- Chimera-users - RBVI Mailing Lists

RMSD supports symmetry?
by Kevin Wu 11 Sep '09

11 Sep '09

Hi all, I'm wondering if the RMSD function in Chimera will correctly calculate RMSD when two molecules are compared. For example, if a benzene ring is flipped, will the RMSD stay the same? Furthermore, how does Chimera do this comparison? Thanks! Kevin

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Zalman 3D
by Miles Pufall 11 Sep '09

11 Sep '09

Hi Guys - I got a Zalman 3D - it's pretty cool with Coot and Pymol. Your site says the row-interleaved stereo view under camera will work with this monitor, but I wasn't having much success. Do you have some more detailed instructions for this particular monitor? I can drop by and visit with it, or you can come see me if you's like. Thanks! Miles in Yamamoto Lab S574 Genentech Hall

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Re: [Chimera-users] [chimera-dev] suggestion for feature addition to chimera
by Eric Pettersen 09 Sep '09

09 Sep '09

On Sep 4, 2009, at 5:09 PM, Rocco Varela wrote: > Hello, > > I have a small suggestion for an additional feature for Chimera that > I think would be useful. I often look at structures of multiple > small molecules, some artificial and some real, and I noticed > something interesting with the way Chimera writes mol2 files. > > Here is Scenario 1: > > 1) I open a mol2 file that contains multiple molecules flagged as > "separate" MOLECULEs. > > 2) I save the loaded file as mol2 and select "a single file > [combined @MOLECULE section]" for the "Save multiple models in" > option. > > > 3) After saving and reloading this new mol2 file that now has a > single MOLECULE section, all the "names" of the previous molecules > have been lost. (ex. s-030, s-048, s-055, etc...) Instead in the > SUBSTRUCTURE section "UNK0" is used. > > It would useful if Chimera could name the components of the new > single molecule with the proper names. I could easily write a > script to fix this after the fact but I thought it might be a useful > option for other people too? Okay, I changed the Mol2 writer to use the model name instead of the residue type under the following conditions (only): 1) Combining models into a single @MOLECULE 2) All models are a single residue 3) Model names are unique and residue types are not This change will be in tonight's build. > Scenario 2: > > 1) Same as 1 above. > 2) Now I want to save all the MOLECULEs in the file as separate mol2 > files but with the proper "names" that are listed in the original > file loaded. Currently the only option is to provide a common name > and to append the "model number". It would be nice if we were > allowed to NOT provide a common name and allow it to name all the > files according to the molecule "names" not model numbers. This seems like a reasonable enough request. I will open a ticket in our Trac database for it, with you on the recipient list so you'll know when it gets done. It's a tad more work than the preceding change because aside from adding code to support it, the interface has to be changed to allow for the option and the documentation has to be updated to describe it -- whereas the other change can sneak in under the radar. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Can you morph a ligand
by Walter Fast 09 Sep '09

09 Sep '09

Hi! Chimera is great - thanks again! I use it all the time for research and teaching. I have a quick question: We have two different product-bound structures, but when I morph between the two we loose the active site metal ions and the active-site ligands. Is there a way to include these as well? Thanks, Walt -- Walter Fast, Ph.D. Associate Professor The University of Texas at Austin College of Pharmacy The Division of Medicinal Chemistry Phone: (512) 232-4000 Fax: (512) 232-2606 Lab: (512) 471-5839 Email: WaltFast(a)mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html

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Re: [Chimera-users] [chimera-dev] Suggestion: define selection name for startup chimera
by Jean Didier Pie Marechal 09 Sep '09

