#slab Clipping works on all types of data in Chimera including atomic models of proteins. For EM data it helps to have Chimera cover the holes left when a contour surface is clipped. This is described here. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#capping Also you can color according to density on the sliced surface. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorc… All of these URLs come from the Chimera guide to volume display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html and you may find other useful features for viewing your EM map there. The following page shows examples of clipping, capping and coloring including a movie of a slab moving through an EM map of a virus particle. http://www.cgl.ucsf.edu/chimera/experimental/viper_em/viper_em.html Chimera reads many density map file formats (CCP4, MRC, SPIDER, O, XPLOR, Purdue image format, ...) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume I do not know if IMAGIC5 uses any of these formats or has its own. Chimera does not read any specific IMAGIC5 format. Tom > From: P Qian <P.Qian(a)sheffield.ac.uk> > Date: October 4, 2006 1:43:50 PM PDT > Subject: Sheffield Qian, how to make cut 3d model > > > > To whom it may concern, > > I'm a new user of Chimera. It is a very good software! > > Here, I would like to ask you a few questions? To show inside of > protein > (3d model),I need to cut it into half (sometime, maybe only part, > for example, > 1/4 etc.). Just like an apple, if I want to show its core, I need > to cut the > apple into two parts from its middle. Does Chimera has such > function? (I think > it has.) My 3d data comes from electron microscopy single particle > analysis > using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so, > which type of > 3d data I should produce for Chimera? It would be a great > appreciated if you > could reply me in your convenience. Hope it will not bother you too > much. > > Sincerely yours, > > > Pu Qian > > Dr. Pu Qian > Department of Molecular Biology > The University of Sheffield > Firth Court, Western Bank > Sheffield, S10 2TN > UK >

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Re: [Chimera-users] Merge PDB Question
by Jonathan Hilmer 28 Sep '06

28 Sep '06

On the issue of using Chimera to write PDB files, would it be possible to change the format of the PDB output Chimera generates? I'm not too well-versed in the details of the pdb file format, but I ran into issues using Chimera-generated structures with a Blender plugin that used BioPython to handle parsing the files. Although I can't remember the details off the top of my head, it involved the use of multiple 'END' statements to separate models (in Chimera-generated files). It was easy enough to write a script to substitute 'MODEL', 'ENDMDL' pairs, but I'm sure it would be better implemented in whatever library handles the file IO in Chimera. Jonathan > Date: Thu, 28 Sep 2006 10:38:00 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Merge PDB Question > To: "Jared Godar" <jared.godar(a)vanderbilt.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <4F99156D-A681-4EFB-AC6C-5A0C57D029E0(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Jared, > Currently you cannot bond different models, and the only way to > "merge" is to put the atoms in the same file before opening it. > There are actually other reasons your command wouldn't work: > > - seems to me that there is no model 1, only 1.1, 1.2, 1.3 and 1.4, > so the first part would specify zero atoms > - the ampersand & stands for intersection (logical AND, not english > and) and should be omitted, e.g. > command: bond #1.1:504.b@c #1.1:505.b@n > > What I've done in the past to handle similar cases (splicing stuff > from an NMR structure onto a Xray structure) is to first put the tail > (with a few extra residues to overlap with residues that are already > present) into a file by itself. Then I open that new file, so it > will be a new, separate model. I then match that model onto the > original model using atoms in the overlapping part. Then, write out > another PDB file of the tail relative to the untransformed original > model. Using text-editing, remove the part that overlaps since it > was just there for positioning purposes. FINALLY (text-editing > again) make another PDB file that combines the new tail with the > original protein. They may need to have the same chain ID as well. > Sorry this is such a long process. If you think you can hand- > position the tail sufficiently well you could skip the parts about > having the extra atoms, using them for matching, and deleting them. > > If you remove any intervening TER, the bond will already be there > when you open the new file. > > I hope this helps, > Elaine

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Re: [Chimera-users] [chimera-dev] chimera help
by Eric Pettersen 28 Sep '06

28 Sep '06

If you have a large number of PDBs then you might want to use Python, where you have access to loops and variables. Say you had the PDBs listed in a file, one per line, named "mypdbs". Then you might use a Python script like this: -------------------------------------- import chimera from chimera import runCommand f = open("mypdbs", "r") for line in f: pdbID = line.strip() runCommand("open " + pdbID) runCommand("scale 1.5; ~disp; ribbon; ribrepr smooth; rainbow") runCommand("copy file %s.png png supersample 5" % pdbID) runCommand("close all") -------------------------------------- Note that the "runCommand" function allows you to do things that you know the Chimera command for without knowing what the Python equivalent is. Assuming you name the script file with a ".py" ending so that Chimera can recognize it as Python, then you can run the script with any of the ways that Chimera opens files (File...Open dialog, "open" command, startup shell command argument). Also, Chimera needs the graphics window to be showing and not obscured by other windows in order to render the images. If you are doing a lot of images you may have to turn off your screen saver so that it doesn't hide the Chimera window. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Sep 28, 2006, at 9:14 AM, Elaine Meng wrote: > Hi Vishal, > Actually you can do this with a Chimera command script, as opposed > to programming in Python. A command script just contains the same > commands you would enter in the Command Line. I'm not sure of what > type of saving you had in mind, " but the "copy" command can be > used to save an image file, "save" to save a session, and "write" > to save a PDB file. > > This page links to all the command man pages, plus it discusses > command scripts (at the bottom): > http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/ > framecommand.html > > Just opening the command file will execute the commands. > Here are links to a couple of example command files: > http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/tutorials/ > setup.com > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/ > 1gfl.com > > And here is another, between the dashed lines: > ----------------------------------------------------------------- > open 1hxx > open 1pho > modelcolor coral #0 > modelcolor cornflower blue #1 > ~disp; rep bs; ribbon; ribrepr smooth > matchmaker #0 #1 > ----------------------------------------------------------------- > > I guess the main difficulty if you are saving images is how to get > a good view of the structures. Usually some rotation, scaling, etc. > is done interactively to make a better picture. > I hope this helps, > Elaine > > > On Sep 27, 2006, at 7:29 PM, Vishal Pua wrote: > >> Hi, I was wondering if there was a way to create a script, that >> would open pdb files, render them to look a certain way ex. wire >> or ribbon, then save, automatically? this would have to work for a >> number of pdb files? I have little programming experience, and >> wonder if there was an easy way to do this, thanks >> >> Vishal Pua >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > ----- > 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-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Merge PDB Question
by Jared Godar 28 Sep '06

