Regarding blender
Hi guys, I saw on the mailing list some information on exporting/importing 3D files. However, I can't really figure out what would be the best way to export chimera scene so that blender can import them. Is the x3d format the best? Which plug-in do you use? Is there another way better? Cheers, JD -----Mensaje original----- De: chimera-users-bounces@cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] En nombre de chimera-users-request@cgl.ucsf.edu Enviado el: lunes, 13 de octubre de 2008 21:00 Para: chimera-users@cgl.ucsf.edu Asunto: Chimera-users Digest, Vol 66, Issue 12 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Helix-Numbers (skmolugu@miners.utep.edu) 2. automating ensemble clustering in chimera (Katryna Cisek) 3. Re: Printing on white background (Elaine Meng) 4. Re: Helix-Numbers (Elaine Meng) 5. Re: save reply log from chimera python script (Katryna Cisek) 6. Re: Pruning pdb graphically (Elaine Meng) 7. Re: save reply log from chimera python script (Thomas Goddard) ---------------------------------------------------------------------- Message: 1 Date: Sun, 12 Oct 2008 13:21:53 -0600 From: <skmolugu@miners.utep.edu> Subject: Re: [Chimera-users] Helix-Numbers To: chimera users <chimera-users@cgl.ucsf.edu> Message-ID: <BLU105-W44550A870C50C9AE487BFD85370@phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Hi, I was wondering if there is a way in chimera for numbering the helices in the map fitted with coordinates. I Basically wanted to explain the location of helix in the map by means of numbering it, so that it will be easy for me to explain in my paper. thank you very much for your time, sudheer. ------------------------------ Message: 2 Date: Sun, 12 Oct 2008 15:42:47 -0400 From: "Katryna Cisek" <cisek.2@osu.edu> Subject: [Chimera-users] automating ensemble clustering in chimera To: chimera-users <chimera-users@cgl.ucsf.edu> Message-ID: <1bd6604c0810121242j2c9b4d48kc030b8a225af66d9@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Chimera Users, How can I automate/import the Ensemble Cluster (Structure Comparison, MD/Ensemble Analysis; cluster members of a conformational ensemble, determine cluster representatives) module into a python script? Thanks, Katryna ------------------------------ Message: 3 Date: Sun, 12 Oct 2008 13:09:33 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Printing on white background To: Christian Schudoma <Schudoma@mpimp-golm.mpg.de>, Francesco Pietra <chiendarret@gmail.com> Cc: Chimera BB <chimera-users@cgl.ucsf.edu> Message-ID: <350D2312-C5FB-4B46-B6B5-023FE8BA7875@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Thanks, Christian! Besides the ways you mentioned, there is also the "set" command, for example: set bg_color white <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> Francesco and others may also be interested in the "tips on preparing images" page, which covers background color and other issues: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> Elaine ----- Elaine C. Meng, Ph.D. meng@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 Oct 12, 2008, at 8:50 AM, Christian Schudoma wrote:
Hi Francesco, you can change the background colour in Chimera: Actions->Color-
background, then Actions->Color->[choose your colour like you would for colouring atoms etc.]. Then just save your image as usual and it should be on a white background.
Also, some of the Publication Options in the Presets menu automatically set the background colour to white.
Maybe there is a command line call for changing the background as well? I don't know... Cheers, Christian ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu ] On Behalf Of Francesco Pietra [chiendarret@gmail.com] Sent: 12 October 2008 12:44 To: chimera Subject: [Chimera-users] Printing on white background
When mapping protein residues around a ligand I would like to have a printout of the enlarged binding site area, so as to put remarks by pencil on the printout. However, on a white background, in order to save ink. Is that a problem of working out the image (I have Gimp only, of which I never gained expertise), or can Chimera provide directly?
Thanks francesco pietra
------------------------------ Message: 4 Date: Sun, 12 Oct 2008 13:26:20 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Helix-Numbers To: <skmolugu@miners.utep.edu> Cc: chimera users <chimera-users@cgl.ucsf.edu> Message-ID: <F5081034-A931-431B-B612-2A930580D98F@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Sudheer, Sounds like you want 2D labels (Tools... Utilities... 2D Labels): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels. html
Since these labels don't move when you rotate the structure, you would first find the position you want to show in your figure, and then add the labels. Alternatively, for labels in 3D that move with the structure, you could just label one atom in each helix and then manually change what is in the label (for example with "Actions... Label... other..."). However, for figures I think 2D labels are much better, since they allow more control over location and can include symbols such as Greek letters, and it is easier to change their sizes and colors. Some example images with 2D labels: <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> <http://www.cgl.ucsf.edu/chimera/feature_highlights/2fma-density.png> <http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities-larg e.png
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@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 Oct 12, 2008, at 12:21 PM, <skmolugu@miners.utep.edu> wrote:
Hi, I was wondering if there is a way in chimera for numbering the helices in the map fitted with coordinates. I Basically wanted to explain the location of helix in the map by means of numbering it, so that it will be easy for me to explain in my paper. thank you very much for your time, sudheer.
