- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Re: stereo viewing on Windows
by Eric Pettersen 12 Sep '05

12 Sep '05

Hi Virginia, Another thing to note is that in the target field, the path to the Chimera executable is embedded in double quotes (e.g. it is something like: "C:\....\chimera.exe"). To add the --stereo option, you need to add it outside the ending double quote and separated by a space, like this: "C:\...\chimera.exe" --stereo . Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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phi psi angles
by Zenon Grabarek 12 Sep '05

12 Sep '05

Hello, I am looking for a script that would allow me to change the phi psi angles in a selected residue (allowing the C-terminal part of the chain to move) and output the coordinates. Chimera has a very nice interactive tool to do that, but I need to do it systematically in small increments over a specified range of angles. I would be grateful for any help in this matter. Zenon Grabarek Ph.D. Boston Biomedical Research Institute 64 Grove St. Watertown MA 02472 tel: 617-658-7805 email: Grabarek(a)BBRI.org

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Re: stereo viewing on Windows
by Virginia B. Pett 09 Sep '05

09 Sep '05

We have windows XP machine in one of our labs. The machine is running chimera. We want to run chimera in stereo mode on this machine. as per the documentation, create a shortcut of chimera on the desktop and then append "--stereo" options in target mode. But target mode does not recognize this. Which file helps start the stereo mode on windows machine, so that i can put that file path in target? ________________________________________ Virginia B. Pett Professor of Chemistry Department of Chemistry, The College of Wooster 943 College Mall, Wooster, OH 44691 Telephone: 330-263-2114 Fax: 330-263-2386 On Sep 7, 2005, at 3:00 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://www.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. creating a symmetric tetramer from a PDB file for a monomer? > (gtseng(a)mail2.vcu.edu) > 2. Re: creating a symmetric tetramer from a PDB file for a > monomer? (Elaine Meng) > 3. Visualizing Electrostatic Potential of *.grd format? > (Anna Feldman-Salit) > 4. Re: Visualizing Electrostatic Potential of *.grd format? > (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 06 Sep 2005 15:53:41 -0400 > From: <gtseng(a)mail2.vcu.edu> > Subject: [Chimera-users] creating a symmetric tetramer from a PDB file > for a monomer? > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <200509061953.PAA18668(a)despina.vcu.edu> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Chimera creators: > Could you please let me know whether it is possible to create a > tetramer structure with 4-fold symmetry from a PDB file for a monomer? > Specifically, I want to create a structure of a voltage-gated K > channel which has 4 monomers surrounding a central pore symmetrically, > beginning with the PDB file for a monomer. There is no 'transformation > matrix' in the PDB file to allow me to create the tetramer easily. > Thank you very much for your help! > > Gea-Ny Tseng > > ------------------------------ > > Message: 2 > Date: Tue, 6 Sep 2005 13:48:50 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] creating a symmetric tetramer from a PDB > file for a monomer? > To: <gtseng(a)mail2.vcu.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <7485CA73-9B1A-492C-9F71-FB36FBF5B103(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hello Gea-Ny, > The Chimera features that generate multimers (the tools Unit Cell > and Multiscale Models) all use matrix information in the PDB file. > Multiscale Models uses BIOMT, MTRIX, SMTRY, and/or CRYST1 records, > and Unit Cell uses MTRIX, SMTRY, and/or CRYST1. > > It sounds like you don't have any of those in your PDB file. > > You could either > (A) figure out what information should be in such a matrix line > and edit it into your file before using one of the Chimera tools, > or > (B) open four copies of your monomer and try to position them > by hand. If you know what the axis of rotation should be, you > can use Constrained Move (Tools... Movement... Constrained Move > in recent versions) to define and use an axis of rotation. > http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ > constrained/constrained.html > > Neither of these is very easy, but I don't know of any way to > automatically position the monomers without the matrix information. > It sounds like BIOMT (REMARK 350) records would be the most > appropriate. Even with an appropriate example, you would still > have to change the values. > > REMARK 350 is described at the PDB web site (you have to scroll > down to get to the description of REMARK 350): > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_31.html > > Here is an example from 1fav (threefold): > REMARK 350 > REMARK 350 BIOMOLECULE: 1 > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 > REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 > REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.81900 > REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 > REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 > REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 17.90950 > REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.02016 > REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On Sep 6, 2005, at 12:53 PM, <gtseng(a)mail2.vcu.edu> wrote: > >> Dear Chimera creators: >> Could you please let me know whether it is possible to create a >> tetramer structure with 4-fold symmetry from a PDB file for a monomer? >> Specifically, I want to create a structure of a voltage-gated K >> channel which has 4 monomers surrounding a central pore symmetrically, >> beginning with the PDB file for a monomer. There is no 'transformation >> matrix' in the PDB file to allow me to create the tetramer easily. >> Thank you very much for your help! >> >> Gea-Ny Tseng >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > ------------------------------ > > Message: 3 > Date: Wed, 07 Sep 2005 13:14:05 +0200 > From: Anna Feldman-Salit <anna.feldman-salit(a)eml-r.villa-bosch.de> > Subject: [Chimera-users] Visualizing Electrostatic Potential of *.grd > format? > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <431ECB7D.8090203(a)eml-r.villa-bosch.de> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Dear All, > > I would like to ask you a question regarding the visualization of > electrostatic potential on msms. For this purpose, of course, I need a > readable format for Potential Map. > In the past I used to work with DelPhi for potential calculations and > then visualize the outputted *.14 file by Chimera. > Today I calculate potentials by using UHBD program, while output files > are saved in /phi/ format with .grd extension (could be written either > in binary or ascii form). > Unfortunately, the Chimera doesn't recognize this format. > > Dear Chimera users, do you know the way to convert the *.grd files to > the *.phi ones readable by Chimera, or any other trick? > I can't recalculate the potentials by DelPhiController, because I have > only one dat-file for both radii sizes and charges (it also doesn't > work > in the simple way). > > I'd very appreciate any help of yours! > > Yours sincerely, > > Anna. > > ------------------------------ > > Message: 4 > Date: Wed, 7 Sep 2005 09:16:40 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Visualizing Electrostatic Potential of > *.grd format? > To: Anna Feldman-Salit <anna.feldman-salit(a)eml-r.villa-bosch.de> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <6902E794-4AAB-438D-A8D8-FB8E8849D7D6(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Anna, > Actually, Chimera does read UHBD grids, the binary version. The older > approach to displaying potential on a surface, DelPhiViewer, is being > phased out in favor of the newer and more general tool, Surface Color > (Tools... Surface/Binding Analysis... Electrostatic Surface Coloring > or Tools... Volume Data... Surface Color both open this tool). > > Surface Color can color surfaces based on any of the volume data (3D > grid) formats that can be read by Volume Viewer (which include UHBD > binary): > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ > volumeviewer.html#formats > > Surface Color is relatively new. It is available in the snapshots > 1.2154 (linux, mac) and 1.2143 (windows). It is also available in > 1.2105, but I don't recommend using that one because we have made it > easier to use in the more recent snapshots. Here is the man page for > Surface Color in version 1.2154: > http://www.cgl.ucsf.edu/chimera/1.2154/docs/ContributedSoftware/ > surfcolor/surfcolor.html > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Sep 7, 2005, at 4:14 AM, Anna Feldman-Salit wrote: > >> Dear All, >> >> I would like to ask you a question regarding the visualization of >> electrostatic potential on msms. For this purpose, of course, I >> need a readable format for Potential Map. >> In the past I used to work with DelPhi for potential calculations >> and then visualize the outputted *.14 file by Chimera. >> Today I calculate potentials by using UHBD program, while output >> files are saved in /phi/ format with .grd extension (could be >> written either in binary or ascii form). >> Unfortunately, the Chimera doesn't recognize this format. >> >> Dear Chimera users, do you know the way to convert the *.grd files >> to the *.phi ones readable by Chimera, or any other trick? >> I can't recalculate the potentials by DelPhiController, because I >> have only one dat-file for both radii sizes and charges (it also >> doesn't work in the simple way). >> >> I'd very appreciate any help of yours! >> >> Yours sincerely, >> >> Anna. >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 29, Issue 5 > ********************************************

