- Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] Map Oddities
by Thomas Goddard 22 Sep '06

22 Sep '06

Hi Albion, When you are running Chimera and it opens a Python code file with suffix .py and there is an older byte compiled version of the same file with suffix .pyc then Python automatically recompiles the .py file and you should see that the date on the .pyc file is updated. You never need to compile Python files by hand. Here are 3 ideas about how to make some programs that read MRC maps establish equivalent map positions. As I mentioned in my previous email some programs may fail with certain maps to associate the x,y,z axes with the correct data axes. And some may ignore all header info about positioning. So there are alot of different cases. I'm only going to make suggestions for the simple problems. One idea is to have Chimera print out the difference between the origin that a crystallography program would use versus the MRC 2000 origin. You could insert a little code in the Chimera mrc_format.py file to print this difference for MRC 2000 files. Specifically after the line self.data_origin = (v['xorigin'], v['yorigin'], v['zorigin']) add lines # Print difference between crystal and mrc 2000 origins ncs_nrs_nss = v['ncstart'], v['nrstart'], v['nsstart'] nxs, nys, nzs = ncs_nrs_nss[xa], ncs_nrs_nss[ya], ncs_nrs_nss[za] from VolumeData.griddata import scale_and_skew x0,y0,z0 = scale_and_skew((nxs,nys,nzs), self.data_step, self.cell_angles) print 'Origin difference ', self.name, '=', print x0 - v['xorigin'], y0 - v['yorigin'], z0 - v['zorigin'] The origin difference will be printed to the Chimera reply log and you can somehow apply it in other programs. A second idea is to try to modify the MRC 2000 map header so that the crystal origin is the same as the xorigin, yorigin, zorigin header values. This is generally not possible since the former uses integers while the latter uses float values. But if you don't care where the origin is as long as all programs agree, you might adjust xorigin, yorigin and zorigin to match the crystal origin. You would need some simple program to modify the map header. A third approach is to modify Chimera mrc_format.py so it never uses the MRC 2000 xorigin, yorigin, zorigin. If Chimera always uses the crystal origin that would probably more often agree with other software packages. I would recommend against this approach. You will later install a new version of Chimera without the modification and your fit PDB models will no longer align with their maps and you will probably forget why and scream. Tom > From: Albion Baucom <baucom(a)msg.ucsf.edu> > Subject: Re: [Chimera-users] Map Oddities > Date: Fri, 22 Sep 2006 17:12:51 -0700 > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Hi Tom, > Im going to take this off list since my inquiries get more specific > now, but you are welcome to post this back to list if you think it is > within the scope of the Chimera Users list. > > So, you were right. There is indeed a X, Y and Z origin field in the > map header. Thanks for pointing that out and giving me the code to > print those values to the reply log. > > A quick question regarding my modification to the mrc_format.py. I > don't know Python very well yet, and am wondering what happens when I > modified the source code. The modifications worked of course, but > Chimera did not recompile the code into a .pyc file. When are > the .pyc files accessed? > > OK, back to the original question :) > > So, offhand, could you suggest a fix for me so that other programs > that use the "other" origin can interpret the data the same as > Chimera? Naturally what is going to have to happen is I will have to > translate the PDB file a set distance based on the discrepancy > between the origin conventions. I would like to do this translation > as accurately as possible. > > What I noticed from an empirical re-docking of the PDB file into the > density in another program was it had to be moved approximately ~116A > in all 3 axes. This appears to be close to the following calculation > (for the x axis in this case) > > ( | xorg | - xlen) + (xlen/2) > > where xorg (-224) is the MRC2000 origin, and xlen (213.423) is the > xtal origin. In this case this comes out to be > > (224.000 - 213.423) + (xlen/2) = 117.289 > > Applying this to the model as a translation in all 3 axes looks > almost exactly like what I see in Chimera. > > Does this make any sense? This is all I could come up with that gave > an answer close to my empirical docking translation numbers. > > Thanks Tom. I really appreciate your help. > > Albion

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Map Oddities
by Albion Baucom 22 Sep '06

