Hi James, Yes, undoubtedly in nogui mode there is no Reply Log dialog for you to access. If you are using Python, there are far more direct ways to get an atom's coordinates than using getcrd and trying to parse the reply log anyway. Such as: from chimera.selection import OSLSelection sel = OSLSelection("#0:%s.%s@CA" % (snpPos, chain)) a = sel.atoms()[0] crd = a.coord() # or a.xformCoord() for transformed coordinates I've attached a PDF of a handout from a Chimera development class we just taught here at UCSF. It covers a bunch of handy resources and tips. The first resource it lists, the Programmer's Examples, is something you should look over. They cover how Chimera's molecular data is laid out, how to deal with selections, and so forth. --Eric On Aug 20, 2008, at 9:37 AM, James A. Cleland wrote:

Ok, I ran this in chimera (gui) and I see how it is working now, the reply contains space-separated coordinates at the end of the string and get_coords picks these off from the end (-1, -2, -3). Perhaps this is another “headless” issue as there is no dialog? If so, maybe there’s somewhere else I can pick off the reply information for getcrd?

Thanks!

From: James A. Cleland [mailto:jcleland@jamescleland.com] Sent: Wednesday, August 20, 2008 12:32 PM To: 'Eric Pettersen' Subject: RE: headless chimera issues

This worked like a charm, thank you! I have run into another issue that I thought you may be able to help with.

We are attempting to draw a pointer indicating the alpha carbon for a particular residue. This has been done in the past, but no longer works. This may have been something that you helped with.

The function that is currently failing is called “get_coords()”. Here’s what I have:

def _get_coords(): from chimera import dialogs, Vector coords = Vector(0,0,0) r = dialogs.find('reply') text = r.text.get('1.0', 'end') coordString = text.splitlines()[-2] coordString = coordString.split(' ') print coordString coords[2] = float(coordString[-1]) coords[1] = float(coordString[-2]) coords[0] = float(coordString[-3]) return cords

Prior to calling get_coords(), there is a command executed that seems to provide the dialog information, if I’m understanding correctly:

runCommand("getcrd #0:%s.%s@CA" % (snpPos, chain))

The line that appears to be failing in get_coords() is the fourth in the function, r.text.get(). It looks like dialogs.find() returned None.

Do you have any suggestions as to how I might get these coordinates or what we might be doing wrong?

Thanks! James From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, August 19, 2008 7:41 PM To: James A. Cleland Cc: Tom Goddard Subject: Re: headless chimera issues

That's right -- the patch just prevents the error. It doesn't do the coloring. Hopefully Tom Goddard will be able to help you with that.

--Eric

On Aug 19, 2008, at 4:21 PM, James A. Cleland wrote:

Thank you for the quick reply! I applied this patch manually by just adding the import and the condition. I had commented the conditional statements prior to writing you and this worked fine, but the surface model didn’t appear to be colored according to the Delphi output. Is it correct for me to assume that, after this patch is applied, I’m still not seeing the electrostatic potential in the surface coloring?

Thanks again, James

From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, August 19, 2008 6:56 PM To: James A. Cleland Cc: Tom Goddard Subject: Re: headless chimera issues

Hi James, That exception would be a bug -- SurfaceColor should not be trying to bring up a dialog if Chimera is running in nogui mode. I've committed a fix for this and it will be in tomorrow's daily build. Here's the diff if you want to correct your version:

*** ChimeraExtension.py 6 May 2008 04:20:05 -0000 1.12 --- ChimeraExtension.py 19 Aug 2008 22:51:36 -0000 *************** *** 50,56 **** from VolumeViewer import open_volume_file vlist = open_volume_file(path, ftype, open_models = False, show_data = False, show_dialog = False) ! if len(vlist) > 0: from SurfaceColor.gui import show_surface_color_dialog d = show_surface_color_dialog() d.use_electrostatics_colormap() --- 50,57 ---- from VolumeViewer import open_volume_file vlist = open_volume_file(path, ftype, open_models = False, show_data = False, show_dialog = False) ! import chimera ! if len(vlist) > 0 and not chimera.nogui: from SurfaceColor.gui import show_surface_color_dialog d = show_surface_color_dialog() d.use_electrostatics_colormap()

I've cc'ed Tom Goddard on this mail since he is the expert on Chimera's volumetric API and can hopefully provide advice on coloring your map programmatically.

--Eric

Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

On Aug 19, 2008, at 1:32 PM, James A. Cleland wrote:

Hi Eric,

My name is James Cleland and I am currently working with Dr. Rachel Karchin at JHU. I had corresponded with Greg Couch over running Chimera without an X server and he had directed me toward a build designed to run headless. I have been using this for a couple of weeks without problems, but I encountered an issue the other day.

I am trying to import a surface for electrostatic potential that was generated using Delphi. The trouble is, this is causing an error (see below).

Executing test.py...Opening pdb1a01.ent... 1 model opened

Traceback (most recent call last): File "/home/pipeline/chimera/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 384, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1345, in open File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython File "test.py", line 15, in <module> runCommand("open 1a01.phi") File "CHIMERA/share/chimera/__init__.py", line 2026, in runCommand File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand File "CHIMERA/share/Midas/midas_text.py", line 918, in doOpen File "<string>", line 1, in <module> File "CHIMERA/share/Midas/__init__.py", line 1352, in open File "CHIMERA/share/chimera/__init__.py", line 1345, in open File "CHIMERA/share/SurfaceColor/ChimeraExtension.py", line 55, in open_cb File "CHIMERA/share/SurfaceColor/gui.py", line 613, in show_surface_color_dialog File "CHIMERA/share/chimera/dialogs.py", line 77, in display File "CHIMERA/share/chimera/dialogs.py", line 62, in find File "CHIMERA/share/chimera/baseDialog.py", line 435, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 121, in __init__ File "CHIMERA/share/chimera/tkgui.py", line 63, in <module> ImportError: No module named Togl Error while processing test.py: ImportError: No module named Togl (see reply log for Python traceback info)

From what I can gather, the call to open is trying to present a dialog for choosing surface colors and limits. I’ve seen this when running Chimera with an X server. The trouble is, I need to skip this dialog and, possibly, specify volume in some other fashion.

We used to use the following python code in our Chimera script:

from chimera import openModels, MSMSModel runCommand("set bg_color black") surf = openModels.list(modelTypes=[MSMSModel])[0] from VolumeViewer.volume import Volume vol = openModels.list(modelTypes=[Volume])[0] from SurfaceColor import color_by_volume color_by_volume(surf, vol, (-30, 0, 30), ((1,0,0,1.0), (1,1,1,1.0), (0,0,1,1.0)))

This was run using an older version of Chimera and used an X server. We ran into problems using this version with –nogui, which is what led me to the headless version.

I have been playing around with SurfaceColor/ChimeraExtensions.py, specifically line 55-56, trying to figure out how to at least get color on the surface using the default volume. It appears that, by commenting the aforementioned lines, I get no surface coloring at all.

Can you provide some direction for me on this? Any help is appreciated!

Thanks,

James A. Cleland (w) 1(703)392-1357 (c) 1(703)402-5447 jcleland@jamescleland.com