January 2007 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

I made the change (please, see document attached to be sure I did it right). When I restarted Chimera and tried to record a movie there was an error message (see reply log attached). Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 4:16 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Ok, so the bug is not fixed in Chimera version 1.2304. I made a note of that in our bug database. Here is a suggestion from the original bug report that solved the problem in that case: Edit the file in you Chimera 1.2304 distribution chimera/share/MovieRecorder/RecorderHandler.py using any text editor to change line 97 from image = chimera.viewer.pilImages() to width, height = chimera.viewer.windowSize image = chimera.viewer.pilImages(width, height, supersample = 1, opacity = False) Make sure to use the same indentation as the original code since this is important in the Python language. Then restart Chimera and try movie recorder again. Let me know if that fixes the problem. Tom

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

I see. Thanks. I am using the version 1.2304, and the platform is Windows XP. Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 1:45 PM To: Zoghbi, Maria Subject: Re: [Chimera-users] Movie resolution Hi Maria, This is a bug. The movie capture should work for any window size without artifacts. This Chimera bug was reported earlier: http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3151&database=ch imera Pressing the "view audit trail" button on that bug report page gives more info -- more than you want to konw. Supposedly that bug was fixed in Chimera version 1.2297. If you are using a newer version of Chimera than that and you still have this problem, then send me email with your Chimera version number and platform (Windows, Linux, Mac). Tom

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bond rotation buglet
by Eric Pettersen 17 Jan '07

17 Jan '07

I just found out that the current release has a bug where it sometimes claims that a bond is terminal (and therefore won't let you rotate it) when it isn't. This occurs when there is already an active bond rotation adjacent to the desired new rotation, and the atom in common would have all its bonds in rotations. You can work around the problem by deactivating the other rotation (in the panel showing the rotations, click on the label for the rotation (under "Bond") which brings up a menu of actions, one of which is Deactivate). I also have a code fix that I could send to people that need it -- just drop me an email. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

Hello, I'm trying to make a movie, but the only format that I have been able to make work is the VCD (Video Compact Disc), which produces a low resolution movie (457x240). As soon as I change to a different standard format the recorded images are totally wrong (rotated, shifted, wear lines, etc). I have tried to choose my own resolution and the only one that has worked is when high=3/2width, but only when high ≤ 300. Are these restrictions for the resolution of the movies normal or am I doing something wrong? How can a make a higher resolution movie? I appreciate any help. Thanks Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu

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Re: [Chimera-users] Export idatmType
by Eric Pettersen 17 Jan '07

17 Jan '07

Hi Brady, Tom forwarded your mail to me. There almost is a way. In the 1.2318 snapshot, the Render By Attribute tool allows you to save attribute values to a file using that tool's "File->Save Attributes..." menu item (saved in the format that Define Attribute accepts). So, why "almost"? The idatmType attribute is screened out of the list of available attributes since it can be expensive to compute the values -- and since you could already select by IDATM type using the regular selection menu. But now that save exists I will have to improve Render By Attribute so that it can know that idatmType values are strings ahead of time (so it doesn't have to ask for any values to figure that out). Anyway, for your purposes it is not too hard to force Render By Attribute to show you idatmType. First, get the 1.2318 release. Then edit the file <your Chimera>/share/ShowAttr/__init__.py (on a Mac: Chimera.app/Contents/Resources/share/ShowAttr/__init__.py) and edit line 24. It will look like this: 'name': False, 'idatmType': False, 'idatmIsExplicit': False, change it to: 'name': False, 'idatmIsExplicit': False, Save the file and thereafter Render By Attribute should show you the idatmType attribute. --Eric > hi tom - is there a quick way to save the atom types from idatmType > to a text/log file along with the atom name or number?

