December 2013 - Chimera-users - RBVI Mailing Lists

select all side chains
by Zhou, Ming (NIH/NCI) [C] 09 Dec '13

09 Dec '13

Dear Elaine: I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? Thanks Ming Zhou

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Silhouette toggle
by Luca Pellegrini 05 Dec '13

05 Dec '13

Hi, I have set Silhouette ON in the Effects tab of the Viewing panel, and now I would like to toggle it off for one specific object. However, the Attributes window from Model Panel does not show the Silhouette option (it should feature between 'ribbon spline' and 'stick scale'). Can anyone please advice? I am using Chimera 1.9 (build 39137) for Mac . Kind regards, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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calculate buried surface area
by Bala subramanian 05 Dec '13

05 Dec '13

Friends, I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface. I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps. Thanks, Bala -- C. Balasubramanian

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Problem of Launching Chimera Remotely on a Mac
by Anindito Sen 05 Dec '13

05 Dec '13

Dear All, I am having difficulty to launch Chimera remotely with the following Error message on my Mac. I understand that the current OS X (version 10.8.5) and the latest Xcode has some issues and cannot handle the process ?! Is there a way out of this ? Thanks and Best Wishes Andy [andy@****** ~]$ chimera Xlib: extension "NV-GLX" missing on display "localhost:15.0". Xlib: extension "NV-GLX" missing on display "localhost:15.0". X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1354 Current serial number in output stream: 1354 Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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Electrostatic potential values at each residue
by Tatsuhito Matsuo 04 Dec '13

04 Dec '13

Dear All, I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? Thank you very much in advance, T.M.

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Re: [Chimera-users] Surface area with positive electrostatic potential
by Tom Goddard 04 Dec '13

04 Dec '13

Hi T.M., To find the surface area with positive electrostatic potential would require computing the potential at surface points. Chimera does not compute solvent accessible surface (SAS) points (although it does compute total area). So there is no simple way to get the SAS area for positive potential points. Chimera does compute the solvent excluded surface (SES) using menu Actions / Surface or command "surface". For an SES surface a little Python code can give the fraction of the surface area colored red. I've attached that Python code red_area.py. You color the surface using the normal red-blue electrostatic coloring. The red_area.py code adds a command called "redarea" that computes the area of the surface that is more red than blue. Here's an example from the header of the red_area.py file. # Example use. # # menu File / Open..., red_area.py, Creates the new redarea command. # # open 1a0m # surface # coulombic -10 red 0 white 10 blue #0 # redarea #0 # # menu Favorites / Reply Log # -> "Surface MSMS main surface of 1a0m, red area 1400, total area 1888, ratio 0.7414" This script and other odd Python code for doing computations is on the Chimera developer web site: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom On Dec 3, 2013, at 9:05 PM, Tatsuhito Matsuo wrote: > Dear Tom, > > Thank you very much for the reply and I'm sorry for inadequate information on what I've done (your guess is completely right). What I'd like to know is the ratio of the solvent accessible surface (SAS) with positive (or negative) potential values to the total SAS. The total SAS value is automatically calculated by the surface plot, and I need the value of SAS having positive/negative potential values. > At first, I thought the ESP value of "Attributes of Residues" is relevant to the one at the corresponding protein surface area. I now understand that this was wrong. Could you teach me how to get the SAS having positive/negative potential values? > > Best regards, > > T.M. > > On 2013/12/04, at 12:19, Tom Goddard wrote: > >> Hi T.M., >> >> I think you've left out details about what you have done -- how did you get this value_Coulombic_ESP attribute? Did you use values at atom positions? Did you use the "compute grid" option in the Coulombic Surface Coloring dialog? I guess you did that. And you say you use Attributes of Residues -- is that an average of the atom attribute obtained from the values at atom positions dialog? I can't be sure what you've done, but here's a guess at what your problem is. The Chimera Coulombic Surface Coloring dialog computes the potential at points 1.4 Angstroms out from the solvent excluded molecular surface and colors the surface points using that value. If you instead use a potential value interpolated at the center of an atom, that will give a much different value -- in fact it should tend to give an extremely large value because if the atom is charged the potential at the atom center is infinite using the simple Coulomb calculation. But because you are (I think) using a value interpolated from a grid you don't get an infinite value, just a very large value. So I think your problem is you are not considering that the electrostatic potential varies rapidly in space and you are comparing colors using potential values at different positions in space. >> >> Tom >> >> >> >> On Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote: >> >>> Dear All, >>> >>> I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? >>> >>> Thank you very much in advance, >>> >>> T.M. >>> >>> <ubiquitin.py><ubiquitin.pyc>_______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >

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request for removal from mailing list
by Aani Homeira 03 Dec '13

03 Dec '13

Thanks . . . . . . . . . . . . . . . . . . . A n i . H o m e i r a . A m i r k h a n i .

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Re: [Chimera-users] reading PDB-format alignment files
by Tom Duncan 03 Dec '13

03 Dec '13

Eric, It's not the structural info I want to extract - just the sequence alignment info. See the remarks in the file header. Thanks, Tom ----------------------------------------------------- Thomas M. Duncan, Ph.D. Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY On Dec 3, 2013, at 3:00 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > Date: Tue, 3 Dec 2013 11:27:02 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Tom Duncan <duncant(a)upstate.edu> > Cc: chimera-users BB <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] reading PDB-format alignment files > Message-ID: <9EF6E8D1-3C93-4C30-AD51-2B110CF5C813(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Dec 3, 2013, at 7:47 AM, Tom Duncan <duncant(a)upstate.edu> wrote: > >> Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. > > Hi Tom, > Well, this "PDB" file doesn't conform to the PDB standard in a variety of ways, but the one you care about is the extra two columns on the ATOM records. The presence of those columns causes Chimera to skip those records. If you simply edit them out then Chimera displays the structure. I've attached an edited version of your file. I will open an enhancement-request ticket in our bug-tracking database for having Chimera ignore non-standard columns past the coordinate records (there are some standard columns that are supposed to be there!) and put you on the notification list for that ticket. > > --Eric

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reading PDB-format alignment files
by Tom Duncan 03 Dec '13

03 Dec '13

Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. Thanks Tom ----------------------------------------------------- Thomas M. Duncan, Ph.D. Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY

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<< measuring areas >>
by Hatuey Hack 03 Dec '13

03 Dec '13

Hellos ChimeraUsers, It could be possible to measure different parts of a surface according to a given parameter? For example, from the electrostatic potential surface, I would like to know the respective area surface with positive and/or negative values. Best regards, Hatuey

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