- Chimera-users - RBVI Mailing Lists

gaussian filter
by Mike Strauss 30 Apr '12

30 Apr '12

Hi, I've been using the gaussian filter for a number of years to help me display my noisy data. I'd like to understand what it's doing a bit better, and so I need help with the following code: ijk_linewidths = map(lambda step: linewidth / step, g.step) what is the resulting length of ijk_linewidths? I can't seem to figure out what type of data type g.step is. Is it a feature of the image itself, or where does it come from? Best Regards, mike

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About volume viewer in chimera 1.6.1
by Yuhong Li 30 Apr '12

30 Apr '12

Dear Chimera developers, Hi! I am a student from Sun Yat-Sen University. I recently began using the Chimera for my study, but I have a problem about how to read the displayed information in volume viewer. Here I attach a picture and inside the picture there are two places I've point out with arrows which represent two different map files in mrc fornat. Now I was wondering if you could spare some time to explain it to me that what do those different numbers mean? Hope to hear from your reply in very soon. Best Wishes, Yuhong Lee

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addaa command
by Mahendra B Thapa 27 Apr '12

27 Apr '12

Dear chimera users, I also added an amino acid residue at the N-terminus of a small protein following the posting: [Chimera-users] Using addaa at the N-terminus?*[ posted date:Fri Sep 30 10:36:31 PDT 2011]* The residue is added at the n-terminus but the added residue is not connected to rest of the protein structure in the graphical display [i.e, a little gap between the added residue and the rest of the protein at N-terminus]. Is this due to wrong command ? Thanks, Mahendra Thapa Graduate student Department of Physics University of Cincinnati, OH

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Per model clipping not working ?
by Damien Larivière 27 Apr '12

27 Apr '12

Dear all, I try to use the Per-Model clipping tool but this error is returned, whatever the PDB file: Model cannot currently be clipped [no valid bounding box] Do I make something wrong? I use Chimera version 1.6.1 (build 35849). My configuration is Windows 7 64bits, ATI Mobility Radeon HD5650. Many thanks for your help! Damien

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loading trajectories with no box line
by Michael F. Bruist 25 Apr '12

25 Apr '12

Is there a way to load trajectories that do not have box lines? I have trajectories from which most solvent and ions have been stripped. They were written with ptraj as amber coordinate files with the "nobox" option. I cannot get these to stay in register for MD movie. I do not have this problem for trajectories for which the box line has not been removed. Mike Bruist Dr. Michael F. Bruist Associate Professor of Biochemistry Department of Chemistry & Biochemistry Griffith Hall 147 University of the Sciences in Philadelphia Philadelphia, PA 19104-4495 Phone (Office & Voice Mail): (215) 596-8530 Department Phone: -8839 Department Fax: -8543 E-mail: m.bruist @usp.edu web page: http://tonga.usp.edu/bruist

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saving transformed map
by Elaine Meng 25 Apr '12

25 Apr '12

On Apr 25, 2012, at 9:04 AM, Ariane Briegel wrote: > Dear Elaine, > I have been using chimera to align several EM maps in respect to each other. > These maps are generated by imod (mrc format). I know I can save the transformed maps in chimera when I use the 'save session' command, but that only allows me to use the transformed maps inside chimera. I would like to save the individual transformed maps- either in mrc or CCP4 format. > I tried to find any info about that in the manual, then checked the old chimera list comments. I found a similar question from the year 2006 (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-July/000864.html) but at that time your conclusion was it is not possible. > Do you know if there is a way to do this now? > Thank you so much for your answer, > Ariane Hi Ariane, The map formats don't include transformation information, so there is no way to save EXACTLY the same data, except transformed. However, you can resample the map onto a new grid, and then save the new map. The values at the new grid points are determined by interpolation, so there will be some (generally minor) data loss. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> The resampling of one map onto the grid of another can be done with command "vop resample" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> For example: vop #1 resample onGrid #0 To save the resampling result to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its "save" option. 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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Re: [Chimera-users] Chimera-users Digest, Vol 108, Issue 25
by Boaz Shaanan 25 Apr '12

