- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] chimera utility help
by Elaine Meng 17 Sep '12

17 Sep '12

Dear Sotirios, You would use Join Models option "C-N peptide bond" as described in these instructions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> "C-N peptide bond - specialized case of joining two peptides. The N-terminal N of one peptide and the C-terminal (carbonyl or carboxyl) C of the other should be selected. Each selected atom must be bonded to only one carbon; however, it may also be bonded to hydrogen and/or OXT, and if so, these atoms will be replaced as appropriate by the new peptide bond." If you do not see that option, maybe you have an older version of Chimera and should upgrade to a newer version. If you do see that option and you have followed the instructions as above but are still not able to apply, please save a session file and use menu "Help... Report a Bug" and attach the session file to the bugreport. I just tried it on two example proteins and seemed OK, but maybe there is something different about your structure. Thanks! 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 Sep 17, 2012, at 9:10 AM, Sotirios Katsamakas wrote: > Dear Elaine C. Meng, > I followed your suggestion and I created a separate side chain of the 25 amino acids with specified phi and psi values for its residues. But I am still not able to Join Models, through the homonymous section. I am selecting the C terminus of the constructed side chain (#0:25@C) and the N terminus of the protein (#1:26@N) respectively, but when I go to the panel the apply button stays inactive. I am sure it must be something obvious but it eludes me. Thank you in advance and I am looking forward in hearing from you. > > Best Regards, > Sotirios Katsamakas.

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Difference between atoms' coordinates on screen and in a PDB file
by Mateusz Dobrychłop 14 Sep '12

14 Sep '12

Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz

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Denaturing a protein
by vamsee 14 Sep '12

14 Sep '12

Hi Elaine, Thanks for the answer for the previous question. I am back with one more :) Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera? Thanks again Vamsee

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sphgen format
by Brian Fochtman 13 Sep '12

13 Sep '12

Hello, I read in the release notes for version 1.6 that Chimera is now able to input files in the dock .sph format. Thank you for this feature, it will be very helpful. Unfortunately I am having some trouble using it. (File -> Open -> file.sph) declares a syntax error for the following file (I've only included the beginning of the file because the output says the synax error is on line 2). Is there another method to read in these files? Thank you, Brian Fochtman cluster 1 number of spheres in cluster 72 1 20.51900 -17.55400 15.86300 0.700 1 2 21.04300 -18.55700 16.07400 0.700 2 3 22.17700 -17.60500 16.24100 0.700 3 4 22.17500 -17.84200 15.30900 0.700 4 5 21.41300 -20.08800 15.15700 0.700 5 6 20.64000 -20.83100 16.58800 0.700 6 7 21.63200 -18.65500 14.15300 0.700 7 8 23.13800 -16.98900 16.54500 0.700 8 9 21.18800 -21.21200 14.71200 0.700 9 10 17.88800 -26.45300 19.89900 0.700 10 11 21.83900 -17.33000 12.81300 0.700 11 12 21.28600 -20.42100 13.28900 0.700 12 13 23.77100 -15.65400 16.91100 0.700 13 14 21.15100 -21.76500 13.92000 0.700 14 15 21.38500 -19.46300 12.20200 0.700 15 16 20.39500 -21.75600 13.41100 0.700 16

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Gromac .xtc format
by Eric Pettersen 13 Sep '12

13 Sep '12

Hi, For you Chimera/Gromacs users out there, the current daily build allows you to use .xtc format coordinates now as an alternative to .trr . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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chimera utility help
by Sotirios Katsamakas 13 Sep '12

13 Sep '12

Dear sir or madam, I am a recent user of the chimera software on Linux-Ubuntu (11.10) operating system and I confronted a dead end on the following issue. I reconstructed a missing side chain of 25 amino acids in a PDB file but I cant seem to find how to set the secondary structure and so on for these 25 residues. So they are stuck in a linear formation externaly from my protein. For your consideration I am attaching also the PDB file. Thank you in advance and looking forward in hearing from you regarding my problem. Best Regards, Sotirios Katsamakas

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Re: [Chimera-users] Match->Align command line option?
by Eric Pettersen 12 Sep '12

