- Chimera-users - RBVI Mailing Lists

Problem in Surface depiction
by Kshatresh Dutta Dubey 31 Mar '10

31 Mar '10

Dear All, I am using chimera 1.41 and 1.4 on a 3 GB Core 2 duo machine. When i draw surface for any ligand or residue then suddenly it get closed. This problem occurs in both versions 1.4 and 1.4.1. Kindly suggest me to fix this problem. Regards Kshatresh Dutta Dubey

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Re: [Chimera-users] named selections
by Elaine Meng 30 Mar '10

30 Mar '10

Hi Ajith, We are very happy to hear you will be the "Chimera guy" for your group, and that the tutorials are useful! But sometimes it is hard to find certain things, which is why we have the chimera- users(a)cgl.ucsf.edu list (recommended rather than sending mail to me individually). It sounds like you really want to use aliases rather than named selections. See the "alias" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> and also how to specify particular models, residues, chains, etc: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierar… > For example, to alias residues 10-42 and 55 in chain A and 80-100 in chain B: alias myresidues :10-42.a,55.a,80-100.b color red myresidues These would be the residue numbers in the structure, which are not always the same as in a sequence file. Session files are not friendly/intended for viewing as text. Aliases are saved in sessions, but you would just use the alias command without arguments to list the definitions of the existing aliases. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 30, 2010, at 8:05 PM, Ajith Harish wrote: > Hi Elaine, > I will not bother you with too many questions after this last one > (at least for a while ;-)). There are a lot of features to explore > and I am playing with it and have learnt quite bit today. Also the > tutorials on the website are very helpful. I am soon going to be the > "Chimera Guy" of our group ;-) > > But there was one feature I could not figure out. Is it possible to > name sections without actually selecting the sequence from the GUI. > I need color different parts of large ensembles. Different domains > in multiple chains of a single pdb file. For now I open the sequence > of one chain at a time form the "Tools > sequence > sequence" and > then pick the residues (amino/nucleotide) based on the numbering > from the corresponding Fasta file from PDB and then name it from > "Select > Name Selection". Is it possible to assign names on a FASTA > file? > > I also looked into the session.py file. I could not relate the > numbers corresponding to my names in the session file to the residue > numbers or the residues. It would be great if I could assign names > in a file and then acess the names to color. Even better would be > assign colors to those named selections. > > Thanks much for your help. > Best wishes, > Ajith >

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Matching RGB color code from Adobe Illustrator
by Ajith Harish 30 Mar '10

30 Mar '10

Hello, I would like to color different regions of a molecule corresponding to RGB colors from Adobe Illustrator. Chimera RGB ranges from 0.000 to 1.000 where as the Illustrator RGB ranges from 0 to 255. Could you please let me know how these two scales are related? Thank you very much, Ajith

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Trouble with thermal ellipsoids
by sherden＠caltech.edu 30 Mar '10

30 Mar '10

I can't seem to get the thermal ellipsoids to work. I have a number of .cif files that are all perfectly good files (have been cif-checked) and all of which I know for a fact have anisotropic data as I can get thermal ellipsoids to display from these files in other programs like Diamond (which we are trying to move away from). But any time I select an atom or group of atoms and use either the "aniso" command or the "Show Thermal Ellipsoids" dialogue box I just get: "No atoms chosen had anisotropic information." This is just not true though, I can open up the .cif files in question and see the anisotropic data listed for the given atoms with my own two eyes. Any thoughts? I am probably doing something immensely stupid, that is usually the case with such situations. --Nat (Nathaniel Sherden) California Institute of Technology Department of Chemistry

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RMSD
by Beale, John 29 Mar '10

29 Mar '10

What is the best way to use Chimera to compute the RMSd value of an MD trajectory snapshot relative to the crystal structure of the protein? Thanks! John M. Beale, Jr., Ph,D. Professor of Medicinal Chemistry and Pharmacognosy St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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zones and residue name/number
by Francesco Pietra 29 Mar '10

29 Mar '10

Hi: I was trying to detect all residues (or atoms) within a given distance from a single-atom ligand in model #0 (PDB file). There are several such single-atom ligand atoms in model #0 (practically invisible in chimera as they are not shown at their relative vdw size), each specified by different residue and atom numbers. I want to carry out the task for each single-atom residue. Therefore I can't use the standard command select #0:single-atom-ligand z(or za)<given.distance because that applies to all those single-atom-ligands. Unless the residue can be specified differently (the residue number in place of residue name did not work), the only way that I found to come out was to set different names for the different single-atom ligands. Is anything better? Secondary question: is there any plan to support psf/dcd format (which I am now using for MD with namd) beyond reading movies? Thanks francesco pietra