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Rotation Angle
by Huang, Zhong 07 Sep '05

07 Sep '05

Hi, dear chimera developers' I am a Chimera user of UT Medical school at Houston . Here I want to know how chimera rotates the loading structure. I wish to know what the rotation parameters mean? Which coordinate sysmtem they refere to? I check the on-line tutorial. Unfortunately, I didn't get the answer. Best Zhong Huantg

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[Chimera-users] Visualizing Electrostatic Potential of *.grd format?
by Anna Feldman-Salit 07 Sep '05

07 Sep '05

Dear All, I would like to ask you a question regarding the visualization of electrostatic potential on msms. For this purpose, of course, I need a readable format for Potential Map. In the past I used to work with DelPhi for potential calculations and then visualize the outputted *.14 file by Chimera. Today I calculate potentials by using UHBD program, while output files are saved in /phi/ format with .grd extension (could be written either in binary or ascii form). Unfortunately, the Chimera doesn't recognize this format. Dear Chimera users, do you know the way to convert the *.grd files to the *.phi ones readable by Chimera, or any other trick? I can't recalculate the potentials by DelPhiController, because I have only one dat-file for both radii sizes and charges (it also doesn't work in the simple way). I'd very appreciate any help of yours! Yours sincerely, Anna.

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Suggestion re Docking Results
by Philip Crawford 06 Sep '05

06 Sep '05

Hi. I like Chimera and hit a limit yesterday. (Windows version.) We are running DOCK using the ZINC databases, which produces very large output_scored.mol2 files. I tried using Chimera to open and sort one of these. After an hour, I killed Chimera. John Irwin suggested (via the Dock-fans list) that I recommend you set a limit on the size of output file to be opened. An alternative may be to set a limit on the number of records which will be read, regardless of file size. Thanks for a useful product. Cheers, Philip Crawford __________________________________________________ Philip Crawford, B. Comp. Sc., MIEEE Structural BioInformatics and Drug Design Group http://www.sbio.med.unsw.edu.au/sbio School of Medical Sciences The University of NSW Phone: +61-2-9385 2564 Mobile: +61-419-294 698 Fax: +61-2-9385 1059 Email: <mailto:p.crawford@unsw.edu.au> p.crawford(a)unsw.edu.au __________________________________________________

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changing the rendering of distanced dotted lines
by Boaz Shaanan 06 Sep '05

06 Sep '05

Hi, Distances between pairs of atoms are marked as dotted lines by the 'distances' panel. Is it possible to make those dots bigger by scaling them up somehow so that they are seen more clearly ? They obviously get larger when I zoom in but sometimes I'd rather stay in the zoom-out view but make the dots more visible. Please let me know. Thanks, Boaz

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[Chimera-users] Save pdb files only have 5 subunits at 5-fold at virus?
by Jason 04 Sep '05

04 Sep '05

Hi all Is it possible to save pdb files that only have 5 subunits at 5-fold after using mulitscale tools buliding virus paritle. And this pdb file can open at other programs too, ex: DeepView, PyMOL. When I use File/Save PDB chimera can save pdb file, but this file(model) only can show correctly at chinera. If I opened this file at PyMOL or DeepViewit only show the origional 3(A, B, C)chain model thanks Jason

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Using the Chimera Tutorial
by Gea-Ny Tseng 31 Aug '05

