September 2009 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] select opt
by Eric Pettersen 23 Sep '09

23 Sep '09

On Sep 21, 2009, at 7:27 AM, Victor MuÃ±oz wrote: > I'd like to know if there's a way to select the select mode "append" > using the > command line instead of the visual interface. Hi Victor, There isn't a way to do that, but it typically isn't necessary. The "|" and "&" characters perform union and intersection operations respectively. So for example you can add all LYS residues to the current selection with: sel sel | : LYS or you could intersect the current selection with LYS residues with: sel sel & :LYS If you really need to change the mode for some reason, let me know what that reason is and maybe we can add something. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. The "|" character is a vertical bar, not a capital i, in case that's not clear in the font you're using.

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Re: [Chimera-users] question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear Elaine: Thank you very much for your instruction. We'll follow your guide. Best wishes WU Xue >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: 吴雪<wuxue(a)nankai.edu.cn> >Subject: Re: [Chimera-users] question about Chimera >Date: Tue, 22 Sep 2009 11:00:11 -0700 > >Dear Wu Xue, >There are several different distance and angle cutoffs that depend on >the donor and acceptor atom types. For example, the distance and >angle cutoffs for finding a H-bond donated from hydroxyl -OH to >carbonyl =O will be different than from amine -NH3 to carbonyl =O. >The cutoff values are taken from tables in this paper: > > Three-dimensional hydrogen-bond geometry and probability >information from a crystal survey. Mills JE, Dean PM. J Comput Aided >Mol Des. 1996 Dec;10(6):607-22. > >As discussed in the FindHBond documentation, > findhbond.html#criteria> > >the criteria in this paper were based on very high resolution crystal >structures of small molecules. Typically the structures in the PDB >are not so high resolution and so the criteria are relaxed. For >example, if a strict criterion from the paper is 2.8 Angstroms >cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms. >We set the default relaxation amounts to what we felt gives >reasonable results on most PDB structures. However, we made them >user-adjustable so that if you don't like them, you can change the >values to whatever you want. > >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 Sep 22, 2009, at 4:18 AM, 吴雪 wrote: > >> Dear colleague: >> I have a question about the "find hydrongen bond" in Chimera. >> The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". >> I don't understand the meaning of the parameter. 20 degree may >> means the angle bias the line,but I can't figure out what is the >> 0.04nm. >> The cutoff of the hydrogen is 0.4nm, and the angle is about 90 >> degree or some other parameters depending on the strength of the >> hydrogen bond. >> If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds >> are found. I don't know the criteria. Can you give me some advice >> so that I can follow your instruction? >> Sincerly Yours >> WU Xue > >

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.sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera
by Xarana 22 Sep '09

22 Sep '09

Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this inner surface with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie

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question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear colleague: I have a question about the "find hydrongen bond" in Chimera. The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". I don't understand the meaning of the parameter. 20 degree may means the angle bias the line,but I can't figure out what is the 0.04nm. The cutoff of the hydrogen is 0.4nm, and the angle is about 90 degree or some other parameters depending on the strength of the hydrogen bond. If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds are found. I don't know the criteria. Can you give me some advice so that I can follow your instruction? Sincerly Yours WU Xue

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Write out phi/psi angles
by David Belnap 21 Sep '09

21 Sep '09

I've read on the archived lists that Chimera does not have a Ramachandran plot viewer. I found phi/psi angles by selecting "Actions", "Inspect", then inspecting "Residue". Can I output the phi/ psi angles to a text file? If so, how do I write out that information? Thanks. David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David.Belnap(a)byu.edu ============================================

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Zooming and orthographic projection mode
by James Conway 21 Sep '09

21 Sep '09

I am struggling a bit and would be interested in any pointers from the knowledgeable folk here. It seems that I cannot use the mouse to get arbitrarily close to a surface in orthographic mode, but I can in perspective mode. In orthographic mode (Viewing -> Camera -> Projection) if I try to zoom in, the camera instead moves in until the front surface clips, but without much actually zooming. (True for the different "Center of Rotation" methods). In the Viewing -> Side View panel, the width of the field is represented by red lines that I cannot control but which I really want to move close together. According to the help for the Viewing -> Camera panel: horizontal field of view (allowed range 1.0-179.0°) - how much perspective is used; does not affect the orthographic projection. The vertical field of view will change along with the horizontal field of view, but their exact relationship depends on the aspect ratio of the graphics window. In fact, with the nightly builds of 1.4 this parameter *does* affect the orthographic projection, and does zoom in (or out) without clipping. Is there an updated explanation of how this works, and if it has changed since 1.3 as I seem to find? Am I looking in the wrong place for help on nightly builds? Thanks, James Conway

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Fit MAP to MODEL
by Michael Schmid 21 Sep '09

21 Sep '09

HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.

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select many atoms by serial number
by Stefano Meliga 21 Sep '09

21 Sep '09

Hello, I use a clustering algorithm to find partitions of proteins. The output is the list of node indexes belonging to each cluster. I would like to plot the clusters in different colours. I successfully managed to select one atom in the graphical interface using: Select > Atom Specifier and typing @\serialNumber=n Nevertheless, I need to select many atoms from a list of serial numbers, what can I do? Cheers, Stefano

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measurements to planes
by Elaine Meng 18 Sep '09

18 Sep '09

Hi Serge, Dave, Jim, et al., In recent daily builds of Chimera, you can now define planes and measure distances and angles to these objects. The planes are shown as disks, and you can perform plane-plane, axis-plane, and atom-plane measurements, in addition to the axis-axis and atom-axis measurements we had earlier. The tool formerly known as Axes is now "Axes/Planes," and we anticipate it will eventually include centroids. The updated documentation isn't there today but should show up tomorrow at <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > and the interface is mostly self-explanatory anyway. Each of you had asked about planes at some point (possibly a while ago), in case you are wondering why I addressed this message to you. 8-) Enjoy! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Cannot open pdb files with older versions of Chimera
by Hiroshi Nikaido 17 Sep '09

17 Sep '09

Hello, I sometimes have to use older versions of Chimera (1.2350 or 1.2422) because the more recent versions refuse to calculate surfaces for my protein. They used to work fine in my old computer running windows xp, but with my new computer (still running xp) an attempt to try any pdb files on my hard disk produces an error message (TypeError: argument 1 should be a str.). How could this problem be fixed? Your help will be greatly appreciated. Hiroshi

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