09 Sep '09

Hi Eric, "binding site" was an idea more than anything else but I realize from your e-mail that we don't really need. Strangely, though using @/display frequently I never thought about using it for selecting. Think I can do without the shortcut... Sorry! Cheers JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological 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 ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Dimecres, Setembre 9, 2009 8:46 pm Assumpte: Re: [chimera-dev] Suggestion: define selection name for startup chimera > On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote: > > > In the new builts of chimera, you have change the initial > > representation of the protein so that binding sites immediately > > appear and the rest of the protein is in ribbon (which is a > great > > idea by the way). That means that you have a automatic analysis > of > > binding site recognition. I wonder if you couldn't include a > > selection named "binding site" (or something similar), that > would > > appear as a named selection and that we could call at the early > > beginning of the session. > > Hi JD, > I could. I definitely wouldn't want to call it "binding site" > since > it includes waters and residues not necessarily involved in > binding, > not to mention the entire structure for small-molecule structures. > > It's also a misleading name for structures without ligand present - > - > since their binding sites won't be selected by it. FInally, it's > also > somewhat confusing as to what should happen if you open multiple > structures over the course of a session. > So it could be called "smart display atoms" I suppose. If some > other > users thought it'd be useful I'd do that (anyone?). In the > interim, > you can pretty easily create the selection yourself with these > commands after opening the structure: > > sel @/display; namesel smart atoms; ~sel > > You could alias that to something snappier. :-) > > --Eric > >

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Re: [Chimera-users] [chimera-dev] Suggestion: define selection name for startup chimera
by Eric Pettersen 09 Sep '09

09 Sep '09

On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote: > In the new builts of chimera, you have change the initial > representation of the protein so that binding sites immediately > appear and the rest of the protein is in ribbon (which is a great > idea by the way). That means that you have a automatic analysis of > binding site recognition. I wonder if you couldn't include a > selection named "binding site" (or something similar), that would > appear as a named selection and that we could call at the early > beginning of the session. Hi JD, I could. I definitely wouldn't want to call it "binding site" since it includes waters and residues not necessarily involved in binding, not to mention the entire structure for small-molecule structures. It's also a misleading name for structures without ligand present -- since their binding sites won't be selected by it. FInally, it's also somewhat confusing as to what should happen if you open multiple structures over the course of a session. So it could be called "smart display atoms" I suppose. If some other users thought it'd be useful I'd do that (anyone?). In the interim, you can pretty easily create the selection yourself with these commands after opening the structure: sel @/display; namesel smart atoms; ~sel You could alias that to something snappier. :-) --Eric

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label
by Bala subramanian 09 Sep '09

09 Sep '09

Friends, Is there any possiblity to move a 3D label along a particular axis in chimera 1.4. I labelled the residues of a DNA molecule using rlabel command. Some residue labels are displayed behind the base of the DNA. I tried to change the lighting also but it vain. Thanks, Bala

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Problem with benzenes split across crystal unit cell
by Tom Goddard 04 Sep '09