22 Sep '06

Hi, I am trying to work out how maps are handled in various graphics programs so I can easily move between programs and expect to see the same thing in each session. Unfortunately at the moment that isn't working so well, and I would like to resolve this issue. Basically I have a situation where I have a PDB model and a CCP4 format EM density map in Chimera that are docked. When I open the exact same map and model in other programs such as O or Pymol, the map and the model are no longer in agreement. What I have noticed is that if I draw the unit cell for the map (P1 symmetry since this is an EM reconstruction), in Chimera, the model and map live in the center of the unit cell and are docked. If I draw the unit cell for O or Pymol, the map lives at the origin of the unit cell, at (0,0,0), which is in the corner, and model is outside of the unit cell offset by what appears to be some arbitrary translation (I have tried using half the unit cell dimensions as a translation, but that unfortunately gets me _very_ close to being correctly docked in the map, but off by some 10A). It appears Chimera is handling the map and model differently than the other packages and I am trying to get an idea of what happens when this map is loaded. I am including a listing of the map header from MAPMAN below. Thanks! Albion Grid = 96 96 96 Origin = -48 -48 -48 Extent = 96 96 96 Cell = 213.423 213.423 213.423 90.000 90.000 90.000 UVW = 1 2 3 Spcgrp = 1 Nr of points = 884736 Density min = -6.915E-01 Max = 2.397E+00 Average = 7.247E-11 Sigma = 2.290E-01 Variance = 5.243E-02 Mappage Prod= 8.257E+01 Plus = 57 Dyn. range = -6.903E-01 To = 2.398E+00 Cell vol. = 9.721E+06 Voxel vol. = 1.099E+01 Grid vol. = 9.721E+06 %Cell vol. = 100.00 Origin frac = -0.50000 -0.50000 -0.50000 Origin Cart = -106.712 -106.712 -106.712 Top frac = 0.48958 0.48958 0.48958 Top Cart = 104.488 104.488 104.488 Spacing = 2.223 2.223 2.223 Top = 47 47 47 Changes = F

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Movement Mouse Mode Extension
by Jared Godar 22 Sep '06

22 Sep '06

I have installed the Movement Mouse Mode Extension, but I get the following error whenever I try to select anything other than the 'Normal' movement mode on the drop-down menu. ImportError: cannot import name functionCallables (see reply log for Python traceback info) Any insight on how I can get this feature to work for me? Thanks, Jared (Log info below) Traceback (most recent call last): File "C:\Program Files\Chimera\share\__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in init tkgui.eventLoop() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, in eventLoop app.mainloop() File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 170, in <lambda> set_variable_cb = lambda v=self.variable, n=name: v.set(n) File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 780, in set self.tk_variable.set(value) File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 191, in set return self._tk.globalsetvar(self._name, value) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1751, in __call__ _reporterror(self.func, args) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1814, in _reporterror displayerror(msg) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1377, in displayerror _errorReportFile.write(text + '\n') File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 832, in cb callback() File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 800, in tk_variable_changed_cb cb() File "C:\Program Files\Chimera\share\MoveSelection\gui.py", line 64, in mode_changed_cb move.set_mouse_mode(mmap[self.mode.get()]) File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 569, in set_mouse_mode m = mover(create = True) File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 598, in mover the_mover = Selection_Mover() File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 36, in __init__ self.original_move_callbacks = self.wrap_mouse_modes() File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 42, in wrap_mouse_modes from chimera.mousemodes import addFunction, functionCallables ImportError: cannot import name functionCallables -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

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Connolly surface and Triangulation
by Nihshanka Debroy 21 Sep '06

21 Sep '06

Hi, 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 his algorithm? Also, when the surface information is saved by Chimera, 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 Chimera creates the triangulation. 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, Nihshanka

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AMBER netCDF trajectory
by Mingfeng Yang 20 Sep '06

20 Sep '06

Dear Chimera developers, The latest release of AMBER supports netCDF format trajectory. Is there any plan for Chimera to support AMBER's new format? Best, Mingfeng

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Chimera secondary-school use
by Thomas Goddard 19 Sep '06