12 Sep '12

On Sep 12, 2012, at 11:16 AM, Chetanya Pandya wrote: > Hello, > > I want to superimpose multiple structure sets and get the corresponding multiple sequence alignments using Chimera. I've been using the Match->Align option from the Tools menu. Now, I want to automate the process using the Python interface. > > Unfortunately, I'm unable to find a command line option which does this. Can you help me out with this? Hi Chetanya, It's a little ambiguous if you are asking about a command version of Match->Align, or how to call it from Python. The issue is moot though since there currently is no command version of Match->Align, so you have to call it from Python! I don't know how familiar you are with Python or programming with Python, but the Chimera Programmer's Guide has some info to help. http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html If you don't know Python at all, follow the link in the Guide to the Python Tutorial and work through that, or at least the first few sections of that. Then for some Chimera-specific info, look at some of the Examples and the "basic primer" linked on the page. Assuming you've written a script that has gotten to the stage where the structures are already open and superimposed, here's the info you'll need to use the Match->Align API: 1) Getting the list of open molecules: from chimera import openModels, Molecule mols = openModels.list(modelTypes=[Molecule]) 2) Getting the list of chains to use. This example code assumes they're chain A: chains = [m.sequence('A') for m in mols] 3) Call Match->Align to create the alignment. from StructSeqAlign import makeAlignment mav = makeAlignment(chains) Note that the makeAlignment call will only return the Multalign Viewer instance starting with tomorrow's daily build (i.e. I made that change today!). Also, the makeAlignment call has a lot of optional arguments to change the parameters used in computing the alignment (e.g. cutoff, iteration, reference chain). Look at <your Chimera>/share/StructSeqAlign/__init__.py to see what the options are if you need to change the default behavior. (On a Mac, "<your Chimera>" is Chimera.app/Contents/Resources). 4) Save the alignment to a FASTA format file (named "x.fa") and Quit the MAV instance: f = open("x.fa", "w") from MultAlignViewer.formatters.saveFASTA import save save(f, mav, mav.seqs, mav.fileMarkups) f.close() mav.Quit() I hope this helps. Since this is pretty Python-intensive, I set followups to go to the chimera-dev mailing list rather than chimera-users. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Visualization of protein aqueous solution
by Nikolay Igorovich Rodionov 10 Sep '12

10 Sep '12

Hi all, Could anyone tell me how I could solvate my protein in a solution of a specific molarity solution with both water molecules and Na+ Cl- ions. I have no trouble adding the water molecules, but I am not sure how to go about adding the ions into the visualization. I've tried using add-ion but I haven't had good results. Are there any other options? This is for purely visual purposes, I'm creating a conceptual image, so I don't need the system to be 100% accurate or capable of conducting calculations. Much Thanks! Nikolay Rodionov

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color by RMSD
by Daniel Gurnon 10 Sep '12

10 Sep '12

Hi everyone, To color a trajectory by RMSD, comparing each frame to the final frame. My approach was to save the last frame of the trajectory as a pdb, load it as a separate model, and then run something like this script: mm #0 #1 show true rangecolor mavRMSD min white mid pink max red This works, but of course my screen quickly fills with multialign-viewer windows. Without "show true" in the script, coloring doesn't work past the first frame. Is there a way to do this without displaying the MAV window? thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Ribbon gradient coloring
by vamsee 10 Sep '12

10 Sep '12

Hi All, Is there a way to color the ribbon with a gradient? In my case, it has to be an increasing and then decreasing gradient. Ex: Let's say I have data that shows that a certain region of a protein is highly dynamic. This region consists of approx 11 residues and the most dynamic region in these 11 are the residues 5,6 and 7. Now, I need to color the ribbon in such a way that residues 1 and 11 are the same color (green), 2 and 10 (yellow), 3 and 9 (light orange) 4 and 8 (orange) 5,6 and 7 (red). I could do this by coding it but it becomes a step gradient and it doesn't look so good plus if I need to do this for residues in a bunch of proteins/peptides, the task quickly becomes tedious. I would rather write 2 lines of code for the complete protein than write 1 line/residue/protein. Any ideas? Thanks in advance Vamsee

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selection of multiple atoms in a session with multiple pdb structures
by Anindito Sen 09 Sep '12

09 Sep '12

Dear All, I have a Chimera session where 4 different atomic structures (pdb files) are docked in the computed density map of a macromolecular complex. I need to select multiple amino acids positioned at different places of the different docked atomic structures. To explain the situation- Say the 4 docked Atomic structures are A, B, C & D I need to select 276aa of A, 15aa of B, 246aa of C and so on... How can I do that ? Thanks 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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Distance between two benzene rings
by George Tzotzos 06 Sep '12

06 Sep '12

Hi everybody, I'm trying to work out stacking interactions between two benzene rings. Is there a way to measure the distance from the center of the benzene rings of a Tyr to the center of the benzene ring of a Phe residue? Your help suggestions / help much appreciated as always Regards George

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Fwd: [Chimera] #11323: Chimera using local GLUT installation (was: Chimera bug report submission)
by George Tzotzos 05 Sep '12