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Converting SDF files to Mol2 Format
by Nancy 29 Mar '10

29 Mar '10

Hi Elaine, I need to convert a large number of PubChem SDF files into Mol2 format. When I convert an SDF file into Mol2 format, I add partial charges and run energy minimisation on the molecule, as this is necessary for the program I am inputting the files into. So far, I have only used Chimera in this method to convert individual files. Is there a way to convert a large number of SDF files to Mol2 format at once, and also preserve the filenames? Thanks in advance, Nancy

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Question related to chimera H-bond constraints
by snoze pa 26 Mar '10

26 Mar '10

Dear Chimera Users, I have a question related to number of hydrogen bonds. 1. When I am using the Relax H-bond constraints then chimera is showing 76 H-bonds as shown below figure (h bonds are shown in cyan color) http://img260.imageshack.us/img260/6467/screenshotau.png 2. If I will select the option color H bonds not meeting precise criteria differently, then still it shows 76 H bonds with some bonds that do not meet the criteria in red color http://img690.imageshack.us/img690/5607/screenshot1ks.png In 2, Why the red H bonds are different from 1 though H bonds are relaxed. If it is true then why chimera is showing these bonds in Relax H-bond constraints in 1. 3. However, if I will not choose the option to relax H bonds constraints then it is showing 50 H bonds as shown below http://img153.imageshack.us/img153/3822/screenshot2kr.png Thank you very much for your time and help. S

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Binding Pocket Internal Volume Calculation
by ppwanjari 24 Mar '10

24 Mar '10

Hello Everyone, I want to determine the inside volume of a pocket shaped molecule. Does anyone know how can I do it with Chimera? I am only able to measure volume of pocket-making atoms with Chimera, but not the inside volume. Thanks. Piyush

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Chimera crashes on my mac even after a reinstall
by David Chenoweth 23 Mar '10

23 Mar '10

Hi! I recently downloaded a new version of Chimera (Mac OS X (Cocoa, Intel, 64-bit)MD5: e54f53e4313817e26dbc68450bd5312d) and it's been running great until today. After using the program all day it finally crashed just as I was trying to save a session and I didn't get the crash message. I restarted the program and as soon as I tried to open a file the program crashed. I tried shutting my computer down and this didn't help so I deleted that version of chimera from my computer and downloaded it again. After reinstalling the program I still have the same problem and now I'm a bit stumped! I have a lot of work saved in session files from today and I can't seem to get the program to run at all. I am using a new 15 inch Macbook pro (OSX 10.6.2). Any suggestions? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Dimer construction from a monomer generated using Modeller
by akshita kumar 23 Mar '10

23 Mar '10

Dear Members, Using 1T3D as template, we have generated a homology model via Modeller. As the biological unit is a trimeric structure we need to generate trimer of the model too. Therefore we undertook structural alignment of the model and individual template 1T3D chains ("a, b , c"). However in our model the loop region that falls at the interface between two dimers is much longer and as a result the loops between dimer overlap each other. Can anybody please suggest a solution for generating a dimer/trimer from the monomer built using homology modelling. Thanks Akshita

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Re: [Chimera-users] Scripting to write / save multiple models into single pdf file
by Eric Pettersen 23 Mar '10