25 Apr '12

Hi, Elaine is correct in that newly deposited structures (since a year or so?) have to have their TLS information converted to aniso B and have those values in the appropriate place on the ATOM card. However, this was not the case for the older entries. The 1ss8 entry seems to have been refined by refmac5 from the ccp4 package. In this package there is a program called tlsanl which will do the job of converting the TLS infotmation to B-aniso. (a several seconds job) So maybe Steve could use it and thus solve his problem? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Tuesday, April 24, 2012 7:19 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 108, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: remote session (Greg Couch) 2. Rendering TLS information in Chimera ? (Steven Ludtke) 3. Incomplete chain contain many dotted lines while displaying (Junfeng Huang) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Apr 2012 12:05:41 -0700 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] remote session Message-ID: <4F95A805.1080609(a)cgl.ucsf.edu> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" The error is that the OpenGL library is looking for a NVidia-specific extention to the remote protocol and failing when it is not there. That is a driver bug -- it shouldn't matter what graphics driver you have on either of the systems. There are two things I'd do to try and fix it: (1) try updating the NVidia driver on the remote computer that is running chimera (not the computer displaying chimera), and (2) try uninstalling the NVidia driver on the remote computer, and reverting to the software implementation of OpenGL (mesa). The first option is preferable if it works, because the proprietary (NVidia/AMD) drivers have been faster and less buggy than the mesa driver for most uses. Good luck, Greg On 04/20/2012 02:25 PM, Hernando J Sosa wrote: > > Hi > > I used to be able to run chimera remotely from a machine with an X- > windows server (the one that comes with Cygwin in this case). But now > I get the following error: > > Xlib: extension "NV-GLX" missing on display "localhost:10.0". > > X Error of failed request: BadRequest (invalid request code or no > such operation) > > Major opcode of failed request: 148 (GLX) > > Minor opcode of failed request: 181 () > > Serial number of failed request: 12779 > > Current serial number in output stream: 12784 > > I t does work fine if run directly from the computer where chimera is > installed. Any idea what the problem could be? > > Thanks > > Server computer: > > Chimera v 1.5 (similar problem with 1.6) > > OS: Linux OpenSuse 11.3 64b > > Client computer: > > OS: Windows 7 64. > > Graphics: ATI Radeon HD 5450 >

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electron density ven diagram
by Terry Lang 25 Apr '12

25 Apr '12

Hey Guys, I am interested in making kind of a ven diagram between two maps for electron density (see attached). What I would like to do is where the density is above a certain threshold for both maps, color the map grey, and where it is above the threshold for map A only, color red, and for map B only, blue. Plan #1 --superimpose maps (have this working) --create a third map (have this working) --do a direct < > = point-by-point comparison between map A and B and reset the values of the third map to be -1 (map A only), 0 (both maps) or 1 (map B only) --color the map using the histograms PROBLEM: The maps are not gridded the same. After some careful thought, I don't think I actually can get them gridded the same for technical reasons. Plan #2 --superimpose maps (have this working) --create copy of map A (coarser map) with map A gridding (have this working) --use interpolation function to interpolate map B (finer map) onto map A gridding --create copy of map A and do a direct < > = point-by-point comparison between map A and interpolated map B and reset the values of the fourth map to be -1 (map A only), 0 (both maps) or 1 (map B only) --color the map using the histograms QUESTION: Is there an easier way to do this with tools that already exist in Chimera? If not, can I get a little bit of info on how the data is stored in the ccp4 style maps (eg start at origin and loop over x, loop over y, loop over z or something else?) Let me know if you need more details or clarification on this rats nest. Thanks! Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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Incomplete chain contain many dotted lines while displaying
by Junfeng Huang 25 Apr '12

25 Apr '12

Hello Everyone， I have a problem while display PDB file. I extract the residues from protein-protein interface by ligplus into a new PDB file, and want to display and analysis it. As the file contain only the residues form interface, they are discontinuous. While display with pymol, it is OK. However, While using Chimera, there are many dotted lines between the residues. I know what the dotted lines are, but I do want to hide all these lines, can somebody please give me some hints? I sent two figures in the attachment. It's the first time I used mail-list, if it doesn't support figures, please check here: Interface display by pymol http://bbs.sysu.edu.cn/attach/Pictures/1335235173.JPG Interface display by Chimera http://bbs.sysu.edu.cn/attach/Pictures/1335235254.JPG Thank you very much!

