September 2006 - 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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Chimera-users September 2006