31 Aug '05

Dear Chimera creators: I am trying to learn how to use Chimera by using your on-line Tutorial. Is there a printable version of the Tutorial and User's Guide? I am not sure how to read the Tutorial and then try out the commands using one single monitor (that is all I have). Or did I miss something obvious? Your help is highly appreciated? Gea-Ny Tseng, PhD Physiology Virginia Commonwealth University

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helices display in latest snapshots
by Boaz Shaanan 30 Aug '05

30 Aug '05

Hello, I the latest snapshots (Windows 2143 and linux 2154) helices show up as thin worms when I ask for 'ribbons' under action (they used to look like nice ribbons in previous releases). I found the tools/depiction/ribbons display and managed somehow to change the look of the ribbons (still, they looked nicer before) but failed to change the look of the helices. Where can I do this now ? Thanks, Boaz

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[ViewDock] wrong bonds
by Aurelien GROSDIDIER 29 Aug '05

29 Aug '05

Hi all ! I'm currently trying to use the ViewDock plugin to visualize results coming from our in house docking program, which dumps PDB files. These PDBs are them transformed into in a DOCK3/DOCK4 compliant format. First, I should say I haven't seen a clear description of this format, and the script gathering together PDB files is very empirical. The problem I see might come from a mistake of our docking program. Urls to fock3/4 specifications are thus welcome :) Problem context: ---------------- The problem happens when dealing with ligands having several distinct residue numbers or if the docking coordinates do not consist only of a ligand, but also a set of sidechains of its receptor (also with distinct residue number). Problem symptoms: ----------------- The representation loaded using ViewDock show bonds between each and every atoms of the ligand (and the sidechains, if any), no matters their atom type or how far they are. This is kinda of weird, as the representation is perfect when these PDB are loaded from individual PDB files (not using ViewDock). I am a newbie on this mailing list, and unfortunately this problem should be solved withing a few days or so. I would like to apologize in advance in case this help request should go somewhere else. And in case you need a clearer description of the problem (with figures, input files and so on), feel free to contact me either directly or using the ML :) Thanks a lot for your help, Aurélien Grosdidier

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regarding coloring
by moumita dutta 24 Aug '05

24 Aug '05

Dear Sir, How can I use more than one color to highlight different area using the UCSF chimera software in a 3d refined model of a virus ? Regards, M.Dutta --------------------------------- Start your day with Yahoo! - make it your home page

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problems reading delphi phi map under XP
by Boaz Shaanan 24 Aug '05

24 Aug '05

Hello, When I try to read a delphi phi map under XP I get the error message: Return code: -2147483641 and the program exits. The same map would be read OK under linux and under Win2k. I'm using the latest win32 snapshot (the same happens with the official release though). I would appreciate if you could let me know what has gone wrong. Thanks, Boaz

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ATI catalyst 5.7 drivers with R9600SE video card crash winxp when creating surfaces (or running surface benchmark) in chimera-1.2143
by Sabuj Pattanayek 22 Aug '05

22 Aug '05

Hi, I had upgraded ATI's catalyst drivers from 5.4 (or 5.5) to 5.7 for my R9600SE video card under winxp sp2. In Chimera-1.2143 when I tried to create a surface representation or tried the surface benchmark the screen would go black (monitor led goes from green to orange) and the system would crash (no longer responds to pings). Downgrading to catalyst 5.6 fixed the problem. I sent a trouble ticket to ATI. Has anyone had a similar problem with Radeon (non-firegl) cards? Thanks, Sabuj Pattanayek

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Re: [chimera-dev] accelerators and stereo
by Eric Pettersen 18 Aug '05

18 Aug '05

Hi Justin, Chimera doesn't have a function to directly save a stereo image. Instead, what you do is save separate left-eye and right-eye images and place them appropriately in your presentation or paper -- for a cross-eye image that would be the left-eye on the right and vice versa. You save the images by bringing up the Side View (under Favorites) and clicking on the "Camera" tab. There is a "camera mode" menu under that tab that lets you select left-eye/right-eye views. Then just use the regular image-saving process. This is also described in the Images tutorial (near the end): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html We want to make this easier to do but haven't gotten to it yet. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Aug 18, 2005, at 7:06 AM, Justin Wu wrote: > Hi > Would you please let me know how to make a cross-eye figure from > Chimera? I do not where to look for this function. > Thanks > Justin > ************************************************ > Justin Wu > Rm 752, Biological Science Building > 484 West 12th Ave, > Columbus, OH 43210 > Tel: (614)247-5040, Fax: (614)292-6773 > ************************************************ > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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Re: [Chimera-users]
by Eric Pettersen 09 Aug '05

09 Aug '05

Hi Sabuj, It is the indentation. In Python, indentation is meaningful and statements at the same "level" have to have the same indentation. I've appended the critical part below. Note the the "self.rulerTexts..." and "x += ..." statements are indented one space further than the preceding if/else and "text = ..." statements. To Python, the extra space starts a new indented block of statements, which is only legal after 'if' statements and so forth. Take a space away from the front of the last two statements and I think things will work. --Eric for chunkStart in range(self.seqOffset, end, 10): seq1index = self.seqs[0].gapped2ungapped (chunkStart) if seq1index is None: dispText = "?" else: dispText = str(seq1index+1) text = self.mainCanvas.create_text(x, y, anchor='s', font=self.font, text="%s" % (dispText)) self.rulerTexts.append(text) x += self.chunkGap + 10 * (self.fontPixels[0] + self.letterGaps[0])

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by Pattanayek, Sabuj 09 Aug '05

09 Aug '05

Hi all, Is there a modification I can do to the multi-align viewer code so that "-" (gaps) characters are not counted in the alignment numbering (but are still displayed for alignment purposes) from a fasta file in the multi-align viewer? The numbering should correspond to the first sequence found in the fasta file (i.e. I don't care about the numbering due to gaps in the second, third, etc sequences). Thanks, Sabuj Pattanayek

