July 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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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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substitute single residue
by Andrew P. Hinck 01 Sep '09

01 Sep '09

Dear all, I was hoping to make some single amino acid substitutions in the context of a protein binding interface. I've only briefly poked around, but so far the only way I see to do this is to delete existing atoms/bonds one by one, and then rebuild (the alternate amino acid) atom-by-atom/bond-by-bond. Is there an easier way (like, telling the program to substitute an Asp for a Lys, or something akin to this)? Thanks in advance for any suggestions. Andy Hinck Andrew P. Hinck, Ph.D. Professor, Department of Biochemistry, MC 7760 University of Texas Health Science Center at San Antonio San Antonio, TX 78229-3900 office: 210-567-8780 mobile: 210-725-4438 fax: 210-567-8778 email: hinck(a)uthscsa.edu websites: http://hincklab.uthscsa.edu http://nmr.uthscsa.edu

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Chimera --send command
by cdlau＠ucsd.edu 24 Aug '09

24 Aug '09

Hi, I am currently running chimera remotely on a computer using "ssh" commands. I have been using the "chimera --send" command to send cmd and python scripts to a computer running chimera. I was wondering if it were possible for me to run 2 or more instances of Chimera on a computer and control which instance of Chimera the "--send" script is executed by. Thanks for your help, Chris

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Using Command Line
by cdlau＠ucsd.edu 30 Jul '09

30 Jul '09

Hi, I was wondering there was a command similar to the --geometry (feature in the system command line option (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#script)) but for the Command Line. I know there is a command "windowsize" in which the user can specify the dimensions of the chimera instance, however where the chimera instance is located cannot be specified with this command. I want to be able to use a feature similar to --geometry where I can specify X and Y offsets of the top left corner of the window from the top left corner of the screen. Thanks, Chris

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projection view for publication
by Tom Duncan 30 Jul '09

30 Jul '09

I have seen some good recent comments on settings for saving publication-quality images, but I wonder if there is a general preference (by users or or journals) for use of perspective versus orthographic projection when generating images for publication. Thanks, Tom Duncan ----------------------------------------------------- Thomas M. Duncan, Ph.D. Research Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY

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Re: [Chimera-users] domains as ellipsoids?
by Elaine Meng 30 Jul '09

30 Jul '09

On Jul 24, 2009, at 7:20 AM, Stefano Ciurli wrote: > Hello Elaine, > I am writing to ask you the following: I need to define the > relative orientation of two domains of a protein, and I am not sure > about how to do it. I was thinking of approximating the domains as > ellipsoids and then calculate the angles between the axes of the > ellipsoids. I wonder if you have a better way to define the > orientation, or if Chimera can do things like calculate ellipsoids > axes and their orientation. > Regards > Stefano Hi Stefano, There is an Axes tool (under Tools... Structure Analysis). It does not give ellipsoids, just the long axis, shown as a cylinder. You can define axes for helices or for any set of atoms (e.g. a domain), and then choose any two axes for an angle calculation. For details, see <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes> or just click the Help button on the dialog to see your local copy of this information. Eventually we want to also allow defining centroids and planes, but only the axes measurements are available currently. Please send chimera questions to chimera-users(a)cgl.ucsf.edu rather than to me personally, unless private data are included. This allows others to benefit, or to answer the question if I am unavailable. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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] Display all rotamers
by Eric Pettersen 29 Jul '09

29 Jul '09

In the daily build the Rotamers tool will now allow you to add multiple rotamers to a residue, using alt locs to distinguish them. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu > On Dec 6, 2008, at 9:35 AM, daniel.hilger at lrz.uni-muenchen.de > wrote: > > > > I´m really sorry for my imprecise question. I will concretize it. I > > know > > the rotamer tool, but I don´t want to replace only one rotamer into > > another. I will have them all in the structure and in the according > > pdb-file. With the rotamer tool, it is only allowed to choose one > > rotamer > > out of the rotamer list before clicking "Apply". This is my problem, > > and I > > didn´t found an appropriate answer in the manual and help menu. > > Hi Daniel, > I'm sorry for misunderstanding - > > It's true that Apply only puts one copy in the structure, but if you > don't Apply and simply keep the Rotamer list dialog and choose all of > its lines, that displays all of the rotamers at the same time. Maybe > that would allow you to do what you want. The Rotamer list dialog > allows calculating clashes and H-bonds, plus selecting the rotamer > atoms so you can control their appearance with the Actions menu. > > The issue is that the structure can't have multiple indistinguishable > atoms (with the same name and residue number). We have talked about > allowing multiple rotamers to be applied to the structure by giving > them different "alternate location" ID codes, but that has not been > implemented yet. Also, some residues may have more rotamers than the > number of possible alternate location ID codes. Nevertheless we will > make sure it is on one of our requested features lists. > > So currently you can't save PDB with multiple rotamers, but you can > save/restore the session in the state where all of the rotamers are > displayed. > I hope this helps, > Elaine

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Convert the structure
by Abeer Shokeer 29 Jul '09

29 Jul '09

Hello I would like to convert the model structure that I have prepared 90 degree or in different position. Can I do that with Chimera? Thanks Abeer

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fusion proteins
by Brennal Pierre 28 Jul '09

28 Jul '09

Hi, I would like to know if it possible to create fusion proteins by merging two pdb files, or if it is possible in any other way, thanks Bren. _________________________________________________________________ Bing™ brings you maps, menus, and reviews organized in one place. Try it now. http://www.bing.com/search?q=restaurants&form=MLOGEN&publ=WLHMTAG&crea=TXT_…

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Chimera-users July 2009