- Chimera-users - RBVI Mailing Lists

how to setup a default settings for a new pdb model?
by Xing Zhang 07 Feb '12

07 Feb '12

Hi, I have many different pdb models that need to be displayed at exactly the same settings, including color, background, stick scale and so on, so I want to set all these settings for the first model, and then apply these settings to a newly opened pdb model. Is there any way to save and load a default setting for a new pdb model? Thanks much. Xing

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Rotamer copying
by Ahir Pushpanath 07 Feb '12

07 Feb '12

Hello there, I have a question regarding MODELLER in Chimera and the ability of chimera to adjust the model using some inbuilt features quickly(i.e. automatically, instead of interactively) Firstly, I am trying to model the "holo" form of an enzyme with known apo-form structure. I did this usinig the two independent domains of the apo form as a template (in a bid to get the domains accurate) and for the holo-form closure I used a very similar homologue that has been solved in the holo form. The results were good and I got a decent model that had closed up like the homolog. However, I noticed that in the model a lot of the sidechains have not been modelled with the right rotamer. This is odd, as I gave it the two independent domains as a template, so it had all the information it needed to get that perfectly right. Either way, this means, I need to manually "copy" the rotamers from the apo form onto the "holo model", which is time consuming. I know from the homolog that only two or three residues in the active site change rotamer upon apo-holo conformational change. So, I just want an easy way to edit the rotamers in the holo-model to copy the rotamers of the apo-form for all residues. Is there an easy way to do this, is it possible to this with a script? I have no idea how to script, mind you! Ahir

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associating multiple structures and sequences
by Uppal, Karan 07 Feb '12

07 Feb '12

Hi, I am writing a custom extension based on MultiAlign Viewer that highlights regions in a multiple sequence alignment based on numerical values stored in an external file. I modified the RegionBrowser.py script, and added a function that works just like "showSS". It works fine for one structure and sequence combination. However, I am trying to associate multiple copies of the same protein structure and its sequence. So, the structures are identical and so are the sequences in the sequence alignment, but each copy represents different information. My problem is that the sequences in the alignment viewer dialog box are highlighted in a random fashion. And, I want the sequences to be highlighted in an ordered fashion starting from first sequence to last sequence since we want to be able to map the highlighted regions back to the external file. Is there a way to control the order in which the sequences are highlighted in the alignment viewer dialog? Or is there a way to get the model # associated with a particular sequence and using the model # to highlight the alignment viewer? I would highly appreciate your help. Thank you, Karan Uppal Application Developer Emory University ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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minimization with nonstandard atoms
by Jon N. Rumbley 07 Feb '12

07 Feb '12

I was hoping to minimize a homology model containing two heme groups. To understand how I might do this I have been starting with the known structure 1a6m. As suggested in the documentation I begin with Dock Prep and calculate charges etc. To my surprise Chimera alpha version 1.6 (build 34702) actually assigned charges to the heme. The problem is with the minimization itself. Within Minimize Structure I turn off all of the Dock Prep steps and simply try to minimize the structure but get an error,"Element Fe (atom #0:154.A@FE) is not currently supported". I was assuming the charge calc was going to be the hard part but now I am stuck at this subsequent step. Is there something I can do to get the heme atoms recognized or is this simply not possible? Thank you, Jon Rumbley Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 Life Sciences 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

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Manipulating representation during MD movie
by Jean Didier Pie Marechal 07 Feb '12

07 Feb '12

Hi guys, I have a MD movie I generated that I want to record. However, I would need to ask on the graphical representation at given frames (i.e. frame 60) so that the system changes (i.e. change the representation en stick or add a given label). Is there a way to do so directedly? Or should I go for a command file? In this case, how would I mix the MD movie with my own succession of events? All the best, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dilluns, Febrer 6, 2012 9:00 pm Assumpte: Chimera-users Digest, Vol 106, Issue 7 > 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. Rotamer copying (Ahir Pushpanath) > 2. Re: Rotamer copying (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 6 Feb 2012 18:51:22 +0000 > From: Ahir Pushpanath <ahir29(a)googlemail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Rotamer copying > Message-ID: > <CAMVKkxyEoXbnQUo7hxa+m2-u5wLCvMJn7DDY=hzZPJEbC_OvSw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello there, I have a question regarding MODELLER in Chimera and the > ability of chimera to adjust the model using some inbuilt features > quickly(i.e. automatically, instead of interactively) > > Firstly, I am trying to model the "holo" form of an enzyme with known > apo-form structure. I did this usinig the two independent domains > of the > apo form as a template (in a bid to get the domains accurate) and > for the > holo-form closure I used a very similar homologue that has been > solved in > the holo form. The results were good and I got a decent model that had > closed up like the homolog. > > However, I noticed that in the model a lot of the sidechains have > not been > modelled with the right rotamer. This is odd, as I gave it the two > independent domains as a template, so it had all the information it > neededto get that perfectly right. > > Either way, this means, I need to manually "copy" the rotamers from > the apo > form onto the "holo model", which is time consuming. I know from the > homolog that only two or three residues in the active site change > rotamerupon apo-holo conformational change. So, I just want an easy > way to edit > the rotamers in the holo-model to copy the rotamers of the apo-form > for all > residues. > > Is there an easy way to do this, is it possible to this with a > script? I > have no idea how to script, mind you! > > Ahir >