23 Mar '10

Hmm, it seems that you have the Model Panel set to autostart in your preferences. Now, Chimera probably should ignore autostarting tools when it is in nogui mode, but currently it doesn't. So what you will have to do for now (until we fix this) is to start Chimera normally, turn off the autostart of the Model Panel (and any other graphical tools probably), save the new preferences, and then run your script. If you look in the "Preferences" preference category, it will show the location of the preferences file. You could squirrel away your original preferences file somewhere, make the version with no autostarting, copy that somewhere, and then put your original version back. You would then be able to use the no-autostarting preferences by specifying it's location with the --preferences startup option. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 8, 2010, at 7:32 PM, Sumitro Harjanto wrote: > Hi Eric, > > Thanks for the suggestion. I don’t really script, I usually use a c+ > + code / excel to generate the command (.cmd) files. Should be okay > for the automation for now, if I run into any problem then I will > post it up here again. =] > > Mean while I try running the command “chimera.exe –nogui” in PATH/ > chimera/bin but got the following error message. I followed the > instruction and copy over the debug message (below). any advise? I’m > on a win7 X86 platform btw. > > Thanks, > Sumitro > > ----------------------------------------------------------------------------------------------------- > > Chimera failed abnormally; the exit code was: 1 > Use –debug command line option for the full error message. > > -------------------------------------------------------------------------------------------------- > Cannot execute 'gzip': no automatic decompression of .Z files > Traceback (most recent call last): > File "E:\Chimera\share\__main__.py", line 65, in <module> > value = chimeraInit.init(sys.argv) > File "E:\Chimera\share\chimeraInit.py", line 401, in init > extension.startup(startExtensions) > File "E:\Chimera\share\chimera\extension\base.py", line 1056, in > startup > manager.autostartTools(extNames) > File "E:\Chimera\share\chimera\extension\base.py", line 959, in > autostartTools > > emo.activate() > File "E:\Chimera\share\ModelPanel\ChimeraExtension.py", line 23, > in activate > display(self.module('base').ModelPanel.name) > File "E:\Chimera\share\chimera\dialogs.py", line 77, in display > dialog = find(name, create=1) > File "E:\Chimera\share\chimera\dialogs.py", line 62, in find > return d() > File "E:\Chimera\share\chimera\baseDialog.py", line 523, in __init__ > BaseDialog.__init__(self, master, *args, **kw) > File "E:\Chimera\share\chimera\baseDialog.py", line 244, in __init__ > self.fillInUI(self.__top) > File "E:\Chimera\share\ModelPanel\base.py", line 217, in fillInUI > self._addColumns() > File "E:\Chimera\share\ModelPanel\base.py", line 436, in _addColumns > self._buildTable() > File "E:\Chimera\share\ModelPanel\base.py", line 454, in _buildTable > % len(filter(lambda s: s == 1, self.shownColumns))) > File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 1306, in __init__ > cnf, kw) > File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 307, in __init__ > self.tk.call(widgetName, self._w, *extra) > _tkinter.TclError: invalid command name "tixScrolledHList" > Return code: 1 > Press return or enter to to exit >

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question concerning volumetric data
by Eric Pettersen 22 Mar '10

22 Mar '10

Hi, I have a EM map, spider file and the data are scaled by a factor of 3.6. I need to expand the map by this factor. How can I do this with chimera? Thank you very much for your help Best Regards Stefan

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Regarding backbone images for protein structures
by Saurabh Gupte 17 Mar '10

17 Mar '10

Hello, I have been using Chimera for observing the 3D model of protein structures. For viewing the backbone structure, I used the following commands: show backbone or show minimal But in the latest production version 1.4, I am not able to view the backbone/minimal structure. The 3D structure is rendered properly but the above command do not seem to work. Have there been any changes in the format for above commands or have they been substituted by some other commands? Thanks, Saurabh

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Step size in MD Movie
by Francesco Pietra 16 Mar '10

16 Mar '10

Hi: In my hands, with "chimera alpha version 1.5 (build 30193) 2010-03-06 09:27:34 GMT" linux 64bit (Debian lenny) the step size in MD Movie is always "1", no matter how higher it is set. I did not check if the stable version has the same problem. Could please users verify what happens on changing the step size? thanks francesco pietra

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Volume surface colors
by Will Moore 15 Mar '10

15 Mar '10

Hi, I'm trying to write a script to change the surface colors of volumes in Chimera: This is what I have so far. for m in chimera.openModels.list(): print m.surface_colors m.surface_colors = [(1.0, 0.0, 0.0, 1.0)] print m.surface_colors This seems to alter the surface colors, but has no effect on what the maps look like in the UI. Do I need to call something else for the UI to be updated, or am I using the wrong approach entirely? Also, I would like to only select the volumes in the first line but I don't know what modelTypes this is: for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): Many thanks, Will. William Moore Wellcome Trust Centre for Gene Regulation & Expression College of Life Sciences MSI/WTB/JBC Complex University of Dundee Dow Street Dundee DD1 5EH United Kingdom Phone 01382 386364 http://openmicroscopy.org.uk

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file format conversion using chimera
by snoze pa 12 Mar '10

12 Mar '10

Dear Chimera Users, I want to save/convert a pdb file into .mrc or .ccp4 format using chimera I think I did it before using chimera but don't remember exactly how! I will highly appreciate your help. Thank you S

