September 2009 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Grouping models
by Tom Goddard 23 Dec '09

23 Dec '09

-------- Original Message -------- From: Thomas C. Marlovits To: Tom Goddard Date: 9/22/09 2:04 AM > HI Tom, > > I was wondering, whether one can "group" a few models in chimera. At > the moment, I have more than 40 models open simultaneously, some of > which I would like to group in order to make coloring, selection, etc > ... more easily. It might be that the feature is present, but > couldn't spot it so far. > The other thing that I would appreciate, if there is a simple way to > assign the model nr manually (at the moment it is done automatically, > and it appears that the order is somewhat random ...) > Best, > Tx, > -T. > Hi Thomas, You can used "named selections" to give a short name to several models or to any combination of selected items. Use menu entry Select / Name Selection... You can use the names in Chimera commands or use the "Select / Named Selection / name" menu entry. I don't know of a command to name a selection. Is there such a command (other Chimera developers)? You can set the model number if you open your models with a command, for example, open 5 twisty.pdb to open a model as model number 5. After the model number has been assigned it unfortunately cannot be changed. Tom

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Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

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mouse selection not working
by lorenzo 05 Oct '09

05 Oct '09

Hi everybody, I just installed chimera-1.3-linux.exe on an atom netbook. The OS is ubuntu 9.04. My problem is that the mouse selection tool does not work. To complete the scenario I add a few details 1) I don't have the green outline and setting Fill mode for selection highlighting in Preferences does not work around the problem (probably just a screen setting problem). 2) Other forms of selections work. For example by Select -> Chemistry -> Element -> H and then by Actions -> Atoms/Bonds -> Delete I can delete hydrogens. 3) I cannot delete anything that I select by ctrl + mouse left button. 4) libgl1-mesa-glx and libgl1-mesa-dri are installed. Thanks for your attention Lorenzo Bongini

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segmentation fault
by Francesco Pietra 01 Oct '09

01 Oct '09

Hi: On Debian Linux i386 squeeze I had the X system broken while attempting to install the gnome cd burner "brasero". I purged everything about that bad code, installed and reconfigured the X system, however something is still broken. Attempts at launching CHIMERA returned "segmentation fault". That also sitting in the directory where chimera is installed ( /usr/local/chimera/bin). As I had an old version, I reinstalled chimera-1.3-linux.exe, while that did not solve the above problem. I do not remember where to put the hands in such cases. Thankful for reminding me about that. francesco@deb32:~$ gcc --version gcc (Debian 4.3.4-2) 4.3.4 francesco pietra

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Re: [Chimera-users] Solvent Accessible Surface Area
by Elaine Meng 01 Oct '09

01 Oct '09

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am using Chimera for identifying the surface residues. > > I select areaSAS > 0.05 square angstroms, is this same as saying > areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq > angstroms have these been switched some how or are they curiously > the same in the following statement? > > I just need some help in understanding. > Thank You > Sincerely > -Thiru Ramaraj Hi Thiru, In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms. Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state. See for example the GetArea server, which gives "Ratio(%)": <http://curie.utmb.edu/area_man.html> However, what Chimera reports is just the surface area of the atom or residue in your structure. To choose surface residues, I'd probably use a bigger cutoff, say select :/areaSAS>10 but it depends on what you are going to do with the results. You can try different values and see what looks reasonable. 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

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Transparent Spheres
by Waight, Andrew 30 Sep '09

30 Sep '09

Hello everyone again. I apologize for a potentially embarassing question but is it possible to display sidechains as transparent spheres with solid stick representation inside. Seeing as I also can't find an image in the Chimera gallery where it is represented as such, I am wondering if it is possible to individually color (and set opacity) on spheres. I am also aware that vdw will create dots of varying density, but is it alternatively possible to display vdw as solid surface with opacity. Thanks to all for your patience. Drew ------------------------------------------------------------ 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. =================================

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Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 26
by vamsi krishna 30 Sep '09

