- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues
by Elaine Meng 08 Mar '11

08 Mar '11

On Mar 8, 2011, at 1:03 PM, Ingmar Buerstel wrote: > Dear Elaine, > thanx a lot for your quick answer. In fact I have already a modelled structure (made with swiss model) of the protein. > I was looking for a possiblitiy to fit a 4Fe4S-cluster in the position of the original cluster. The cysteines are conserved, thus, I just need to copy/paste the 4Fe4S-cluster into my structure. I would be glad, if you could help me concerning this problem. Dear Ingmar, You could superimpose your model and the related structure that does contain this cluster (residue SF4) and then merge the SF4 residue into your model. However, the result may be rough, depending on how well the structures match in 3D. It might be better to start over and use Modeller as described in my previous message, because it can make a model that already includes the cluster. However, if you want to try the superimposing approach, here are more details. (a) In Chimera, open your model and then open the known related structure that contains the cluster. (b) Superimpose the two structures, for example with the Matchmaker tool. Here is some discussion of different ways to superimpose structures in Chimera. You will want to make sure that the structures match well at the four cysteines. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (c) Delete everything in the known structure except for the part you want to paste into your homology model, and then combine the two models into one. For example, if your model is open as #0 in Chimera and the known structure is open as #1, you could use commands delete #1 & ~:sf4 combine #0,1 The delete command gets rid of all atoms in #1 except the SF4 residue. The combine command creates a new model, #2, by merging the SF4 residue in #1 with the homology model in #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> You can save the new model #2 to a file (for example, with File... Save PDB). However, you would hope that the cysteine sidechains in your model are pointing in the correct orientations to bind the cluster. If not, you might have to paste in those residues from the known structure too, and delete them from your homology model, before merging. Then you might have to manually text-edit the PDB to add bonds between the merged cysteines and the rest of the homology model. Again, it might be better just to start over and use a modelling method that can include the cluster in the first place. 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 > > > > Subject: Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues > > From: meng(a)cgl.ucsf.edu > > Date: Mon, 7 Mar 2011 09:38:45 -0800 > > CC: chimera-users(a)cgl.ucsf.edu > > To: ingmar_b(a)hotmail.com > > > > Dear Ingmar, > > It sounds like you want to model your whole protein including the 4Fe4S cluster, am I right? Or is there a structure of your protein but that does not include the cluster? > > > > I would not recommend modeling this "from scratch" (building one atom by one atom) in Chimera but instead, homology-modeling your protein and cluster from the structure of a related protein that contains the cluster. Of course, this all depends on the existence of a known structure for a related protein. > > > > Chimera includes an interface to the Modeller program for homology-modeling. To use it, you would have to first go to the Modeller website > > <http://www.salilab.org/modeller/registration.html> > > and register to get a license key (free for academic use). In Chimera, you could choose "Tools... Sequence... Blast Protein," paste in the sequence of your protein, and then blast it against the PDB to see if there are any structures related to your protein. If there is a hit that seems good enough to you, you could use the Blast results dialog to open the structure and also the alignment of the two sequences. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/blast.html> > > Then, in the sequence alignment window, choose "Structure... Modeller Tools" to show the interface to Modeller. Use "Advanced Option" to "Include non-water HETATM residues from template" so that the FeS cluster will be included in the model. > > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> > > > > Or, you could simply see if there is already a model of your protein available in ModBase by using "File... Fetch by ID" in the Chimera menu. However, those models probably wouldn't contain the FeS cluster. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html> > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html> > > > > Some related references I just saw but didn't read in detail: > > > > Fee, J. A.; Castagnetto, J.M.; Case, David A.; Noodleman, L.; Stout, C.D.; Torres, R.A.; "The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters". J. Biol. Inorg. Chem. 2003, 8: 519-526. > > <http://dx.doi.org/10.1007/s00775-003-0445-8> > > > > Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein. > > (2002) J.Mol.Biol. 315: 1155-1166 > > <http://dx.doi.org/10.1006/jmbi.2001.5292> > > (goes with PDB entries 1iqz, 1ir0 ... I see that the residue name of the cluster is SF4, so you could also use the searching tools at the PDB website to find structures that have this cluster) > > > > I hope this helps, > > Elaine > > > On Mar 6, 2011, at 6:44 AM, Ingmar Buerstel wrote: > > > Dear users, > > > i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. > > > > > > So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster > > > Thanx in advance, > > > Ingmar > >