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Re: [Chimera-users] Chimera: Display map around atoms
by Elaine Meng 12 Mar '10

12 Mar '10

Hi Greg, That "bv" shortcut creates a new, larger map (periodically extended as needed to cover the atoms), which sounds like the opposite of what you want. You can limit the density display to a zone around selected atoms. Choose "Zone" from the "Features" menu in the Volume Viewer dialog to add the relevant controls to the dialog. The zone feature is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… > For future questions, it's better to send Chimera questions to the chimera-users(a)cgl.ucsf.edu list rather than to me directly. That way it won't fall through the cracks if I'm on vacation, or sick, or don't know the answer. I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 12, 2010, at 1:24 PM, Greg Friedland wrote: > Hi Elaine, > Thanks for your earlier help with Chimera. I'm currently have > difficulty displaying a density map. I'd like to only display the > density around protein atoms, not the full symmetry density. I tried > the shortcut 'bv' according to http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/003002.html > but the new map still contains lots of the symmetric molecule > density. Is there another way? > Thanks, > Greg > > Greg Friedland > Postdoc > Sandia National Lab > Joint BioEnergy Institute

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Recording trajectory
by Francesco Pietra 11 Mar '10

11 Mar '10

Hi: I am interested in following the pathway of a ligand forced to leave a protein. I can follow that path with the movie (NAMD format) but I would be interested to also have a trace of the pathway recorded. I would like to show around the protein the various traces for different pathways of exit of the same ligand. thanks francesco pietra

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Re: [Chimera-users] Recording trajectory
by Eric Pettersen 09 Mar '10

09 Mar '10

On Mar 9, 2010, at 2:17 PM, Francesco Pietra wrote: > Hello Eric: > I have seen your later correction mail. > > I had a bad day, that is little time for chimera and with little > success. Please try to guess were I was faulty. > > francesco@tya64:~$ chimera --version > chimera alpha version 1.5 (build 30193) 2010-03-06 09:27:34 GMT > francesco@tya64:~$ > This is amd64, at the moment I have no 32bit computer. > > <select ligand> selects too much. > > <select :residue.number> > <select :residue.name> > do select exactly what I want (which is a small ligand of HEME ligand > of the protein. > > The problem was with <define> command > > MD-movie...Per-Frame "define centroid :residue.number" ... Apply > > then activating the movie gave the same view as not going through the > Per_Frame, i.e., the small ligand does not leave any sphere on the > path. I did not investigate if the sphere are too small to be seen at > the magnification I used, ore have the same color as the background > (black). Very likely, I did some other major mistake. Not sure what to say. Works for me. I've appended an image of centroids tracing the motion of a small ligand in an RNA binding site. I used a step size of 10 and this 'define' command: define centroid raiseTool false radius 1.0 color goldenrod sel "raiseTool false" prevents 'define' from trying to bring up the Axes/ Planes/Centroids tool (and update that tool's table) for every centroid created. The other options control the size and color of the centroid. I had the small ligand selected so 'sel' is my atom spec. I tried it a second time with ":35" (which also selects the small ligand) and that worked too. FYI, "~define" will get rid of all the centroids. I hope this helps somehow. Are you sure you had the "Interpret script as" part of the per-frame dialog set to "Chimera commands"? I can't imagine that you didn't, since you would have gotten some kind of error if it had been interpreted as Python. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Scripting to write / save multiple models into single pdf file
by Elaine Meng 08 Mar '10

08 Mar '10

On Mar 7, 2010, at 5:12 AM, Sumitro Harjanto wrote: > Hi Meng, > I would like to use chimera to help me with a process of combining > receptors and ligands that were modelled separately (in separate > files) > > So here is my intended framework: > > For each iteration: > • open “template.pdb” template file (which contains the receptor/ > ligand complex) I used to model the receptor and ligand > • open the receptor_model.pdb > • open the ligand_model.pdb > • match receptor to template > • match ligand to template > • close template.pdb > • save the models in their current position into a single new pdb > file. > > I was exploring the feasibility of using the command “write” but I > am not too sure if it will allow me to save the complex as a single > pdb file..? > > On a side note, if it’s possible, any suggestion on how to optimise > the run time since I might be running this for a large number of > iterations ..? I read somewhere about switching off the GUI to save > time, does it help..? > > Thanks! > Cheers, > Sumitro Hi Sumitro, You can't save multiple models in one file with the "write" command, but you can use "write" multiple times, one for each model you want to save. If you make sure to save each model "relative" to the same model, they will be in the correct positions with respect to each other when you reopen the files. See the "relative" keyword: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> Or, if you really need to have them in a single file, you can use the "combine" command to create a new single model from multiple models. You would do that after the matching, but before saving the PDB file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> I can't answer about how to script for multiple models, or how much faster it might be to use noGUI, so I'm sending this to the chimera- users list. In the future, please send Chimera questions to the chimera-users(a)cgl.ucsf.edu list, because I might be away from work or (like now) others may be better able to answer the question. I hope this helps, ----- 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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Problem with energy minimization
by Bill McIntire 05 Mar '10