04 Sep '09

Hi Mike, The Chimera unit cell dialog is behaving as expected in the cases where the asymmetric unit contains half of a benzene ring. First, parts of the asymmetric unit are not moved relative to other parts of the asymmetric unit, so as you observe the half benzenes in asymmetric unit copies sometimes lie outside the unit cell. All unit cell dialog just puts the center of the asymmetric unit in the unit cell box. A second problem is that a half benzene ring from one asymmetric unit will not be joined to a half benzene ring from another asymmetric unit. They will line up perfectly but Chimera does not see bonds between the two halfs so for instance, selecting aromatic rings won't pick those up. I guess the first problem could be handled by moving each connected group of atoms so its center lies in the unit cell. I think it could lead to undesired results. For example a protein with a bound ligand might have the ligand outside the unit cell causing it to be moved to some other asymmetric unit's binding site. The trouble with that is that the protein and ligand are part of one molecule model in Chimera, so now you have taken the ligand in that molecule and placed it with the protein of another copy of the molecule. That may not be what you want. Another answer to the first problem, is that I added to the unit cell dialog the ability to make multiple asymmetric unit copies to fill multiple unit cells. If you make several unit cells, then the half benzenes lying outside one unit cell do join up with the half benzenes from a different unit cell. If you were trying to make a figure and you didn't want half-benzenes floating around -- you could simply select them and delete them (Actions / Atoms / Delete). The second problem is harder. Chimera could guess that the half-benzenes should be joined since they have exactly coincident atoms. (This relies on the strange inconsistency that the half-benzenes in the PDB files you sent contain 4 atoms instead of the expected 3 atoms. So it doesn't actually represent an asymmetric unit since there is an extra atom that will be duplicated in other asymmetric units.) But Chimera can't join them because covalent bonds can't be formed between different molecule objects -- it would require making a new molecule to contain all the atoms. Creating extra molecule models to join the half benzenes is possible but weird. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard Date: 9/4/09 12:41 PM > Hi Tom, > > Thanks. It looks like the issue is mostly resolved. > > The is a problem with molecular units sitting at symmetry element in > non-primitive cells, for now I've found it in C2/c (iat03.pdb) and > Fdd2 (ta21.pdb) which I've attached. As far as I can tell this is not > unique to chimera, some programs handle this okay, many don't. You'll > see that in these two cases benzene molecules land outside of the cell > or fail to complete a pair. > > If I had to lobby for any particular ticket on your list it would be > #201. What I would add in way of description on that ticket is that > I'm not talking about using SHELX in Chimera. What I meant to say is > for Chimera to read a standard format CIF file containing the > reciprocal space transform of the real space electron density. The fft > routines to transform back to real space have been around forever and > are in most all modern languages. > > All crystallography packages can write this type of file containing > h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in > degrees). This the preferred format for sending data to the PDB. > > I'm not looking to add a bunch of "stuff" to your already huge pile > but I thought most of this was already in the public domain. After > all, nothing is impossible for the guy that doesn't have to do it. > It's all easy and straightforward, right? ;0) > > As for the issue of reading the CIF, P21/n is a very common alternate > setting of P21/c and the PDB symmetry list does not contain it. > > Thanks again!! > Cheers, > Mike > > <<< > ------------------------------------------------------------------------>>> > Dr. Michael W. Day > Director - X-ray Crystallography Lab & Molecular Observatory > California Institute of Technology > Mail Code 139-74 > Pasadena, CA 91125 > > <<< > ------------------------------------------------------------------------>>> > > On Sep 2, 2009, at 5:54 PM, Tom Goddard wrote: > > Hi Mike, > > I've fixed the unit cell dialog to handle inverting symmetries. It > was a simple change. Will be in tonight's daily builds. > > We could have Unit Cell work with CIF files but that is an > enhancement that will have to compete for time with the hundreds of > other feature requests we're looking at. My list of requests is here > > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests > > and Eric and other developer maintain their own off-line lists. So > you need to make a good case. It could be an easy task if our > third-party CIF file reader already parses the needed symmetry > operators. If it does not provide those then it could be a > significant bit of work. > > Tom > > > -------- Original Message -------- > Subject: Re: [Chimera-users] Centro-symmetric space groups > From: Michael Day > To: Thomas Goddard > Date: 9/1/09 1:19 PM >> Hi Tom, >> >> Thanks. >> >> Another option you might consider is to have the Unit Cell tool work >> also with CIF files then only coordinate transformations are needed >> as the symmetry operators are included. An advantage is that if >> someone uses a non-standard setting of a space group the symmetry >> operators are still valid for the coordinates. >> >> Thanks for all your work. All of you on the Chimera team (Elaine, >> Eric and Greg) set the bar pretty high! My hats off to you. >> >> Cheers, >> Mike >> >> <<< >> ------------------------------------------------------------------------>>> >> Dr. Michael W. Day >> Director - X-ray Crystallography Lab & Molecular Observatory >> California Institute of Technology >> Mail Code 139-74 >> Pasadena, CA 91125 >> >> <<< >> ------------------------------------------------------------------------>>> >> >> On Sep 1, 2009, at 9:27 AM, Thomas Goddard wrote: >> >> Hi Mike, >> >> Thanks for the suggestions. The coordinate transformations are >> routine. The trouble is that the Chimera Molecule C++ code takes the >> transformation matrix and orthonormalizes it to a proper rotation. >> So the inversion operator of "P -1" gets changed to inverting x and >> y axes but not the z axis. The orthonormalization is supposed to >> just fix tiny round-off transformation problems, like matrices read >> from a PDB file that have only 5 digits of precision. Really we >> should be warning if a transformation is very far from a proper rotation. >> >> I'll let you know when the problem is fixed in the daily builds. >> >> Tom >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Centro-symmetric space groups >> From: Michael Day >> To: Thomas Goddard >> Date: 8/31/09 7:54 PM >> >>> Tom, >>> Thanks again. Awesome! >>> I suspect mirrors and therefore glide planes could be an issue as >>> you don't see them in proteins. >>> I don't know what your overall strategy is for applying space group >>> operators but to avoid issues I would suggest; >>> 1) deorthogonalize into crystallographic coordinates as fractions of >>> cell edge >>> 2) apply symmetry operators in turn to the original set (x,y,z) to >>> get (x',y',z') for each operator >>> 3) calculate the centroid for each equivalent set of coordinates >>> (x',y',z') >>> 4) move centroids into unit cell as needed so they are x=0,1 y=0,1 >>> and z=0,1 >>> I suspect you already know this but it never hurts to say it. My >>> students think I overstate the basics at times but it sure helps all >>> of us get on the same page. >>> Cheers, >>> Mike >>> <<< >>> ------------------------------------------------------------------------>>> >>> Dr. Michael W. Day >>> Director - X-ray Crystallography Lab & Molecular Observatory >>> California Institute of Technology >>> Mail Code 139-74 >>> Pasadena, CA 91125 >>> > >>> <<< >>> ------------------------------------------------------------------------>>> >>> On 31 Aug, 2009, at 6:14 PM, Thomas Goddard wrote: >>>> Hi Mike, >>>> >>>> Oops. The symmetries that invert coordinates don't work in the Unit >>>> Cell tool. This is because it sets the transformation matrix >>>> (rotation and shift) for the asymmetric unit copies but it can only >>>> handle proper rotations. Chimera is generally used for proteins >>>> which are handed (not symmetric under inversion) so such space >>>> groups generally don't occur for proteins. But of course for small >>>> molecules they can. >>>> >>>> I'll fix this soon, maybe later this week. I'll have to change >>>> atom coordinates instead of setting the transform matrix for the >>>> asymmetric unit copies. >>>> >>>> Tom