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Searching chimera-users archive
by Tom Goddard 08 Mar '11

08 Mar '11

Hi Conrad, Searching the Chimera mail archives from the Chimera documentation web page does not work at all well. http://www.cgl.ucsf.edu/chimera/docindex.html I tried searching for "Beale" and it produced no results. > Your search - *Beale site:www.cgl.ucsf.edu/pipermail/chimera-users > -filetype:gz* - did not match any documents. > > Suggestions: > > * Make sure all words are spelled correctly. > * Try different keywords. > * Try more general keywords. > * Try fewer keywords. > There is a message in August 2010 from John Beale. If I search for that message using www.google.com (chimera "startup options" John Beale) I do get the message. So it has been indexed. Some other revealing problems. Searching the Chimera archives from the documentation page for "chimera" produces only 20 hits, all but 5 are attachments. Likewise a search for "windows" produces just 4 hits (one from 2005, one 2006, one 2007, one 2010). Obviously this isn't working. Maybe we should remove the search field from the documentation until we have time to fix it because users (even ones who should know better like me) sometimes believe the search results that there are no archived messages on the topic. Tom > On Mar 8, 2011, at 10:58 AM, Tom Goddard wrote: > >> Hi Eric, >> >> How do I reply to an old chimera-users message and keep my reply in >> the same mailing list thread? I guess there is some mail header line >> that allows the mailing list to recognize which messages belong to >> the same thread. But I don't have the old chimera-users email I want >> to reply to. The web interface to the archive doesn't appear to >> provide a way to reply. > > Well, I don't know for sure, but I assume it is threaded based on the > In-Reply-To header and/or the References header. Now, the archive > doesn't show you either of those so I assume they're buried in some > internal location, so you're stuck. Besides, threading is broken > across month boundaries anyway, so isn't the point moot really? > > --Eric >

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saving charmm layout
by Francesco Pietra 07 Mar '11

07 Mar '11

Hello: Is it possible to save pdb conserving as much as possible charmm layout (in particular the segments (P1, P2, etc)? I find speedy to edit graphically with Chimera but, afterward, much time is required to restore charmm layout. thanks francesco pietra

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How to model a 4Fe4S cluster on conserved Cys residues
by Ingmar Buerstel 07 Mar '11

07 Mar '11

Dear users, i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster Thanx in advance, Ingmar

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question on volume viewer usage
by Bala subramanian 04 Mar '11

04 Mar '11

Friends, I am using chimera version 1.5 (build 31401 downloaded on 2010-09-16). I have three pdb files (of same protein) and for each pdb file, i have an electro static potential file (.dx file). I opened the three pdb files and then the .dx potential files successively through volume viewer. Each time i open the .dx file, the isosurfaces are mapped on to the first pdb file. Why is it so ?. 1) Precisely 1.dx should be mapped on 1.pdb, 2.dx on 2.pdb...etc. How can i do this ? 2) Is there any way to have a universal setting of volume display options. Like in isosurface threhold (+2 and -2 in my case), color for +ve and -ve surface, transparency etc. Because presently i am doing these settings individually for each .dx file. Thanks, Bala

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1 out of many helices shown as pipe
by odonnell＠chem.fsu.edu 03 Mar '11