05 Mar '10

I used Dock Prep for my modeled structure, and get no error comments. However, when I try to energy-minimize, I get the following message: No MMTK name for atom "HN1" in standard residue "PRO" PRO is at the N-terminus. I cannot find any help in manual. Please help with this problem. Thanks Bill McIntire

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cap color from command line
by Jean-Paul Armache 05 Mar '10

05 Mar '10

Hello, Thank you for all your previous answers. I would like to ask you whether there is a way to change the cap color not only from the Surface capping tool, but the command line as well and declare it maybe in a script (like for example coloring of the maps and models). Thanks, Jean-Paul

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make one chain from two chains ID in PDB
by Dong, Jianbo 04 Mar '10

04 Mar '10

Hello, I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way. May I get some help for this? Is there a easier way to do this? Many thanks, Jianbo

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positive and negative overlaps
by Kshatresh Dutta Dubey 03 Mar '10

03 Mar '10

Dear all, Can anyone tell me the significance of positive and negative overlaps results in structure analysis module of chimera, as i got 140 contacts that contains both positive and negative overlap values? Any help is appreciated. Thanks in advance Kshatresh Dutta Dubey

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show axis ?
by Stefan Bäckström 03 Mar '10

03 Mar '10

Hi. It is possible to show the box of a volume, and I wonder if it is possible to show the X, Y and Z axis as lines ? Best, Stefan Bäckström Medical Biochemistry Göteborg University Sweden

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groups
by Jean-Paul Armache 03 Mar '10

03 Mar '10

Hello, I am often juggling between different sets that are to be turned on/off together. Is there a way of grouping maps/pdbs so that instead of turning 20 pdbs on, i could just click on a group to which they belong ? If there is something like that, could you point me to it ? And if not, would it be possible to have it in the Model Panel? Best regards, Jean-Paul Armache

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chimera-users@cgl.ucsf.edu
by Jozef Lewandowski 03 Mar '10

03 Mar '10

Hi everybody, I am trying to get a list of all hydrogen atoms within certain distance from a specific atom. I found an old thread suggesting using findclash for that. When I use: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 everything works fine and I get the list of all the atoms within the desired distance limits. However, I get all types of atoms. To select only for contacts to hydrogens, I have tried to add the "test" option but when I type: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 test @H the procedure does not report on any contacts. Am I misunderstanding the syntax? What is the way to get only the distances between :4@c and all hydrogens within ~10A? Moreover, I am ultimately interested in the sum of all reported distances (or more specifically sum of (1/r)6 where r is the distance). Is there simple way to get this value calculated in Chimera (e.g. simple script)? Unfortunately, I have no idea about Python coding, so right now I have to import the list to Excel and calculate what I need in there (which is fine for a few atoms but slightly tedious when you have to check several hundred of them...). Any help would be appreciated. Thanks, Józef

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Sum of distances
by Jozef Lewandowski 03 Mar '10

03 Mar '10

Hi everybody, I am trying to get a list of all hydrogen atoms within certain distance from a specific atom. I found an old thread suggesting using findclash for that. When I use: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 everything works fine and I get the list of all the atoms within the desired distance limits. However, I get all types of atoms. To select only for contacts to hydrogens, I have tried to add the "test" option but when I type: findclash #0.265:4@c overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 test @H the procedure does not report on any contacts. Am I misunderstanding the syntax? What is the way to get only the distances between :4@c and all hydrogens within ~10A? Moreover, I am ultimately interested in the sum of all reported distances (or more specifically sum of (1/r)^6 where r is the distance). Is there simple way to get this value calculated in Chimera (e.g. simple script)? Unfortunately, I have no idea about Python coding, so right now I have to import the list to Excel and calculate what I need in there (which is fine for a few atoms but slightly tedious when you have to check several hundred of them...). Any help would be appreciated. Thanks, Józef