30 Sep '09

Dear all, I am using chimera to calculate solvent accessibility of residues , may i ask you what cutoff is appropriate to identify surface residues significant for substrate binding . Thank you vamsi 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: Solvent Accessible Surface Area (Elaine Meng) > 2. Re: Solvent Accessible Surface Area (Thiruvarangan Ramaraj) > 3. Re: Solvent Accessible Surface Area (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 Sep 2009 12:14:48 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Thiruvarangan Ramaraj <thiruvaranganr(a)yahoo.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Solvent Accessible Surface Area > Message-ID: <E24233F9-9564-4824-8D82-6D9506261ACB(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > > >> Hi Elaine, >> I am using Chimera for identifying the surface residues. >> >> I select areaSAS > 0.05 square angstroms, is this same as saying >> areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq >> angstroms have these been switched some how or are they curiously >> the same in the following statement? >> >> I just need some help in understanding. >> Thank You >> Sincerely >> -Thiru Ramaraj >> > > > Hi Thiru, > In Chimera there is no percentage (%) measurement, it is only the area > value in square angstroms. Some other programs give % exposed for a > residue, which is a ratio of the area of that residue in your > structure to the area of the same type of residue in some theoretical > unfolded state. See for example the GetArea server, which gives > "Ratio(%)": > <http://curie.utmb.edu/area_man.html> > > However, what Chimera reports is just the surface area of the atom or > residue in your structure. To choose surface residues, I'd probably > use a bigger cutoff, say > > select :/areaSAS>10 > > but it depends on what you are going to do with the results. You can > try different values and see what looks reasonable. > 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 > > > > > ------------------------------ > > Message: 2 > Date: Mon, 28 Sep 2009 13:49:00 -0700 (PDT) > From: Thiruvarangan Ramaraj <thiruvaranganr(a)yahoo.com> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Solvent Accessible Surface Area > Message-ID: <842106.2825.qm(a)web53905.mail.re2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks,? Elaine for the information. > > Also I am having problems with installing Chimera on Linux Fedora 11(32 bit version). I am able to download it and install it. When I start chimera it comes up and then crashes immediately, the only message it gives is Segmentation Fault. > > Is there anyway I could resolve this problem. > > Thank You > > -Thiru Ramaraj > > --- On Mon, 9/28/09, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Solvent Accessible Surface Area > To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Date: Monday, September 28, 2009, 1:14 PM > > On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > > >> Hi Elaine, >> I am using Chimera for identifying the surface residues. >> >> I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers? 5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement? >> >> I just need some help in understanding. >> Thank You >> Sincerely >> -Thiru Ramaraj >> > > > Hi Thiru, > In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms.? Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state.? See for example the GetArea server, which gives "Ratio(%)": > <http://curie.utmb.edu/area_man.html> > > However, what Chimera reports is just the surface area of the atom or residue in your structure.? To choose surface residues, I'd probably use a bigger cutoff, say > > select :/areaSAS>10 > > but it depends on what you are going to do with the results.? You can try different values and see what looks reasonable. > 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 > > > > > > >

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Using Chimera to read SMILES string into structure
by Miriam Gochin 29 Sep '09

29 Sep '09

I have downloaded the latest build (Aug 30, 2009) and don't seem to be able to input a SMILES string. I have tried both the Utilities -> Structure Diagram and the Structure Editing -> Build Structure tool, and in both cases I can see a box to input the SMILES string, but the copy and paste mechanism won't work. I can enter text in the box, but cannot paste it in, which I need to do. Thanks for your help. Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Zoom factor for model when first opened
by Tom Goddard 25 Sep '09

25 Sep '09

Hi Kevin, The camera settings (position, amount of zoom, angular field of view) all contribute to how much of the Chimera window is filled when you open a map. How those are initially set when you start Chimera and open a map has changed a few times over the last year or two so if you run different Chimera versions (Help / About Chimera... to check version number) you may see different initial sizes. Tom -------- Original Message -------- Subject: chimera question From: Kevin Koehntop To: goddard Date: 9/24/09 6:34 PM > Hi Tom, > > I have a quick chimera question. When I open the same EM map in two > different chimera sessions, even though the scale factor, origin, > voxel size, and isosurface threshold level are exactly the same, the > map appears much smaller in one of the windows and I can't determine > why. Is there another parameter that I need to check? Thank you > > Kevin

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Re: [Chimera-users] [chimera-dev] select opt
by Eric Pettersen 23 Sep '09

23 Sep '09

On Sep 21, 2009, at 7:27 AM, Victor MuÃ±oz wrote: > I'd like to know if there's a way to select the select mode "append" > using the > command line instead of the visual interface. Hi Victor, There isn't a way to do that, but it typically isn't necessary. The "|" and "&" characters perform union and intersection operations respectively. So for example you can add all LYS residues to the current selection with: sel sel | : LYS or you could intersect the current selection with LYS residues with: sel sel & :LYS If you really need to change the mode for some reason, let me know what that reason is and maybe we can add something. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. The "|" character is a vertical bar, not a capital i, in case that's not clear in the font you're using.

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Re: [Chimera-users] question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear Elaine: Thank you very much for your instruction. We'll follow your guide. Best wishes WU Xue >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: 吴雪<wuxue(a)nankai.edu.cn> >Subject: Re: [Chimera-users] question about Chimera >Date: Tue, 22 Sep 2009 11:00:11 -0700 > >Dear Wu Xue, >There are several different distance and angle cutoffs that depend on >the donor and acceptor atom types. For example, the distance and >angle cutoffs for finding a H-bond donated from hydroxyl -OH to >carbonyl =O will be different than from amine -NH3 to carbonyl =O. >The cutoff values are taken from tables in this paper: > > Three-dimensional hydrogen-bond geometry and probability >information from a crystal survey. Mills JE, Dean PM. J Comput Aided >Mol Des. 1996 Dec;10(6):607-22. > >As discussed in the FindHBond documentation, > findhbond.html#criteria> > >the criteria in this paper were based on very high resolution crystal >structures of small molecules. Typically the structures in the PDB >are not so high resolution and so the criteria are relaxed. For >example, if a strict criterion from the paper is 2.8 Angstroms >cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms. >We set the default relaxation amounts to what we felt gives >reasonable results on most PDB structures. However, we made them >user-adjustable so that if you don't like them, you can change the >values to whatever you want. > >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 > >On Sep 22, 2009, at 4:18 AM, 吴雪 wrote: > >> 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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.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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