03 Mar '11

Hi all, I have a pdb with many alpha helices but I only want one or two to stand out as a pipe. I tried highlighting that particular sequence(s) and going to Depiction => pipesAndPlanks but it will change all of them. Many thanks for a push in the right direction. -Jason ------------------------------------------------------------------------- Sent via webmail for Chemistry & Biochemistry @ Florida State University https://webmail.chem.fsu.edu -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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ambient lighting mode for simple drawing style missing
by Benda, Christian 03 Mar '11

03 Mar '11

Hi possibly a simple question but it has kept me buffled for two weeks now, so I decided to ask: how can I set lighting mode to ambient? I am trying to create images using a simple drawing style like exemplified in http://www.cgl.ucsf.edu/chimera/ImageGallery/ p53 simple drawing or Clathrin but I don't find ambient lighting mode in the viewing tools - lighting menu. The only options given are lights (head light, 1, 2) or quality (normal, glossy). I am using Chimera 1.5 build 30417 fir darwin 64bit, aqua on a MacBook Pro with Mac OS X 10.6.6. Many thanks in advance Christian ________________________________ Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: benda(a)biochem.mpg.de

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Re: [Chimera-users] Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 02 Mar '11

02 Mar '11

Thank you, I had missed the settings on that other place. Now it works quite well. (barring some issues with external monitor) I also noticed that overlay setting in same menu should be on or whole desktop would get blurry (with or without stereo glasses on). -vpk On 3/1/11 10:36 PM, Greg Couch wrote: > If both Chimera and PyMol are complaining, then you've haven't > configured OpenGL stereo correctly. The NVidia Quadro driver > configuration has two places to setup stereo. There are the > "Stereoscopic 3D" settings that are not helpful for chimera (except for > making NVIDIA's stereo image viewer work). So in addition to that, you > want to setup stereo in the "3D Settings / Manage 3D Settings" dialog. > In there, turn on "Stereo - Enable" and select the appropriate kind of > stereo in "Stereo - Display mode". > > Good luck, > > Greg > > On 02/28/2011 09:11 PM, Veli-Pekka Kestilä wrote: >> >> I have done all of these and as I said in my original e-mail I got the >> full screen tests nvidia provides working. Problem is that when I try to >> start Chimera or PyMol it fails complaining that 3d vision mode isn't >> available. So question still basically is if it's possible to get it >> working with Quadro 880M >> >> On 2/23/11 4:40 PM, Sabuj Pattanayek wrote: >>> also see : >>> http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#NVidia_NVision… >>> >>> . It has some instructions on how to setup 3d vision on windows. >>> >>> On Wed, Feb 23, 2011 at 8:36 AM, Sabuj Pattanayek<sabujp(a)gmail.com> >>> wrote: >>>> IIRC there's an option in the windows nvidia configuration utility >>>> that enables and disables nvidia 3d vision. I assume that's the setup >>>> you're trying to use, so check that to see if it's enabled or >>>> disabled. >>>> >>>> 2011/2/23 Veli-Pekka Kestilä<veli-pekka.kestila(a)helsinki.fi>: >>>>> Hi Tom, >>>>> >>>>> On 2/22/11 8:12 PM, Tom Goddard wrote: >>>>>> Hi Veli-Pekka, >>>>>> >>>>>> This is either a driver configuration problem or driver limitation or >>>>>> driver bug. Your driver is from Oct 2010 and there are newer ones. >>>>>> The >>>>>> following 266.58 driver was released Jan 18, 2011 and the notes >>>>>> say it >>>>>> adds support for various "3d vision notebooks". Maybe the new >>>>>> driver is >>>>>> needed. >>>>>> >>>>>> http://www.nvidia.com/object/notebook-win7-winvista-64bit-266.58-whql-drive… >>>>>> >>>>> I installed back the newest driver and problem still persist. So it's >>>>> problem either with driver or the card. >>>>> 880M isn't very high end on the Quadro Cards. >>>>> >>>>>> If it is a driver configuration problem, I don't know about that. Our >>>>>> expert on stereo and Windows is on vacation this week but can >>>>>> advise you >>>>>> next week. >>>>> Seems that I will be waiting for that. Thank you for your reply. And >>>>> hope to hear from you next week. >>>>> >>>>> -vpk >>>>> >>>>>> Tom >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I have problem with Nvidia Quadro FX 880M and Stereoscopic view. >>>>>>> When I >>>>>>> switch the stereoscopic view on in Chimera it gives me following >>>>>>> error: >>>>>>> >>>>>>> stereo viewing (Unable to find hardware stereo support >>>>>>> (couldn't choose pixel format >>>>>>> Couldn't configure togl widget)). >>>>>>> >>>>>>> I have installed the Quadro drivers version 259.57 in Windows 7 >>>>>>> 64bit. >>>>>>> And separate 3D driver for Quadro. >>>>>>> >>>>>>> Greetings, >>>>>>> Veli-Pekka Kestilä >>>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> University of Helsinki / Institute of Biotechnology / >>>>> veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, >>>>> Biocenter 3 >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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odd output from surfnet
by Irene Newhouse 02 Mar '11