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Making and Breaking bonds in Chimera
by David Chenoweth 04 Aug '05

04 Aug '05

Dear Chimera users, Does anyone know how to make a new bond or delete a bond between two atoms within a PDB file using chimera? -Thanks DC

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Coloring by Delphi potential in Chimera
by Elaine Meng 29 Jul '05

29 Jul '05

Hi Zach, DelPhiViewer got removed because other tools can do the same things in a more general and flexible way. Unfortunately in the latest snapshot (1.2129, June) it is confusing to get to these newer features, but they are all there, and I'll explain how. I'll assume you are using that latest snapshot and that you have an electrostatic potential file in the format from DelPhi. ------------------- First, open the electrostatic potential file with File... Open. If the file is named ending in .phi you can set the File type to "all (guess type)" or "DelPhi or GRASP potential". This will automatically start Volume Viewer. (A) IF you want to look at contour (isopotential surfaces), keep using Volume Viewer. Open the Volume Viewer man page by clicking the Help button on the dialog. You probably want to go to the "Surface or Mesh" section of the man page, under "Display Panel". Otherwise... (B) IF you want to color the molecular surface or GRASP surface based on the potential, click the Unshow button on Volume Viewer and then the Close button on Volume Viewer. Open the molecule and show its surface that you want to color, or open the GRASP surface you want to color (this can also be opened with File... Open). The tool for coloring a surface by potential is Surface Color (Tools... Surface/Binding Analysis... Surface Color). Pick the surface of interest from the menu next to "Color surface" and choose the electrostatic potential data from the menu next to "Using volume data or geometry". You probably want to change the "Color scheme" to "3 color symmetric" - then you have something similar to the DelPhiViewer surface coloring interface. Click the Help button on the Surface Color dialog if you want to see the man page. -------------------- We realized this is pretty confusing and have tried to make it better (and the improvements will show up in the next release). The improvements are that you will be able to color a surface according to electrostatic potential by choosing Tools... Surface/Binding Analysis... Electrostatic Surface Coloring, and then you can open the electrostatic potential using a Browse button on that tool (avoiding Volume Viewer entirely). It will also start with the 3-color scheme when opened this way. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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[Chimera-users] coloring of nearly identical protein sequences in multialign viewer
by Sabuj Pattanayek 29 Jul '05

29 Jul '05

Hi all, I have a clustal aln file or a fasta file with two nearly identical aligned protein sequences. When I view them in the multialign viewer I would like to change the color of the consensus style. That is, residues which are both identical should be just black (rather than red and capitalized) and residues that are not identical should be red (or some other color that contrasts against black). Is there anyway to do this? Better yet would it be possible to not use the consensus at all and color the entire non-matching column a color of my choice? Thanks, Sabuj Pattanayek

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gopenmol files in chimera?
by syma 25 Jul '05

25 Jul '05

HI, I was just wondering if it is possible to import gopenmol plt files in chimera either directly or by going through a (freely available) conversion code? Thanks in advance for your help, -Syma *************************************************** Dr Syma Khalid Lab. of Molecular Biophysics, Department of Biochemistry, University of Oxford South Parks Road, Oxford OX1 3QU U.K. ***************************************************

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insertion codes and residue selection
by Moo Cow 11 Jul '05

11 Jul '05

I would be very grateful for advice. Some coordinates contain residue 51 residue 51A (a residue with an insertion code) If I select #0:51 then both residues are selected. Is there any way to persuade chimera to just select residue 51, but not 51A ? Many thanks -- ___________________________________________________________ Sign-up for Ads Free at Mail.com http://promo.mail.com/adsfreejump.htm

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How to append functional groups to a residue
by C. Parry 01 Jul '05

01 Jul '05

Hi Chimera Peoples - My question is how does one append a functional group (say, nitro, bromine, ..., or metal) to a residue (say, tyrosine, ..., adenine). This would involve replacing some atom or group. I am aware of 'swapa,' 'swapna' commands but these are straight forward one-for-one changes of whole residues. Thanks. C. Parry __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Exporting 3D File Formats
by peter allen 30 Jun '05

30 Jun '05

Hello, Does your software have any way of exporting 3d file formats. DXF OBJ 3DS IGES STL DWG etc Many Thanks Peter Allen

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Gallery PDB source
by David Piper 24 Jun '05

24 Jun '05

Chimera Folks, I was looking at the gallery images and noticed that one is of the FlAsH molecule. Are the PDB coordinate available somewhere for this molecule? Or ReAsH? Thanks, David

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Electron density
by C. Parry 22 Jun '05

22 Jun '05

Could anyone help with loading and displaying CNS or XPLOR electron density maps in Chimera. I have tried many times and also the dialog boxes in the user guide do not exactly correspond to the version (12/2004) of Chimera I have. Thanks. ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com

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mutation tool?
by ROBERT LAVIERI 17 Jun '05

17 Jun '05

I am exploring/using the program and I was wondering if there was any sort of point mutation tool? Such that one could graphically see say a mutation like ser23trp? Thanks, Robert R Lavieri

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how to open bug-report dialog in v1.2105
by Sabuj Pattanayek 13 Jun '05

13 Jun '05

Hi, In v1.2105 (irix) the report a bug command under the help menu is not available (as stated in the current development documentation I assume for v1.2129). How do I open the bug report submission dialog from the command line or from the menus even if a crash or error has not occurred? Thanks, Sabuj Pattanayek

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Stereo monitors
by Thomas Goddard 06 Jun '05