28 Sep '06

I have an incomplete pdb crystal structure of a homohexameric protein containing six ~25AA tails. In the incomplete model, two of these six tails are complete (A and F) and the other four are truncated at various positions (B,C,D, and E). I have used the either the A or F complete tails as templates and generated appropriate length segments to compleate each of the truncated B-E tails by selecting the appropriate residues and saving the selected atoms as a new PDB. Currently, I have all six tails completed and saved as a single PDB. I would like to use the Bond command to covalently link the extended chains, but my single PDB is segregated into models 1.1, 1.2, 1.3, 1.4, and 1.5. When I use the Bond command as follows "bond #1: 504.b@c & #1.3:505.a@n", I get an error that only one atom is selected. Does Chimera consider #1 and #1.1 to be different models? If so, how can I merge these 5 models into one to allow me to create the bond? Thanks, Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Department of Molecular Physiology & Biophysics 708 Light Hall 2215 Garland Ave. Nashville, TN 37232-0615 Work: 615.322.7898 Fax: 615.322.7236 jared.godar(a)vanderbilt.edu

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Re: [Chimera-users] [chimera-dev] chimera help
by Elaine Meng 28 Sep '06

28 Sep '06

Hi Vishal, Actually you can do this with a Chimera command script, as opposed to programming in Python. A command script just contains the same commands you would enter in the Command Line. I'm not sure of what type of saving you had in mind, " but the "copy" command can be used to save an image file, "save" to save a session, and "write" to save a PDB file. This page links to all the command man pages, plus it discusses command scripts (at the bottom): http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/framecommand.html Just opening the command file will execute the commands. Here are links to a couple of example command files: http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/tutorials/ setup.com http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/ 1gfl.com And here is another, between the dashed lines: ----------------------------------------------------------------- open 1hxx open 1pho modelcolor coral #0 modelcolor cornflower blue #1 ~disp; rep bs; ribbon; ribrepr smooth matchmaker #0 #1 ----------------------------------------------------------------- I guess the main difficulty if you are saving images is how to get a good view of the structures. Usually some rotation, scaling, etc. is done interactively to make a better picture. I hope this helps, Elaine On Sep 27, 2006, at 7:29 PM, Vishal Pua wrote: > Hi, I was wondering if there was a way to create a script, that > would open pdb files, render them to look a certain way ex. wire or > ribbon, then save, automatically? this would have to work for a > number of pdb files? I have little programming experience, and > wonder if there was an easy way to do this, thanks > > Vishal Pua > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev ----- 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

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how to get nonbonded distance and torsion angle list
by Prem Prakash Pathak 28 Sep '06

28 Sep '06

Hi! I am using the chimera for the visualizing protien form *.pdb file. I wanted to get the nonbonded distance , *.upl file and angle constraint files. Would you please help me in solving the problem. PremPrakash

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"longbond" in scripts
by Eric Pettersen 26 Sep '06

26 Sep '06

We've made some improvements to the "longbond" command (breaks non- physical bonds that show missing structure segments) which are not backward compatible with the previous version. We are wondering if anyone makes any significant use of the longbond command in scripts. If you do, we would consider making a new command with the improved behavior and leaving the longbond command unchanged for backwards compatibility. So speak up if this affects you. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Connolly surface and Triangulation
by Nihshanka Debroy 25 Sep '06

25 Sep '06

Hi, Not sure if this went the first time, so sending it again: ----------------------------------------------------------------------------------------------- I have been using Chimera to generate the Connolly surface for several different proteins and saving the surface information in X3D format. I was wondering what algorithms are used in the Connolly surface generation. Is it the same approach that Michael Connolly had come up with in his 1983 paper on Analytical Molecular Surface Calculation, or is it a variation of that algorithm? Also, when the surface information is saved by Chimera in X3D, it breaks the surface into triangular faces. I noticed that the coordinates of the points comprising the triangles are completely different from the atomic coordinates. I am interested in learning more about how the triangulation is created. If you could direct me to a link or paper that would help me better understand the algorithms involved in these two processes, that would be great! Thanks. Sincerely, Nihshanka

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chimera ubuntu/debian package?
by Javier Díez 25 Sep '06

25 Sep '06

Hy: Is there a chimera version for ubuntu or debian? I would like to add the url to my sources.list if it exits. Thank you any way. Javi

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