02 Mar '11

I'm trying to get an image of channels in the attached protein. It's actually a dimer, & the surfaces looked bizarre for the dimer, so I thought maybe surfnet was choking on the repeated residue numbers when you use chain ID, so I clipped it down to the monomer. That' still odd. I've attached a png of the result, using the defaults, & the pdb file of the monomer. What am I doing wrong? Is there a way to get the n largest channels, instead of all of them? Thanks! Irene Newhouse

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morph problem
by Andres Palencia 02 Mar '11

02 Mar '11

Dear Chimera Users, I am trying to morph the complex1 and complex2 from the same system (protein-RNA) to make a video monitoring the conformational changes. As complex 1 is missing one domain and a helix (not visible in the crystal structure), I need to remove these parts in complex 2 to have an equal number of atoms in both complex and could morph it. The resulting video is not so nice because shows the gaps corresponding to the missing part. So, to avoid that, I have modelled the missing part in the complex 1 to have the same atoms, and afer morph it again to make the video, but this is not working. In the transition between complex 1 and complex 2, the RNA encounter one helix on the way that needs to move out to let the RNA to get the position observed in complex 2. If I take out this helix, the video can perfectly be done, but still is not perfect because show gaps. Anybody could give an idea in how to solve the problem? We need the video to include in a publication,. Thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: palencia(a)embl.fr phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/

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3-D
by Jason Bouvier 02 Mar '11

02 Mar '11

Hi, how do I view proteins in 3-D in Chimera? And would I use standard 3-D glasses or are special ones required? I viewing in stereo with some old 3-D glasses that I had around but to no avail. Thank you. Cordially, Jason Bouvier Jason Bouvier | Graduate Student, <http://mcb.illinois.edu/departments/biochemistry/> Biochemistry | <http://www.life.illinois.edu/gerltlab/research.html> Gerlt Lab | <http://www.igb.illinois.edu/> Institute for Genomic Biology | Rm 3200 | <http://illinois.edu/> University of Illinois at Urbana-Champaign | 1206 W. Gregory Dr. | MC-195 | Urbana, IL 61801 | office 217.333.2673 | lab 217.333.2699 | <mailto:jbouvier@illinois.edu> jbouvier(a)illinois.edu

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Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 01 Mar '11

01 Mar '11

Hello, I have problem with Nvidia Quadro FX 880M and Stereoscopic view. When I switch the stereoscopic view on in Chimera it gives me following error: stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I have installed the Quadro drivers version 259.57 in Windows 7 64bit. And separate 3D driver for Quadro. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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chimera ?
by Alexander Spyros Maris 01 Mar '11

01 Mar '11

Hi, I was attempting to start part of the tutorial by fetching "1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this? Thanks! -- Alex Maris

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Internal water molecules
by Beale, John 28 Feb '11

28 Feb '11

Hello, Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation. Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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hem group
by "dr. R�szer Tam�s" 28 Feb '11