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Charge data
by Nikolay Igorovich Rodionov 25 Apr '12

25 Apr '12

Hi everyone, I know chimera does not produce PQR files, but I was wondering if it is possible to create a data text file with the atoms' three dimensional coordinates and charges after applying the amber forcefield? Sincerely, Nikolay Rodionov

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Rendering TLS information in Chimera ?
by Steven Ludtke 24 Apr '12

24 Apr '12

Hi. A question about rendering B-factor information: Over the last decade, rather than simple anisotropic B-factors, it has become increasingly common to represent local "motion" using the translation-libration-screw (TLS) model, which provides for anisotropic representation of such motions. Is there a good way to represent this data in Chimera ? Here is an example. If you render the PDB structure 1OEL as atoms, and color the atoms by B-factor, you can immediately observe regions of high variability in the apical domain. This same data was later re-refined using a TLS model as PDB structure 1SS8. When you render this structure in Chimera in the same way, you see high B-factors only for a few specific sidechains. The overall large-scale variability is gone, presumably because the TLS parameters have absorbed it, and the "B-factor" is now only a residual B-factor. However, I can't see any obvious way of rendering the TLS information. Any tips ? ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Associate Professor Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu) Co-Director CIBR Center (www.bcm.edu/research/cibr) Dept of Biochemistry and Mol. Biol. (www.bcm.edu/biochem) Baylor College of Medicine sludtke(a)bcm.edu stevel(a)alumni.caltech.edu

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remote session
by Hernando J Sosa 23 Apr '12

23 Apr '12

Hi I used to be able to run chimera remotely from a machine with an X- windows server (the one that comes with Cygwin in this case). But now I get the following error: Xlib: extension "NV-GLX" missing on display "localhost:10.0". X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 148 (GLX) Minor opcode of failed request: 181 () Serial number of failed request: 12779 Current serial number in output stream: 12784 I t does work fine if run directly from the computer where chimera is installed. Any idea what the problem could be? Thanks Server computer: Chimera v 1.5 (similar problem with 1.6) OS: Linux OpenSuse 11.3 64b Client computer: OS: Windows 7 64. Graphics: ATI Radeon HD 5450

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Displaying atoms within a distance
by Nikolay Igorovich Rodionov 21 Apr '12

21 Apr '12

Hi everyone, I am trying to display waters within a set distance from a solvated protein. Can someone please tell me how I can use the display or show commands to selectively show only the residues that are within a specific distance from a residue type? I've looked at the chimera manual and I am still confused on how these commands function. Thank you, Nikolay Rodionov

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Charge calculations PDB2PQR
by Nikolay Igorovich Rodionov 20 Apr '12

20 Apr '12

Hi all, Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem? Sincerely, Nikolay Rodionov

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Volume Viewer Mesh
by Terry Lang 20 Apr '12

20 Apr '12

Hey Guys, I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser? Thanks, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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modeller interface
by Sadler, Evan 19 Apr '12

19 Apr '12

Hi, I'm trying to construct what I think should be a simple homology model and it's failing as below whether I use the web server or run modeller locally: Target seq: VWF_CK Template structures: 2TGI.pdb (#0)Run locally, the Modeller binary location: /Library/modeller-9.10/bin/mod9.10 Now, modeller is running locally... <type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <function command at 0x17982770> (type: <type 'function'>) Args: () Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 700, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerDialog.py", line 579, in Apply veryFast=self.veryFastVar.get(), tempPath=self.pathTempOpt.get().strip(), **kw) File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 247, in model if loopData: <type 'exceptions.UnboundLocalError'>: local variable 'loopData' referenced before assignment UnboundLocalError: local variable 'loopData' referenced before assignment File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 247, in model if loopData: See reply log for Python traceback. My version of Chimera is alpha version 1.7 build 36205, running under Mac 10.6.8. Do you have any advice? Thanks, Evan Sadler -- J. Evan Sadler, M.D., Ph.D. Chief, Division of Hematology Department of Medicine Washington University 660 S. Euclid Ave., Box 8125 St. Louis, MO 63110 Tel: 314-362-9067 FAX: 314-454-3012 email: esadler(a)wustl.edu