06 Jun '05

Steve Ludtke reports what his lab is using for hardware stereo. Tom ------- Start of forwarded message ------- Date: Mon, 6 Jun 2005 12:59:39 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: Chimera Suggestion We have the Sharp 15" one. As I said, it works ok as long as you stay in the sweet spot, but gives me a nasty headache (which the glasses do not). We haven't tried any of the high-refresh LCD's yet. We still use CRT's for that at the moment. We're about to try a homebrew polarized glasses solution. We do actually have a (800x600) high refresh projector for use with the shutter glasses which works well. - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Asst. Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | instant messenger: sludtke42 | Those who Do, Are http://ncmi.bcm.tmc.edu/~stevel | The converse also applies On Mon, 6 Jun 2005, Thomas Goddard wrote: > Hi Steve, > > Our stereo monitor that requires no glasses was a 20" flat panel > type display from Opticality (formerly X3D). I just found out we have > returned it because it worked so poorly. I'd be curious what > make/model you have. Also have you tried any normal flat panels with > fast refresh rates and LCD glasses? > > Tom > ------- End of forwarded message -------

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Red / blue stereo
by Thomas Goddard 06 Jun '05

06 Jun '05

Steve Ludtke would like red / blue stereo. Tom ------- Start of forwarded message ------- Date: Sat, 4 Jun 2005 02:13:29 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Chimera Suggestion We've had a minor resurgance of stereo work in the lab recently. We have a couple of SGI's still with the standard shutter-glasses, and a single PC with a CRT and an active stereo capable projector. We tried the Sharp autostereographic monitor, but it works only so-so, and gives me a headache almost instantly. It would be really useful to have simple stereo set up for occasional use on all of the desktop machines in the lab (which have normal LCD panels now). Anyway, I was just wondering if you guys thought about implementing analglyph (red/blue glasses) stereo ? I've done this manually for snapshots using the 'left eye' and 'right eye' mode in chimera to get the separation right, and it works surprisingly well as long as you don't mind sacrificing color. It would be very useful to have this available for interactive use. Any chance ? (it's also very useful for posters, since many people can't do the eye-crossing thing). Just a suggestion :^) - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Asst. Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | instant messenger: sludtke42 | Those who Do, Are http://ncmi.bcm.tmc.edu/~stevel | The converse also applies ------- End of forwarded message -------

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Selection question in --nogui mode
by Miguel Ortiz Lombardia 26 May '05

26 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello. I'm trying to execute this: $chimera --nogui cmd:findselhbonds where the file findselhbonds contains: open 01.pdb select :59-62 hbonds selRestrict any saveFile tmp.bonds In the graphic mode those instructions work as expected, however in the - --nogui mode I get this error: Opening 01.pdb... warning: Ignored bad PDB record found on line 1 warning: Ignored bad PDB record found on line 2 Computed secondary structure assignments (see reply log) Model 0 (01.pdb) appears to be a protein with no secondary structure assignments. Computing assignments for it using the ksdssp algorithm (Kabsch and Sander Define Secondary Structure of Proteins) with an energy cutoff of - -0.5, minimum helix length of 5, and minimum strand length of 4. If these parameters don't produce good results for this structure, you can rerun the algorithm with different settings using the 'compute SS' button in the model panel (under 'infrequent' actions) or via the 'ksdssp' command in the Midas emulator. The model panel will also allow you to save new default parameters. 1 model opened Opened 01.pdb containing 1 model, 632 atoms, and 62 residues Error while processing cmd:forchimera: NameError: global name 'selMode' is not defined (see reply log for Python traceback info) Traceback (most recent call last): File "/usr/local/linux_prg/Chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 287, in init prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1043, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 17, in func File "CHIMERA/share/Midas/midas_text.py", line 88, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand File "CHIMERA/share/Midas/midas_text.py", line 1039, in doSelect File "CHIMERA/share/Midas/__init__.py", line 620, in chimeraSelect File "CHIMERA/share/chimera/tkgui.py", line 1604, in selectionOperation NameError: global name 'selMode' is not defined Any clues? Thank you very much! Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: miguel.ortiz(a)cnio.es - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées >>> And the boring bits follow... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.6 (GNU/Linux) iD8DBQFCleiGF6oOrDvhbQIRAi6cAJ415IJkwKrdjmhOofNbff34aEM3OQCeMdHj GNtxhKnI0DVyUDenbeAHOmw= =VDTj -----END PGP SIGNATURE----- **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión 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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Dipole
by Miguel Ortiz Lombardia 18 May '05

18 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, Maybe a silly question, but I couldn't find anything in the docs. Given one structure pdb and an electrostatic potential calculated by delphi, can Chimera display the resulting dipole as a vector? Thank you very much! Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: miguel.ortiz(a)cnio.es - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées >>> And the boring bits follow... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.6 (GNU/Linux) iD8DBQFCi3u+F6oOrDvhbQIRAsvpAJ40rweZtnhVlp3HPYt8sVDODfzEjgCfdAyq efdpkP4wOqyWcrCTT23aJCM= =rxYo -----END PGP SIGNATURE----- **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión 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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Re: [Chimera-users] New 64-bit Linux version of Chimera
by Thomas Goddard 17 May '05

17 May '05

The 64-bit Linux Chimera 1.2123 installer was broken. A packaged file did not have execute permission. The fixed version is on the download page now with the same version number and date. If you got the broken version (by downloading in the past 8 hours), please try again. Sorry for the gaff. Tom

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Draw user specified object
by Reza Khayat 17 May '05

17 May '05

Hi, I was wondering if there is a way to draw a user specified object. For example, draw a cylinder (bond) from vertex x to vertex y. Thank you. Reza rkhayat(a)scripps.edu

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New 64-bit Linux version of Chimera
by Thomas Goddard 17 May '05

17 May '05

A new 64-bit Linux Chimera snapshot (version 1.2123) is available on the Chimera download page. http://www.cgl.ucsf.edu/chimera/download.html Unless you are viewing large data sets (> 1 Gb), we suggest you use 32-bit versions of Chimera on 64-bit Linux systems. 32-bit versions will likely run faster and use less memory. The 32-bit versions are more likely to be compatible with your Linux distribution. We are not yet making regular distributions for 64-bit linux so our 32-bit version will usually be newer. Tom

