- Chimera-users - RBVI Mailing Lists

Error when fetching pdb by ID
by Kenward Vaughan 21 Oct '08

21 Oct '08

Hmm... is this my system or outside it? I'm at home behind a firewall and have never seen such an error before. I'm not sure where I should look for an answer... Fetch by ID. The error log: Opening 1ai2 Error reading 1ai2: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') Done opening 1ai2 It doesn't fail at work, so I'm suspicious of my home network. ??? Both my workstation and gateway/firewall are Debian/Sid boxes. What port is the call made on?? Thanks for any ideas! Kenward -- ."^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Chair, Physical Science Department |,;| Bakersfield College / ', \ 1801 Panorama Drive / o O \ Bakersfield, CA 93305 (oOoOOoOo) http://www2.bc.cc.ca.us/kvaughan ---========--- ???$$MM$$???

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Fwd: Pruning pdb graphically
by Francesco Pietra 21 Oct '08

21 Oct '08

Hi Elaine: LEaP does not understand capping, with a pdb file that Chimera understands perfectly. I have asked for light at both the Amber and Dock sites. Even Dock uses LEaP for amber score. LEaP adds and exta H to the terminal/beginning and OXT to the terminal/last. Moreover, it tries to join the first ACE with last NME. I have not tried separating the capping residue with TER. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Tue, Oct 21, 2008 at 10:34 AM Subject: Re: [Chimera-users] Pruning pdb graphically To: Elaine Meng <meng(a)cgl.ucsf.edu> Hi Elaine: I had fully protonated histidine and left the chain amino group of lysine in basic form! No excuse for that. Now the charge is 5.0000 so that I expect that dockprep (avoiding add-h!) will work. In my (brief) experience, Chimera is an excellent tool also for capping, especially if Add-H is revised for the cases of capped residues. In some cases (12 residues capped in my case) that is important. Also because I want to run MD under various pH conditions, so that capping will change (constant pH MD is not possible with Amber under explicit medium conditions). That Amber has updated to PDB rules is good news. Perhaps I was so suspicious because a few days ago I found a bug with the latest version of ambpdb (Amber's tool to get a pdb file from inpcr/prmtop): the N-hydrogen names for LEU as first residue are written incorrectly. A revised ambpdb is forthcoming. Regards francesco On Tue, Oct 21, 2008 at 12:49 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > After looking at more parameter files, I now believe that Amber and PDB atom > names in standard residues, including hydrogens, are the same. My previous > information was old (I haven't run Amber for 10 years!), sorry about that. > You would still need to worry about correctly naming any atoms changed or > added with Build Structure, though. > > Besides the Amber *lib files mentioned before, you can also look up the > standard atom names in the links from this PDB page: > http://remediation.wwpdb.org/downloads.html > > Elaine > > > On Oct 20, 2008, at 2:39 PM, Elaine Meng wrote: > >> I forgot to mention that usually you don't need to worry about the atom >> names, as Add Charge knows which PDB names go with which Amber >> names/charges, and AddH uses the standard names. >> >> I think you only have to worry about the names of atoms that were changed >> or added "manually" in Build Structure, and if the nonhydrogen atoms have >> the standard names (PDB = Amber for nonhydrogen atoms in standard residues), >> AddH will use correct names for the hydrogens later added to those atoms. >> If you use hydrogens added by Build Structure, however, you have to fix >> their names. >> >> Elaine >> >> > >

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Residue Accessibility
by Luis Alberto Alvarez 21 Oct '08

21 Oct '08

Hello, I am trying to calculate the relative surface accessibility of residues (It will come to getting the solvent accessibility I guess) and the only information I found is from a post in the mailing list dating to 2005 ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-October/000482.html)I am just wondering if there is anything new in this front or I should just follow the 2005 instructions. Thank you -- Luis Alvarez alvarez(a)lcp.u-psud.fr Laboratoire de Chimie Physique Université Paris-Sud à Orsay microscope: 01 69 15 30 31 (80% du temps) bureau: 01 69 15 56 15

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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) ________________________________________________________

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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

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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

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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?

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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

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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

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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 *********************************************

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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

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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

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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

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Re: [Chimera-users] Helix-Numbers
by skmolugu＠miners.utep.edu 12 Oct '08

12 Oct '08

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.