19 Sep '06

Follow up on "[Chimera-users] first time use of chimera". ------------------ From: "Rich Kaufman" <richkaufmanpv(a)hotmail.com> To: goddard(a)cgl.ucsf.edu Subject: Chimera, afterthought Date: Tue, 19 Sep 2006 11:38:26 -0500 Dear Tom, Just to mention a few more details, I am trying to use electron density maps we generated in the lab using a Spider processing of cryo-EM photos .I will be downloading PDB's from the RCSB to dock with these. After properly hand docking the PDB, I will then load the density map and the hand-aligned PDB into a Normal Mode Flexible Fitting package ( NMFF ) for fine-tuning of the fit, to give a higher resolution picture of the electron density map. I've been working on this project for about three months. I had never heard of any of these things prior to that. It's been an amazing learning curve for me....quite interesting. Sincerely, Rich Kaufman, ( background....mainly physics; teacher of high school chemistry and physics ) P.S. One goal of this project is to enable me to use these techniques at the secondary education level. I don't know if that's doable....suggestions welcomed. --------------------- Date: Tue, 19 Sep 2006 10:00:38 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: richkaufmanpv(a)hotmail.com Subject: Re: Chimera, afterthought Hi Rich, Oh! I sent my previous email before I read this one about what you are actually doing. You're doing some fancy stuff. If you hand-align a PDB model in the SPIDER map you can then do a local position optimization within Chimera using menu entry Tools / Volume Data / Fit Models in Maps This moves the model using a rigid rotation and translation to maximize the map values at selected atom positions. Here's a page describing how to use it: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… The bottom of the following tutorial also gives step by step instructions for placing a PDB model in a map: http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/07-VolumeData/tut… In fact, most of the tutorials on the following page do this kind of fitting: http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html The normal mode fitting you will do is fancier, allowing the model to deform to fit into the map. The following page explains alot of the Chimera features for working with density maps. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html The myosin animation on the following web page shows fitting a model into a map: http://www.cgl.ucsf.edu/chimera/animations/animations.html Finally, here are some databases that show some cryo-EM maps of viruses and other systems. http://viperdb.scripps.edu/tnumlist.php?N=all http://www.ebi.ac.uk/msd-srv/emsearch/AccEMServ?criterion=Retrieve+All&valu… I'm sure this is more than you wanted to know! Tom

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visualizing a confocal image stack
by William Beaver 19 Sep '06

19 Sep '06

Hello. I have a stack of intensity images (8bit) taken from confocal microscopy of dapi expression in Drosophila that I'd like to visualize. I cannot figure out the format that the volume viewer requires to view the data; more specifically, none of the formats in 'registered file types' are familiar to me and I've been unable to find anything about them to sort out which format I should convert to. I have read the image sequences into matlab (3d matrix) and can write output to just about anything from there if I know the format. Does anyone have an idea for what the best/easiest/only format I should use? A pointer to a spec on the format if it's not something trivial (like matlab 'save stack.txt varname -ascii') would be appreciated. If it makes a difference, at some point soon I'd like to visualize more channels that just dapi (dll, for example) simultaneously. Thanks in advance. I really do appreciate it! -William ------------ William Beaver wbeaver(a)cs.ucsd.edu

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Re: [Chimera-users] Movie Question: EM Densities about robbon structures
by Thomas Goddard 18 Sep '06

18 Sep '06

Hi Jared, If you use Chimera commands that specify how many frames to rotate, shift, scale, fade over, ... then it does not matter how fast or slow your machine is. Each frame is recorded only after it is drawn, and none will be skipped. Only when you move a model by hand with the mouse will it matter how fast the machine is. Here are some problems with smooth transitions I have observed. Fading out a PDB model in stick mode produced all kinds of weird flickering of the bonds. This I believe is a bug in Chimera transparency of bonds and I plan on submitting a bug report for that. Smoothly changing the contour level does not produce a very smooth change in surface appearance. Little spots pop up or disappear at discrete contour levels. This is because the contouring algorithm (marching cubes) changes the surface triangulation in discrete ways when the contour level passes through a grid point data value. I don't know of any remedy although using surface smoothing (volume dialog under surface and mesh options) may help. Let me know what problems you encounter. I am interested in improving the Chimera movie capabilities. Tom > Date: Mon, 18 Sep 2006 13:11:39 -0500 > From: "Jared Godar" <jared.godar(a)vanderbilt.edu> > Sender: jared.godar(a)gmail.com > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Movie Question: EM Densities about robbon structures > > I did, thank you much... I have successfully installed the additional > extensions and am attempting to incorporate them into a .CMD script for my > movie. So far that is going fairly smoothly, with the exception of frames > involving fading in/out of structures are taking significantly longer than > others resulting in a jumpy movie. I'm going to attempt to try it on a > fastest machine and see if that helps. > > The independent rotation is working, the fade in/out of specific models is > good, and I'm going to try the contour transition next. > > Thanks again, > > Jared

