October 2008 - Chimera-users - RBVI Mailing Lists

Presets and multiple structures
by James Nettles 16 Oct '08

16 Oct '08

Something that often comes up is that I have some number of aligned protein structures with nicely color coded secondary features and specific side chains. I then want to fit another molecule in this same space and apply a "preset" graphic mode to the new structure without undoing the previous molecular views. I expect this is possible, but I haven't gotten it to work yet. I've tried making only my molecule of interest "active" in the Model Panel, but the preset still effects everything. I'm using Alpha build 2557 2008/09/13 at the moment. Thanks, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine Laboratory of Biochemical Pharmacology (LOBP) Computer Assisted Discovery Research Environment (CADRE) ________________________________________________________

3 3

Building ACE, NME (peptide caps)
by Elaine Meng 16 Oct '08

16 Oct '08

On Oct 16, 2008, at 6:22 AM, Francesco Pietra wrote: > Hi Elaine: > Thanks. > Is it possible with Chimera to cap the the protein termini (once the > work below is carried out) with ACE and NMA residues? I have no > experience with such a procedure. > francesco Hi Francesco, I wouldn't recommend doing it in Chimera. If you are using AMBER anyway, do it with that program. In Chimera, you could do it by using Build Structure (under Tools... Structure Editing), Modify Atom section. It would take several cycles of atom modification, being careful to name the residues ACE and NME and to give the atoms the correct types and names as you build out. For the first atom in the new residue you would use "change modified residue's name to ACE" (or NME) and then for the rest of the atoms in the residue, leave the residue name unchanged. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht… > Then, because the names of hydrogens added while building aren't standard for those residues, either delete all the hydrogens and re- add them using AddH, or use Modify Atom to change the hydrogen names to what AMBER expects (shown below), or just write out the file and use a text-editor to change their names. It is easy to make mistakes in this long process. In addition, I just found a bug where addh still thinks the first amino acid has a free N-terminus even though it is capped by ACE, so if you use addh, you would then have to delete the two hydrogens on the first amino acid's nitrogen and then use Build Structure (Modify Atom) on that nitrogen to make it trigonal and get one hydrogen back, and then change the name of that hydrogen to H. THEN you would get correct charges from addcharge. The atom names that AMBER (and addcharge) expect: for ACE: C O CH3 HH31 HH32 HH33 for NME: N H CH3 HH31 HH32 HH33 If you are capping the residues to avoid terminal charges on residues that are not really the termini, there is no need to do this. AddH looks at the SEQRES information in the file to decide what is really a terminal residue. If it is not a real terminus (for example, the structure starts at residue 5 because 1-4 are disordered), the residue will still be treated as an internal residue starting with NH-CA- (etc.) not as NH3+-CA-(etc.). The C-terminus is handled similarly, (...)C(=O) if not a real terminus instead of (...)CO2 minus for the real C-terminus. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)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

1 0

imposing symmetry
by Anindito Sen 16 Oct '08

16 Oct '08

Hi I have a density map with symmetry C8. I have docked the monomer crystal structure. I was wondering if there is any way I can put crystal structures in rest of the 7 monomers without doing it manually. Thanks for your reply in advance. Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

2 1

error
by Linnemayr Charlotte 16 Oct '08

16 Oct '08

Hello, I have a problem opening a file, I got it from a friend, who also installed chimera recently. On her computer it works nicly. But I get an errormessage and a white window, with some of the files text. I see the model for about 2 seconds, before the window turns white. Do I need an extra plugin?

2 1

Contact mapping
by Beale, John 16 Oct '08

16 Oct '08

Is there a way in Chimera to generate interresidue contact maps for proteins from MD data? Thanks! John M. Beale, Ph,D, Associate Professor of Medicinal Chemistry and Pharmaceutics St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