05 Sep '12

Apologies for sending this to the List but I haven't received any information regarding the bug report below. Maybe I missed the mail. I have reinstalled Chimera but I get the same error message. Any suggestions how to solve this problem? Many thanks George Begin forwarded message: > From: Chimera <chimera-bugs-admin(a)cgl.ucsf.edu> > Subject: Re: [Chimera] #11323: Chimera using local GLUT installation (was: Chimera bug report submission) > Date: August 27, 2012 7:12:02 PM GMT+02:00 > To: Undisclosed recipients: ; > Reply-To: chimera-bugs(a)cgl.ucsf.edu > > #11323: Chimera using local GLUT installation > ---------------------------------+------------------------------------- > Reporter: gtzotzos@… | Owner: gregc > Type: defect | Status: assigned > Priority: normal | Milestone: Release 1.7 > Component: Platform | Version: 1.6.2 (b36855) > Severity: normal | Resolution: > Keywords: | Blocked By: > Blocking: | Notify when closed: > Platform: Mac OS X (Cocoa 64) | Project: chimera > ---------------------------------+------------------------------------- > Changes (by pett): > > * status: new => assigned > * component: Unassigned => Platform > * project: => chimera > * platform: => Mac OS X (Cocoa 64) > * version: => 1.6.2 (b36855) > * milestone: => Release 1.7 > * owner: pett => gregc > > > -- > Ticket URL: <http://plato.cgl.ucsf.edu/trac/chimera/ticket/11323#comment:1> > Chimera <http://plato.cgl.ucsf.edu/trac/chimera> > Chimera Issue Tracker

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H-bond analysis in case of TIP4P water model ?
by Marek Maly 04 Sep '12

04 Sep '12

Hello, it seem to me that Chimera is not able to do H-bond analysis between water molecules when TIP4P water model is used. Am I right or I overlooked something ? Thank you very much for the answer in advance ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Ligand parametrization
by Miro Moman 04 Sep '12

04 Sep '12

Hello, When energy minimising protein-ligand complexes, I have observed that Chimera seldom, if ever, complains about missing parameters. However, when I try to generate a Pmrtop file for the same complexes, quite often sLeap is unable to complete the request due to its inability to recognise certain atom types.. Provided that the minimization engine (MMTK) is using the Amber force filed, I was wondering: Are parameters computed in the same way? If not, what are the differences? Maybe a different forcefield version? In addition, is there a way to inspect the parameters that have been generated for minimising a given ligand or non-standard residue? Kind regards, Miro

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saving spheres
by MARY VARUGHESE 04 Sep '12

04 Sep '12

Hi, I saved the combined sph(two clusters) file. But the file contains two clusters with single ID, so i cant create the box including both clusters, since in the box.in file of dock i can give only one cluster number. How can i assign both clusters into single cluster. or any other suggestion. Thanking You.

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Fwd: Installation problems
by prashant kurkute 04 Sep '12

04 Sep '12

Respected sir, Sorry for making you disturb. I am novice to linux. I am trying to install chimera in ubuntu 12.04 LTS. I follow following instruction. sudo chmod +x chimera-1.6.2-linux_x86_64.bin ./chimera-1.6.2-linux_x86_64.bin (I also triied with root sudo ./chimera-1.6.2-linux_x86_64.bin) I got following reply bash: ./chimera-1.6.2-linux_x86_64.bin: cannot execute binary file Sir please help me to solve problem. I will be greatly thankful to your help. With Best wishes and regards.

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volume of an ensemble
by R. Andrew Byrd 31 Aug '12

31 Aug '12

Dear Chimera Team, Is it possible to get the total volume that encompasses an ensemble of structures? For example, if a docking or structure calculation produces an ensemble of structures, can one calculate the volume that encompasses all the members of the ensemble? A docking calculation may have one component superimposable and the second component represent an ensemble, and it is that ensemble that I would I like a measure of the total volume. Thanks! Andy

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adjust resolution of alignment .eps in Multalign viewer
by Gesa Volkers 30 Aug '12

30 Aug '12

Hi all, I would like to extract a high resolution publication quality image from my alignment from the Multalign viewer. Only option I see is to save it a as .eps, but when I open that file the resolution is not sufficient. Is it possible to get a higher resolution image? Thanks, Gesa

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reasonable minimization times
by David Belnap 30 Aug '12

30 Aug '12

I am trying to link the crystal structure of an Fc domain with two Fab structures. I am using the command "minimize spec sel fragment true" on the command line. When various options come up, I've selected "if alternate locations, keep only highest occupancy", "add hydrogens", "add charges", "consider each model in isolation from all others", "also consider H-bonds", and AMBER ff12SB and ANTECHAMBER to assign charges. I've had jobs run overnight that didn't finish. What is a reasonable time for about 8-10 residues to be minimized? Can you suggest any ways to speed this up? Thanks, David

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problem with loading color scheme in Multalign viewer
by Gesa Volkers 29 Aug '12

29 Aug '12

Hi all, I encountered a problem when I tried to open a color scheme (tried it with custom.par from the Chimera website) in the Multalign viewer. I get the following error: "File "C:\Program Files\Chimera 1.6.2\share\MultAlignViewer\PrefDialog.py", line 69, in addColorScheme self._resColorOpt.set(colorFile) See reply log for Python traceback." I reported a bug. Though has anyone found a way to solve this problem and is able to open a .par file again? Thanks, Gesa

