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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