2 1

automating ensemble clustering in chimera
by Katryna Cisek 15 Oct '08

15 Oct '08

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

3 4

Regarding blender
by Dr. Jean-Didier Maréchal 15 Oct '08

15 Oct '08

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(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] En nombre de chimera-users-request(a)cgl.ucsf.edu Enviado el: lunes, 13 de octubre de 2008 21:00 Para: chimera-users(a)cgl.ucsf.edu Asunto: Chimera-users Digest, Vol 66, Issue 12 Send Chimera-users mailing list submissions to chimera-users(a)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(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)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(a)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(a)miners.utep.edu> Subject: Re: [Chimera-users] Helix-Numbers To: chimera users <chimera-users(a)cgl.ucsf.edu> Message-ID: <BLU105-W44550A870C50C9AE487BFD85370(a)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(a)osu.edu> Subject: [Chimera-users] automating ensemble clustering in chimera To: chimera-users <chimera-users(a)cgl.ucsf.edu> Message-ID: <1bd6604c0810121242j2c9b4d48kc030b8a225af66d9(a)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(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Printing on white background To: Christian Schudoma <Schudoma(a)mpimp-golm.mpg.de>, Francesco Pietra <chiendarret(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Message-ID: <350D2312-C5FB-4B46-B6B5-023FE8BA7875(a)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(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 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(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu > ] On Behalf Of Francesco Pietra [chiendarret(a)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(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Helix-Numbers To: <skmolugu(a)miners.utep.edu> Cc: chimera users <chimera-users(a)cgl.ucsf.edu> Message-ID: <F5081034-A931-431B-B612-2A930580D98F(a)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(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 Oct 12, 2008, at 12:21 PM, <skmolugu(a)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. ------------------------------ Message: 5 Date: Mon, 13 Oct 2008 12:22:59 -0400 From: "Katryna Cisek" <cisek.2(a)osu.edu> Subject: Re: [Chimera-users] save reply log from chimera python script To: "Tom Goddard" <goddard(a)cgl.ucsf.edu> Cc: chimera-users(a)cgl.ucsf.edu Message-ID: <1bd6604c0810130922m35b031c4sc4694d7e46f6ce81(a)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(a)cgl.ucsf.edu> wrote: > Hi Katryna, > > I don't think there is a command to save the text in the reply log. In 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(a)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(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Pruning pdb graphically To: "Francesco Pietra" <chiendarret(a)gmail.com> Cc: chimera <chimera-users(a)cgl.ucsf.edu> Message-ID: <DD923F0C-8D7F-478E-991A-FD8E054B7E81(a)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(a)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 ------------------------------ Message: 7 Date: Mon, 13 Oct 2008 10:49:43 -0700 From: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] save reply log from chimera python script To: Katryna Cisek <cisek.2(a)osu.edu> Cc: chimera-users(a)cgl.ucsf.edu Message-ID: <48F38A37.5080803(a)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: > 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(a)cgl.ucsf.edu> wrote: >> Hi Katryna, >> >> I don't think there is a command to save the text in the reply log. In 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(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 66, Issue 12 *********************************************

3 2

Re: [Chimera-users] Chimera-users Digest, Vol 66, Issue 13, 1. Regarding blender ( Dr. Jean-Didier Mar?chal )
by Jonathan Hilmer 14 Oct '08

14 Oct '08

> 1. Regarding blender ( Dr. Jean-Didier Mar?chal ) > ---------------------------------------------------------------------- > Message: 1 > Date: Tue, 14 Oct 2008 18:16:29 +0200 > From: " Dr. Jean-Didier Mar?chal " <jeandidier.marechal(a)uab.cat> > Subject: [Chimera-users] Regarding blender > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <004a01c92e18$37236890$a56a39b0$%marechal(a)uab.cat> > Content-Type: text/plain; charset=iso-8859-1 > > 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 Quite a while ago I wrote a VRML importer for Blender that was specifically designed for Chimera-generated surfaces. It worked acceptably, but the X3D importer mentioned previously (http://blenderartists.org/forum/showthread.php?t=107126) looks like a much better overall solution. If that importer isn't working for some particular aspect of a Chimera scene, I could probably help adapt it to get what you're looking for. The only other good solution I know of is to import your structures directly into Blender, and use Blender to generate the scene from the base primitives. That approach gets very complicated for representations such as helices, and I wouldn't recommend it unless you have very specific needs. Jonathan

1 0

save reply log from chimera python script
by Katryna Cisek 13 Oct '08

13 Oct '08

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

3 3

Pruning pdb graphically
by Francesco Pietra 13 Oct '08

13 Oct '08

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

2 1

Chimera-users October 2008