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making a movie problem
by Boskovic.Jasminka 29 Aug '12

29 Aug '12

Hi, I am trying to make a movie with chimera but instead of filming just a molecule's movement the program is making the frames of all the chimera window showing the "File, Select, Actions etc" bottoms and the command line? How can I remove this option and film just the molecule window? Thank you in advance! Best regards, Jasminka Boskovic, PhD Centro Nacional de Investigaciones Oncologicas-CNIO (Spanish National Cancer Research Centre-CNIO) Melchor Fernandez Almagro 3 28029 Madrid Spain Tel.: + (34) 917 328 000 (ext 3031) Fax: + (34) 912 246 980 e-mail: jboskovic(a)cnio.es **NOTA DE CONFIDENCIALIDAD** Este correo electr�nico, y en su caso los ficheros adjuntos, pueden contener informaci�n protegida para el uso exclusivo de su destinatario. Se proh�be la distribuci�n, reproducci�n o cualquier otro tipo de transmisi�n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Trivial question
by George Tzotzos 28 Aug '12

28 Aug '12

It seems that a standard feature of Chimera is upon loading a pdb file of a complex, a number of nearby residues also show up. My question is whether there's a rule, let's say a cutoff distance, or other. Thanks in advance for any advice on this Regards George

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Batch energy minimisation
by Miro Moman 24 Aug '12

24 Aug '12

Hello, Searching through the archives, I have found that performing DockPrep in batch mode is quite straightforward: http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html I have also noticed that, when working from the GUI, energy minimisation involves a previous DockPrep step. I would like to perform the energy minimisation of several protein-ligand complexes, can this be easily done in batch mode? Furthermore, I would also be interested of computing the binding energy both prior and after minimisation (possibly including APBS-computed electrostatic terms...). However, this is of secondary importance as it can be easily achieved with other tools. Best regards, Miro Moman

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graphics problems after update from UCSF-Chimera64-1.5.3 to UCSF-Chimera64-1.6.2
by Dieter Blaas 21 Aug '12

21 Aug '12

Hi, I replaced the previous version of Chimera, UCSF-Chimera64-1.5.3 with the new one UCSF-Chimera64-1.6.2 on our cluster running Linux l22 2.6.32-131.17.1.el6.x86_64 #1 SMP Wed Oct 5 17:19:54 CDT 2011 x86_64 x86_64 x86_64 GNU/Linux whereas everything was perfect so far I now get the error message: X Error of failed request: GLXBadContextTag Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1352 Current serial number in output stream: 1352 followed by a crash. This is annoying since I need the new version for compatibility with some sessions saved with the new version on another machine. Thanks a lot for hints, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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a problem with silhouettes
by Alja Oblak 20 Aug '12

20 Aug '12

Dear Chimera users, I am trying to create an image for a publication using Chimera 1.6.1. Whenever I turn on "silhouette" dark spots appear on the screen and on the saved image. They seem totally random but they move along with the structure when rotated. When I zoom on them they look like small "umbrella-shaped" discs. The "show shadows" option is turned off. Does anybody know what are those spots and how to get rid of them? Thank you very much for any help. Regards, Alja Oblak

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how to use antechamber?
by 何永辉 16 Aug '12

16 Aug '12

Hello, Can you show me how to use the ambertool antechamber in Chimera? Thanks! Yonghui Dr. Yonghui He Central South University 932 Lushan South Road Changsha, China.

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em fit refinement
by Bala subramanian 15 Aug '12

15 Aug '12

Friends, I used "fit" command to fit a structure onto a EM map and obtained a list of fits. Now i want to choose the best fit and refine it further. I would like to know if there is any way to refine a fit produced by fit command in Chimera. Or can i use any other software for the same, which can take chimera's fit as input and refine it further. Thanks, Bala -- C. Balasubramanian

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Mountain Lion
by John (Jack) Johnson 13 Aug '12

13 Aug '12

Are there any issues with the current Mac version of Chimera (1.6.2) and Mac OS 10.8 (Mountain Lion)? Also, for a MacBook Pro (latest version) should one be using 32 or 64 bit version of Chimera. Thanks, Jack John E. Johnson Elden R. Strahm Professor of Structural Virology PHONE 858-784-9705 Department of Molecular Biology, MB31 FAX 858-784 -8660 The Scripps Research Institute EMAIL jackj(a)scripps.edu<mailto:jackj@scripps.edu> 10550 N. Torrey Pines Rd. La Jolla, CA 92037 http://johnsonlab.scripps.edu/ Virus Partcle ExploreR (VIPER) http://viperdb.scripps.edu/ ******************************************************************************** Olive Ireland PHONE 858-784-2947 Administrative Assistant EMAIL ireland(a)scripps.edu<mailto:ireland@scripps.edu>