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Printing on white background
by Francesco Pietra 12 Oct '08

12 Oct '08

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

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Re: [Chimera-users] problem of sleap for solvation
by Eric Pettersen 09 Oct '08

09 Oct '08

Hi JD, I am now able to reproduce your problem. It should be fixed in the next daily build. You can fix it in your build directly by copying C: \Archivos de programa\Chimera\inst\cygwin1.dll into C:\Archivos de programa\Chimera\bin\amber10\exe . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 9, 2008, at 12:32 AM, Dr. Jean-Didier Maréchal wrote: > Hi Eric, > > I followed your instructions. I cleaned my previous chimera, > installed 08/10/2008 build, fetch for 1gcn, went to > ToolsàAmberàsolvate. Asked from 4ang box, with TIP3PBOX. The > hydrogens have therefore been built but then it came with the same > message: > > Terminii for #0 determined from SEQRES records > Chain-initial residues that are actual N terminii: HIS 1.A > Chain-initial residues that are not actual N terminii: > Chain-final residues that are actual C terminii: THR 29.A > Chain-final residues that are not actual C terminii: > 15 hydrogen bonds > Hydrogens added > > tempDir: d:\docume~1\jean\config~1\temp\tmpesjllr > command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\ > \sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmpesjllr\ > \solvate.cmd'] > Running sleap command: C:\Archivos de programa\Chimera\bin > \amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmpesjllr > \solvate.cmd > Failure running sleap > Check reply log for details > > Best, > JD > > De: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Enviado el: jueves, 09 de octubre de 2008 2:57 > Para: "Dr. Jean-Didier Maréchal" > CC: chimera-users(a)cgl.ucsf.edu > Asunto: Re: [Chimera-users] problem of sleap for solvation > > Hi JD, > I tested solvating 1gcn with the Windows daily build and > it worked fine. You shouldn't need to install all those things you > tried. You have to realize that when Chimera runs sleap that > various environment variables are set that will cause sleap to find > files that it won't find it you run it standalone without those > environment variables set. > Can you try installing a "clean" version of the daily > build and see if you can solvate 1gcn (4 angstrom box) without > error? If you get an error, save the contents of the reply log and > mail it to me. If you don't get an error then try your structure. > If that fails, you will have to send it to me if I'm going to have a > chance to debug the problem... > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Oct 8, 2008, at 7:12 AM, Dr. Jean-Didier Maréchal wrote: > > > > Dear all, > > I tried yesterday's build on windows and tested the solvation plugin. > I had a first crash that reply log message I give here: > > command: ['C:\\Archivos de > programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', > 'd:\\docume~1\\jean\\config~1\\temp\\tmp7wpvvm\\solvate.cmd'] > Running sleap command: C:\Archivos de > programa\Chimera\bin\amber10\exe\sleap -f > d:\docume~1\jean\config~1\temp\tmp7wpvvm\solvate.cmd > Failure running sleap > Check reply log for details > > Running C:\Archivos de programa\Chimera\bin\amber10\exe\sleap alone, > I saw > that cygwin1.dll was missing. So I installed it in the same directory. > > Then came a second crash: > > tempDir: d:\docume~1\jean\config~1\temp\tmp6m0sm0 > command: ['C:\\Archivos de > programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', > 'd:\\docume~1\\jean\\config~1\\temp\\tmp6m0sm0\\solvate.cmd'] > Running sleap command: C:\Archivos de > programa\Chimera\bin\amber10\exe\sleap -f > d:\docume~1\jean\config~1\temp\tmp6m0sm0\solvate.cmd > (solvate) [gtkleap]$ source leaprc.ff03 > (solvate) Error: can not find file leaprc.ff03 in all > the search > path. > Failure running sleap > Check reply log for details > > Though I located the leaprc.ff03 file in another directory and > copied it in > the running one, I can not pass over this problem. > > All the best! > > JD > > > *************************************************** > Dr. Jean-Didier Maréchal > Lecturer > Computational Bioorganic and Bioionorganic Chemistry @ Transmet > Unitat de Química Física > Departament de Química > Universitat Autònoma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal(a)uab.es > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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export scene to maya, obj, iges, stl, dwg-dxp?
by Eli Kuslansky 08 Oct '08

