- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Export idatmType
by Eric Pettersen 18 Jan '07

18 Jan '07

On Jan 17, 2007, at 10:47 PM, Brady Bernard wrote: > is there a way to do this with --nogui so that i can automate it in > a script? > > thanks, > brady It's pretty easy to make a Python script that opens a file, loops through open molecules and then their atoms, and prints our the atom identifier and IDATM type to that file. Here's an example: import chimera f = open("types.txt", "w") for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print>>f, a, a.idatmType f.close() If you save the above into a file with a ".py" suffix (e.g. types.py), then you could save all the types of 1gcn with "chimera -- nogui pdb:1gcn types.py", which would create a file named "types.txt" (in the same folder as types.py) with the types listed. BTW, you need to preserve the indentation of the Python code above -- it matters to Python. If you're automating this in a shell script, it may be simpler to just print the info to standard output and redirect that into a file, rather than open the file in the Python script. The command would then be "chimera --nogui --nostatus pdb:1gcn types.py > 1gcn_types.txt" (note the "--nostatus" flag so that status messages don't get mixed into the output). The Python script becomes: import chimera for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print a, a.idatmType --Eric > ----- Original Message ----- > From: Eric Pettersen > To: Brady Bernard > Cc: Thomas Goddard ; Elaine Meng > Sent: Tuesday, January 16, 2007 4:40 PM > Subject: Re: Export idatmType > > 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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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 18 Jan '07

18 Jan '07

Now it works perfectly! Thanks 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 5:04 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Sorry the code I suggested was not correct. The new lines should have images = ... instead of image = ... Otherwise your change looks correct. Tom

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For Chimera mac users
by Eduardo Sanz-Garcia 18 Jan '07

18 Jan '07

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 18 Jan '07

18 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 18 Jan '07

18 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 18 Jan '07

18 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 17 Jan '07

17 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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