November 2009 - Chimera-users - RBVI Mailing Lists

coarse-grained MD
by Francesco Pietra 11 Nov '09

11 Nov '09

I know that questions about coarse-grained MD wit amber have already been raised. However, I wonder whether any plan is going on - if feasible at all - to implement in the ambertools something like the cg builder of vmd. Or ask chimera software if a conjoint effort may allow us amber users to approach cd md "at home", benefitting of the amber's secure code. thanks francesco pietra

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Re: [Chimera-users] Coloring range for residues
by Eric Pettersen 10 Nov '09

10 Nov '09

Hi Ibrahim, I'm glad it helped. I've opened a Trac ticket for your request for restricted rainbow coloring, so you'll get a notification when it gets implemented. It could be quite some time before I get to it, though if others request it also it could happen sooner. --Eric On Nov 9, 2009, at 8:28 PM, Ibrahim Moustafa wrote: > Hi Eric, > > Thank you very much, as usual, I got the help I expected from > chimera team. > > Actually, the conformational change for the structure I have is > dramatic and involves wide range of residues. It is really painful > for the eye to follow the structural change for a certain element. > Coloring the residues in few colors did the job; however, the > rainbow coloring using the script you sent did a much better job. > It would be useful if this command can be added to the chimera!. > > Many thanks, > Ibrahim > > -------------------------------------------------------------------------------------------------------------------------- > Ibrahim M. Moustafa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., University Park > Pennsylvania State University > PA 16802 > > Tel. (814) 863-8703 > Fax (814) 865-7927 > > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Monday, November 09, 2009 7:29 PM > To: Ibrahim Moustafa > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Coloring range for residues > > Hi Ibrahim, > I'm not 100% sure why you want to rainbow the > highlighted part of your structure, rather than use a single color, > or color the rest of the structure dark gray, or make the rest of > the structure semi-transparent, or many other possible highlighting > schemes. > Anyway, there's no way to do it without resorting to > (simple) Python. Put the following in a file that ends in ".py": > > import chimera > residues = chimera.selection.currentResidues() > residues.sort() > for i, r in enumerate(residues): > r.highlightNum = i+1 > > Then select the residues you want highlighted in > Chimera. Run the Python script by opening it with the "open" > command or with the File->Open dialog. Then run this Chimera command: > > rangecolor highlightNum,r min blue mid white max red sel > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Nov 9, 2009, at 11:14 AM, Ibrahim Moustafa wrote: > > > Dear Chimera team, > > I wonder if there is a way to color a certain range of residues > using rainbow. > I tried to use the rainbow command with atom_spec but it applied for > the whole chain. > > What I want to do is to color part of the structure as a rainbow > (from blue-white-red) with an increasing order of residues number. > I just wanted to highlight a region of conformational change so the > eye can follow which part of the structure has changed dramatically. > > > Thanks in advance for your help. > > Ibrahim > > -- > Ibrahim M. Moustafa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., University Park, > Pennsylvania State University > PA 16802 > > Tel. (814) 863-8703 > Fax (814) 865-7927 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Re: [Chimera-users] Coloring range for residues
by Elaine Meng 10 Nov '09

10 Nov '09

Hi Ibrahim, Just thought I would mention that there are some other interesting ways to show conformational changes or conformational variability in a single picture. Some images are attached at the bottom. You can assign attributes to residues, and then show those attribute values on one or more structures with color and/or "worms". If two or more structures are associated with an alignment and you show the alignment "RMSD" header, that automatically creates the residue attribute named mavRMSD, where the values are the alpha-carbon RMSDs for residues in the same column of the alignment. If you only have two structures it boils down to the CA-CA distance between the two residues in each column of the alignment. You are probably thinking "but I don't have an alignment!" -- however, in Chimera it is easy to make one. If you have > 2 structures already superimposed, you can use Match->Align (under Tools... Structure Comparison) to create and display the sequence alignment. If you have 2 structures, you can use MatchMaker to both create the pairwise sequence alignment and superimpose the structures. Here is an example with a G protein in the "on" and "off" conformations, using the command version of MatchMaker: open 1tad open 1tnd del ~ :.a mm #0 #1 show true That will create the pairwise sequence alignment with RMSD header shown. Then in the alignment window, choosing "Structure... Render by Conservation" brings up the dialog for mapping colors and/or worm fatness onto the structures. In that dialog, change the attribute from "mavConservation" to "mavRMSD" to see the histogram of values. Then use the Colors or Worms section in the dialog to map the values. You can do it for either or both structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html… > I attached images for the example above, where mavRMSD is shown with: (a) worms for both structures (b) color on one structure (c) both color and worms on one structure You could also do the coloring with command "rangecolor" instead of with the dialog <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> The example uses two conformations of the same protein, but it will also work with different proteins along as they are similar enough for Matchmaker to create a good alignment. Or instead of using an alignment, you can create your own attribute in a text file and then use "rangecolor" or the "Render by Attribute" tool (under Tools... Depiction), actually the same dialog used above for showing mavRMSD, to show your custom attribute on the structure. There is a description of the file format <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > and example files <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Probably more information than you wanted 8-) 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] External SAS calculation
by Yasser Almeida Hernández 10 Nov '09