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How to save high resolution image?
by Yogendra 19 Apr '12

19 Apr '12

Dear Sir, I am a new user of Chimera software. I am using this software for academic purposes (i.e. research publications). I am trying to save the image with more then 600 dpi but every time i am ending up with an image of 96 dpi. I am using the POV-Ray method for image improvement but everything is going to the drain when taking the final print of the document. Can you please help me ho can i save a high resolution image? I am briefly describing my protocol of image generation: 1) I am making a density map of particular PDB file. 2) loading in the Chimera and adjusting the volume by volume viewer option 3) Coloring it using described colors 4) Using Pov-Ray for increasing effects on plane 5) Increasing the pixels to about 5000 in the pixel option 6) finally trying to save an image with 600 or 1200 dpi. But at the end of this, i am just getting an image of 96 dpi every time. Can you please help me out to make an image of higher dpi (600, 1200 or more if possible). It will be very much helpful for me if can do it. I am stuck at this point.I am badly waiting for your reply whether i can do it or should i look for some another software. Regards Yogendra S Rathore Research Scholar ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202

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Methanesulfinamide Stability and Synthesis
by Nancy 19 Apr '12

19 Apr '12

Hello All, I would greatly appreciate it if anyone has information on the stability of methanesulfinamide (SMILES: C[S](=O)N([H])[H]), as well as it's stability in water. Thank you.

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Command line "Render by attribute"
by rswett＠chem.wayne.edu 19 Apr '12

19 Apr '12

So, I"m wondering if there's a way to call "Render by Attribute" command line for movie making purposes. I have several Defined Attributes and i'd like to be able to recolor surfaces by the various attributes at different points in a movie. What would the format for that type of command be? Thanks for any help you guys have! ~Rebecca

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Check Marks in 2D Labels
by Paul Cernek 17 Apr '12

17 Apr '12

Hello, I'm having trouble inserting a check mark (Unicode page here: http://www.fileformat.info/info/unicode/char/2713/index.htm) into a 2D label, using the Chimera Daily Build from April 10 2012 on Windows Vista. I know that you can reference a special character via its Unicode escape sequence (in this case \u2713). Indeed, when I specify such text from the command line, or when I copy/paste the check mark into the text box of the 2D Labels window, it displays exactly what I want IN THE 2D LABELS WINDOW. However, in the main Chimera model display window the check mark is NOT properly depicted in the label. Instead, I get that empty square you get whenever a program encounters an unrecognized character. Other more conventional symbols (such as the Greek letter 'alpha') display normally. Why would the "2D Labels" window display the check mark properly, while the main display window does not? Any assistance in this matter is very much appreciated. Thanks, -Paul

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APBS maps
by Rebecca Swett 12 Apr '12

12 Apr '12

Hey guys, i'm working with some electrostatic potential maps and am interested in doing a difference map. Two nearly homologous proteins with nearly identical surface shapes, and radically different electrostatics. I"m thinking a difference map would illustrate the differences well, but in looking at the APBS output I have no idea how to do that manually. Does anyone here have an idea about how to do that in chimera?

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Re: [Chimera-users] [Dock-fans] Help with antechamber
by Trent E. Balius 10 Apr '12