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how to find salt bridge
by Bishwajit Das 04 Feb '12

04 Feb '12

how to find salt bridge in a docked structure........plz help me -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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Coloring electrostatic potential
by George Tzotzos 03 Feb '12

03 Feb '12

Hi everybody, I'm using SiteHound for ligand binding identification sites. I'm comparing the highest affinity sites for two superimposable receptors. I'm attaching an example where the sites favourable to protein 1 are shown red, whereas those for protein two blue. I've opened in Chimera the file that contains the red and blue clusters (difference.pdb) as well as the corresponding potential file (potential.dx). I used the Volume Viewer to different affinity areas but had .... no luck. Any help would be greatly appreciated Best regards George

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export saved session
by Gabor PAPAI 02 Feb '12

02 Feb '12

Dear Chimera team, Is it possible to export a session with all of its files to a different location - for e.g. to a USB flash drive for portability reason? I'd like to open a session saved to a server on an offline computer (during travel). I know that I can do it manually just I'm searching for quick solution. Thank you in advance for the help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-88655748

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selection based on ring names
by Bala subramanian 02 Feb '12

02 Feb '12

Friends, I have two ligands with a common benzoxadiazole ring. I want to do the rmsd comparison only on the ring, but the names of the atoms forming the benzoxadiazole ring are different in both the ligands. Is there any way to use ring name as a string the compare the rmsd. ie. rmsd of benzoxadiazole of ligand 1 and benzoxadiazole ring of ligand 2 -- C. Balasubramanian

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stereo with zalman monitor
by Jose Miguel Mancheno 01 Feb '12

01 Feb '12

Dear colleagues, I am trying to see stereo images with chimera (candidate version 1.6 for mac) using a Zalman monitor ZM240W which works OK with COOT, which is connected to an iMac. As far as I know, I have to select (within the camera mode) the option: row stereo, right eye even (or odd). However, none of these options provided stereo images. If I select sequential stereo (or reverse sequential stereo) I see the image flickering, as expected, but this is not synchronized with the zalman glasses. Any suggestion about how to proceed to see in stereo mode? Thank you very much in advance. José Miguel --

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Selecting equivalent surfaces
by Ankush Aggarwal 01 Feb '12

01 Feb '12

Hi, I am opening up a viperDB file of a T=3 virus in Chimera. I want to select the 60 equivalent copies of a protein, so that I can change their color together. I am able to select selecting each of them separately. Is there a smarter way to do it? Also, after I rotate the view, is there a command to reset it to the default. Right now, I am "undoing" the move, but it can be a pain if I have moved the model a few times. Thanks, Ankush.

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Notebook
by Miguel Ortiz Lombardía 01 Feb '12

01 Feb '12

Dear all, Was the notebook feature implemented in Chimera? I found a message from some time ago but nothing else? Any plans to include a session notebook? I would ask for something really simple, just apt for text notes. Currently, I create text files with the same name than sessions but with .txt extension, however I think it would be useful to have this built-in in Chimera. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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Re: [Chimera-users] HIV ligands
by Eric Pettersen 31 Jan '12