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Elongating TMV capsid
by Jeremiah Gassensmith 13 Aug '12

13 Aug '12

Hello, I've downloaded the tobacco mosaic virus structure from the PDB and used Multiscale Models to build the biological unit. Unfortunately, only about 45 or so of the 2200 protein monomers show up. Is there a way I can multiply the biological unit to elongate the TMV structure? I don't need all 2200 monomers, but something a bit longer would be helpful. Thanks! Jeremiah Dr. Jeremiah J. Gassensmith Stoddart Mechanostereochemistry Group Northwestern University 2145 Sheridan Road Evanston, IL 60208-3113 Phone (W) +1(847)467-5936 Fax +1(847)491-1009

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Chimera inquiry: .py to .u3d conversion
by Will Jones 13 Aug '12

13 Aug '12

Hello, My name is Will. I'm a researcher at the University of Iowa. Our group has been using your Chimera software to visualize a model of our protein of interest. It's been very helpful but I've run into a small issue that I'd like to ask your advice on. I'm trying to convert the 3d image of the saved .py file into a universal 3D file (.u3d). I have tried several types of conversion software including polytrans/nugraph, 3DVIA Composer, and CS5 Adobe Photoshop with no success. Could you please tell me if conversion of .py to .u3d is possible, and if so how I might go about it. Thank you, I appreciate your time. Sincerely, Will -- Department of Biochemistry University of Illinois Urbana-Champaign Class of 2012

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Saving Images
by Hobbs, Merlin Eric 09 Aug '12

09 Aug '12

We are having trouble saving images to look a certain way. More specifically we are trying to make an image with the distance from a residue to a metal ion shown. The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick. Thanks Eric -- Merlin Eric Hobbs | Graduate Student, Biochemistry and Biophysics | Raushel Lab | Rm 2510 | Texas A&M University | College Station, TX 77842 | 979-845-9163 | eric0zero(a)tamu.edu

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Re: [Chimera-users] Rapid Access - a different question/request
by Eric Pettersen 08 Aug '12

08 Aug '12

On Aug 8, 2012, at 2:25 PM, Boaz Shaanan wrote: > OK Eric, thanks. I'll wait for the scroll bar since my window is already stretched to the limit. Okay, there will be a scrollbar in tonight's daily build. Worked fine in my tests. Speak up if it turns out I botched something! --Eric

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Rapid Access - a different question/request
by Boaz Shaanan 08 Aug '12

08 Aug '12

Hi Eric, I actually find the Rapid Access very convenient, however I wonder: is the list limited to the n most recent sessions/pdb ? I actually am missing the option of paging further down the list to jobs that are not in the list but which are quite recent. Is there already an option to do this? The browse button does other things (at list in my hands). Cheers, 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: Monday, August 06, 2012 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 112, Issue 6 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. Modelling of missing regions ussing Chimera (Gleb Novicov) 2. (no subject) (Merced Malabanan) 3. Re: Rapid Access file list (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Sat, 4 Aug 2012 15:44:12 +0400 From: Gleb Novicov <gnovikov87(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Modelling of missing regions ussing Chimera Message-ID: <CAN=J6WkT9_GH8YYT8U=Nbt-3hhor_YvNHrndwXK6L4ix75uHvA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear Chimera's users! I need to model some missing segments ( In particular case I need to build missing N and C termi ) of my protein ussing Modeller's options. Could you tell me about possible solution of that issue ? On my win7 I have installed Chimera as well as Modeller v 9.10 suite. I've defined Modeller pathways in the Chimera's Model pool options but when I've selected option Prune seection to define region of interest I didnt obtain anythinf from both of Chimera or Modeller. On other hand the option Structure -> Modeller tools also not available for me. Does it means that I've installed modeller incorrectly ? Also I've used runmod.dat script with defined variables from which I obtained the below C:\Users\own\Desktop\worktemp>runmod.bat usage: mod9.10 script [...] Doest this means that all work fine ? By the way after executing of that script I could not launch modeller by means of mod9.10.exe from modeller folder. The error from modeller was C:\Program Files\Modeller\bin>mod9.10.exe FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete MODELLER in stallation Could you explain me whats I've done wrong and how I could fix this problem? Thanks for help Gleb

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Modelling of missing regions ussing Chimera
by Gleb Novicov 08 Aug '12