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first time use of chimera
by Rich Kaufman 18 Sep '06

18 Sep '06

9/18 To whom it may concern: I would like an abbreviated guide to loading a pdb and an electron density map into chimera for comparison and hand docking. I have only worked with visualization software for a few months and still, frequently, can't do what I want with it. Chimera was suggested as the easiest or perhaps only software to do what I need to do. Currently, I only have only got VMD downloaded, but can install chimera if its worthwhile. Sincerely, Rich Kaufman, U.KS. biochem. dept, Kansas City, Ks.

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Movie Question
by Jared Godar 15 Sep '06

15 Sep '06

Hello there, I have a few technical questions about a movie I am trying to make with chimera. I have PDB files for three predicted structural elements of a larger protein whose structure my lab is resolving through cryo EM. I've converted these PDB files to MRC's of the desired resolution we are trying to obtain with the reconstruction. In an effort to produce animation which highlights structural elements of these three subdomains, I have encountered a couple difficulties translation the movie I envision through Chimera. I would like to start with the three subunits spaced across the X axis and rotating about the central y axis of each subunit. Then, one at a time, have a single unit grow and translate to the center, then while the other two subunits fade away, then return to it's original position. I've been able to script this type of motion for each of the individual subunits, but I hit a problem when I try to incorporate all three. - Is there a way to have multiple proteins roll about their own respective y axis instead of orbiting about the central y axis of the scene? - Is there a way to selectively show / hide (fade over specified number of frames) PDB's or MRC's like you can show / hide / fade text? Thank you in advance for your help. -Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

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Movie Question: EM Densities about robbon structures
by Jared Godar 15 Sep '06

15 Sep '06

Hello there, I have a few technical questions about a movie I am trying to make with chimera. I have PDB files for three predicted structural elements of a larger protein whose structure my lab is resolving through cryo EM. I've converted these PDB files to MRC's of the desired resolution we are trying to obtain with the reconstruction. In an effort to produce animation which highlights structural elements of these three subdomains, I have encountered a couple difficulties translation the movie I envision through Chimera. I would like to start with the three subunits spaced across the X axis and rotating about the central y axis of each subunit. Then, one at a time, have a single unit grow and translate to the center, then while the other two subunits fade away, then return to it's original position. I've been able to script this type of motion for each of the individual subunits, but I hit a problem when I try to incorporate all three. - Is there a way to have multiple proteins roll about their own respective y axis instead of orbiting about the central y axis of the scene? - Is there a way to selectively show / hide (fade over specified number of frames) PDB's or MRC's like you can show / hide / fade text? Thank you in advance for your help. -Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

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Dual monitor display
by John Hatten Jr. 15 Sep '06

15 Sep '06

Hi all. I'm a bit of a chimera newbie. I've been using DOCK for a while, and chimera has turned into a natural choice for combing through the results. I've noticed that chimera quits when I try to run it in dual display with XP. I get an error message that there is a driver conflict. Is there a way to fix this? I would love to have my display window on one screen and the tool windows on the other. Thanks for the wonderful software, its a great tool. Sincerely, John Hatten jahatten(a)duke.edu

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16,000 molecules slow
by Thomas Goddard 13 Sep '06

