- 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 08 Sep '05

08 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 02 Jul '05

02 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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