08 Aug '12

Dear Chimera's users! I need to model some missing segments ( In particular case I need to build missing N and C termi ) of my protein ussing Modeller's options. Could you tell me about possible solution of that issue ? On my win7 I have installed Chimera as well as Modeller v 9.10 suite. I've defined Modeller pathways in the Chimera's Model pool options but when I've selected option Prune seection to define region of interest I didnt obtain anythinf from both of Chimera or Modeller. On other hand the option Structure -> Modeller tools also not available for me. Does it means that I've installed modeller incorrectly ? Also I've used runmod.dat script with defined variables from which I obtained the below C:\Users\own\Desktop\worktemp>runmod.bat usage: mod9.10 script [...] Doest this means that all work fine ? By the way after executing of that script I could not launch modeller by means of mod9.10.exe from modeller folder. The error from modeller was C:\Program Files\Modeller\bin>mod9.10.exe FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete MODELLER in stallation Could you explain me whats I've done wrong and how I could fix this problem? Thanks for help Gleb

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Re: [Chimera-users] Chimera-users Digest, Vol 112, Issue 2
by vamsee 07 Aug '12

07 Aug '12

Hello, I am trying to script distance measurements (distance monitor) between the Calpha of a residue and a few Hydrogens. I have pretty much everything working except that I am not able to figure out how to change the attributes (color, line style etc..) of the distances (pseudo-bonds). I know it can be changed using the GUI but I would rather script it. Any suggestions? Thank you Vamsee On Thu, Aug 2, 2012 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > 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. combining mrc maps (Daniel Murin) > 2. Re: combining mrc maps (Elaine Meng) > 3. Re: combining mrc maps (Tom Goddard) > 4. double bonds visualization ? (Marek Maly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Aug 2012 18:58:53 -0700 > From: Daniel Murin <cmurin(a)scripps.edu> > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] combining mrc maps > Message-ID: > < > 83025BE3F3B8D644AA9F8CAA21F2640801A3D700C402(a)EXCH-CCR01.lj.ad.scripps.edu> > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I was wondering if it is possible to combine two mrc volumes into a single > volume and save that as a new mrc file? I haven't really been able to find > anything and I suspect that this may not be possible with Chimera. > > Thank you for your help, > > Daniel > > > > Charles Daniel Murin > Graduate Student - Ward/Ollmann-Saphire Labs > Department of Molecular Biology > Kellogg School of Science and Technology > The Scripps Research Institute > 10550 North Torrey Pines Road, CB 227 > La Jolla, CA 92037 > > Work: 858.784.9053 > Fax: 858.784.8218 > email: cmurin(a)scripps.edu > > > > ------------------------------ > > Message: 2 > Date: Thu, 2 Aug 2012 10:06:36 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Daniel Murin <cmurin(a)scripps.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] combining mrc maps > Message-ID: <20D05B2F-142C-4433-B4A3-A8BAB0242919(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Daniel, > You can add or subtract maps to make a new map using the "vop" command: > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html> > > That command has various other filtering and scaling options that may also > be of interest. You can save the new map to a file using the Volume Viewer > dialog (its File menu) or the "volume" command. > > 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 Aug 1, 2012, at 6:58 PM, Daniel Murin wrote: > > > Hi, > > I was wondering if it is possible to combine two mrc volumes into a > single volume and save that as a new mrc file? I haven't really been able > to find anything and I suspect that this may not be possible with Chimera. > > Thank you for your help, > > Daniel > > > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Aug 2012 10:07:18 -0700 > From: Tom Goddard <goddard(a)sonic.net> > To: Daniel Murin <cmurin(a)scripps.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] combining mrc maps > Message-ID: <501AB3C6.2050900(a)sonic.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Daniel, > > Yes, just add the two map with the volume operation command > > vop add #1,2 > > This will extend the grid of map #1 to cover map #2 then interpolate map > #2 on that grid and add it. You may also want to scale the values of > one map so that the two maps have comparable density ranges using the > "scaleFactors" option. > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#add > > Tom > > > > Hi, > > > > I was wondering if it is possible to combine two mrc volumes into a > single volume and save that as a new mrc file? I haven't really been able > to find anything and I suspect that this may not be possible with Chimera. > > > > Thank you for your help, > > > > Daniel > > > > > > > > Charles Daniel Murin > > Graduate Student - Ward/Ollmann-Saphire Labs > > Department of Molecular Biology > > Kellogg School of Science and Technology > > The Scripps Research Institute > > 10550 North Torrey Pines Road, CB 227 > > La Jolla, CA 92037 > > > > > > ------------------------------ > > Message: 4 > Date: Thu, 02 Aug 2012 20:00:51 +0200 > From: "Marek Maly" <marek.maly(a)ujep.cz> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] double bonds visualization ? > Message-ID: <op.wifdnpi4lc8gdf(a)pocitadlon.ujep.cz> > Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes > > Hello, > > I am just curious if it is possible to visualize double bonds > as double bonds now similarly like in case of rings one > can visualize them nicely (aromatic ring/disc). > > Thanks for the info in advance, > > Best wishes, > > Marek > > > -- > Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: > http://www.opera.com/mail/ > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 112, Issue 2 > ********************************************* >

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(no subject)
by Merced Malabanan 06 Aug '12

06 Aug '12

Hi, I'm trying to get used to the new Rapid Access interface of chimera. But how do you remove the list (or items on the list) on the right side of the interface? Thanks.