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Fwd: chimera to rebuild crystal
by Eric Pettersen 16 Jan '07

16 Jan '07

Hi Tom, Brady's question below seems more up your alley somehow. It also seems like one of those things that should be cross-posted to the chimera-users or -dev lists for "community building" purposes, though I'll leave that up to your discretion. --Eric Begin forwarded message: > From: "Brady Bernard" <bradyb(a)u.washington.edu> > Date: January 11, 2007 5:06:21 PM PST > To: "Eric Pettersen" <pett(a)cgl.ucsf.edu> > Subject: chimera to rebuild crystal > > hi, > > i am interested in using distance-dependent statistics in a scoring > function and i would like more than the default 3x3x3 repeating units > to rebuild a crystal using cryst1 data in pdb files. how can i do > this with chimera? i will need to do this for thousands of files and > am familiar with scripting and using the -nogui option with cmd files, > etc. > > thanks in advance for your help, > > brady bernard > uw bioengineering

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Chimera doesn't display AMBER molecular dynamics trajectories with periodic boundary condition.
by juyong Lee 16 Jan '07

16 Jan '07

Hi, I'm using chimera 1.2309 version. And I found out that MD movie module in chimera doesn't display AMBER trajectory file with periodic condition correctly. I works well only with non-periodic condition trajectory file. Another visualization program, VMD, has two seperated options for AMBER trajectory file: with periodic condition and not. I prefer display style of chimera. So, I really hope to see my AMBER trajectory with Chimera. Do you have any tips for this problem? or have plan to add the format, with periodic boundary condition. :-) Thanks again for your great program and have a nice day! ============================================= Lee, juyong Ph.D student, Department of chemistry, Seoul National University, Korea. drfaust23(a)gmail.com

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Re: [Chimera-users] other/2169
by conrad＠cgl.ucsf.edu 16 Jan '07

16 Jan '07

Synopsis: interface with QPACK State-Changed-From-To: open->closed State-Changed-By: conrad State-Changed-When: Tue Jan 16 10:18:12 2007 State-Changed-Why: QPACK interface available as experimental feature. See http://www.cgl.ucsf.edu/chimera/experimental/experimental.html for more information. http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=2169&database=chime…

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Re: [Chimera-users] Select atom by serial number.
by Jean Didier Pie Marechal 16 Jan '07

16 Jan '07

Hi Elaine and thank you very much for your help. I am pleased to see the selection specifications are OK. Coming back from the WE, I retried this selection on my structure and... it works perfect... For once, it seems I needed a reboot more than my desktop... My apologies for your waste of time. Regards, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdonyola (Barcelona) Tel: +34.935814988 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dijous, Gener 11, 2007 8:59 pm Assumpte: Re: [Chimera-users] Select atom by serial number. > > Hi JD, > We also tested Chimera 1.2309 on Windows, and these specifications > > work correctly. Example: > Command: sel @/serialNumber=232 > will select NZ of Lys 27 in chain A of the PDB entry 1zik. The > only > other thing I can think of (besides what was in the previous > message) > is to check if your PDB file is correctly formatted. The > ATOM/HETATM > serial number is supposed to be in columns 7-11 and right-justified. > Best, > Elaine > > On Jan 11, 2007, at 11:39 AM, Elaine Meng wrote: > > > Hi JD, > > You are using the correct specifications - both of your examples > > > should work. I tested both approaches in Chimera 1.2304 on Mac > OSX > > and they worked correctly. We'll have to look into your > specific > > version/platform and get back to you. If you want, you could > send > > me the PDB file you are using so I could test if there is some > > issue specific to that structure. To be clear: the serial > number > > is the number shown in the column after ATOM (or HETATM) in the > PDB > > file, regardless of what order the atoms are really in. That > is, > > if the first ATOM has 2 in that column, its serial number is 2 > and > > not 1. > > Best, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > > UCSF Computer Graphics Lab and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > > > > > > On Jan 11, 2007, at 10:47 AM, Jean-Didier Maréchal wrote: > > > >> Hi Everyone, > >> > >> > >> > >> > >> > >> I am desperately trying to select an atom of my pdb by its > serial > >> number. > >> > >> Looking at the archives, it seems that I should put something > like > >> @/serialNumber=525 > >> > >> I tried “sel #0@/serialNumber=525” in the commandl ine and “@/ > >> serialNumber=525” in the Atom Specifier. None of these > selections > >> worked. Can someone tell me the right way to do this, please ? > >> > >> > >> > >> Cheers > >> > >> JD > >> > >> > >> > >> Current running chimera: version 1 build 2309 > >> > >> OS: windows > >> > >> > >> > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Numeric/numpy revisited
by Randy Heiland 12 Jan '07