10 Nov '09

It would be nice that Chimera also compute and save the SAS (like a grid), since there're a few softwares to do this task spacifically. I hope this will avaible in the future... Anywere, thanks a lot for your helps -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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Re: [Chimera-users] problem with surface representation
by Miriam Gochin 10 Nov '09

10 Nov '09

Outstanding! That worked perfectly! Thank you so much, Tom. Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463 ________________________________________ From: Tom Goddard [goddard(a)cgl.ucsf.edu] Sent: Monday, November 09, 2009 10:07 PM To: Miriam Gochin Subject: Re: [Chimera-users] problem with surface representation Hi Miriam, I think the cusps (two points) are just parts of the surface. The surface is obtained by rolling a sphere of a 1.4A radius over the molecule and the surface is all points reached by that rolling sphere. The cusps happen because that sphere does not fit between the residue 36 and 104 HE2 atoms. If you reduce the probe radius to 1.2 A then you get rid of the cusp but the surface is slightly different. You would change probe radius in the same dialog where you changed vertex density. Tom -------- Original Message -------- Subject: Re: [Chimera-users] problem with surface representation From: Miriam Gochin <miriam.gochin(a)tu.edu> To: Tom Goddard <goddard(a)cgl.ucsf.edu> Date: 11/9/09 9:31 PM > Hi Tom, > > Thanks for the suggestions. That does improve things a bit, but not completely. Maybe I just have bad geometry at that position? I attach the pdb file. The residues involved are #36 and #104, if you have time to take a look at it. > > Best, > > Miriam > Touro University - CA > miriam.gochin(a)tu.edu > 707-638-5463 > ________________________________________ > From: Tom Goddard [goddard(a)cgl.ucsf.edu] > Sent: Monday, November 09, 2009 8:50 PM > To: Miriam Gochin > Cc: Chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] problem with surface representation > > Hi Miriam, > > I guess the surface is being divided into two few triangles. You can > increase the number of triangles by increasing the "vertex density" > parameter. To do this, select the surface (ctrl-click it), use > inspection selector (menu Actions / Inspect), set the "Inspect" menu in > the inspector dialog to MSMS Surface, increase the "vertex density" > parameter, say from 2 to 5, and press the Enter key after typing in the > new number. That should give a smoother surface. > > Another step that can improve the lighting of the surface is to enable > glossy lighting in the Lighting panel. Menu Tools / Viewing Controls / > Lighting, quality -> glossy. Some old graphics cards don't support this. > > Tom > > -------- Original Message -------- > Subject: [Chimera-users] problem with surface representation > From: Miriam Gochin > To: Chimera-users > Date: 11/9/09 8:07 PM > >> I am having trouble with some pointed edges to my surface (attached). It only happens in one location - everywhere else the surface is smooth. I appreciate any suggestions. >> >> Thanks, >> Miriam Gochin >> Touro University - CA >> miriam.gochin(a)tu.edu >> >> > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Re: [Chimera-users] External SAS calculation
by Yasser Almeida Hernández 10 Nov '09

10 Nov '09

Hi Tom... I'm actually interested in compute and save the accesible surface as a grid (like DMS). If Chimera doesn't compute the SAS surface (with MSMS code), why it ask for the probe radius in Favorites > Preferences > New Surfaces? Thanks -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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problem with surface representation
by Miriam Gochin 09 Nov '09

09 Nov '09

I am having trouble with some pointed edges to my surface (attached). It only happens in one location - everywhere else the surface is smooth. I appreciate any suggestions. Thanks, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Coloring range for residues
by Ibrahim Moustafa 09 Nov '09

09 Nov '09

Dear Chimera team, I wonder if there is a way to color a certain range of residues using rainbow. I tried to use the rainbow command with atom_spec but it applied for the whole chain. What I want to do is to color part of the structure as a rainbow (from blue-white-red) with an increasing order of residues number. I just wanted to highlight a region of conformational change so the eye can follow which part of the structure has changed dramatically. Thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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External SAS calculation
by Yasser Almeida Hernández 09 Nov '09

09 Nov '09

Hi all.. In the Chimera source where is located the sources files for the calculation of SAS. I'm writing a python script for calculate the SAS and i want to call the Chimera's routines to do this task... Best regards -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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access rotation and translation matrices
by Lori Nyland 05 Nov '09

05 Nov '09

Hello, I have been trying to rotate a large volume relative to a reference volume using the vop resample command. The problem is that both volumes are nearly 2GB. However, If I were to bin the volumes (by n) and had access to the rotation R(alpha, beta, gamma) and translation T(x,y,z) matrices I could perform the rotation in an alternate program via R and nT. Thanks! Lori

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Chimera-users November 2009