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SASA vs. MSA
by Nikolay Igorovich Rodionov 05 Aug '12

05 Aug '12

Hi all, I was wondering if you could help me conceptualize what is going on in this situation. I ran both solvent accessible surface area and solvent excluded (molecular) surface area calculations. When I compared the output for both of these calculations I found that, overall, atoms that contribute to the SASA are buried 1-3 angstroms deeper in the protein than those that contribute to the MSA. I don't really understand how this could be unless the deeper buried SASA atoms have a much larger van der waals radii than MSA atoms (I get that some atoms contribute to both). Thanks!

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trajectory rmsd
by George Tzotzos 03 Aug '12

03 Aug '12

I'm writing to find out if it is possible to determine the rmsd of specific residues, say 20-120 (backbone atoms only) from a trajectory against the corresponding residues of an X-ray structures. I used the Movie tool to load the trajectory having loaded prior to it the reference structure. I couldn't find a way to compute what I described above. Your help as always is much appreciated Best regards George

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Inifinite lattice minimisation
by Kyle Morris 03 Aug '12

03 Aug '12

Dear all, I am trying to do minimisations on a crystal system. I wonder if when chimera knows the unit cell will it minimise as an infinite lattice or do the copies need to be explicitly created before minimisation proceeds? Really appreciate any help/insight. Best wishes, Kyle

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combining mrc maps
by Daniel Murin 02 Aug '12

02 Aug '12

Hi, I was wondering if it is possible to combine two mrc volumes into a single volume and save that as a new mrc file? I haven't really been able to find anything and I suspect that this may not be possible with Chimera. Thank you for your help, Daniel Charles Daniel Murin Graduate Student - Ward/Ollmann-Saphire Labs Department of Molecular Biology Kellogg School of Science and Technology The Scripps Research Institute 10550 North Torrey Pines Road, CB 227 La Jolla, CA 92037 Work: 858.784.9053 Fax: 858.784.8218 email: cmurin(a)scripps.edu

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double bonds visualization ?
by Marek Maly 02 Aug '12

02 Aug '12

Hello, I am just curious if it is possible to visualize double bonds as double bonds now similarly like in case of rings one can visualize them nicely (aromatic ring/disc). Thanks for the info in advance, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Re: [Chimera-users] FW: FW: problem in visualising metal- atoms in simulated
by Mahendra B Thapa 31 Jul '12

31 Jul '12

Dear Dr. Elaine, May I send my pdb file? I could not fix the problems; I tried my best as far as I can , with possible alternatives. Thanks, Mahendra Thapa University of Cincinnati On Mon, Jul 30, 2012 at 12:58 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Monday, July 30, 2012 10:58:32 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] FW: problem in visualising metal- atoms in > simulated > > The atom names of the ions should not be lined up with the other names, > and the last field should be CA not C. So there are at least two problems > with these lines. Please see the format description in the link in my > previous message. > > Some additional problems are that the ion lines should probably be HETATM > not ATOM, and the names CA not CO. So I would fix those things too. > Best, > Elaine > > On Jul 30, 2012, at 9:46 AM, Mahendra B Thapa wrote: > > > Dear Dr. Elaine, > > > > The last few lines of the file are as follows: > > ATOM 1212 OXT GLN 76 17.333 31.515 17.211 1.00 0.00 > O > > TER > > ATOM 1213 CO CAL 77 35.029 27.971 38.126 1.00 0.00 > C > > TER > > ATOM 1214 CO CAL 78 37.868 20.307 30.270 1.00 0.00 > C > > TER > > > > I also tried with Ca instead of C in the last column , but no > improvement. > > > > Thank you for help, > > Mahendra Thapa > > University of Cincinnati > > > > > > On Mon, Jul 30, 2012 at 12:34 PM, Thapa, Mahendra (thapamb) < > thapamb(a)mail.uc.edu> wrote: > > > > > > > > ________________________________________ > > From: Elaine Meng > > Sent: Monday, July 30, 2012 10:34:51 AM (UTC-06:00) Central America > > To: Thapa, Mahendra (thapamb) > > Cc: chimera-users(a)cgl.ucsf.edu > > Subject: Re: [Chimera-users] problem in visualising metal- atoms in > simulated > > > > Hi Mahendra, > > Probably the format is slightly wrong for the lines with the calcium ion > coordinates. For example, the name CA for the calcium ion should *not* line > up with the name CA in the protein alpha-carbon lines. > > > > In the ATOM and HETATM lines of PDB files, > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coo… > > > > > > ...the ion name CA should be in columns 13-14, whereas the alpha-carbon > name CA should be in columns 14-15. > > > > Misalignment of ion names is a common problem with the output of many > programs. > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#mis… > > > > > > 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 Jul 30, 2012, at 9:21 AM, Mahendra B Thapa wrote: > > > > > Dear Chimera Users, > > > I converted amber-12 generated rst-file in netCDF format [ > test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the > cpptraj command of amber 12. When I loaded it in chimera, the protein > structure looks fine but two calcium atoms that the protein binds could > not be visualised, although the pdb file-format looks good. > > > Let me help in this respect. > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Unable to visualize density maps
by Anindito Sen 30 Jul '12