13 Sep '06

Email exchange with Brittany Morgan about slow ball and stick display when displaying 16000 molecules. ---- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Tue, 12 Sep 2006 20:52:39 -0400 I am working with molecules, and it has problems redrawing them in ball-and-stick representation, although I expect that at larger system sizes other functions will start slowing down as well. If I look at the memory usage while it is redrawing them, Chimera seems to be using only about 1/4 of the available memory, but creating a paging file nonetheless. It will work, it just takes about 15 minutes to redraw about 64,000 atoms, and I need to go to system sizes much larger. If I need more memory, that is possible, I just wasn't sure if that was the issue because it didn't appear that Chimera was using all of the available memory. I am using Chimera in a non-standard way (I'm not displaying proteins, but rather many small (unrealistic) molecule-type objects). Thank you for your help! Brittany ----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Tuesday, September 12, 2006 9:22 PM To: brmorgan(a)clarku.edu Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Memory allocation Hi Brittany, Thanks for the detailed information. I do not think memory is the problem. Display of 58,000 atoms (pdb 1uf2) in ball and stick took 10 seconds on my 4 year old laptop. That is the time to make the intial drawing. Then it update at about 2 frames per second when rotating the model on this rather old machine. Your problem is likely caused by one of two issues. First, if your "molecule-type objects" contain many (tens or hundreds) small rings within a residue then Chimera will bog down trying to compute the chemical atom types (aromaticity...). This is a problem we have recently analyzed when using Chimera with molecules that do not have reasonable chemical structure. We plan on fixing this problem by being able to tag molecules in Chimera as "non-chemical". But we do not have a version of Chimera available with that feature yet. So currently the only solution is to modify your non-molecule model using multiple residues to avoid having many rings in a single residue. The ring computation is not done in wire display style but is invoked when switching to ball and stick style because atom radii are needed and are based on the chemical types. The second possible problem is that you are not using hardware accelerated 3D graphics. On Linux systems you usually need to install a graphics driver to get hardware acceleration. Windows and Mac systems usually already have the appropriate driver. Rendering computations can be 100 times slower if it is done in software instead of by the graphics chip. Ball and stick display style is much more time consuming to render than wire frame. If you are able to rotate the 64,000 atom ball and stick model after it is first displayed (15 minutes) and it updates reasonably fast (> 1 frame per second) then you have hardware acceleration and this is not the problem. Tom ----- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Tue, 12 Sep 2006 21:34:09 -0400 Hi Tom, I can rotate it after it is first displayed with no difficulty, so I would think that the problem is likely the first. My toy model molecules consist of 4 "atoms" in a linear configuration, so these are very small molecules, and I wouldn't have any rings within a residue, if I understand this correctly. However, would the fact that I have so many molecules be an issue (if I have 64,000 atoms, I have 16,000 molecules)? I can tell you more explicitly what I am attempting to display (and how) if that would be of use. Since I guessed, more or less, on how to output the data to get it to display what I want, it is likely that I am doing this in a less than optimal way. Brittany -------- Date: Tue, 12 Sep 2006 18:51:58 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Hi Brittany, Ok it's not rings. Very likely something is slow when dealing with your large number of molecules. The typical Chimera use involves only a handful of molecules, twenty or thirty is considered alot, and 16,000 may be a record! Another Chimera developer Eric Pettersen will know more about efficiency with large numbers of molecules. (I work primarily on volume data.) So I've sent this email to him and he may have advice. If it is possible I think you would be better off making your 4 atom chains be a single residue with all chains in a single molecule. Chimera is likely to handle that much better. An immediate problem is that if you are using the PDB file format its residue number field is only 4 digits (max 9999 residues). It is awkward but you could use multiple PDB chain identifiers (single letter a-z, A-Z, 0-9) to handle up to ~600,000 chains. Another approach is to put all the chains in a single residue. But a residue with 64,000 atoms may also cause poor Chimera performance. I'll also warn you that Chimera