08 Oct '08

Hi Greg, I'm trying to export proteins using Chimera to a Maya file for animations and presentation, but when I export to an .obj file it has no geometry. How can I assure there is geometry in the file? Best regards, Eli Kuslansky

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problem of sleap for solvation
by Dr. Jean-Didier Maréchal 08 Oct '08

08 Oct '08

Dear all, I tried yesterday's build on windows and tested the solvation plugin. I had a first crash that reply log message I give here: command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmp7wpvvm\\solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmp7wpvvm\solvate.cmd Failure running sleap Check reply log for details Running C:\Archivos de programa\Chimera\bin\amber10\exe\sleap alone, I saw that cygwin1.dll was missing. So I installed it in the same directory. Then came a second crash: tempDir: d:\docume~1\jean\config~1\temp\tmp6m0sm0 command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmp6m0sm0\\solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmp6m0sm0\solvate.cmd (solvate) [gtkleap]$ source leaprc.ff03 (solvate) Error: can not find file leaprc.ff03 in all the search path. Failure running sleap Check reply log for details Though I located the leaprc.ff03 file in another directory and copied it in the running one, I can not pass over this problem. All the best! JD *************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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coloring seperate domains
by Anindito Sen 08 Oct '08

08 Oct '08

HI all I was wondering how to color the c and n terminals of the crystal structure docked in the density map different. Thanks Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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"extended" Zone specifier
by Francesco Pietra 08 Oct '08

08 Oct '08

What I would like to do is a global search of which residues of model #0 are within a certain distance from which residues of model #1. Where "model" stands for a protein in both cases. That would save time in simulations of docking (not using DOCK) between proteins. I can locate with Chimera key residues, but their number is large. Thanks francesco pietra

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incorporate chimera commands into a shell script
by shyamala 07 Oct '08

07 Oct '08

Hi, I am fairly new to Chimera. I am trying to calculate the RMSD of the heavy atoms across two different ligand (small molecule) coordinate files. I don't need a least square fit performed, hence using rmsd as opposed to match. I have to do this comparison for around 200 docked conformations against the native ligand conformation, hence I am thinking shell script that can call chimera to execute this command is the way to go. I am not sure how to first select the two small molecules and then use the rmsd command when I start chimera in nogui mode. Any help, examples, pointers will be very much appreciated. Thanks a lot, Shyamala

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Re: [Chimera-users] symmetric fitting
by Tom Goddard 07 Oct '08