Hi Katryna,
I don't think there is a command to save the text in the reply log. In
------------------------------ Message: 5 Date: Mon, 13 Oct 2008 12:22:59 -0400 From: "Katryna Cisek" <cisek.2@osu.edu> Subject: Re: [Chimera-users] save reply log from chimera python script To: "Tom Goddard" <goddard@cgl.ucsf.edu> Cc: chimera-users@cgl.ucsf.edu Message-ID: <1bd6604c0810130922m35b031c4sc4694d7e46f6ce81@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Chimera Users, Could someone please point out the syntax error in this code: def save_reply_log("/tmp/tmplog.txt"): <<--- error should be here based on error info from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open('/tmp/tmplog.txt', 'w') f.write(text) f.close() ---------------------------chimera error info from reply log------------------------------- <type 'exceptions.SyntaxError'> Exception in Tk callback Function: <function command at 0x132d230> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 244, in command None File "CHIMERA/share/chimera/baseDialog.py", line 453, in OK None File "CHIMERA/share/OpenSave/__init__.py", line 161, in Apply None File "CHIMERA/share/SimpleSession/gui.py", line 41, in _openCB None File "CHIMERA/share/chimera/__init__.py", line 1344, in open None File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython None <type 'exceptions.SyntaxError'>: invalid syntax (refalignrotatewholesymmetrysavelog.py, line 58) -------------- Thanks, Katryna On Wed, Oct 8, 2008 at 10:33 PM, Tom Goddard <goddard@cgl.ucsf.edu> wrote: the
Python function the variable path is the path to the file, for example "/tmp/mylog.txt".
Tom
Katryna Cisek wrote:
Hi Chimera users, Is there a new way to save the reply log from a chimera python script, other than below (from Chimera Archive 2006)?
def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open(path, 'w') f.write(text) f.close()
If not, what is the filename given to the reply log in this function? Is it possible to designate the name? Thanks, Katryna _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
------------------------------ Message: 6 Date: Mon, 13 Oct 2008 10:02:10 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Pruning pdb graphically To: "Francesco Pietra" <chiendarret@gmail.com> Cc: chimera <chimera-users@cgl.ucsf.edu> Message-ID: <DD923F0C-8D7F-478E-991A-FD8E054B7E81@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Francesco, As usual in Chimera, there are several possible ways to do this, and what is "best" depends not only on what you plan to do with the result, but also your personal preferences and working style. I would probably start by using either zones or Find Clashes/Contacts with a conservative cutoff to select all the residues you want to keep, which would probably also include several extra residues. If you used Find Clashes/Contacts, one option selects the contacting atoms, and you would press the keyboard up arrow to promote the selection to whole residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas h.html
Next, invert the selection (for example with Select... Invert (all models)) to include the residues you do NOT want, then undisplay them (for example with Actions... Atoms/Bonds... hide). Then you can manually get rid of the few extra residues here and there: Ctrl-click to select one atom or bond in an unwanted residue, press keyboard up arrow to promote to whole residue, undisplay as before. Repeat as needed. I don't know if you meant you wanted to just undisplay atoms or actually delete them. If you wanted to delete them: you could save PDB(s) and choose the option to include only the atoms that are displayed. Alternatively, you could use the approach described above except instead of undisplaying atoms, deleting atoms (for example with Actions... Atoms/ Bonds... Delete) and then save PDB(s). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht ml#deletion
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 12, 2008, at 10:05 AM, Francesco Pietra wrote:
I would like to remove several parts from a complex protein, just leaving the portion where a complex has been created with amberscore. Which is the besr way in Chimera, while observing the pruning on the screen? Thanks francesco pietra
Hi Chimera Users, Could someone please point out the syntax error in this code:
def save_reply_log("/tmp/tmplog.txt"): <<--- error should be here based on error info from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open('/tmp/tmplog.txt', 'w') f.write(text) f.close()
---------------------------chimera error info from reply log-------------------------------
<type 'exceptions.SyntaxError'> Exception in Tk callback Function: <function command at 0x132d230> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 244, in command None File "CHIMERA/share/chimera/baseDialog.py", line 453, in OK None File "CHIMERA/share/OpenSave/__init__.py", line 161, in Apply None File "CHIMERA/share/SimpleSession/gui.py", line 41, in _openCB None File "CHIMERA/share/chimera/__init__.py", line 1344, in open None File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython None <type 'exceptions.SyntaxError'>: invalid syntax (refalignrotatewholesymmetrysavelog.py, line 58)
--------------
Thanks, Katryna
On Wed, Oct 8, 2008 at 10:33 PM, Tom Goddard <goddard@cgl.ucsf.edu> wrote:
Hi Katryna,
I don't think there is a command to save the text in the reply log. In
------------------------------ Message: 7 Date: Mon, 13 Oct 2008 10:49:43 -0700 From: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: Re: [Chimera-users] save reply log from chimera python script To: Katryna Cisek <cisek.2@osu.edu> Cc: chimera-users@cgl.ucsf.edu Message-ID: <48F38A37.5080803@cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Katryna, The original code defines a function. You leave it unchanged and add a line at the end to call it as follows. Tom def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open(path, 'w') f.write(text) f.close() save_reply_log("/tmp/tmplog.txt") Katryna Cisek wrote: the
Python function the variable path is the path to the file, for example "/tmp/mylog.txt".