31 Jan '12

On Jan 30, 2012, at 5:27 PM, Forbes J. Burkowski wrote: > Hi: > > I think I have found a bug or least a small inconsistency... > > If you fetch 3NDW and do the menu invocation: > > Select... Residue... > > The list in the submenu offerings includes RIT. > > In a command line, I can use: > > sel :RIT > > to get the same selection. > > Now, repeat the above invocations for 2FDE. > > The Select... Residue... leads us to believe that the ligand can be > accessed as 385. But when I use: > > sel :385 > > I do not get a selection. > > This alternate strategy to do the selection is important for me > because I > am getting the same problem when I put this command into the > runCommand > string within a script. > > The same problem seems to exist for 3SM2 and 3SO9. Both have the > ligand > designated by a number so I have a suspicion that one must do > something > different in the sel command when a number is used to designate the > ligand > instead of a character triplet (such as RIT). > > Is this a bug or am I missing something in the syntax of the sel > command? Hi Forbes, Pedantically speaking, the single-colon (e.g ":532") syntax takes a residue sequence number afterward, whereas the lesser-known double- colon syntax (e.g. "::ala") takes the residue name. Now, as a convenience, if you type something that is not an integer after the single colon, then it assumes you mean the residue name and switches over to interpreting it like the double colon does. But in your case you have character strings that you always want interpreted as residues names regardless of whether they look like integers, so you should just use "::" all the time. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] how2 select named selections using command-line [chimera1.5.3]
by Eric Pettersen 31 Jan '12

31 Jan '12

On Jan 31, 2012, at 2:34 PM, frederick lee wrote: > thanks VERY much eric and elaine. > > last question: how do i find out about the alias definitions, if > any, stored > in a session from within chimera instead of looking inside the > python script > (of that stored session). Hi Fred, "alias" with no arguments will list all current aliases in the reply log. --Eric

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how2 select named selections using command-line [chimera1.5.3]
by frederick lee 31 Jan '12

31 Jan '12

dear chimera users, i can defined named selections and they work under the select menu. however, i canNOT use the command line to select them; e.g., i have 4 named selections 0a,0b,1a,1b dis 0a | 1a works sel 1a NOT working sel :1a NOT working (said selection cleared) i like to be able to select multiple named selections and further apply filters on them; e.g., "select 1a and 1b and atoms=side chain atoms" how do i accomplish this? as always thank you very much. fred

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Re: [Chimera-users] structural movement when removing ligand
by Elaine Meng 31 Jan '12

31 Jan '12

On Jan 30, 2012, at 6:24 PM, Benny Lo wrote: > Hi, Elaine: > I am using chimera to remove ligand from the protein structure and am curious why there are structural movement of the protein? > Thank you for your response, > Ben Hi Ben, If you are just deleting some atoms, the other atoms should not move. To say anything else, would need more details on what you actually did. Questions should be sent to chimera-users(a)cgl.ucsf.edu, or if you believe it is a bug, you should use Help... Report a Bug in the Chimera menu to send us everything needed to reproduce the problem (for example attaching your input file and describing each step that you did). 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

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Biology infrastructure at the XFEL
by Tim Wiegels 31 Jan '12

31 Jan '12

The European Molecular Biology Laboratory (EMBL) and the European X-ray Free Electron Laser (XFEL) at DESY, Hamburg, Germany, have a keen interest in the development of FEL-based applications in structural biology. Within this framework the EMBL, together with international collaborators from Russia, Sweden and Germany, propose to construct a biology infrastructure at the XFEL facility (expected completion in 2016) to enable biological experiments using the high brilliance, ultrashort pulse duration and high repetition rate coherent X-ray radiation. The proposed biological sample infrastructure facility will provide: - support to the international life-science community in generation and handling of challenging samples in immediate proximity to XFEL instruments. - appropriate selection, quality control and evaluation of samples, including correlative imaging, immediately prior to XFEL experiments. - standardized technology for data interpretation, including computation and validation of structural models. In order to ensure efficient operation of the facility and provide optimal services for the international biological community we seek your input to identify the requirements necessary to support these novel biological imaging experiments. We would appreciate your input in the web-based questionnaire available at http://www.embl-hamburg.de/xfel_cgi-bin/questionnaire The results of this survey will be used to identify the most pressing needs that should be taken into account during planning and construction of the infrastructure. We thank you in advance for your cooperation. __________________________________ Tim Wiegels Predoc @ Lamzin Group, EMBL Hamburg __________________________________ EMBL Hamburg c/o DESY Notkestrasse 85 DE-22603 HAMBURG GERMANY Phone 0049 40 89902-184 Fax 0049 40 89902-149

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Regarding Bonding Pattern and all residue
by Vivek Keshri 30 Jan '12

30 Jan '12

Dear Sir / Madam, I Vivek Keshri writing from Uttar Pradesh India, I am opening docked PDB file in Chimera 1.5.3 and want to identify all residue of receptor and ligand which are involved in binding. Waiting for favorable response... Yours Sincerely, Vivek Keshri +91-8005261512