07 Oct '08

Hi Sudheer, This means your GroEL map does not have the cylinder axis along z. When you press the Orient button in the volume dialog you can see the orientation, the screen horizontal axis is x, the screen vertical axis is y, and in/out of the screen is z. I've attached a Python script that can produce the symmetry matrices for different cylinder axes. You run it by opening it in Chimera and the output is seen in the Reply Log (Favorites menu). You'll need to edit the script to use the correct axis. Tom skmolugu(a)miners.utep.edu wrote: > Hi Tom, > I have used the matrix file you have gave me and could succesfully generate the coordinates file. After saving the pdb file with the new coordinates, I reopened the saved pdb file that has 14 subunits and it is turns out to be perpendicular to map that has been used. How can I avoid this problem? > thank you very much for your time, > sincerely, > sudheer. > ---------------------------------------- > >> Date: Mon, 6 Oct 2008 12:06:32 -0700 >> From: goddard(a)cgl.ucsf.edu >> To: skmolugu(a)miners.utep.edu >> CC: chimera-users(a)cgl.ucsf.edu >> Subject: Re: [Chimera-users] symmetric fitting >> >> Hi Sudheer, >> >> Figuring out the symmetry matrices for using the symmetric fitting >> capability >> >> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#symcop… >> >> requires some work. First note that the symmetry matrices you want are >> those that transform (rotate and shift) the volume data to an identical >> configuration. >> >> Your case is 2 stacked 7-mer rings. Assuming the z axis is the >> symmetry axis of the map (need to set origin so the center of the >> cylinder is at xyz = 0,0,0 in the volume dialog Coordinates panel) you >> could just compute the needed rotation matrices >> >> cos(a), sin(a), 0 >> -sin(a), cos(a), 0 >> 0, 0, 1 >> >> Could write a script (python script attached) or use a calculator. Also >> you want to flip around x axis by 180 degrees to get 7 more rotations >> with the two 7-member rings exchanged. With that approach I get the >> following lines to add to the PDB file: >> >> REMARK 350 BIOMT1 0 1.000000 0.000000 0.000000 0.000000 >> REMARK 350 BIOMT2 0 -0.000000 1.000000 0.000000 0.000000 >> REMARK 350 BIOMT3 0 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 1 0.623490 0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 1 -0.781831 0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 2 -0.222521 0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 2 -0.974928 -0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 3 -0.900969 0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 3 -0.433884 -0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 4 -0.900969 -0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 4 0.433884 -0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 5 -0.222521 -0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 5 0.974928 -0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 6 0.623490 -0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 6 0.781831 0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 7 1.000000 -0.000000 0.000000 0.000000 >> REMARK 350 BIOMT2 7 -0.000000 -1.000000 0.000000 0.000000 >> REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 8 0.623490 -0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 8 -0.781831 -0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 9 -0.222521 -0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 9 -0.974928 0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 10 -0.900969 -0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 10 -0.433884 0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 11 -0.900969 0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 11 0.433884 0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 12 -0.222521 0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 12 0.974928 0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 12 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 13 0.623490 0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 13 0.781831 -0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 13 0.000000 0.000000 -1.000000 0.000000 >> >> If your map origin is not the center of symmetry or an x-axis flip is >> not a symmetry then these matrices won't work. You can try to set the >> correct origin -- the right value can be found with some tricky use of >> the output of the Fit in Map tool, fitting one copy of the map into >> another copy. Or you could fit one copy of the map to another and use >> the matrixget command to output that symmetry matrix to a file, then do >> that for all symmetries to create the needed matrix text. >> >> As you see this process has not yet been made easy. >> >> Tom >> >> >> >> >> >> skmolugu(a)miners.utep.edu wrote: >> >>> HI, >>> In the symmetric fitting model session that explains about the symmetry generation, i did not understand the method to generate the matrix. I am working on a chaperonin protein called GroEL. It has 14 subunits with seven fold symmetry. can you please explain me how to update the pdb and the matrix values that i need to put in the pdb file. >>> thankyou, >>> sudheer >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> # Chimera script to print symmetry matrices for GroEL 14-mer. format = '''REMARK 350 BIOMT1 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT2 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT3 %3d %10.6f %10.6f %10.6f %10.6f''' axis = (0,0,1) import Matrix as m flip = m.rotation_from_axis_angle((1,0,0), 180) # 180 degree rotation about x. flip = [r + (0,) for r in flip] # Zero translation. for i in range(14): a = 360.0*i/7.0 t = m.rotation_from_axis_angle(axis, a) # Rotation by i/7 turn about z. t = [r + (0,) for r in t] # Zero translation. if i >= 7: t = m.multiply_matrices(flip, t) # Exchange top and bottom ring. print format % ((i,) + t[0] + (i,) + t[1] + (i,) + t[2])

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obtaining rotation angles
by Jaap Brink 06 Oct '08

06 Oct '08

Hi, I'm trying to figure out how I can obtain angles from chimera. I have a 3D object that I have to rotate in order to see certain features. I'd like to know those angles. Is there is a way to get this info? Thanks in advance, Jaap Brink

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Re: [Chimera-users] symmetric fitting
by skmolugu＠miners.utep.edu 06 Oct '08

06 Oct '08

HI, In the symmetric fitting model session that explains about the symmetry generation, i did not understand the method to generate the matrix. I am working on a chaperonin protein called GroEL. It has 14 subunits with seven fold symmetry. can you please explain me how to update the pdb and the matrix values that i need to put in the pdb file. thankyou, sudheer

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Failure of Surface Display
by Charles Letner, Ph.D. 04 Oct '08

04 Oct '08

Hello, I am trying to display a surface using the Actions > Surface>Show menu. The surface is not displaying and the following error is in the reply: C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 1 Calculation of some surface components failed (code 5). Falling back to single-component calculation. C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 I am using Chimera version: production version 1 build 2540 2008/07/09 Platform is Windows Vista 64 bit. The file I am working with contains 2 subunits. If I split the two subunits into separate files and open individually in the same session, the surfaces display without any issue. I am trying to show the surface of the two subunits associated, not the surface of each individual subunit. Any help will be appreciated. Cheers, Chuck

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