January 2012 - Chimera-users - RBVI Mailing Lists

Attribute Error!
by Asma Tahir 10 Jan '12

10 Jan '12

Greetings! I encountered error while using the Modeller tools from the Structure Menu. I have tried this function using .aln , .pir, .ali files but i encountered problem. The error is as below: *Attribute Error: Templateseq instance has no attribute 'status'.* ** If I will try to fetch PDB through ID, it is giving me error of "Error during PDB fetch". I read the archives of the chimera on site and changed the www.rcsb.org to the IP Address, as written, in init.py and fetch.py but still the same error. I am using Windows 7. The downloaded chimera version is 1.5.3 win 64. Kindly advice. Thanks in advance, *Asma Ishaq Tahir* *Research Technical Assistant*

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superimposing an all-atom structure to a reduced one
by Damien Larivière 10 Jan '12

10 Jan '12

Dear all, I have two instances of the same protein. One is the original pdb structure which has been locally deformed and saved as the second pdb structure. I would like to match the 2 pdb structures. However, one structure is a reduced version of the other in that it contains only the carbon-alpha trace plus one or two atoms of the side chain. I get an error message when I use MatchMatcher. What can I do to superimpose the all-atom structure onto the reduced one? Many thanks for your help! Damien ps: I can join the two pdb structures if necessary

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APBS -> Chimera plugin - why not?
by Boaz Shaanan 09 Jan '12

09 Jan '12

Hi Elaine, Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too? Happy New Year to you all (still not too late). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Friday, January 06, 2012 2:22 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 105, Issue 5 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: APBS (Elaine Meng) 2. Re: APBS (Elaine Meng) 3. Re: APBS (Anjana Ramnath) 4. Re: How to place a metal ion in protein model (Suneel N.A.) 5. Re: How to place a metal ion in protein model (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Thu, 5 Jan 2012 12:04:22 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Anjana Ramnath <anjanaram1(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] APBS Message-ID: <4CE9538A-80A1-4A3B-B99D-D4F401A73A6E(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hello Anjana, Are you sure you're using Chimera? As far as I know there is no APBS plugin for Chimera, only for Pymol. In Chimera, (A) there are several ways to show distances, including selecting two atoms (Ctrl-click on one atom, Shift-Ctrl-click on the second atom) and using command: distance sel (B) there is no tool especially for aromatic interactions, but you can use the tool Find Clashes/Contacts or command findclash to identify contacts between two sets of aromatic residues. For example, to identify contacts between aromatic amino acids in chain A and aromatic amino acids in chain B, command: findclash :.a&aromatic test :.b&aromatic overlap -1 hb 0 (You would probably also want to display all atoms so you can see where the contacts are.) The same thing could be done using the Find Clashes/Contacts graphical interface, in the menu under Tools... Structure Analysis. GUI documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas…> Command documentation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> 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 Jan 4, 2012, at 9:02 PM, Anjana Ramnath wrote: > Hello all, > My question is simple: im trying to install the APBS plugin but have so far been unsuccessful. I am also trying to show the interactions between aromatic residues on a PDB molecule. how do i do this? im also having trouble with showing the distance between 2 residues. im using Fedora 12 and also WindowsXP. please do let me know. thank you very much! > sincerely, > Anjana. ------------------------------ Message: 2 Date: Thu, 5 Jan 2012 12:23:49 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Anjana Ramnath <anjanaram1(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] APBS Message-ID: <5BAFC2C8-8868-4D58-A577-C2EE7DD1C6CE(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Anjana, After showing a surface, you can either (A) open an electrostatic potential (ESP) map previously calculated with some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it to color the surface with "Electrostatic Surface Coloring" (in menu under Tools... Surface/Binding Analysis) or command "scolor" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html> or (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or command "coulombic" to calculate Coulombic ESP and color the surface based on those values <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> ... for example, as in this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> 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 Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote: > thanks so much for your prompt response! well actually, i was wondering if there was a way to show the electrostatic surface in chimera? > ------------------------------ Message: 3 Date: Fri, 6 Jan 2012 01:56:19 +0530 From: Anjana Ramnath <anjanaram1(a)gmail.com> To: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] APBS Message-ID: <CAAwO1H_Lt3ZRSnjqTNx+qXDpYa7jhF3=-hf+F5TMM1QRjGnj8w(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" thanks so much Elaine! let me just say that Chimera user support is waayy better than any other popular graphics program ive come across! youve got a chimera fan here now. :) On Fri, Jan 6, 2012 at 1:53 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Anjana, > After showing a surface, you can either > > (A) open an electrostatic potential (ESP) map previously calculated with > some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it > to color the surface with "Electrostatic Surface Coloring" (in menu under > Tools... Surface/Binding Analysis) or command "scolor" > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> > < > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo… > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html> > > or > (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or > command "coulombic" to calculate Coulombic ESP and color the surface based > on those values > < > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi… > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> > > ... for example, as in this tutorial: > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> > > 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 Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote: > > > thanks so much for your prompt response! well actually, i was wondering > if there was a way to show the electrostatic surface in chimera? > > > >