28 Feb '11

Hello, I would like to add HAEM group to a protein reconstructed from pdb data. I am working on Windows platform. Could you please help me how can I do that? many thanks Tamas

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How to
by M. Amin Arnaout 28 Feb '11

28 Feb '11

I am running Cimera 1.5.2 on Mac. I am now unable to show a cabonyl O, N or CA of a residue while ribbon is also displayed. Could do that in the earlier version. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Chimera-users] [chimera-dev] clashes and contacts with hidden models
by Elaine Meng 28 Feb '11

28 Feb '11

On Feb 28, 2011, at 5:28 AM, Elisabeth Ortega wrote: > > I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? > Hi Elisabeth, With either the graphical interface of Find Clashes/Contacts or the command findclash, you can specify which two groups of atoms to examine for clashes. The remaining atoms will be ignored. I believe it doesn't matter whether the atoms are displayed or active. With the command, it would be something like findclash #1 test #2 [other options] Another example: findclash ligand overlap -0.4 hb 0 test aromatic Use command "help findclash" to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> With the GUI, the procedure is slightly different: you would select one group (say #1), click Designate, choose option "second set of designated atoms", select the second group (say #2), click "Designate selection as second set", Apply. Click the Help button to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas…> This is more of a chimera-users(a)cgl.ucsf.edu question (how to use Chimera) than chimera-dev (programming related to Chimera), so I'm also CC-ing the former list. 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

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suggestion: sym option
by Dougherty, Matthew T 25 Feb '11

25 Feb '11

add an SYM command option to specify the model number of the resulting model Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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morph shape/bild objects
by Do-Nyun Kim 25 Feb '11

25 Feb '11

Hello, I'm using shapes in bild format to make spheres and cylinders in Chimera. Is there a way of morphing these shapes, spheres in one conformation to spheres in another conformation? Thanks you. Best regards, Do-Nyun Kim.

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Chain/Structure ID as label
by Berhane Temelso 25 Feb '11

25 Feb '11

Hi, I often read in 1-30 hydrogen-bonded molecular clusters from XYZ files and tile them for analysis. It would be great to label each cluster/model with its chain ID or file name. Labeling them using the 2Dlabel command is inconvenient especially when I have a large number of models. Is there an easy way of doing this? Thanks in advance. Berhane

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Inter-helical angle?
by Brian Cannon 24 Feb '11

24 Feb '11

I need to calculate the angle between two helices in a protein. Do you have any instruction about how I could go about doing this? Any help would be greatly appreciated. Thanks! Brian

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color key creation
by Bala subramanian 23 Feb '11

23 Feb '11

Friends, I am using chimera version 1.5 (build 31401 downloaded on 2010-09-16). I have opened two pdb files A and B. I also opened two attribute files corresponding to A and B and colored the ribbon based on the attribute. I want something like the following A B Colorkey 1 Colorkey2 My problem is creating the individual Colorkey. I chose model A (in the Depiction-> render by attribute -> create color key ) and created Colorkey1. When i did the same for model B and use my mouse for colorkey2 creation. Colorkey1 is deleted and Colorkey2 is created below the model B. Is it a bug. Precisely, if i hve to create two Colorkeys corresponding to two different models, how can i do that ? Thanks, Bala

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X,Y,Z coordinates in GUI
by Sujata Sovani 23 Feb '11

23 Feb '11

Wondering if it is possible to see the X,Y,Z coordinates of a particular atom in the GUI using a command? Thanks, Sujata

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need coordinates from volume data
by Terry Lang 23 Feb '11

23 Feb '11

Hey Everyone, I'm am trying to do some unorthodox analysis of volume data using a script. As part of the analysis, I need to access the x,y,z coordinates of each of the points of a ccp4 map. How would I go about that in Chimera scripting once the data is read in? Thanks, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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Displaying double-bonds of small molecules
by Rocco Varela 23 Feb '11

23 Feb '11

How do I display double-bonds of small molecules in Chimera?

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