June 2013 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Flip handedness of map
by Tom Goddard 05 Jun '13

05 Jun '13

Hi Michael, To flip the hand of map #0 use vop zflip #0 This makes a copy of the map with the z-planes in reverse order. Tom On Jun 4, 2013, at 9:09 PM, Michael Stowell wrote: > Tom, > > There used to be a simple way to change the handedness of a map in Chimera, just use a negative voxel number. However, this no longer works but rather gives an error. Is there a new way to achieve this. This is very helpful when assessing the handedness of EM maps. > > Thanks > > m > > Michael H. B. Stowell > MCD Biology and Mechanical Engineering Departments > University of Colorado > Boulder, CO

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Request for assistance
by Zachary W. Carpenter 04 Jun '13

04 Jun '13

Dear Chimera, I have been a long time user and really love your software. Recently I have used and cited Chimera in 4 high impact publications. One in mBio, two in nature medicine, and a final one in review at Nature Genetics. I have used Chimera to make beautiful images of mutations that we identify in NGS data of tumors. My role has become interpreting the effects of mutations on crystal structure. Thus far this has not been difficult as the effects of the mutations have been obvious. A recent finding however has left me extremely perplexed and I have need for greater accuracy of structural modeling of the mutations. I was wondering if you can put me in the right direction for creating models of mutations that are more reliable then just using Modeller or I-Tasser with the mutant in the sequence to be predicted. I know this is an elaborate question but I'd like to know which Chimera tools I can use to help me along this path. Or if I need to use totally new software/ methods. Thanks for your time, Zach -- Zachary W. Carpenter Department of Pharmacology College of Physicians and Surgeons Columbia University 630 West 168th Street New York, NY 10032 Email: ZWC2101(a)Columbia.edu

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To build ssDNA to base pair with the other strand of DNA
by Wei Shi 04 Jun '13

04 Jun '13

Hi all, I am working on solving the crystal structure of a protein-DNA complex. I could complete one strand of the DNA to fit the electron density using Coot, but for the other strand, the density for several bases at each end of the DNA is not clear and it's missing several bases at each end of the DNA. I am wondering whether in chimera, there is a function I could use to build the missing bases in one strand of the DNA to base pair with the other strand of DNA which is complete. Thank you so much! Best, Wei

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Re: [Chimera-users] Just starting out
by burt.goldberg＠gmail.com 03 Jun '13

03 Jun '13

Dear Elaine, it is very hard for Senior faculty to audit a class. As for the Biochemistry well I have been teaching it for several decades. My interest is to learn how to use Chimera better and I will be working with a post doc experienced in using Chimera. I just want to read so I can ask intelligent questions. I am employing this in an on going research project. Thank you again for you help. ------Original Message------ From: Elaine Meng To: burt.goldberg(a)gmail.com Cc: chimera-users(a)cgl.ucsf.edu List ReplyTo: chimera-users(a)cgl.ucsf.edu List Subject: Re: [Chimera-users] Just starting out Sent: Jun 1, 2013 12:53 PM Hi Burt, This forum is meant for questions about the Chimera program. Proteomics and informatics are vastly broader areas. You might want to look for recent textbooks and journal articles on those topics, and/or audit some classes, and/or attend the group meetings and seminars of academic researchers in those areas. It's not clear whether learning Chimera should be one of your goals at this point. Which tools and programs are needed depend on the research problem at hand, and the types of data that are available for tackling that problem. If you do want to learn how to use Chimera, there are indeed several step-by-step tutorials. Before doing any tutorials you can explore the website just to get a better sense of what the program is for: <http://www.cgl.ucsf.edu/chimera/index.html> The "Quick Links" section on that page includes tutorials. 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 On Jun 1, 2013, at 9:34 AM, burt.goldberg(a)gmail.com wrote: > Dear all, after 40+ years doing wet work I had to leave the bench, medical reasons, and so although my students continue doing work at the bench I have decide to go the route of proteimics and informatic for myself. The informatics is fine. How do I get started on the proteimics? Does the tutorial help? Any thing some one can suggest I read first? Thank, Burt > Sent via BlackBerry from T-Mobile Sent via BlackBerry from T-Mobile

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How to calculate the deviation of two ligands in the same pocket
by felipe vasquez 03 Jun '13

03 Jun '13

Hi, I am working on the modeling of one ligand in a native and mutant receptor. The ligand occupies different positions in the binding cavity, and I am interested in estimate this difference. However, if RMSD is calculated via MatchMaker, the ligand in mutant receptor (non-reference) is moved from its original position to try to minimize the deviation compared to ligand in native receptor (reference). How can I calculate the difference in the ligand position between the two receptors, in an appropriate manner? Best regards, * * *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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How to force Chimera to properly analyze and visualize in each MD movie frame the ribon representation of the protein structure ?
by Marek Maly 01 Jun '13

01 Jun '13

Dear all, I just found that if one loads several frames from the simulation (Amber prmtop + inpcrd, *.rst files) chimera calculate/set the character of ribons (random colil, beta sheet, alpha helix) just using the first loaded frame and even if structure of the protein is changing in the next frames (e.g. forming beta sheet structure from the originally random coil), the visual ribon representation is not changed. I found this, when I loaded just the isolated frame from the simulation and saw nice forming of the local beta sheet which was nicely highlighted by proper ribon representation (wide arrow) in the palce where was originally (in the initial frame) just random coil. But when I loaded both (initial frame and that after some MD simulation), chimera keep to use random coil representation for both frames. I did also reverse experiment i.e. first loaded later frame from MD simulation and then the initial frame and this time chimera fixed for both frames beta sheet representation in that protein area. Please is there any possibility to prevent such unwanted behavior and to force Chimera that analyses properly protein configuration at each loaded frame and eventually changes properly the ribon representation ? Thank you in advance for any useful advices ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera-users June 2013