- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] mutating amino acid side chain_deleting single atom
by Gary Laco 24 Apr '07

24 Apr '07

Hi, How can I mutate an amino acid side chain in a protein to another residue using Chimera? Also, how do I delete a single atom on an amino acid (for example a hydrogen). I looked through all the tools and did not find a way to do it. Thanks, Gary Gary S. Laco, Ph.D. Assistant Professor of Biochemistry Lake Erie College of Osteopathic Medicine-Bradenton 5000 Lakewood Ranch Blvd. Bradenton, FL 34211 Office: 941-782-5666 Fax: 941-782-5729 E-mail: <mailto:glaco@lecom.edu> glaco(a)lecom.edu

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movie and 'side view'
by jean-francois menetret 23 Apr '07

23 Apr '07

Is it possible to include the 'side view' during movie recording ? 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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Secondary Structure Editing
by anat＠chem.ch.huji.ac.il 23 Apr '07

23 Apr '07

Hi, I would like to know if it's possible to edit (manually) the secondary structure attribute of single amino acid in the computed sequence given by Chimera (e.g. from strand to helix). Thank you for your help, Anat, the Hebrew university of Jerusalem. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [Chimera-users] Chimera-users Digest, Vol 48, Issue 17
by Puey Ounjai 21 Apr '07

21 Apr '07

Dear all; I am wondering can we manually assign secondary structure to each residues in the PDB file in chimera? Thanks Puey

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Chimera crash
by hsosa＠aecom.yu.edu 20 Apr '07

20 Apr '07

Hi, I'm having problems later with chimera. Sometimes when rotating molecules or volumes the whole computer freezes for a while. Sometimes recover and will freeze again after a few more molecule movements. Sometimes the whole system crash with blue screen and reboot. It seems like a new problem as I've bee using chimera for a while and it didn't' happen before. As far as I know everything is the same in the computer. I'm running the latest snapshot release of chimera but that doesn't seem to be the problem. I deinstalled this version and installed the latest production release and got the same problem. Any ideas what the problem may be ?. Thanks Hernando System details UCSF chimera version 1.2382 (or 1.2304) OS: Windows XP service pack-2 Computer: Dell Precision 530 with Dual Xeon 1.4 GHZ processors and 1 GB RAM Graphic Card: NVDIA Quadro 900 XGL Video BIOS version 4.25.00.27.05 ForceWare version 91.36 -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Transform Molecule Coordinates
by rkhayat＠scripps.edu 19 Apr '07

19 Apr '07

Hi, I was wondering if there is a stand alone version of the "Transform Molecule Coordinates" Chimera extension available. Alternatively, how will I be able to use this feature outside of Chimera? Thanks. Reza

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Re: [Chimera-users] rotating maps in chimera
by Tom Goddard 19 Apr '07

19 Apr '07

Hi Preethi, Here's what caused the misalignment when you opened "subtracted map 2", let's call that one map 3, into Chimera where the original map 2 and reoriented map 1 were already opened. When you open map 3 Chimera needed to give it an initial transformation. Maps 1 and 2 had different transforms. Chimera chooses the transform of the map with the lowest id number (shown in Model Panel, menu entry Favorites / Model Panel). Map 1 must have had the lowest id number, so it got the transform of map 1 instead of the transform of map 2. Chimera had no way of knowing that map 3 was just a modified version of map 2. When you open data in Chimera it assigns an id number to it (shown in Model Panel). The id number is 0 for the first opened data set, then 1 for the next, .... In general it assigns the lowest available id number when a new data set is opened. When restoring Chimera sessions maps get their original model id numbers in Chimera versions 1.2354 and later, but are assigned new model id numbers in older versions. Since the data sets with lowest id number determines the transform of all newly opened models it is best to think of that data set as defining the reference frame. You can use the Model Panel / Transform As... button to correct the transform of a newly opened model. In the case you described you would need to transform map 3 as map 2 to fix the misalignment. This is probably easier than editing a session file. Tom preethi(a)bu.edu wrote: > Hi Tom, > > Chris I think had already discussed with you about how we transform > the PDB files that were originally fit into a brix map so that it now > fits into an MRC file in chimera. > > I am just repeating that here because I came across a problem when I > did this. > > I saved a session in chimera where I had rotated a MRC map say map 1 > w.r.t another MRC map 2 and then used the "fit map into map" feature > to align map 1 into map 2.So I saved the session(which would save the > transformation matrix) and then used the matrix to move certain PDB > files(using "transform as"). > > Now I did some zoning and volume erasing on map 2(the unrotated map) > and then saved the resulting map and then with another program outside > chimera subtracted the zoned out volume from the whole volume of map 2. > > SO when I read in the subtracted file into chimera it is now rotated > w.r.t the map 2 instead of being read with the original matrix that > was used for map2. I fixed this problem by going into chimera session > file and maunally changing the rotation and translation values for > this map to match that of map2. > > Also, if I opened chimera afresh and didnt restore the session where I > had done all the transformations but just opened map 2 and the > subtracted map then it reads them correctly without displacing one map > w.r.t the other. > > So I was just wondering why chimera automatically rotates the > subsequent MRC files that are read into a session where a > transformation was applied to some files only ? > > -Preethi > > > > > >

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rotating 2 models side-by-side
by jean-francois menetret 19 Apr '07

19 Apr '07

How can I make two models rotate side-by-side around their respective centers using chimera ? 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] Proper display of oligosaccharide
by Greg Couch 18 Apr '07

18 Apr '07

To followup, I just tried the first Human milk saccarides example on the Sweet webside, 2'-Fucosyllactose, and the PDB file it generates doesn't display at all because of the non-standard data in columns 67-72. We have decided that we're being too strict in this case and will change chimera. In the iterim, if you're on a UNIX system (Linux, Mac OS X, etc.), you can truncate the lines with the following: awk '{if (/^ATOM/) print substr($0, 1, 67); else print $0}' < original > fixed with appropriate filename replacements for original and fixed. Greg Couch UCSF Computer Graphics Lab

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Proper display of oligosaccharide
by R. Andrew Byrd 18 Apr '07

18 Apr '07

We study protein:carbohydrate interactions, and we use chimera for protein displays. We have a model built for an oligosaccharide using the SWEET server at http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php The file is in pdb format, but it has neither amino acid residue names nor nucleotide names. Hence, the molecule is invisible in Chimera. How could we make this a recognizable molecule so that we can examine various visualizations and modeling efforts using Chimera? Thanks! Andy P.S. I can send the file if you want.

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