is not at good as other molecular graphics programs (PyMol, and VMD) at handling systems larger than 100,000 atoms. Chimera uses much more memory (about 3 Kbytes per atom). PyMol and VMD I am told are 5-10 times more memory efficient on a per-atom basis. Chimera may be better for doing custom types of analysis though. Tom Is it OK if I forward your last email to the chimera-users mailing list? That may help others with similar problems. ----- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Wed, 13 Sep 2006 13:57:36 -0400 Hi Tom, Feel free to forward anything that you think would be of use to others. Unfortunately, 16,000 is only a moderately large system for me. I'm looking to be able to get up to around 112,500 atoms and a little under 30,000 molecules. I only need the visualization aspects of Chimera, all analysis I do on my own. Do you think PyMol would be able to handle something like that? I can try making them all a single molecule, but I also suspect that having a chain with 112,500 atoms would cause problems. Thanks again, Brittany ---- Date: Wed, 13 Sep 2006 11:07:59 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Hi Brittany, There are two difficulties you are likely to run into: PDB file format limits on number of atoms (100,000) and number of residues (10,000), and poor software performance for such large systems. If you are primarily concerned with visualization rather than analysis than PyMOL I believe will give better performance. But you may have a hard time with the file format issues. I think you will get better support solving the file format problems with Chimera since we have 5 developers while PyMOL has just one. Having 100,000 atoms in a single PDB chain is not a problem. I believe also that Chimera can handle a modification of PDB file format where the atom number starts in column 6 instead of column 7 allowing up to 1,000,000 atoms. Eric would know. Tom ---- From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Date: Wed, 13 Sep 2006 12:26:30 -0700 Hi Brittany, I confess I find your problem somewhat mysterious. I wrote a Chimera Python script (attached) that can either generate a single molecule with 16000 4-atom residues or 16000 4-atom molecules (depending on whether the 'singleMol' variable is True or False). While Chimera is better with the single-molecule system (on my mac, taking about 5 seconds each to run the script and to change to ball- and-stick), it isn't that much worse using the 16000-molecule system (about 20 seconds each -- not nearly 15 minutes!). It also took about twice as much memory (~1GB vs ~480 MB; this was using the 1.2255 snapshot). You can try it out yourself by using File..Open to open the script and changing the "singleMol = False" line in the script beforehand to choose modes. You should check that Chimera is using your graphics card rather than software rendering. One way to do that is to use Help->Report A Bug.. and click the Next button in the resulting dialog. The ensuing panel will have a "Bug Description" field that reports your OpenGL vendor and renderer. What does it say? If it says something involving "Mesa" then you are using software rendering and should try to update the driver for you card by visiting your card manufacturer's web site. You can click "Cancel" in the bug dialog to dismiss it. As Tom mentioned, we allow a modified PDB format where the sixth column of an ATOM record can be a digit, effectively allowing 1 million atoms. There are several gotchas in your situation. Whereas most such large systems are composed of standard residues with known connectivity, you may well need to specify your connectivity -- and CONECT records are strictly limited to 5-digit atom serial numbers. If your molecules do have typical bonding distances, you can let Chimera figure out the connectivity, but you would need to put each molecule in its own residue to prevent the N-squared intra-residue connectivity search from getting out of hand (so you would likely need to use chain IDs once you're past 9999 residues), and you would need to insert TER cards between residues to prevent the implied connectivity between residues (may not actually be necessary in the 1.2255 snapshot). --Eric File manyMols.py follows import chimera singleMol = False if singleMol: m = chimera.Molecule() m.name = "test" mols = [m] for ri in range(16000): r = m.newResidue("UNK", " ", ri+1, " ") prev = None for ai in range(4): a = m.newAtom("C%d" % (ai+1), chimera.Element("C")) r.addAtom(a) if prev: m.newBond(a, prev) crd = chimera.Coord(ri, ai, 0.0) a.setCoord(crd) prev = a else: mols = [] for mi in range(16000): m = chimera.Molecule() m.name = "test%d" % mi mols.append(m) r = m.newResidue("UNK", " ", 1, " ") prev = None for ai in range(4): a = m.newAtom("C%d" % (ai+1), chimera.Element("C")) r.addAtom(a) if prev: m.newBond(a, prev) crd = chimera.Coord(mi, ai, 0.0) a.setCoord(crd) prev = a chimera.openModels.add(mols)