12 Jan '07

I'll post this long-winded thing to the users list although it's really for the developers... I'm revisiting the issue of wanting to have access to the numpy pkg (numpy.scipy.org) for a Chimera plugin - a delayed continuation of the problem discussed here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-April/000743.html Here's my situation: I installed chimera-1.2304-osx_x11.dmg. I then built the numpy pkg (from svn) using my system's python (2.4) via 'python setup.py build' and copied the resulting /numpy dir into the chimera /share dir. I then discover/verify 2 things: 1) using my system's python, I can successfully import both Numeric and numpy - Numeric coming from chimera and the numpy that I just built and copied into chimera's /share dir 2) using the python2.4 bundled with chimera, I cannot import both Numeric and numpy. I can always import one (either one), but then get a bizarre error when trying to import the other. --------------------------- More verbosely: I set PYTHONPATH to /Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/Num eric:/Applications/Chimera.app/Contents/Resources/share Then check the system python: [macmini:~] heiland% pwd /Users/heiland [macmini:~] heiland% which python /usr/local/bin/python [macmini:~] heiland% ll /usr/local/bin/python lrwxr-xr-x 1 root heiland 68 Jul 27 06:19 /usr/local/bin/python@ -> ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/python [macmini:~] heiland% python Python 2.4.3 (#1, Apr 7 2006, 10:54:33) [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric >>> import numpy >>> from numpy.core.multiarray import typeinfo >>> Then check the chimera python: /Applications/Chimera.app/Contents/Resources/share [macmini:Contents/Resources/share] heiland% ../bin/python2.4 Python 2.4.3 (#1, Oct 16 2006, 09:43:37) [GCC 4.0.1 (Apple Computer, Inc. build 5247)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric >>> import numpy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Applications/Chimera.app/Contents/Resources/share/numpy/__init__.py", line 36, in ? import core File "numpy/core/__init__.py", line 8, in ? import numerictypes as nt File "numpy/core/numerictypes.py", line 83, in ? from multiarray import typeinfo, ndarray, array, empty, dtype ImportError: cannot import name typeinfo ----------------------------- OK, it then dawns on me that probably what I really should be doing is building numpy using chimera's python. So, after downloading the chimera (1.2318) OSX headers (http://www.cgl.ucsf.edu/chimera/sourcecode.html ), putting the /include in the /Resources dir, and doing: /Applications/Chimera.app/Contents/Resources/bin/python2.4 setup.py build It all builds fine, but then I have the same bizarre error when trying to import both Numeric and numpy as before. Crap. So I then use 'ldd' to see the dependencies in the different python executables: ldd /Applications/Chimera.app/Contents/Resources/bin/python2.4 /Applications/Chimera.app/Contents/Resources/bin/python2.4: /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 71.1.3) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 47.1.0) [macmini:~] heiland% ldd /Library/Frameworks/Python.framework/Versions/2.4/bin/python /Library/Frameworks/Python.framework/Versions/2.4/bin/python: /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 47.1.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.3) Note the different versions on the libSystem.B.dylib. Some more poking... [macmini:~] heiland% locate libgcc_s.1.dylib /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib [macmini:~] heiland% ldd /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3) [macmini:~] heiland% ldd /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 71.1.3) [macmini:~] heiland% ldd /usr/lib/libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.2) ----------------------------- One thing worth noting is the different gcc builds (my system python used a later build, 5250, cf 5247 for chimera's python). I also installed the latest xcode (2.4.1) before doing all this. If you've stayed with me to the end, I congratulate you :) Basic question - any ideas? Would it be possible for the Chimera OSX developers to verify they have the latest xcode? And secondly, do you know how one can the chimera python have the dependency on libSystem.B.dylib v.88.1.2 instead of 71.1.3 ? Thanks, -Randy Fwiw, this link http://mail.python.org/pipermail/pythonmac-sig/2006-April/017310.html seems related to this thread also.

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