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Re: [Chimera-users] Exporting VRML of MSMS surfaces
by Thomas Goddard 16 May '05

16 May '05

The VRMLoutput/__init__.py I posted in my previous two emails worked for the newly added MSMS surface output, but was broken for volume contour surfaces. Here is the corrected code. Tom ---- VRMLoutput/__init__.py follows: # ----------------------------------------------------------------------------- # Output displayed _surface models as VRML. # # ----------------------------------------------------------------------------- # def surfaces_as_vrml(surface_models): surf_vrml = ['#VRML V2.0 utf8\n', 'Transform {', ' children ['] import _surface import chimera for m in surface_models: if m.display: if isinstance(m, _surface.Surface_Model): glist = filter(lambda g: g.display, m.surface_groups()) for g in glist: vrml = surface_group_as_vrml(g) surf_vrml.append(vrml) elif isinstance(m, chimera.MSMSModel): vrml = msms_surface_as_vrml(m) surf_vrml.append(vrml) surf_vrml.extend([' ]', '}']) vrml = '\n'.join(surf_vrml) return vrml # ----------------------------------------------------------------------------- # def surface_group_as_vrml(g): vertex_rgba = g.vertex_colors() solid_rgba = g.color() m = g.model() mat = m.material shine = mat.shininess / 128.0 srgb = mat.specular if g.display_style() == g.Solid: v, vi = g.geometry() n = g.normals() ts = g.two_sided_lighting() vrml = surface_vrml(v, vi, n, vertex_rgba, solid_rgba, ts, shine, srgb) else: v, vi = g.edges() # Mesh lighting not supported in VRML97. vrml = mesh_vrml(v, vi, vertex_rgba, solid_rgba) return vrml # ----------------------------------------------------------------------------- # def msms_surface_as_vrml(m): vertex_rgba, solid_rgba, mat, shine, srgb = msms_colors(m) # TODO: Use m.drawMode (Filled, Mesh, Dot) to control vrml style vfloat, vint, tri = m.triangleData() v = vfloat[:,:3] n = vfloat[:,3:6] vi = tri[:,:3] ts = True vrml = surface_vrml(v, vi, n, vertex_rgba, solid_rgba, ts, shine, srgb) return vrml # ----------------------------------------------------------------------------- # def msms_colors(m): if m.colorMode == m.Custom: vertex_rgba = colors_to_rgba(m.customColors) elif m.colorMode == m.ByAtom: vfloat, vint, tri = m.triangleData() alist = m.atomMap() vatoms = map(lambda i: alist[i-1], vint[:,1]) vertex_rgba = colors_to_rgba(map(atom_color, vatoms)) else: vertex_rgba = None mol = m.molecule if mol: c = mol.surfaceColor if c == None: c = mol.color solid_rgba = c.rgba() mat = c.material else: solid_rgba = (1,1,1,1) import chimera mat = chimera.MaterialColor(0,0,0).material shine = mat.shininess / 128.0 srgb = mat.specular return vertex_rgba, solid_rgba, mat, shine, srgb # ----------------------------------------------------------------------------- # def colors_to_rgba(color_list): rgba = map(lambda c: c.rgba(), color_list) import Numeric rgba_f32 = Numeric.array(rgba, Numeric.Float32) return rgba_f32 # ----------------------------------------------------------------------------- # def atom_color(atom): c = atom.surfaceColor if c == None: c = atom.color if c == None: c = atom.molecule.surfaceColor if c == None: c = atom.molecule.color return c # ----------------------------------------------------------------------------- # def surface_vrml(vertices, vertex_indices, vertex_normals, vertex_rgba, solid_rgba, two_sided_lighting, shininess, specular_rgb): vrml_template = \ '''Shape { appearance Appearance { material Material { diffuseColor %s transparency %.3f shininess %.3f specularColor %s } } geometry IndexedFaceSet { coord Coordinate { point [ %s ] } normal Normal { vector [ %s ] } coordIndex [ %s ] %s solid %s } } ''' pts = tuple_string(vertices, '%.6g %.6g %.6g') ns = tuple_string(vertex_normals, '%.6g %.6g %.6g') m = polygon_size(vertex_indices) vi_format = ' '.join(['%d'] * m + ['-1']) ci = tuple_string(vertex_indices, vi_format) if vertex_rgba: clrs = tuple_string(vertex_rgba[:,:3], '%.3f %.3f %.3f') cspec = 'color Color {\n color [\n%s]\n }\n' % clrs else: cspec = '' srgb, trans = material_colors(vertex_rgba, solid_rgba) specular = '%.3f %.3f %.3f' % specular_rgb if two_sided_lighting: solid = 'FALSE' else: solid = 'TRUE' vrml = vrml_template % (srgb, trans, shininess, specular, pts, ns, ci, cspec, solid) return vrml # ----------------------------------------------------------------------------- # VRML does not handle normals for lines. # def mesh_vrml(vertices, vertex_indices, vertex_rgba, solid_rgba): vrml_template = \ '''Shape { appearance Appearance { material Material { emissiveColor %s transparency %.3f } } geometry IndexedLineSet { coord Coordinate { point [ %s ] } coordIndex [ %s ] %s } } ''' pts = tuple_string(vertices, '%.6g %.6g %.6g') m = polygon_size(vertex_indices) vi_format = ' '.join(['%d'] * m + ['-1']) ci = tuple_string(vertex_indices, vi_format) if vertex_rgba: clrs = tuple_string(vertex_rgba[:,:3], '%.3f %.3f %.3f') cspec = 'color Color {\n color [\n%s]\n }\n' % clrs else: cspec = '' srgb, trans = material_colors(vertex_rgba, solid_rgba) vrml = vrml_template % (srgb, trans, pts, ci, cspec) return vrml # ----------------------------------------------------------------------------- # def material_colors(vertex_rgba, solid_rgba): if vertex_rgba: srgb = '0 0 0' trans = 1 - max(vertex_rgba[:,3]) else: srgb = '%.3f %.3f %.3f' % solid_rgba[:3] trans = 1 - solid_rgba[3] return srgb, trans # ----------------------------------------------------------------------------- # def polygon_size(vertex_indices): if vertex_indices: return len(vertex_indices[0]) return 0 # ----------------------------------------------------------------------------- # def tuple_string(tuples, format): tuple_strings = [] for t in tuples: tuple_strings.append(format % tuple(t)) tstring = '\n'.join(tuple_strings) return tstring # ----------------------------------------------------------------------------- # def surface_models(): import chimera import _surface mlist = chimera.openModels.list(modelTypes = [_surface.Surface_Model, chimera.MSMSModel]) return mlist # ----------------------------------------------------------------------------- # def write_surfaces_dialog(): import os.path dir = os.path.dirname(__file__) help_path = os.path.join(dir, 'helpdir', 'vrml_output.html') help_url = 'file://' + help_path filters = (('VRML', ('*.wrl', '*.vrml'), '.vrml'),) import OpenSave od = OpenSave.SaveModeless(title = 'Save Surfaces as VRML', filters = filters, defaultFilter = 0, command = write_surfaces_cb, multiple = 0, help = help_url) od.enter() # ----------------------------------------------------------------------------- # def write_surfaces_cb(okayed, dialog): if okayed: paths = dialog.getPaths() if len(paths) == 1: write_surfaces_as_vrml(paths[0]) # ----------------------------------------------------------------------------- # def write_surfaces_as_vrml(path): mlist = surface_models() vrml = surfaces_as_vrml(mlist) f = open(path, 'w') f.write(vrml) f.close()