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Memory allocation
by brmorgan＠clarku.edu 13 Sep '06

13 Sep '06

Does Chimera have a fixed amount of memory allocated to it, and if so, is it possible to increase this amount? I am working with very large system sizes and am trying to reduce the amount of time it takes to perform certain operations.

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Re: [Chimera-users] Memory allocation
by Thomas Goddard 12 Sep '06

12 Sep '06

Hi Brittany, Thanks for the detailed information. I do not think memory is the problem. Display of 58,000 atoms (pdb 1uf2) in ball and stick took 10 seconds on my 4 year old laptop. That is the time to make the intial drawing. Then it update at about 2 frames per second when rotating the model on this rather old machine. Your problem is likely caused by one of two issues. First, if your "molecule-type objects" contain many (tens or hundreds) small rings within a residue then Chimera will bog down trying to compute the chemical atom types (aromaticity...). This is a problem we have recently analyzed when using Chimera with molecules that do not have reasonable chemical structure. We plan on fixing this problem by being able to tag molecules in Chimera as "non-chemical". But we do not have a version of Chimera available with that feature yet. So currently the only solution is to modify your non-molecule model using multiple residues to avoid having many rings in a single residue. The ring computation is not done in wire display style but is invoked when switching to ball and stick style because atom radii are needed and are based on the chemical types. The second possible problem is that you are not using hardware accelerated 3D graphics. On Linux systems you usually need to install a graphics driver to get hardware acceleration. Windows and Mac systems usually already have the appropriate driver. Rendering computations can be 100 times slower if it is done in software instead of by the graphics chip. Ball and stick display style is much more time consuming to render than wire frame. If you are able to rotate the 64,000 atom ball and stick model after it is first displayed (15 minutes) and it updates reasonably fast (> 1 frame per second) then you have hardware acceleration and this is not the problem. Tom > From: "Brittany Morgan" <brmorgan(a)clarku.edu> > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] Memory allocation > Date: Tue, 12 Sep 2006 20:52:39 -0400 > > I am working with molecules, and it has problems redrawing them in > ball-and-stick representation, although I expect that at larger system sizes > other functions will start slowing down as well. If I look at the memory > usage while it is redrawing them, Chimera seems to be using only about 1/4 > of the available memory, but creating a paging file nonetheless. It will > work, it just takes about 15 minutes to redraw about 64,000 atoms, and I > need to go to system sizes much larger. If I need more memory, that is > possible, I just wasn't sure if that was the issue because it didn't appear > that Chimera was using all of the available memory. I am using Chimera in a > non-standard way (I'm not displaying proteins, but rather many small > (unrealistic) molecule-type objects). > > Thank you for your help! > Brittany

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Re: [Chimera-users] Can I use "Chimera" to measure length of a VRML file?
by Thomas Goddard 12 Sep '06

12 Sep '06

Hi Masako, Chimera does not read IMOD files but perhaps I can add a file reader for you. Have you already defined a path in IMOD along the structure you want to measure? Or have you just segmented out the structures. If you have segmentations but no explicitly defined 1 dimensional path then it is not clear how to define the length. Is the IMOD format you are using the following? http://bio3d.colorado.edu/imod/doc/binspec.html Could you send me an example file? Tom > Date: Mon, 11 Sep 2006 17:41:20 -0700 > From: Masako Terada <mterada(a)ncmir.ucsd.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Can I use "Chimera" to measure length of a VRML > file? > > Hi. Thank you for your e-mail. I have tried using volume path tracer > as you instructed. Even though it looks very promising, it is > time-consuming since we have 90 different objects to measure. So I > would like to try your another suggestion, importing trace file into > Chimera and measure lengths. Are you familiar with IMOD segmentation > file format? I tried to import this IMOD file into Chimera, but > unsuccessful, so I am guessing that I have to convert it to something > else... Any more suggestion? > > Masako >

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Can I use "Chimera" to measure length of a VRML file?
by Masako Terada 11 Sep '06

11 Sep '06

Hi. I have a VRML file, which was created with different softwares. Is there anyway I can use Chimera to measure length of this tube-like structure? Thanks, in advance! ---------------------------------------------------- Masako Terada National Center for Microscopy and Imaging Research Center for Research in Biological Systems University of California, San Diego (858)534-7968 mterada(a)ncmir.ucsd.edu ----------------------------------------------------

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