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Computing xray density from structure factors
by Tom Goddard 04 Sep '09

04 Sep '09

Hi Mike, If it is just a matter of computing a Fourier transform that is easy. Chimera already has libraries that does that. The trouble will be parsing the CIF file. Chimera reads molecular structure CIF and mmCIF files using a third party library called mmLib. I don't know if mmLib will read the structure factors. If you send me an example CIF file with structure factors I'll give it a try. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard Date: 9/4/09 12:41 PM > Hi Tom, > > ... > > If I had to lobby for any particular ticket on your list it would be > #201. What I would add in way of description on that ticket is that > I'm not talking about using SHELX in Chimera. What I meant to say is > for Chimera to read a standard format CIF file containing the > reciprocal space transform of the real space electron density. The fft > routines to transform back to real space have been around forever and > are in most all modern languages. > > All crystallography packages can write this type of file containing > h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in > degrees). This the preferred format for sending data to the PDB. > > I'm not looking to add a bunch of "stuff" to your already huge pile > but I thought most of this was already in the public domain. After > all, nothing is impossible for the guy that doesn't have to do it. > It's all easy and straightforward, right? ;0) > > As for the issue of reading the CIF, P21/n is a very common alternate > setting of P21/c and the PDB symmetry list does not contain it. > > Thanks again!! > Cheers, > Mike > > <<< > ------------------------------------------------------------------------>>> > Dr. Michael W. Day > Director - X-ray Crystallography Lab & Molecular Observatory > California Institute of Technology > Mail Code 139-74 > Pasadena, CA 91125 > > <<< > ------------------------------------------------------------------------>>>