1 0

matching scale for different sessions
by jinghua＠ucsd.edu 16 May '05

16 May '05

to our friendly developer, Is there a way to specify the physical size for a view, so that different sized molecule or map is shown at the same physical scale from different sessions. By the way, is there a command to specify the pixel size of the window? the shrink to fit or grow to fit doesn't work well. many thanks! Jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>< Jinghua Tang, Ph.D. Phone: 858-534-5852(o) 4107 Natural Sciences Bldg, MC-0378 858-597-2056(h) Department of Chemistry & Biochemistry Fax: 858-534-5846 University of California, San Diego E-mail: jinghua(a)ucsd.edu La Jolla, CA 92093-0378 http://cryoem.ucsd.edu/~jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><

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by Klinkhardt＠em.uni-frankfurt.de 13 May '05

13 May '05

Hello, I have a question concerning the surface resolution of multiscale models. My intention was to create a surface from pdb data, export it as vrml and reimport it in maya for further animation, shading etc. It works quite well (I had to convert the vrml file in ascii with Deep Explorer first) but the problem is, that I do not get a fine surface with all its convexities and sites for binding. This is important for my work because I would like to animate receptor binding and subsequent signaling in maya. I am looking for a fine surface like these MSMS main surface from pdb data. I do not need many copies of single pdb surfaces but I guess I will only get a #real# surface using the multiscale models tool?? I tried to change the surface resolution (the best result was with resolution: 3, threshold atom density 0.00, smoothing factor 0.5 and smoothing interations 2/3) but I was not able to create a really fine surface. Is there any possibility to get a finer surface (like MSMS main surface) for VRML export? If not, do you have an idea if there are other tools to do that? It would be rally great if you could give me a short reply. Thanks a lot in advance (and sorry for my english...). Best regards Ute

2 2

Scale bar in Chimera
by Haixiao Gao 09 May '05

09 May '05

Hi, I have a problem with the "scale bar" option in Chimera. I was trying to show the scale bar together with a EM density map in spider/brix format. Howerver, it seems that when I changed zoom in/out position, the size change of the "scale bar" is not proportional to the size change of the density map? My chimera version is win32, bata version from 12/15/2004. Thanks for the help! -Haixiao

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Re: [Chimera-users] os x tiger
by Thomas Goddard 05 May '05

05 May '05

We've put code in the Chimera 1.2121 snapshot (released May 5, 2005) to work around a bug in the Apple OpenGL driver that caused Chimera to crash when displaying molecule ribbons. You need to use Chimera 1.2121 or later on Mac OS 10.4. Tom

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beta version of Sequence.py
by Bryan W. Lepore 05 May '05

05 May '05

i'm trying out the secondary structure matching stuff that Eric wrote, and i'm wondering if there is a updated Sequence.py package (that has the StructureSequence functions)? b/c the new MatchMaker/__init__.py trys to import StructureSequence, but its not in chimera/Sequence.py. -bryan

2 1

os x tiger
by Grant Geske 04 May '05

04 May '05

has anyone tried running chimera on the new mac os tiger?? i did and it did not work. does anyone have any suggestions?? grant ________________________________ Grant Geske Blackwell Group University of Wisconsin-Chemistry 1101 University Ave Madison, WI 53706 PH: 608-262-9043 email: chemg(a)mac.com

2 2

circular permuation
by Bryan W. Lepore 04 May '05

04 May '05

i want to test my understanding about the "circular permuation" during matching: is this for proteins that result from gene duplication? -bryan

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Fwd: [Chimera-users] writing alignment
by Elaine Meng 04 May '05

04 May '05

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: Wed May 4, 2005 1:56:54 PM US/Pacific > To: "Bryan W. Lepore" <lepore(a)brandeis.edu> > Subject: Re: [Chimera-users] writing alignment > > > On Wednesday, May 4, 2005, at 01:41 PM, Bryan W. Lepore wrote: >> however i'd like to ask if mmaker is in fact not written to handle >> specific stretches of a model - e.g you can do #1:.a at the least? >> e.g., not something like #1:.a1-10,a15-20... to prune out areas to >> ignore. >> >> -bryan >> > > Hi Brian, > You can specify which chains (like in that example you included > in a previous mail) to construct an alignment with, but not > subparts of those chains. > > However, remember that the structure matching will only use > residues that are actually aligned in the initial sequence alignment. > So, it doesn't matter if the sequences have other parts > that are essentially unalignable. > Elaine >