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Minimisation error
by Kyle Morris 30 Jan '12

30 Jan '12

Hi, I get a minimisation error - Atom type "Br" is not supported by MMTK - when trying to minimise a PDB that contains a bromonaphthalene covalently bound ligand. I have read the post by neelagiri.d at gmail.com and note the Cl substitution does make this work but my Br is part of the molecule and so GAFF/Antechamber should be able to handle it I thought? Really appreciate any help. Best wishes, Kyle

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Re: [Chimera-users] pythonw.exe error
by Gutheil, William 30 Jan '12

30 Jan '12

Im am getting the same error as noted in this post: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005790.html Is this a graphics problem? Any suggestions to fix? THanks

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Images
by George Tzotzos 30 Jan '12

30 Jan '12

Hi everybody, When I'm saving images either as tiff or pgn, the void around the image can ON OCCASIONS be quite large. The example attached below. Is there a way of reducing the void space? Regards George

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Chimera output into Collada .dae file format
by Evan Kantrowitz 30 Jan '12

30 Jan '12

Hi, This is the way I got it to work, I exported Chimera scene to VRML (.wrl). Next you need blender. You can download it from http://www.blender.org/download/get-blender/ Then Open Blender. In the upper right corner in the Scene section right click on Lamp and delete it right click on Cube and delete it right click on Camera and delete it Save this file so you don't have to do this every time. I called mine empty_blender_file.blend Either open empty_blender_file.blend or continue from above and read in the the .wrl file from Chimera File -> import->X3D Extensible 3D (.x3d/.wrl) this reads in the file In Blender you need to delete the three lights that came in from Chimera called TOPO, TOPO.001 and TOPO.002 In the upper right corner in the Scene section right click on TOPO and delete it right click on TOPO.001 and delete it right click on TOPO.002 and delete it Now you need to move around the viewport to get it centered In the upper right corner in the Scene section click on the Viewport then press number pad 0 Press the cube icon below the Scene section Now in the transform section move the location x,y,z. When you have it the way you want it is ready for export. File->export->collada (.dae) Done. This file will read into iBooks Author and have somewhat uniform lighting. By the way, .dae files can be opened an checked in Preview. Its easier than going back and forth into the iPad, since you can rotate the image in Preview. Here is a link to a .dae file of 1crn that you can import into iBooks Author or Preview http://dl.dropbox.com/u/4300550/1crn2_mod.dae Hope this helps, let me know if it works for you and if you have any suggestions. Finally, someone needs to write a one step VRML and/or X3D to collada converter that will work with PyMol and Chimera etc. PS It was a little easier from PyMol, if your interested see the post at https://discussions.apple.com/thread/3670156?start=0&tstart=0 PSS. Okino Computer Graphics makes a .wrl and .x3d to .dae converter http://www.okino.com Have fun! ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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Re: [Chimera-users] Chimera output into Collada .dae file format
by Chris Tomlinson 28 Jan '12

28 Jan '12

Hello, I've tried generating several Collada dae files via Meshlab from stl files exported from Chimera and consistently get: The 3D file “benzene.dae” wasn’t added. The scene couldn’t be loaded. I've tried very simple ones as above and more complex ones such as 1CRN.pdb with no success. I also tried generating an xsd file and then converting to dae via Meshlab and got the message: The 3D file “2HHB.pdb.dae” wasn’t added. The files assets could not be consolidated Perhaps the iBooks Author isn't ready to handle these sorts of files as of yet. Chris

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Re: [Chimera-users] Chimera output into Collada .dae file format
by Chris Tomlinson 28 Jan '12

28 Jan '12

Hello, I've tried generating several Collada dae files via Meshlab from stl files exported from Chimera and consistently get: The 3D file “benzene.dae” wasn’t added. The scene couldn’t be loaded. I've tried very simple ones as above and more complex ones such as 1CRN.pdb with no success. I also tried generating an xsd file and then converting to dae via Meshlab and got the message: The 3D file “2HHB.pdb.dae” wasn’t added. The files assets could not be consolidated Perhaps the iBooks Author isn't ready to handle these sorts of files as of yet. Chris

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Re-order models in function of their rmsd regarding a given structure
by Jean Didier Pie Marechal 27 Jan '12

27 Jan '12

Hi everyone, I have a set of protein and would like to morph between them in the smoothy manner. I'd like then, to re-order following the rmsd regarding a given structure. What would be the command-line, script that could do this relatively easily? All the best. JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

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