- 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

3 3

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 >

2 1

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

2 3

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

2 2

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

2 1

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

3 3

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

3 2

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

3 6

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

2 4

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 --------------------------------------------------------

2 3

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

6 8

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 >

3 15

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

2 1

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

4 4

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

2 2

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

2 3

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

2 1

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

1 0

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

3 5

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

2 1

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

2 1

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

2 2

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

2 1

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

4 5

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

2 2