December 2009 - Chimera-users - RBVI Mailing Lists

Grouping models
by Tom Goddard 23 Dec '09

23 Dec '09

-------- Original Message -------- From: Thomas C. Marlovits To: Tom Goddard Date: 9/22/09 2:04 AM > HI Tom, > > I was wondering, whether one can "group" a few models in chimera. At > the moment, I have more than 40 models open simultaneously, some of > which I would like to group in order to make coloring, selection, etc > ... more easily. It might be that the feature is present, but > couldn't spot it so far. > The other thing that I would appreciate, if there is a simple way to > assign the model nr manually (at the moment it is done automatically, > and it appears that the order is somewhat random ...) > Best, > Tx, > -T. > Hi Thomas, You can used "named selections" to give a short name to several models or to any combination of selected items. Use menu entry Select / Name Selection... You can use the names in Chimera commands or use the "Select / Named Selection / name" menu entry. I don't know of a command to name a selection. Is there such a command (other Chimera developers)? You can set the model number if you open your models with a command, for example, open 5 twisty.pdb to open a model as model number 5. After the model number has been assigned it unfortunately cannot be changed. Tom

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Grouping of bonds/atoms
by Dipl.-Ing. Thomas Mitterfellner 23 Dec '09

23 Dec '09

Hello! I'd like to group a certain set of bonds (or atoms), so that I can select them quickly without having to select each item manually every time I decide to change a property like size, style or color. I know that selecting a pseudobond and pressing the UP key selects all pseudobonds. Is it possible to do that for a user-defined subset of bonds too? Thank you, Thomas P.S.: Merry Christmas to the Chimera team!

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Linewidth in images
by Dipl.-Ing. Thomas Mitterfellner 22 Dec '09

22 Dec '09

Hello! I am making large images (4096x3072) which use silhouette edges and dashed wire-style bonds. When I increase the width of the silhouette edges, I do see that on the screen, but the output image turns out the same regardless of this setting. The same is true for my dashed bonds. Is this some issue of graphics card (GeForce 6200) or am I missing something? Thank you, Thomas

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selecting zone, minimizing, docking
by Elaine Meng 22 Dec '09

22 Dec '09

On Dec 21, 2009, at 11:30 PM, gytjyb wrote: > hello,Mr meng ! > I have 3 questions. > <1> > I select one residues or animo acid > But how can I made a radius around this residues or animo acid, > I aslo can select neighbor residues or animo acid within some radius. > <2> > If I should add water for model minization and refine, > how can I refine for a new model. > I want to do a mutation,wether I must fix other residues when I do > minization. > <3> > how can I prepare for a docking, dose this software do docking? > thank you for your answer! Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly) and include something meaningful in the "Subject" line. Also, you can use "Help... Search Documentation" in the Chimera menu to look up information by keyword. (1) menu "Select... Zone." You can also specify zones in commands. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones > (2) That is up to your own scientific judgement. As mentioned in an earlier reply, the minimization capabilities in Chimera are rather limited. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… > (3) Chimera does not do docking calculations. You can move two structures together by hand... of course that is only approximate. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html> However, Chimera does have tools that are related to docking: "Dock Prep" for preparing structures for docking or other calculations (with other programs outside of Chimera) and "ViewDock" for looking at docking results output by other programs, mainly DOCK. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.… > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.h… > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> Here is the Web site for DOCK. <http://dock.compbio.ucsf.edu/index.html> They also have tutorials: <http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm> 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

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identifying residues in a surface
by Elaine Meng 22 Dec '09

22 Dec '09

On Dec 21, 2009, at 5:14 PM, gytjyb wrote: > hello:meng! > thank you for your help! > i want to make a surface about protein. > i want to do lipophilicity and electrostatics surface,we had better > label some amino acid on the surface,how can i do? > or i just use differrent color for different amino acid category. > i think the color must be very different from each. > so i can recognize each other,and find out some important different > between homology protein. > thank you very much! > Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly) and include a short description in the "Subject" line. You can show lipophilicity on the surface with menu item "Presets... Interactive 3 (hydrophobicity surface)" where orange is most lipophilic and blue is most hydrophilic. You can show Coulombic electrostatic potential on the surface with "Tools... Surface/Binding Analysis... Coulombic Surface Coloring" The regular labels are not that good when you are showing a surface. They are usually partly inside the surface so you can't read them. If it is for a figure, you can put labels anywhere you want with "2D Labels" (under Tools... Utilities), but those do not move when you rotate the structure. Also, there are pop-ups that say what is under your mouse, but they only show the detailed information when you are not showing the surface. Sometimes I like to use color-coding, a different color for each amino acid type. Of course, you can't have that as the same time as the lipophilicity or electrostatic coloring. There is a command file (rescol.com) linked to the User's Guide that does my favorite residue color-coding: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile > You would save that file to your computer as plain text and just open it (file named *.com) in Chimera to apply the residue color-coding. 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