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hydrogen bond representation
by Bala subramanian 04 Sep '09

04 Sep '09

Friends, Is there any way to represent hydrogen bonds as dotted lines instead of a solid line in Chimera. Sometimes hbond analysis in chimera shows same atom to be involved in two hydrogen bonds, why is it so ? Thanks, Bala

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2D projections
by Ana Luiza 03 Sep '09

03 Sep '09

Hi, Is it possible to build 2D projections from a 3D surface in Chimera? Thanks, Ana Luiza.

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wglMakeCurrent failed
by Stefano Marzi 03 Sep '09

03 Sep '09

Hi, With the new production releases, from 1.2540 to the very last one 1.4_b28596, for windows, I am keeping getting the wglMakeCurrent failure. This happens when I try to make a movie. I have searched in the Chimera-user mailing list archive but I have found only a thread by Greg Couch saying that this bug has been fixed already one year ago, September 2008. Could anyone please help me with that? Thank you, Best Stefano Marzi

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Rendering with nogui
by Kevin Wu 02 Sep '09

02 Sep '09

Hi, It seems like it's not possible to render figures or models in Chimera when using the nogui option. Is there anyway around this? I'd like to use Chimera in a program to render models to display. Regards, Kevin

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chimera latest build
by Bala subramanian 01 Sep '09

01 Sep '09

Friends, 1) I downloaded the chimera's today's build and tried to change the nucleic acid representation using..Depiction in Tools. I get the following error. Kindly write me what is going wrong ? TclError: unknown option -width TclError: unknown option -width File "CHIMERA/share/CGLtk/OptionMenu.py", line 15, in __init__ See reply log for Python traceback. Thanks, Bala

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substitute single residue
by Andrew P. Hinck 01 Sep '09

01 Sep '09

Dear all, I was hoping to make some single amino acid substitutions in the context of a protein binding interface. I've only briefly poked around, but so far the only way I see to do this is to delete existing atoms/bonds one by one, and then rebuild (the alternate amino acid) atom-by-atom/bond-by-bond. Is there an easier way (like, telling the program to substitute an Asp for a Lys, or something akin to this)? Thanks in advance for any suggestions. Andy Hinck Andrew P. Hinck, Ph.D. Professor, Department of Biochemistry, MC 7760 University of Texas Health Science Center at San Antonio San Antonio, TX 78229-3900 office: 210-567-8780 mobile: 210-725-4438 fax: 210-567-8778 email: hinck(a)uthscsa.edu websites: http://hincklab.uthscsa.edu http://nmr.uthscsa.edu

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Chimera works on Snow Leopard
by Thomas Goddard 31 Aug '09

31 Aug '09

Hi John, I tested Chimera 1.3 and 1.4 daily builds on Mac OS 10.6 (Snow Leopard). All the tests worked fine. I ran our test suite using the Aqua Mac Chimera 1.4 snapshot and it all passed. I tested Chimera 1.3 production releases Mac Aqua and Mac X11 by hand opening a few data sets (molecules and volume data) and doing some coloring and encountered no problems. Tom -------- Original Message -------- Subject: Re: Snow Leopard ? From: Elaine Meng To: John Gerlt Date: 8/27/09 9:12 AM > Hi John, > I don't know for certain, so I'm turning over the question to the rest > of the staff (cc'd on this message). To whomever answers: could > include response on chimera-users list if you think others will have the > same question... thanks! > Best, > Elaine > > > On Aug 27, 2009, at 9:08 AM, John Gerlt wrote: > >> Elaine, >> >> Apple is issuing OS 10.6 tomorrow. For reasons I don't understand, I >> like to be current. But, as I recall from the past, when I tried to >> be current and install a new OS (10.5?), Chimera would not work. Do >> you know if Chimera will work with 10.6? >> >> Thanks. >> >> John

