- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] how to export the volume data which is stored in the memory?
by Tom Goddard 05 Dec '07

05 Dec '07

Hi Zhiheng, Here is a script to write out the maps in memory using Chimera 1.2199. You open this script with menu entry File / Open... from the main Chimera window. It will write the files to /tmp. Of course be sure to check those files before closing Chimera. Tom Zhiheng Yu wrote: > Hi Tom, > > I got the following information: > > Beta Version 1 build 2199 2006/01/24 > Platform: linux 2. Windowing system:x11. > > Apparently, it is an older version. > > Thank you very much for your generous help. I really appreciate it. > > Zhiheng > > Tom Goddard wrote: >> Hi Zhiheng, >> >> You must be using an older version of Chimera. Old versions read >> the original file even if the map was in memory when writing out the >> data. Maybe I can give you a script that will write the maps out >> from memory if you tell me what version of Chimera you are running >> (menu entry Help / About UCSF Chimera). >> >> Tom >> # # Write maps to files. For Chimera 1.2199. Only use in-memory copy. # Written for Zhiheng Yu to recover maps lost to failed disk. # from VolumeData import Array_Grid_Data from VolumeData.mrc.writemrc import write_mrc2000_grid_data from VolumeViewer import volume_dialog from os.path import join dir = '/tmp' # Location to write maps. d = volume_dialog() for v in d.data_regions: m = v.full_matrix(read_matrix = False) if not m is None: a = Array_Grid_Data(m, v.data.origin, v.data.step) path = join(dir, v.data.name) write_mrc2000_grid_data(a, path)

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(no subject)
by Julien Orts 04 Dec '07

04 Dec '07

Dear Chimera people, I would like to save a lot of pdb. I have for example 500 pdb. Each saved pdb file should contains 2 pdbs of these 500 pdbs. I can write a script for this but the command write does not work for more than two pdb. Is there any other way? thank you Julien

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question about the model panel
by jean-francois menetret 04 Dec '07

04 Dec '07

Is there is way to reorder the position of the models in the model panel ? (For example putting the mrc files on top and the pdb files at the bottom) Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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Re: [Chimera-users] Question regarding Chimera usage
by Tom Goddard 03 Dec '07

03 Dec '07

Hi Navya, If you have a 3-button mouse you move the atomic model with the middle button. If that is not working then you probably have the mouse modes assigned differently. You can look at and change what the mouse buttons do with menu entry Features / Preferences category Mouse. Usually button 2 is assigned to translate in x and y (second column of table). It may not be assigned to that operation if you have used other tools like volume path tracer or volume subregion selection that reassign mouse button 2. Tom swetha davuluri wrote: > Hi, > > Thanks for your reply. I am trying to move the atomic model using the > mouse. But I can only rotate the model but not transitionally shift it > i.e. I am not able to move the model either up/down and sideways. Not > sure how to do this. Please let me know. > > Thank you, > Navya. > > ----- Original Message ---- > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > To: swethadn(a)yahoo.com > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Sent: Friday, November 30, 2007 9:27:37 AM > Subject: Re: [Chimera-users] Question regarding Chimera usage > > Hi Navya, > > The first step is to move the atomic model using the mouse close to > the correct location in the EM map. The Fit Model in Map tool will not > move the atomic model if its initial position lies outside the map. > Here are instructions on how to do the fitting. > > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… > > Tom > > > > ------------------------------------------------------------------------ > Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See > how. <http://us.rd.yahoo.com/evt=51732/*http://overview.mail.yahoo.com/>

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Remove steric clashes
by Francesco Pietra 02 Dec '07

02 Dec '07

I would like to delete all water residues that are in steric clash with lipid residues. What I have is a single pdb file that includes both types of residues. Can't have the two as different models. Therefore I can't apply the zone tool that I know how to manage for two different models. The only alternative I can figure out is through the "Find Clashes,Contacts", writing a file for all WAT at a specified distance from the lipid residues and then manually deleting, or inventing a script for that (at <=0.6A there are 386 clashes). Hope to have missed an automatic tool from Chimera. If not, I suggest that as a most useful additional tool for cleaning systems. I dropped into the problem when at the first minimization, in view of MD, the system met segmentation fault after a few steps, with gradient decreasing by eight orders of magnitude along those few steps. Then I recognized not to have been careful enough before making the coordinate files for the MD suite. I should have not relied too much in the membrane builder and I had better spent time in checking for steric clashes. Thanks francesco pietra ____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs

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distance measurement
by sette＠uniroma2.it 30 Nov '07

30 Nov '07

Dear all, I would like to measure the distances between all atoms in a molecule, in particular between all hydrogens. I added the H but it seems to me that is possible to measure only the distance between two selected atoms and not between all atoms in a single command. How is possible to do? Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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morphing structures
by Elaine Meng 30 Nov '07

30 Nov '07

> Thank you for your help. I did superimpose the structure with pdv > viewer. I did save as a pdb file but when I open the morph > conformations tool and I add the pdb I am not able to create the > interpolation between the structure. > > Do you know why? > Hi Djemel, I would recommend just using Chimera to superimpose the structures. Starting with the two structures in two separate files, open them with File... Open in the Chimera menu, then superimpose them. There are lots of ways to superimpose them but probably this simple command (show command line with Favorites... Command Line) will work fine: matchmaker #0 #1 In Morph Conformations you have to specify more than one structure. There should be more than one line in the Conformations list. My guess (and it's only a guess) is that the way the other program wrote the file it was considered all one structure, not 2 separate structures. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab 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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Detecting residue from command line
by Francesco Pietra 30 Nov '07

30 Nov '07

Sorry for a question that was surely answered many times. How to detect on the screen (from command line) residues from their resSeq number?. I have two different sets of WAT: 522-9999 and 0-4759 and want to check where 0-521 are located in a protein-ligand-POPC membrane. Thanks francesco pietra ____________________________________________________________________________________ Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ

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morphing movie
by Elaine Meng 30 Nov '07

30 Nov '07

> Actually I would like to do some movie with chimera but I never used > before. I have two crystal structure of two different conformation of > the protein that I work with. I would like to see the trajectory from > conformation 1 to 2. I just downloaded the chimera but I don't know > how to start. > > Could you tell me how to make the movie? I would appreciate you help. > Is that possible to load molecule 1 and 2 and see how the trajectory > is ? Begin forwarded message: From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: November 30, 2007 10:29:41 AM PST It sounds like you want to use the Morph Conformations tool (under Tools... Structure Comparison). If you have two structures, it will "make up" a series of in-between structures to create a trajectory. You have to match (superimpose) the two structures yourself first. There are different options of how to make the in-between structures and how many to make. The trajectory-viewing tool, MD Movie, is automatically started to show the trajectory. From MD Movie you can record the trajectory as a movie file (Quicktime or other formats) or just save it as a PDB file for later viewing in Chimera. Probably you will need to learn a little bit about using Chimera so that you can set the display (ribbons, background color, displaying important sidechains) how you want for the movie. Chimera comes with a User's Guide. You can open it directly or search it from the Chimera Help menu. Also clicking the Help buttons on dialogs will automatically open the corresponding man pages. I will give some links to our Web site, but most of the same pages are included with your download. Tutorial on matching structures and making nice images: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html Manual page for Morph Conformations: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html for MD Movie: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (see the "Recording a Movie" section) For basic Chimera use, there is "Getting Started" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html and a more detailed version of that at our web site (not in the User's Guide): http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html but if you get stuck or have trouble finding something, you can ask me about it. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab 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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Re: [Chimera-users] Question regarding Chimera usage
by Tom Ferrin 30 Nov '07

30 Nov '07

------- Forwarded Message Date: Thu, 29 Nov 2007 20:06:54 -0800 From: swetha davuluri <swethadn(a)yahoo.com> To: tef(a)cgl.ucsf.edu Subject: Question regarding Chimera usage Dear Dr. Ferrin, I have a question Chimera usage. I am trying to fit a model to an EM map. I cou ld lock the map from moving but I am not able to transitionally shift the model . The translational shift box in "Fit Model in Map" is checked. Please let me k now how to transitionally move the model. Regards, Navya. _________________________________________________________________________ ___________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.ya hoo.com/ ------- End of Forwarded Message

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