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Re: [Chimera-users] hide dashed lines
by Elaine Meng 21 Dec '09

21 Dec '09

Hi Vijay, There are a few ways to hide these "missing segments" pseudobonds. Method 1: Ctrl-click to select one of the dashed lines, click magnifying glass on lower right corner of Chimera window to open Selection Inspector, Inspect "Pseudobond group," change "displayed" to "false" Method 2: open PseudoBond Panel (under Tools... General Controls), choose "missing segments" from the left side and click "hide" on the right side Method 3: "setattr" command, e.g.: setattr g display false but that turns off all pseudobonds, not just missing segment. You could also use the setattr command to only undisplay certain pseudobonds but that would require selecting or naming the endpoint atoms in the command, so if you want to retain other pseudobonds the first two methods will be easier. 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 Dec 21, 2009, at 10:52 AM, Vijay S. Reddy wrote: > Hello, If the there is break in the structure, it is shown by dahsed > lines in the Chimera, How can I hide them or turn them off. I am > deliberately trying to show different regions that are not > sequentially contiguous. Thanks very much, > Vijay

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center of molecule
by Bala subramanian 18 Dec '09

18 Dec '09

Friends, Is is possible to find the central x,y,z coordinates of a pdb file in chimera. Bala

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[Chimera] #7448: show axes/major ellipses for thermal ellipsoids
by Dipl.-Ing. Thomas Mitterfellner 18 Dec '09

18 Dec '09

Hello! > #7448: show axes/major ellipses for thermal ellipsoids Thanks for the implementation of this feature! There's just one thing: the major ellipses are displayed very thinly. The ellipse size factor does not seem to change the size of the ellipses (I supposed them to become larger than the ellipsoid with increased scaling factor so that they extend beyond the surface). Can the thickness or the size of the major ellipses be altered? Thomas

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price quote for chimera software
by Yong You 18 Dec '09

18 Dec '09

Dear Sir,/ Madam, I am emailing to inquire about a single user/computer license for the Chimera software for Molecular Modeling. Can I get the price quotes for using it in Windows 32-bit OS (Windows XP) and in Linux 64-bit OS? Thanks a lot! Sincerely, Yong You Integrated DNA Technologies, Inc. 1710 Commercial Park, Coralville, IA 52241 (319) 626 -9606

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single-component calculation
by Bala subramanian 17 Dec '09

17 Dec '09

Friends, When i try to show the surface sometimes, i get a chimera warning that ' calculation of some surface components failed, falling back to single component calculation'. The message in reply log is as follows. Kindly enlighten me on what is causing the problem. Calculation of some surface components failed. Falling back to single-component calculation. /home/cbala/chimera/bin/mscalc 1.400000 2.000000 0 MSMSLIB 1.3 started on RAMANA Copyright M.F. Sanner (March 2000) Compilation flags WARNING: check_SES_edge: weird case, 1 probe full1 and not full2 WARNING: class_arete2: warning hole in a reentrant face 2119 WARNING: classe_aretes2: No cycle in face 3781 (nba=-6) WARNING: classe_aretes2: No cycle in face 11830 (nba=-4) WARNING: classe_aretes2: No cycle in face 19652 (nba=4) WARNING: classe_aretes2: No cycle in face 19653 (nba=-1) WARNING: classe_aretes2: No cycle in face 19663 (nba=-3) RESTART FROM SES: 1 radius of atom 1220 goes from 1.625000 to 1.725000 radius of atom 1221 goes from 1.000000 to 1.100000 radius of atom 1665 goes from 1.700000 to 1.800000 radius of atom 1666 goes from 1.000000 to 1.100000 radius of atom 3490 goes from 1.500000 to 1.600000 radius of atom 3618 goes from 1.000000 to 1.100000 radius of atom 3620 goes from 1.500000 to 1.600000 radius of atom 3621 goes from 1.000000 to 1.100000 radius of atom 5103 goes from 1.625000 to 1.725000 radius of atom 5106 goes from 1.000000 to 1.100000 Partial mode WARNING: class_arete2: warning hole in a reentrant face 2119 RESTART FROM TRI: 2 radius of atom 470 goes from 1.700000 to 1.800000 radius of atom 4231 goes from 1.700000 to 1.800000 radius of atom 4250 goes from 1.480000 to 1.580000 Partial mode Surface black.pdb, category main, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 16352.1 Total solvent accessible surface area = 17959.3

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Chimera-users December 2009