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Centro-symmetric space groups
by Michael Day 31 Aug '09

31 Aug '09

How do you get Chimera to recognize centrosymmetric space groups. If I include the space group on the CRYST1 card of the PDB file all is well for non-centrosymmetric groups but when a center of symmetry enters the picture all bets are off. I'm using Tool->Higher-Order Structure->Unit cell For example adding the space group in column 56 of the PDB P1 as P 1 - all's good P-1 as P -1 - complete nonsense although it recognizes there are two symmetry elements P2 as P 1 2 1 - all's good P21 as P 1 21 1 - all's good P212121 as P 21 21 21 - no problem But; P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell expansion. Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------> >>

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Re: [Chimera-users] Problem building 3D structure from smile text ...(Solved. Thanks)
by Sergio Garay 29 Aug '09

29 Aug '09

Thank tou Alaine. The new chimera version works perfect! On Fri, Aug 28, 2009 at 5:29 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Sergio, > Normally if you want to report an error it is best to use "Help... Report a > Bug" in the Chimera menu since that would automatically include information > about your computer and Chimera version, and let you attach files. > > However, in this case I can immediately see the problem: you need a newer > version of Chimera! > > You would need a version from July 3 or later, for example the August 20 > snapshot: > <http://www.cgl.ucsf.edu/chimera/download.html#snapshots> > > Explanation: The SMILES -> 3D structure conversion is done by a Web server > provided by a group at Indiana University, and a few months ago they changed > how this service is accessed. It was necessary to change Chimera to use the > new, updated service. > > I tested the following command in the snapshot version just now, and it > worked fine: > > open smiles:N[C@@H](C)C(=O)O > > Using this command is the same as entering the SMILES in the Build > Structure dialog. I also checked doing it that way. > > I think you will be pleasantly surprised to see the many improvements we > have made in Build Structure and in other tools, and the many new features > that have been added to Chimera! > > Improvements between 1.3 and the snapshot (and you were using a version > older than 1.3): > <http://www.cgl.ucsf.edu/chimera/1.4_b28596/docs/relnotes/snapshot.html> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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movie image resolution
by Anastasia A Aksyuk 28 Aug '09

28 Aug '09

Hi, It is very easy to specify resolution for a saved image, but not for the images used to create a movie. Is there a way to generate a movie or a stack of images with higher resolution then a display screen? I seem to be limited to 1273x870. Thanks a lot, Anastasia

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Problem building 3D structure from smile text ...
by Sergio Garay 28 Aug '09

28 Aug '09

Hi all I'm trying to build a 3D structure from this smile text: N[C@@H](C)C(=O)O But the program stops and doesn't respond to any key. The log window shows the next message: <type 'exceptions.KeyboardInterrupt'> Exception in Tk callback Function: <bound method BuildStructureDialog._placeAtoms of <BuildStructure.gui.BuildStructureDialog instance at 0x31ca3b0>> (type: <type 'instancemethod'>) 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/BuildStructure/gui.py", line 632, in _placeAtoms None File "CHIMERA/share/BuildStructure/Smiles.py", line 15, in openSmiles None File "CHIMERA/share/BuildStructure/Smiles.py", line 21, in smiles2mol None File "CHIMERA/share/BuildStructure/SOAPpy/WSDL.py", line 61, in __init__ None File "CHIMERA/lib/python2.5/urllib.py", line 82, in urlopen return opener.open(url) File "CHIMERA/lib/python2.5/urllib.py", line 190, in open return getattr(self, name)(url) File "CHIMERA/lib/python2.5/urllib.py", line 325, in open_http h.endheaders() File "CHIMERA/lib/python2.5/httplib.py", line 860, in endheaders self._send_output() File "CHIMERA/lib/python2.5/httplib.py", line 732, in _send_output self.send(msg) File "CHIMERA/lib/python2.5/httplib.py", line 699, in send self.connect() File "CHIMERA/lib/python2.5/httplib.py", line 673, in connect self.sock.connect(sa) File "<string>", line 1, in connect None <type 'exceptions.KeyboardInterrupt'>: Am I doing something wrong? I am working with this chimera version: alpha version, build 2577, 2008/12/09 -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Exporting surfaces as vrml
by Christian Hesketh 28 Aug '09