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Intersurf
by George Tzotzos 07 Jan '12

07 Jan '12

Hi everybody and happy New Year I'm using Intersurf to define the interface between two sub-units of a protein. Intersurf selects the atoms which appear to be far from the interface. Changing the prune distance from the default value of 30 to, say 10 or less has no effect on the atom selection. Is this right? Is there a way to select atoms that lie, say 5 Angstrom on either side of the interface. Thanks and best regards George

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Phosphorylation
by Tombline, Gregory 07 Jan '12

07 Jan '12

Hi I noticed the script/plugin for no natural amino acids... Is it possible to substitute phosphorylated residues? Ie. and see the phosphate Thanks, Greg Sent from my iPhone

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automated selection of most N-terminal residue in model
by michel dedeo 06 Jan '12

06 Jan '12

Hi, I'm trying to measure the distance between the N-termini (or the first known residue) of a batch of dimeric proteins. The two proteins are different chains. I know how to do this by hand, but am exploring different ways to script it. It may be best to avoid using chimera entirely, but I thought I'd check to see if anyone knows a clever way to select the residue closest to the N-terminus when it's not residue #1. Thanks for your help. Michel

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Re: [Chimera-users] APBS
by Elaine Meng 05 Jan '12

05 Jan '12

Hi Anjana, After showing a surface, you can either (A) open an electrostatic potential (ESP) map previously calculated with some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it to color the surface with "Electrostatic Surface Coloring" (in menu under Tools... Surface/Binding Analysis) or command "scolor" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html> or (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or command "coulombic" to calculate Coulombic ESP and color the surface based on those values <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombi…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html> ... for example, as in this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> 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 Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote: > thanks so much for your prompt response! well actually, i was wondering if there was a way to show the electrostatic surface in chimera? >

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APBS
by Anjana Ramnath 05 Jan '12

05 Jan '12

Hello all, My question is simple: im trying to install the APBS plugin but have so far been unsuccessful. I am also trying to show the interactions between aromatic residues on a PDB molecule. how do i do this? im also having trouble with showing the distance between 2 residues. im using Fedora 12 and also WindowsXP. please do let me know. thank you very much! sincerely, Anjana.

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movie quality
by Ernesto Arias 04 Jan '12

04 Jan '12

Hi everyone, I've made some movies using the current Chimera alpha version (alpha version 1.6 build 35109, 2011-12-24) in an ubuntu 10.04 laptop. I've noticed that the quality of the movies is worse that in the version 1.5.3, and I have generated the movies using the same chimera session and the same script. I've seen this for at least avi and mp4 formats. The movie options I'm using in the script are: *movie record supersample 3 movie encode output movie.avi bitrate 5000 framerate 25 mformat avi* Does anybody know why the quality is worse in the newer Chimera version? Thanks in advance, Ernesto.

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Grid on image
by Sukanya Punthambaker 04 Jan '12

04 Jan '12

Hello, I have a quick question about Chimera. When I save an image from Chimera it displays a grid on top of the image. How do I get rid of the grid? Thank you, -Sukanya Punthambaker.

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