30 Jul '12

Dear All, With the latest Chimera version in Daily Build for Mac , I am unable to visualize any density map in the "surface" and the "mesh" mode. On playing around trying to visualize the density maps I get something like the following attached figure. However I can see the maps at the "solid" mode. I am using Snow Leopard 10.6.8. Best Andy Versions Not Working: Mac OS X chimera-alpha-mac.dmg Size: 105982078 bytes MD5: ba098e1169a7fb37f9b80bbac27cae26 Jul 28, 2012 Mac OS X 64-bit chimera-alpha-mac64.dmg Size: 93344817 bytes MD5: 22700ce0b2b0272d3efe060832933ee5 Jul 28, 2012 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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ff dat file
by Nikolay Igorovich Rodionov 30 Jul '12

30 Jul '12

Hi, since I am able to implement various force fields, does that mean that I have the .dat files of those ff buried somewhere in my chimera directory? I want to add my custom ff parameters to PDB2PQR so I need to locate the .dat files of force fields like Amber12 and Amber99SB. Thank you, Nikolay Rodionov

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Re: [Chimera-users] FW: problem in visualising metal- atoms in simulated
by Mahendra B Thapa 30 Jul '12

30 Jul '12

Dear Dr. Elaine, The last few lines of the file are as follows: ATOM 1212 OXT GLN 76 17.333 31.515 17.211 1.00 0.00 O TER ATOM 1213 CO CAL 77 35.029 27.971 38.126 1.00 0.00 C TER ATOM 1214 CO CAL 78 37.868 20.307 30.270 1.00 0.00 C TER I also tried with Ca instead of C in the last column , but no improvement. Thank you for help, Mahendra Thapa University of Cincinnati On Mon, Jul 30, 2012 at 12:34 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Monday, July 30, 2012 10:34:51 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] problem in visualising metal- atoms in > simulated > > Hi Mahendra, > Probably the format is slightly wrong for the lines with the calcium ion > coordinates. For example, the name CA for the calcium ion should *not* line > up with the name CA in the protein alpha-carbon lines. > > In the ATOM and HETATM lines of PDB files, > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coo… > > > > ...the ion name CA should be in columns 13-14, whereas the alpha-carbon > name CA should be in columns 14-15. > > Misalignment of ion names is a common problem with the output of many > programs. > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#mis… > > > > 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 Jul 30, 2012, at 9:21 AM, Mahendra B Thapa wrote: > > > Dear Chimera Users, > > I converted amber-12 generated rst-file in netCDF format [ > test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the > cpptraj command of amber 12. When I loaded it in chimera, the protein > structure looks fine but two calcium atoms that the protein binds could > not be visualised, although the pdb file-format looks good. > > Let me help in this respect. > > > >

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problem in visualising metal- atoms in simulated
by Mahendra B Thapa 30 Jul '12

30 Jul '12

Dear Chimera Users, I converted amber-12 generated rst-file in *netCDF format* [ test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the cpptraj command of amber 12. When I loaded it in chimera, the protein structure looks fine but two calcium atoms that the protein binds could not be visualised, although the pdb file-format looks good. Let me help in this respect. Thanks, Mahendra Thapa University of Cincinnati

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Coulombic Potential Dielectric
by Nikolay Igorovich Rodionov 26 Jul '12

26 Jul '12

Hi, I just have a question about the default dielectric coefficient in the Coulombic surface coloring function. Does the coefficient of 4 correspond to the dielectric of the solvent or the solute (the biomolecule)? I think the latter makes more sense but I just want to make sure. Thanks! Nikolay Rodionov

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Pot.dx to cartesian
by Nikolay Igorovich Rodionov 26 Jul '12

26 Jul '12

Hi all, I was wondering if anyone knows of a program that can take the gridpoint potential matrix from the APBS output pot.dx file and convert it into Cartesian coordinates. Something like: X Y Z Potential 545 5 54 +2.5484 Thanks! Nikolay Rodionov

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how do I open RMF files in chimera on Mac?
by Khuri, Natalia 26 Jul '12

26 Jul '12

Natalia Khuri PhD Student, Graduate Group in Biophysics Laboratory of Andrej Sali UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA

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