10 Apr '12

Hi Brad, I am cc'ing this to the chimera list. I think that you should write a python script to run DOCK prep on the command line. See the following: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html For other example scripts see the following: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html You should not have to specify the AMBERHOME path. This is done internally to chimera. as an aside, It is unnecessary to run antichamber with sudo. I hope this helps, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/ -----Original Message----- From: Brad Ridder <clustro(a)gmail.com> To: dock-fans <dock-fans(a)docking.org> Sent: Wed, Feb 29, 2012 4:38 pm Subject: [Dock-fans] Help with antechamber Hi Dockfans, My name is Brad; I am a grad student in the dept. of chemical engineering at Purdue University. We are experimenting with DOCK for various drug discovery work. At the moment, I am trying to do execute all of the "dock prep" commands through the Terminal, since it is not practical to do large volumes of Dock Prep by hand through the CHIMERA GUI. Corresponding to what is in the DOCK tutorial, I am on "Receptor and Ligand Preparation." I got reduce to work, in order to add hydrogens. Now, I am trying to get antechamber to work, in order to add the charges, but it is not working. Here is the command I am running: sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/3GLRcharged.mol2 -fo mol2 Which returns the error: Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, use "mopac.sh" in the work directory Cannot open CONNECT.TPL , exit The atom number exceeds the MAXATOM, reallocate memory I looked around in the dock6 directory, and found a folder called "parameters/antechamber", which contains CONNECT.TPL. I figured this is what should be the $AMBERHOME directory. For DOCK_HOME, I figured it should be the dock6 folder. Here is what I have in my .bash_profile file in my home folder. export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' export DOCK_HOME='/home/.../DOCK6.5/dock6' I also tried using the "amber11" folder that comes with CHIMERA as AMBERHOME, but to no effect. I don't actually have AMBER installed on my computer, but since CHIMERA can add charges without actually requiring the purchase of AMBER, I do not think that is the problem. I did not know what to do with "mopac.sh." I ran the script, but it says it needs input files. What am I doing wrong that is preventing antechamber from executing correctly? -- Bradley James Ridder Chakrabarti Group Graduate Student School of Chemical Engineering Purdue University _______________________________________________ Dock-fans mailing list Dock-fans(a)docking.org http://mailman.docking.org/mailman/listinfo/dock-fans

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vector of axis
by Gwo-Yu Chuang 09 Apr '12

09 Apr '12

Dear all, I am trying to figure of the principal inertia axis of a protein domain using Chimera. Is there any way to get the vector of the axis (the values), besides just showing it on the screen? Many thanks Yours Sincerely, Paul

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Morph with Cofactors
by Marco Jost 06 Apr '12

06 Apr '12

Hi, I am trying to morph two conformations of a protein that includes multiple cofactors. While the protein structure is morphed just fine, the cofactors are not included in the morph (or in the output PDB). I numbered the cofactors identically in both files and everything else should be consistent as well. Does anybody know how to include cofactors in the morphing and have them be written into the output PDB? Thanks! Marco Jost Ph. D. Student, Department of Chemistry Massachusetts Institute of Technology

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Re: [Chimera-users] [Open Babel] UCSF Dock mol2 files
by Scott Brozell 06 Apr '12

06 Apr '12

Hi, This is a good suggestion. But before implementation, 1) do the DOCK developers or users have any comments ? 2) do the Chimera developers or users have any comments ? In particular, does Chimera use ########## as the lexeme for the DOCK token ? It might be useful to have a consistent lexeme across programs. Or maybe the Babel folks have comments on what would be a more general tag ? thanks, scott On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: > Here you have two example files > http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 > http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2 > > What OB should do (in my mind) is to take "Name:" value as target molecule > name and pass all 3 grid scores (total, vdw and ele) somehow (i guess > comment is a right place, since there is not much choice), so that it can > output it in simmilar manner. > > Maybe it would be easier to have an option "d" (aka. dock) which would copy > ALL the ###### data, and some other one, such as "s" (aka. sufix) to take > suffixed name into account. Disadvantage of above is that it wouldn't work > for other formats. > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > maciek(a)wojcikowski.pl > > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > geoff(a)geoffhutchison.net> napisał: > > > > I have a thought about mol2 files form Dock program, which contain > > > additional information in commentary (###). Those information is being > > lost > > > during openbabel operations, which is a pity. I'd like to propose a > > in/out > > > option for mol2 for Dock'ed mol2's to read/write compatible information > > from > > > those files. Especially conformer ID is important for further anylisis. > > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > > files. > > > > > > If you can give us a selection of example files and a list of what > > information you'd like retained, it's fairly easy to patch the parsers. > > > > Cheers, > > -Geoff

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