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constraints and restraints
by Elaine Meng 02 Mar '10

02 Mar '10

Hello, The Chimera release notes describe what is new or changed in a release: <http://www.cgl.ucsf.edu/chimera/docs/relnotes.html> ... clicking the "1.4" link: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html> The meaning of "constraint" "restraint" and "tether" may change based on which program you are using. Each program should explain it in its own documentation. In programs I've used, "constraints" meant atoms are completely fixed in place (frozen, cannot move) whereas "restraints" use a force constant like a spring, and allowed some movement. I don't have any opinion on the technical definition of "tethering." Again, don't rely on my descriptions as final because different programs may use the words to mean different things. Chimera minimization only allows "fixing" some of the atoms so they can't move at all. It does not allow holding atoms in place with force constants. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… > 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 > nice to give you a letter! > is there a new one ,really? > what is the new feature in the least software? > > I want constraint ,restraint and tether some atoms and backbone. > how can I do constraiting ,restrainting and tethering in > software.how can i set value for constraiting ,restrainting and > tethering. > what is the difference between them? > > thank you! > >

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NAMD trajectory and AMBER topology
by Francesco Musiani 02 Mar '10

02 Mar '10

Hi all, I would like to visualize in Chimera a trajectory obtained with the program NAMD, but I have a .prmtop topology file generated using AMBER instead of a .psf topology file. I have these files beacuse in NAMD is possible to use AMBER format topology. Is it possible to implement an additional feature in Chimera which allows to visualize NAMD trajectory using AMBER topology? Thanks in advance, Francesco -- Francesco Musiani -- Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin 40, I-40127 Bologna, Italy Phone: +39-051-2096236 - Fax: +39-051-2096203 E-mail: francesco.musiani(a)unibo.it Web: http://bioinorg.agrsci.unibo.it

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load pdb files from local PDB mirror
by Mark Moll 02 Mar '10

02 Mar '10

I have a local mirror of all PDB structures (as pdb files). It’d be nice if Chimera could use this, but it seems that Chimera expects a “flat” directory structure rather than the hierarchical directory structure of the PDB. For example, on my machine the pdb file for 1ady is stored in ${HOME}/pdb/ad/pdb1ady.ent.gz, but when I fetch by ID, the file will not be found. Instead, Chimera will download the file and save it in ${HOME}/pdb/PDB/1ADY.pdb. Is there some way to handle both cases (flat & hierarchical directory structure)? -- Mark

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multi-threading
by Jean-Paul Armache 02 Mar '10

02 Mar '10

Hello, I know that this topic might've emerged earlier, but I was curious whether there were any plans to implement multi-threading into Chimera ? Best regards, Jean-Paul Armache

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Re: [Chimera-users] How are chains paired in morphing?
by Eric Pettersen 01 Mar '10

01 Mar '10

The sequences are in input order unless you ask for the return value to be a dictionary (with the 'asDict' keyword). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 22, 2010, at 11:25 AM, Conrad Huang wrote: > There's a comment in Segment.py: > > # Get the chains from each model. If they do not have the > # same number of chains, we give up. Otherwise, we assume > # that the chains should be matched in the same order > > It uses molecule.sequences() to get the chains. Eric, does > sequences() return the chains in input order, or is it random (eg > hash order)? > > Conrad > > On 2/22/2010 10:26 AM, Thomas Goddard wrote: >> Bobby Laird showed me a homo-tetramer with chains A, B, C, D that >> when >> morphed between two states with the Chimera morph conformations tool >> swapped two of the monomers. In other words the 4 chains from one >> state >> weren't correctly paired with the 4 chains from the other state so >> two >> monomers exchanged positions during the morph. The tetramers were >> built >> from dimers 1pfk and 2pfk by using the symmetry of the unit cell with >> other software (coot?). >> >> How does morph conformations decide which chains to pair? >> >> >> Tom >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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saving moved maps
by Erika Mancini 26 Feb '10

26 Feb '10

Dear Chimera users, is it possible, after moving maps around, to save them into their new positions? I tried save map from volume viewer, but maps are saved in their original positions. Thanks! erika

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question
by Huang, Xinlei 25 Feb '10

25 Feb '10

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help. Thanks xinlei

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variable surface visualization
by Zambonelli, Carlo 25 Feb '10

