- Chimera-users - RBVI Mailing Lists

.sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera
by Xarana 22 Sep '09

22 Sep '09

Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this inner surface with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie

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question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear colleague: I have a question about the "find hydrongen bond" in Chimera. The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". I don't understand the meaning of the parameter. 20 degree may means the angle bias the line,but I can't figure out what is the 0.04nm. The cutoff of the hydrogen is 0.4nm, and the angle is about 90 degree or some other parameters depending on the strength of the hydrogen bond. If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds are found. I don't know the criteria. Can you give me some advice so that I can follow your instruction? Sincerly Yours WU Xue

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Write out phi/psi angles
by David Belnap 21 Sep '09

21 Sep '09

I've read on the archived lists that Chimera does not have a Ramachandran plot viewer. I found phi/psi angles by selecting "Actions", "Inspect", then inspecting "Residue". Can I output the phi/ psi angles to a text file? If so, how do I write out that information? Thanks. David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David.Belnap(a)byu.edu ============================================

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Zooming and orthographic projection mode
by James Conway 21 Sep '09

21 Sep '09

I am struggling a bit and would be interested in any pointers from the knowledgeable folk here. It seems that I cannot use the mouse to get arbitrarily close to a surface in orthographic mode, but I can in perspective mode. In orthographic mode (Viewing -> Camera -> Projection) if I try to zoom in, the camera instead moves in until the front surface clips, but without much actually zooming. (True for the different "Center of Rotation" methods). In the Viewing -> Side View panel, the width of the field is represented by red lines that I cannot control but which I really want to move close together. According to the help for the Viewing -> Camera panel: horizontal field of view (allowed range 1.0-179.0°) - how much perspective is used; does not affect the orthographic projection. The vertical field of view will change along with the horizontal field of view, but their exact relationship depends on the aspect ratio of the graphics window. In fact, with the nightly builds of 1.4 this parameter *does* affect the orthographic projection, and does zoom in (or out) without clipping. Is there an updated explanation of how this works, and if it has changed since 1.3 as I seem to find? Am I looking in the wrong place for help on nightly builds? Thanks, James Conway

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Fit MAP to MODEL
by Michael Schmid 21 Sep '09

21 Sep '09

HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.

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select many atoms by serial number
by Stefano Meliga 21 Sep '09

21 Sep '09

Hello, I use a clustering algorithm to find partitions of proteins. The output is the list of node indexes belonging to each cluster. I would like to plot the clusters in different colours. I successfully managed to select one atom in the graphical interface using: Select > Atom Specifier and typing @\serialNumber=n Nevertheless, I need to select many atoms from a list of serial numbers, what can I do? Cheers, Stefano

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measurements to planes
by Elaine Meng 18 Sep '09

18 Sep '09

Hi Serge, Dave, Jim, et al., In recent daily builds of Chimera, you can now define planes and measure distances and angles to these objects. The planes are shown as disks, and you can perform plane-plane, axis-plane, and atom-plane measurements, in addition to the axis-axis and atom-axis measurements we had earlier. The tool formerly known as Axes is now "Axes/Planes," and we anticipate it will eventually include centroids. The updated documentation isn't there today but should show up tomorrow at <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > and the interface is mostly self-explanatory anyway. Each of you had asked about planes at some point (possibly a while ago), in case you are wondering why I addressed this message to you. 8-) Enjoy! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Cannot open pdb files with older versions of Chimera
by Hiroshi Nikaido 17 Sep '09

17 Sep '09

Hello, I sometimes have to use older versions of Chimera (1.2350 or 1.2422) because the more recent versions refuse to calculate surfaces for my protein. They used to work fine in my old computer running windows xp, but with my new computer (still running xp) an attempt to try any pdb files on my hard disk produces an error message (TypeError: argument 1 should be a str.). How could this problem be fixed? Your help will be greatly appreciated. Hiroshi

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Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 16
by Gaël McGill 16 Sep '09

16 Sep '09

Hi Andrew, You might try contacting Monica Zoppe (in Pisa, Italy) - she has experience importing PDB data into Blender. Here is her site: http://www.scivis.ifc.cnr.it/ Her e-mail: Monica Zoppè <mzoppe(a)ifc.cnr.it> Hope this is helpful, -Gael. ------------------------- Gaël McGill, Ph.D. Director of Molecular Visualization Center for Molecular & Cellular Dynamics Harvard Medical School www.molecularmovies.org President & CEO Digizyme, Inc. P.O. Box 1921 Brookline, MA 02446-1921 (617) 232-7676 (phone) (617) 232-5623 (fax) mcgill(a)digizyme.com www.digizyme.com On 9/16/09 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > 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: Exporting from Chimera to Blender - basic questions. > (Tom Goddard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Sep 2009 23:03:03 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Exporting from Chimera to Blender - basic > questions. > To: "Waight, Andrew" <Andrew.Waight(a)med.nyu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4AB07F97.6080108(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Andrew, > > Chimera exports the surface vertex and individual atom and ribbon > residue colors in the X3D and VRML output. If you raytrace a scene > with Chimera File / Save Image... it first exports X3D and then converts > that X3D to input for POVray which does get all the colors right. So I > think your question calls for some expertise with Blender, to find out > what color information it can handle when importing those files. I > don't know anything about Blender. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] Exporting from Chimera to Blender - basic > questions. > From: Waight, Andrew <Andrew.Waight(a)med.nyu.edu> > To: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > Date: 9/15/09 10:31 AM >> Hello all, >> >> I have recently solved the structure of a novel membrane protein, and >> have been using chimera quite a bit for my figures and analysis. In my free >> time I have been playing around with the 3D animation package Blender which I >> must say is a total blast, and makes fantastic movies and animations. However >> exporting from Chimera to Blender is a little tricky, in that when using >> VRML2 or X3D formats while the actual 3D "mesh vertices" import quite well, >> the colors are not imported, and imported items such as cartoon helices seem >> to have totally random materials assigned to nonsensical segments (instead of >> materials assigned by chain for example) . Ideally I would like to perform >> and export the coloring operations using chimera because it's obviously an >> order of magnitude easier to select residues, chains and monomers with >> chimera. Or at least have the grouping of objects imported correctly. This is >> really just for fun so I'd thought I'd ask if anyone here has any experienc! > e ! >> with importing Chimera models into Blender. Of course I have no idea how >> VRML2 actually works. Thanks all. >> >> Andrew Waight >> Wang Lab >> Skirball Institute of Biomedical Sciences >> NYU School of Medicine >> >> P.S. Extra Credit: Does anyone have any idea how to export the calculated >> electrostatic surface into UV mapping for a Blender Object (the surface mesh >> obviously)? >> >> ------------------------------------------------------------ >> This email message, including any attachments, is for the sole use of the >> intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. Any >> unauthorized review, use, disclosure, or distribution is prohibited. If you >> have received this email in error please notify the sender by return email >> and delete the original message. Please note, the recipient should check this >> email and any attachments for the presence of viruses. The organization >> accepts no liability for any damage caused by any virus transmitted by this >> email. >> ================================= >> >> _______________________________________________ >> 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 77, Issue 16 > *********************************************

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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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