28 Aug '09

Hi there, I am trying to export molecular surfaces with varying transparencies to vrml, but the resultant model has a completely opaque surface. Is there anyway to export surfaces with transparent features to a 3D model? I would rather not work with x3d files as there don't seem to be any good 3D modeling programs that can accept this format. Thanks in advance, Christian

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Enabling silhouette edges in a nogui script
by Thomas Goddard 27 Aug '09

27 Aug '09

Hi Davide, There is a new command in Chimera 1.4 daily builds that lets you turn on silhouette edges and set their width set silhouette set silhouette_width 2 and to turn off silhouette edges ~set silhouette Here's the documentation http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html You're right that the "ac" command to run keyboard shortcuts doesn't work in nogui mode. That is because of some sloppy code that tries to create the keyboard shortcut dialog if you use the "ac" command and dialogs cannot be created in nogui mode. I've added an entry to the Chimera request list to fix that. http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests Tom -------- Original Message -------- Subject: Re: [chimera-dev] Generating images in chimera with the --nogui option From: Davide Baú To: Tom Goddard Date: 8/27/09 7:22 AM > Tom, > > how are you? > > I'm just back from (good) holidays! Hope you had good holidays too :-) > > I've tried out the "shape tube" command and it works great. Just one > question. From the sample image you attached to your last email, it > seems to me that silhouettes are toggled on ('ac se'). Is that > true/possible via a command script? Chimera Keyboard Shortcuts > (Accelerators) do not work when called form within a script (Error while > sourcing chimera.cmd: Unrecognized command: "'ac") and I haven't found a > different way (maybe using the set command?) to toggle silhouettes on. > > Thanks againg for your support, > Davide >

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Image not appearing
by MIKALS,KYLE A 27 Aug '09

27 Aug '09

I made a code to make movie and two of the molecules are not appearing in the saved output images. I put in the code where to save them so if something went wrong. This is the code I made and models 18 and 14 display in the window while the code is running, but not in the saved images. I have no idea what is going wrong. Any ideas? Here is my code below. # start capturing frames, in .png format movie record fformat png raytrace true directory /msg/users/kmikals/Chimera_Files #Created Label saying AAV Capsid Assembly 2dlabels create lab1 text 'AAV Capsid Assembly' color khaki size 28 xpos .2 ypos .94 visibility show scale 1.008 50 #Starts action once previous command is complete wait modeldisplay#0 wait 5 turn y -1 35 wait 30 modeldisplay#17 turn y -.6 20 wait 30 modeldisplay#18 wait 30 turn y +1.4 35 wait 30 modeldisplay#3 ~modeldisplay#0 ~modeldisplay#17 ~modeldisplay#18 wait 30 scale 0.992 50 wait 15 turn y -1 65 wait 9 modeldisplay#4 wait 9 turn y -1 35 modeldisplay#5 wait 9 turn y -1 65 modeldisplay#10 wait 9 modeldisplay#9 wait 9 turn y -1 65 modeldisplay#14 wait 9 modeldisplay#11 wait 9 turn y -0.5 30 modeldisplay#12 wait 9 turn y -1 65 modeldisplay#13 wait 9 modeldisplay#6 turn y -1 65 wait 9 modeldisplay#7 wait 9 modeldisplay#8 2dlabels delete lab1 #hide_all_molecules ~modeldisplay#3 ~modeldisplay#4 ~modeldisplay#5 ~modeldisplay#6 ~modeldisplay#7 ~modeldisplay#8 ~modeldisplay#9 ~modeldisplay#10 ~modeldisplay#11 ~modeldisplay#12 ~modeldisplay#13 ~modeldisplay#14 wait 20 scale 0.987 modeldisplay#16 turn y -.3 20 wait turn x -.75 35 wait 30 turn x .75 35 wait 30 turn x -.38 35 wait turn y -1 35 wait 30 turn y 2 180 wait turn x 2 180 wait # stop recording frames movie stop # write status information to reply log movie status # encode a movie in mp4 format from recorded frames movie encode mformat mp4 output /msg/users/kmikals/Chimera_Files -- MIKALS,KYLE A Biochemistry University of Florida