25 Feb '10

Dear All, I am working with a glycoprotein structure and I want to visualize the protein surface as a continuum with the glycans sticking out as sticks. If I visualize the surface of the whole molecule (including sugars), and then I select the sugars only and visualize them as sticks, the surface of the amino acids immediately connected to the sugar (Asn) appear to be clipped. One solution could be to the following: 1. save the model with a different name 2. load the 2 identical structures and align them 3. remove the sugars from one structure only and use it to visualize the protein 4. the second structure is used for visualizing the sugars and not the protein. I used to do something similar with Pymol, and it should work with Chimera as well, but I am sure there is a better/simpler solution. Any suggestion? Thank you for your help. Carlo

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quesitons
by Xinlei Huang 25 Feb '10

25 Feb '10

Hi, Thank you for inventing the software, it rocks! By the way I have a question about viewing the 3D reconstruction image of a Virus like particle containing small nanoparticle cores. When I tried to increase the electron density in order to see the inside cores there always was a box showed up along with the nanoparticle. I want to know is there a way to remove the outside box? Here I attach an image to explain better what I mean. I appreciate you help. Thanks xinlei Chemistry Department Indiana University-Bloomington

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Re: [Chimera-users] [chimera-dev] run chimera's IDLE in terminal on mac os x
by Eric Pettersen 24 Feb '10

24 Feb '10

On Feb 24, 2010, at 5:34 PM, Yang wrote: > Hi Eric > > I want to manipulate with electron density maps, and just use > chimera functions for reading pdb files and density maps. However, > for high-resolution maps, it takes too long to run the my program on > my mac book. So I want to remotely use the server of our department, > which has much larger memory, to complete this task by typing > commands in terminal. Before that, I had everything done in > chimera's IDLE. So I prefer using chimera functions somehow in > terminal assuming chimera is installed first. > > Thanks for your advice. I think you just want to take whatever commands you were using in IDLE and put them in a Python script (file ending: .py). You can then execute them with "chimera --nogui myscript.py". If you need to supply arguments to the script then instead run it like this: "chimera --nogui --script myscript.py -- arg1 arg2 ...". This is described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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version 1.3
by n.prahl＠freenet.de 24 Feb '10

24 Feb '10

Hi everybody, I don`t find a link on your homepage to download the chimera version 1.3. I only find version before or after chimera 1.3. How can I download the version 1.3? I need this version for my studies. Thank you, Nicole Heute schon ge"freeMail"t? Jetzt kostenlose E-Mail-Adresse sichern! http://email.freenet.de/dienste/emailoffice/produktuebersicht/basic/mail/in…

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Re: [Chimera-users] [chimera-dev] run chimera in terminal on mac os x
by Elaine Meng 24 Feb '10

24 Feb '10

On Feb 24, 2010, at 11:45 AM, ylei(a)ecs.umass.edu wrote: > Dear all > Could somebody tell me how to run Chimera in terminal on the system > of mac? > Thanks. > Yang Hi Yang, It is described in the User's Guide page on Chimera startup: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecore.html> See the part about Mac OS X. To summarize, if Chimera is installed as /Applications/Chimera , to start it from Terminal you would type: /Applications/Chimera.app/Contents/MacOS/chimera (or if it is in a different place or you gave it a different name, substitute those instead). Since that is kind of a long thing to type, you may want to make an alias. My aliases are in the file named .tcshrc in my home directory on the mac, but the filename could be different depending on what shell you are using (maybe .bashrc or .cshrc or something like that). 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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Chemical groups
by Mauro Truglio 23 Feb '10

23 Feb '10

Hi, I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g.. It could be useful to add some sort of identifier, like: FG1: atom atom atom FG2: atom atom atom How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.: Group number 1 : [<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>] Group number 2 : [<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>] Thank you Mauro Truglio (Bioinformatics Lab - University of Rome Tor Vergata)

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Rendering a vector/axis
by Richard Stanton 23 Feb '10

23 Feb '10

Hi, Is there a way to render a vector after defining it as an axis in the "Axes/Planes" tab under "Structure Measurements"? I am able to define an axis using the selected atoms in my structure but I am not sure how to visually render and alter its appearance, as there is no visual representation on the graphics screen. I was hoping that after using my selected atoms to define the axis I would then have an arrow or line showing me the axis/vector and I could then create different vectors/axis and view them simultaneously to show the difference between their angles. Is there a way to do this? Thanks in advance for the help! Thanks, Rich

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Chemical groups
by Mauro Truglio 23 Feb '10

