July 2011 - 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

5 7

Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! 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 Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

3 5

font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

2 1

color surface based on NMR Order parameters
by lalit.deshmukh＠huskymail.uconn.edu 08 Sep '11

08 Sep '11

Hello, I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on.. Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way? Thanks in advance, Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269

5 8

centroid trace problems
by Francesco Pietra 01 Aug '11

01 Aug '11

hello: "centroid" works fine to me in getting the trace of a moving molecule in and out of a protein, using command define centroid radius 0.2 color red :residuename when the residue is unique. In fact, the method has produced extraordinarily illustrative (I am using the words of the referee) in a paper that will appear shortly on Chemistry & Biodiversity. Now I have three diatomic molecules, only one of which is made moving around. In this case define centroid radius 0.2 color red :residuename:residuenumber for the moving residue does not work. What happens is that "red balls" for the specified residue are being accumulated at the place of origin of the residue, while the residue is leaving the protein as a short bar, not a ball. Could that be fixed in the above command? thanks francesco pietra

3 5

hide a peptide in Chimera
by C.J. 29 Jul '11

29 Jul '11

Hi,all, I have a pdb file containing several peptides. And I want to hide some of them when visualizing the file in Chimera. Anyone would like to help me to that? I'm appreciated of any suggestions. -- Regards! C.J.

2 3

Hbond in CLI + cacheDA
by Maciek Wójcikowski 29 Jul '11

29 Jul '11

Hello everyone, I'm trying to compute hbonds for quite large molecular database, so i do it in CLI. I've added cacheDA parameter which speeds up whole process at first by 10 times, although after time cache is getting bigger and bigger operations slows down as one can expect, because Chimera is caching every compound. Is there a way to limit the size of a cache, or even better to tell chimera to cache only protein donors and acceptors? ---- Pozdrawiam, | Best regards, Maciek Wójcikowski maciek(a)wojcikowski.pl

2 6

Chimera 1.5.3, nvidia quadro 4000 and stereo
by Veli-Pekka Kestilä 27 Jul '11

27 Jul '11

Hello, I found following problem when trying to use Chimera 1.5.3 with stereo in Nvidia Quadro 4000. When starting the chimera in windows I will get error: Error Initializing OpenGL: Couldn't configure togl widget When stating in OpenGL debug mode it starts without any problem. Nvidia driver is 275.65 and everything works in linux without problem. In Manage 3D settings I have put on Stereo Enable. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

3 4

gtx-470 GeForce cards
by Francesco Pietra 26 Jul '11

26 Jul '11

With GeForce2 MX200 / Debian GNU-Linux i386 wheezy I have no problems in running movie with "define centroid". In contrast, with GeForce gtx-470 (two such cards and PhenomII 1075T (six cores)/ Debian amd64 wheezy, on running movie to get the trace of the centroid, the X server hangs and the keyboard is no more sensed. I have to restart the computer from a ssh-linked desktop. In both cases chimera 1.5.3. Chimera was started as the only application, just after booting the OS (I am saying that because, to run molecular dynamics, I have first to command # nvidia-smi -L # nvidia-smi -pm 1 Any experience to this regard? thanks francesco pietra

2 1

castp .poc file is not opened in restored session (plain text version)
by Boaz Shaanan 26 Jul '11

26 Jul '11

Hi, I save a session in which I used castp .poc file (very nice indeed!). However, after saving the session, the restored session does not open the .poc file. Is that how it's supposed to be? Cheers, Boaz P.S. sent again in plain text format since it seems the previous html version has been mangled up Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

2 4

Chimera-users July 2011