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extending DNA for a figure
by Elaine Meng 27 Aug '09

27 Aug '09

On Aug 13, 2009, at 12:00 AM, Janet G Yang wrote: > Hi Elaine, > > I'm a grad student in Geeta Narlikar's lab, and I've been to a few > of your Chimera tutorials at UCSF and found them very helpful. I > have a less analytical and more aesthetic structural task, and I'm > wondering if you might have any insight. I would like to make a > figure showing the structure of the nucleosome with some extra DNA > docked in at the edges. The crystal structure of the nucleosome > contains 147 bp wrapped around the histone octamer, and I would like > to extend out the DNA on one side. I think I could just take the > structure of the nucleosome, and that of some B form DNA, and > somehow align them together. Is there a good way to do this? > > Thanks a bunch > janet Hi Janet, My guess is that lots of people run across similar aesthetic issues -- making a figure is partly art, after all! Everything you say sounds reasonable. First you would need to get the extra B-form DNA, then position it relative to the nucleosome structure. (1) Getting the extra DNA. This could be from another PDB structure, or built using standard B-form parameters. The NDB atlas <http://ndbserver.rutgers.edu/atlas/xray/index.html > lists nucleic acid structures in categories such as B-DNA; you can use "File...Fetch by ID" in Chimera to fetch using NDB identifiers. Those structures might be shorter or less regular than what you need. Here is a server that will build canonical structures to order: <http://structure.usc.edu/make-na/server.html > (I admit I haven't actually tried using it, but it looks promising) (2) Positioning the extra DNA relative to the nucleosome structure. You could position it by hand and/or by matching overlapping sets of atoms. Positioning by hand requires activating/deactivating models for motion so that they can be moved relative to one another -- you would do that with the checkboxes below the Command Line, or with the "A(ctive)" checkboxes in the Model Panel. Matching would be done with the "match" command. It may be tedious to figure out the atom naming in the two structures and then figure out which sets of atoms to match to get the best result, but I don't really see any way around that trial and error process, unless you are really skilled at just positioning the structures by hand. I would probably do some matching and then maybe make slight manual adjustments depending on how it looked. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> My answer was based on the understanding that you just want the DNA to trail away in a somewhat straight path, rather than continuing on curling as in the nucleosome. If you wanted that continued curling, there might be some fancy ways to do it with several copies of a curved segment and symmetry operators, but that is beyond my skill set! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. 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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is there a way...
by Connie Oshiro 26 Aug '09

26 Aug '09

Elaine, et al-- I have a chimera session that was saved a while back (xxx.py). I can open it and view it in chimera. Question: Is there a way to extract/recontruct the commands that were used to create the view that I have? In this case, all commands were executed on the command line. The history file doesn't go back far enough. I took a look at the python file and didn't find midas/chimera commands. For example, I know I used "rainbow", with some options for the colors, but I don't see "rainbow" in the .py file. thanks for any info. connie

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