23 Feb '10

Hi, I'm a newbie, and I'd like to use Chimera to recognize functional groups on a structure or a ligand, and I need it to write a file with the atoms involved. Now, if I do Select>Chemistry>functional group , search for one, and export the results through "write list", it exports a raw list of atoms without any specification of which atom is involved in which f.g.. It could be useful to add some sort of identifier, like: FG1: atom atom atom FG2: atom atom atom How can I do that? Already tried to modify __init__.py in ChemGroups, but all I obtain is a list of physical addresses of atoms, e.g.: Group number 1 : [<_chimera.Atom object at 0xa455db8>, <_chimera.Atom object at 0xa455dd0>, <_chimera.Atom object at 0xa455de8>, <_chimera.Atom object at 0xa455e00>, <_chimera.Atom object at 0xa455e18>] Group number 2 : [<_chimera.Atom object at 0xa455e30>, <_chimera.Atom object at 0xa455e48>, <_chimera.Atom object at 0xa455e60>, <_chimera.Atom object at 0xa455e78>, <_chimera.Atom object at 0xa455e90>] Thank you Mauro Truglio (Bioinformatics Lab - University of Rome Tor Vergata)

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Defining planes & Thermal ellipsoids
by David Chenoweth 22 Feb '10

22 Feb '10

Hi! Thanks so much for adding the define plane and define centroid features. Is there any way to add the option of defining the border of the plane as a polygon where the selected atoms define the polygon vertices? This would allow a plane in the shape of a hexagon or any other heterocycle to be inset inside of an aromatic ring for example without the edges of the plane being visible outside the bond enclosed area. Also, the thermal ellipsoid feature looks fantastic, however the probability setting doesn't seem to be functioning. Thanks again for adding all these features, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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How are chains paired in morphing?
by Thomas Goddard 22 Feb '10

22 Feb '10

Bobby Laird showed me a homo-tetramer with chains A, B, C, D that when morphed between two states with the Chimera morph conformations tool swapped two of the monomers. In other words the 4 chains from one state weren't correctly paired with the 4 chains from the other state so two monomers exchanged positions during the morph. The tetramers were built from dimers 1pfk and 2pfk by using the symmetry of the unit cell with other software (coot?). How does morph conformations decide which chains to pair? Tom

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Which Mac daily build to use
by Thomas Goddard 21 Feb '10

21 Feb '10

> on another note: which of the daily builds should I be using? aqua, > aqua-intel, intel-cocoa, intel-cocoa-64. > > not sure on the + & -'s > > do not mind taking some crash risks to push sw dev objectives and reporting. > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine/Houston Texas USA Hi Matt, The Mac Chimera builds are far too numerous now. I recommend the 64-bit Cocoa build. That is what I use. It has one very serious issue right now that pressing Option-e or Option plus many other other characters will immediately crash Chimera. It is a Tk Cocoa bug that I reported but I need to put a fix into Chimera while I wait for the Tk developers to fix it. If that sounds too dangerous use the Chimera Aqua build (32-bit only). That uses the Mac Carbon API which is the older Mac API that Apple says they will not provide 64-bit support for. So we will replace that with Cocoa in the Chimera 1.5 release in a few months. My least favorite choice is Mac X11 which is not the native Mac windowing system and is the least well supported. That Chimera version will also be eliminated in the future. For the 32-bit versus 64-bit Chimera Cocoa you should use 64-bit if you have Mac OS 10.6 (Snow Leopard) or 32-bit for older Mac OS versions. We don't offer 64-bit Mac Chimera on Mac OS 10.5 or older Mac OS versions. Mac OS 10.6 is the first version of Mac OS that uses 64-bit by default. I've measured performance of 64-bit Mac Cocoa Chimera and it is as good as 32-bit. For the Chimera 1.5 release we hope to only be offering two production Mac Chimera versions 32-bit and 64-bit Cocoa. The X11 version will be in the unsupported category and the Aqua (= Carbon) will be gone. Tom

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centroid measurements typo
by David Chenoweth 20 Feb '10

20 Feb '10

Hi, Sorry there was a typo in the last message! The centroid feature is great, but I would like to select two centroids or a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Centroid measurements
by David Chenoweth 20 Feb '10

20 Feb '10

Hi, The centroid feature is great, but I would like to select two centroids of a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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command line writing PDB files
by Matthew Dougherty 19 Feb '10

19 Feb '10

Is there a command line string for writing out selected atoms as a PDB file? thanks, matt Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================== ==================================

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