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mmaker
by Bryan W. Lepore 03 May '05

03 May '05

i'm confused about the command "mmaker". `chimera --nogui mmaker` causes a "no such file or directory" error, so i tried `chimera --nogui --mmaker` which isnt' right either. also tried just `mmaker` even though its not in bin/ lib/. so do i make a heredoc script? i suspect i am missing a fundamental point (that i didn't find with `google: mmaker site:www.cgl.ucsf.edu/chimera`) i've tried both the latest official release and the lastest snapshot. -bryan

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by Ihms, Elihu C 02 May '05

02 May '05

I noted that Apple still has X11 availible for download, just that it's not publicized. http://a1408.g.akamai.net/7/1408/1388/20030317/akamai.info.apple.com/X11/us… Keep up the good work on Chimera! -- Elihu Ihms [ ihms(a)tamu.edu ]

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Chimera Surface Area/Volume
by Elaine Meng 27 Apr '05

27 Apr '05

Hi Dieter, Just a few add-ons to Tom's reply: Another approach to getting the surface area of the receptor buried by the ligand is to run Surface Area/Volume (a) on the complex of ligand and receptor (must delete water and anything else first). Then use Attribute Calculator to sum the surface areas of the receptor atoms only. (b) after deleting ligand, run it again on the receptor. The total is all from the receptor, so it is not necessary to use Attribute Calculator. Subtract the value from (a) from this value. Tom gave a link to the development documentation, which is slightly ahead of the Chimera version you have. It is almost the same, except that the Tools menu has been reorganized. Probably in the version you have, both Attribute Calculator and Surface Area/Volume are in the Utilities submenu of the Tools menu. To get the documentation that goes with your version, use the Help buttons on those dialogs or open the User's Guide from the Help menu. If you have the latest snapshot (1.2105, March) there is an "Attributes" tutorial (Help... Tutorials). Part 2 has one example of using Surface Area/Volume and Attribute Calculator. Finally, if anything is confusing or hard to find in the documentation, please feel free to complain to me! 8-) Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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buried surface area
by Thomas Goddard 27 Apr '05

27 Apr '05

Hi Dieter, The surface area / volume tool (menu entry Tools -> Utilities -> Surface Area / Volume) could give buried surface areas if you ran it for the unbound receptor, unbound ligand, and then the complex, and then calculated { Area(receptor) + Area(ligand) - Area(receptor+ligand) } / 2 When you use this tool it reports the total area to the Reply Log (menu entry Favorites / Reply Log) and atoms are assigned an attribute saying how much area they contribute. It is a bit of a pain to run it 3 times and do the math yourself. The surface area is calculated by a web server as described in the Chimera User's Guide http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.ht… so you will need an internet connection to use it. The Chimera User's Guide is only available in HTML as far as I know. It is written in HTML. Tom > From: "Dieter Blaas" <dieter.blaas(a)meduniwien.ac.at> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Date: Wed, 27 Apr 2005 21:38:46 +0200 > Subject: buried surface area > > Hi Tom, > two quick questions: 1/ can Chimera calculate/display > the surface area buried by e.g. a ligand when bound on > a receptor? 2/ is there a documentation other than htlm > (e.g. pdf file)? > Thanx, Dieter >

1 0

Resize a molecule
by Thomas Goddard 27 Apr '05

27 Apr '05

Here is some code to scale a molecule size by a given factor. That is all atoms have their coordinates multiplied by a factor. Tom ------- Start of forwarded message ------- Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi Jinghua, By "virus cage pdb file" I guess you mean you placed atoms at icosahedral positions, and want to show them connected up to show some icosahedral pattern. I think the easiest approach is to open your old session, run a command to change the diameter of the cage, then save a new session. Below is some Python code that provides a "scalemol" Chimera command. Make a directory chimera/share/scalemol in your Chimera distribution and put the code below in file chimera/share/scalemol/ChimeraExtension.py. Then start Chimera, open the cage PDB model, use menu entry Favorites/Command line, and type a command: scalemol 0 1.5 to make model number 0 bigger by a factor of 1.5. If you have more than one model open you can see the model numbers using Favorites / Model Panel, the model number is shown in the left hand column. Tom - ---- scalemol/ChimeraExtension.py code follows: # ----------------------------------------------------------------------------- # def scale_molecule(cmdname, args): from Midas.midas_text import error fields = args.split() try: model_num = int(fields[0]) factor = float(fields[1]) except: error('Syntax error: scalemol <model-number> <factor>') return import chimera mlist = chimera.openModels.list(id = model_num) if len(mlist) == 0: error('scalemol: No model number %d' % model_num) return for model in mlist: for a in model.atoms: x, y, z = a.coord().xyz.data() c = chimera.Coord() c.x, c.y, c.z = (factor*x, factor*y, factor*z) a.setCoord(c) # ----------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('scalemol', scale_molecule) ------- End of forwarded message -------

1 0

get to lighting adjustment
by jinghua＠ucsd.edu 26 Apr '05

26 Apr '05

to whom it may concern, How could I get to the adcanced feature of lighting adjustment? Can I add more lights with different directions? Thanks! Jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>< Jinghua Tang, Ph.D. Phone: 858-534-5852(o) 4107 Natural Sciences Bldg, MC-0378 858-597-2056(h) Department of Chemistry & Biochemistry Fax: 858-534-5846 University of California, San Diego E-mail: jinghua(a)ucsd.edu La Jolla, CA 92093-0378 http://jinghua.ucsd.edu <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><

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