Tom
Katryna Cisek wrote:
Hi Chimera users, Is there a new way to save the reply log from a chimera python script, other than below (from Chimera Archive 2006)?
def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open(path, 'w') f.write(text) f.close()
If not, what is the filename given to the reply log in this function? Is it possible to designate the name? Thanks, Katryna _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 66, Issue 12 *********************************************
On Tue, 14 Oct 2008, Dr. Jean-Didier Mar�chal wrote:
Hi guys,
I saw on the mailing list some information on exporting/importing 3D files. However, I can't really figure out what would be the best way to export chimera scene so that blender can import them.
Is the x3d format the best? Which plug-in do you use? Is there another way better?
Cheers, JD
For chimera, the X3D format is the best export format. So the best solution would be to use a X3D importer for blender. There doesn't appear to be one that comes with blender, so you'll have to google for one (e.g., <http://blenderartists.org/forum/showthread.php?t=107126> looks promising). Looking at the blender documentation, <http://www.blender.org/download/python-scripts/import-export/>, I see that the only common format, that chimera exports and blender imports, is the Wavefront OBJ format. But chimera only exports surfaces in OBJ format, so no spheres, cylinders, lines, nor ribbons. That may or may not be sufficient for you. If you find a solution, please let us know, Greg Couch UCSF Computer Graphics Lab
Hi, Thanks Greg. I have actually tried yesterday the same importer you found. However, I initially concluded that it was not working very well. Today, after having insisted all morning, I found a way to move forward anyways. I have to say that I work on the last released version of blender. Using this .x3d file importer, I saw that importing files that only contains ribbons works ok. However, importing files with sticks and spheres, do not work that well: you just see one sphere at the origin of the 3d world. With time, I figured out that in reality, all the geometrical figures are overlapped in the center of the world. If you guys have the same problem than me then here seems to be the first trick. Import your .x3d file from chimera in blender using the .x3d imported Greg mentioned. Once imported, the 3d window shows the sticks and spheres overlapped at the center of the world. Do the following: select all the mesh (menu select --> select all by type--> mesh), then enter in Grab/move mode (type g) and then you'll see all the sphere and stick back to their places. There are still remaining problems on this. In particular the xyz axis associated to all objects have strange behaviors but I am too short on blender's knowledge to figure out what is going wrong. Matthew may be you'll have some idea? For the moment, with this trick I can get a bit further with blender. Hope we'll have some feedback. Cheers, JD -----Mensaje original----- De: Greg Couch [mailto:gregc@cgl.ucsf.edu] Enviado el: martes, 14 de octubre de 2008 20:52 Para: Dr. Jean-Didier Maréchal CC: chimera-users@cgl.ucsf.edu Asunto: Re: [Chimera-users] Regarding blender On Tue, 14 Oct 2008, Dr. Jean-Didier Maréchal wrote:
Hi guys,
I saw on the mailing list some information on exporting/importing 3D files. However, I can't really figure out what would be the best way to export chimera scene so that blender can import them.
Is the x3d format the best? Which plug-in do you use? Is there another way better?
Cheers, JD
For chimera, the X3D format is the best export format. So the best solution would be to use a X3D importer for blender. There doesn't appear to be one that comes with blender, so you'll have to google for one (e.g., <http://blenderartists.org/forum/showthread.php?t=107126> looks promising). Looking at the blender documentation, <http://www.blender.org/download/python-scripts/import-export/>, I see that the only common format, that chimera exports and blender imports, is the Wavefront OBJ format. But chimera only exports surfaces in OBJ format, so no spheres, cylinders, lines, nor ribbons. That may or may not be sufficient for you. If you find a solution, please let us know, Greg Couch UCSF Computer Graphics Lab
participants (3)
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Dr. Jean-Didier Maréchal -
Greg Couch -
Jean-Didier Maréchal