- Chimera-users - RBVI Mailing Lists

RMSD between ensemble of a protein and its paralogue crystal structure
by Thomas Evangelidis 15 May '12

15 May '12

Dear UCSF Chimera developers, I want to calculate the RMSD between a MD trajectory of a protein and the crystal structure of its paralogue protein. I have looked though the Ensemble Match and RMSD Analysis pages but these applications work for the same proteins (correct me if I am wrong). Is there any way to provide an alignment file to Chimera and calculate the time series of the RMSD between the two paralogues? Thanks in advance, Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Addition of phosphates to PDB structures
by Donado, Carlos 14 May '12

14 May '12

Hi all, I would like to learn how to add a phosphate group to a particular residue, resembling phosphorylation of a particular residue, to a PDB structure. If this is doable using Chimera I would really appreciate any hints on how to do this. Also, I am new to Chimera but I was wondering if there was a way of adding ATP to a designated ATP binding site. I would very much appreciate any responses, Thanks, Carlos Donado The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Chimera-users] semi-transparent ribbon behind semi-transparent surface
by Tom Goddard 14 May '12

14 May '12

Hi Sumitro, I made an image in the style of your image (1a0m.jpg below) using Chimera 1.6.1 and I think it captures the effect of your Chimera 1.5 image (ep.png) very well. The difference is that in your image where the ribbon crosses itself you can sometimes see through the top ribbon. Actually the top ribbon is only transparent in your image in about half of the crossings due to a Chimera 1.5 ribbon transparency bug. In the Chimera 1.6.1 image the ribbon is fully opaque so you do not see through it at places where it crosses itself. I think this produces a better image with less visual depth confusion. Also I think adding silhouette edges as I did in 1a0m_edges.jpg below improves the perception of ribbon crossovers further. I think the main virtue of your image is that the ribbon that is further back is lighter in color so it draws less attention. That is achieved by depth cueing which is the same in Chimera 1.6 and 1.5. My image perhaps does not illustrate depth cueing as well as yours since I used a different PDB model (didn't have yours) and in my view it doesn't vary as much in depth. Tom -------- Original Message -------- Subject: Re: [Chimera-users] semi-transparent ribbon behind semi-transparent surface Date: Sun, 13 May 2012 18:19:39 +0800 From: Sumitro Harjanto To: Tom Goddard Hi Tom, I've attached an image, it's something like this, can you view it? thanks! cheers, Sumitro On 12 May 2012 00:58, Tom Goddardwrote: Hi Sumitro, It is hard to completely understand your problem without seeing an example image made with Chimera 1.5 using the technique you described. If you provide such an image we might have suggestions about how to make something very similar in the latest Chimera. The image link you send before gives permission denied. Tom > Hi Elaine, > > thanks for the reply. I believe you exactly described what I did > with this paragraph: > "In Chimera 1.5 each surface could have its own single-layer > transparency. Thus you could still have multiple transparent > layers overall, but only the top layer of each surface. I'm > guessing the image is something like that (I don't have permission > to view it)." > Sadly, I resorted to re-installing CHIMERA 1.5 cos even if I use > pastel colours in Chimera 1.6, the effects were far from what I've > got using the multiple-single layer transparency previously. Is > there any plan to make the transparency setting more customisable > in the future? that will be of great help! thanks! > > Cheers, > Sum > > On 4 May 2012 00:18, Elaine Meng wrote: > > > On May 3, 2012, at 8:05 AM, Sumitro Harjanto wrote: > > > Hi Elaine, > > I used to use CHIMERA 1.5 to generate some molecular images. > and I was able to show a "hint of shadow" of ribbon behind a > semitransparent molecular surface. but I realised that I can > no longer do that from Chimera 1.6 onwards. I have tried > fiddling with the new "single layer transparency" value, but > either option did not provide me with the visual effect that I > could previously get in chimera 1.5. when I turned off the > single layer transparency, the molecular surface became very > messy with multiple shades and the color is visibly darker. > but If I leave it on, the semi-transparent ribbon was not > displayed at all. is there anyway that I can achieve a similar > effect in Chimera 1.6? i.e if you're wondering what effect I > am talking about here is an example: > http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/n… > <http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/n…> > > Thanks, Elaine! > > Cheers, > > Sumitro > > Hi Sumitro! > In Chimera 1.5 each surface could have its own single-layer > transparency. Thus you could still have multiple transparent > layers overall, but only the top layer of each surface. I'm > guessing the image is something like that (I don't have > permission to view it). > > In Chimera 1.6 the choices are only either a single layer of > transparency, or all transparent layers. > > In Chimera 1.5 if you turn off single-layer transparency for > each surface, the result is the same as in Chimera 1.6 if you > turn off global single-layer transparency. However, I realize > that does not help, since you don't want to show all layers > (it's often ugly, as you describe). > > I don't know if there is any way to get exactly what you had > before, but in 1.6 I suggest trying this: use single-layer > transparency (which is the default), make only the surface > transparent, keep the ribbon opaque. If you want the ribbon > to be less bold, try making it a pastel color. > > I am not involved in the graphics programming -- I CC'd the > list since the other developers may have suggestions (and > other users might find the discussion informative). > 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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Surface atoms and charges
by Nikolay Igorovich Rodionov 14 May '12

14 May '12

Hi all, I was wondering if any of you knew of a way to determine exactly what atoms occur on the surface of a molecule or how to get the exact charge at a point on a surface. Thank you, Nikolay Rodionov

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AMBER ff99SB Documentation
by Nikolay Igorovich Rodionov 12 May '12

12 May '12

Hi all, Could someone point in the direction of some good documentation on ff99SB, how it functions, and what calculations it performs? Thank you, Nikolay Rodionov

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Using Chimera from non-chimera python scripts
by Dan Cohen 11 May '12

11 May '12

Hello, I would like to use Chimera python classes from a python script running outside Chimera (part of a larger python project). I saw another post that explained that this could be done but I was unclear which of the Chimera functionality can be used in this case. In case I want to create an image (e.g. load pdb files, do some editing and then create an image to a file) - can I use the "chimera" class or do I need to use something else? (I saw a reference to "midas" classes) Is there an example for doing that? Processing a file and creating an image in a non-GUI scenario running outside chimera? Thank you, Dany

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Re: [Chimera-users] semi-transparent ribbon behind semi-transparent surface
by Elaine Meng 11 May '12

11 May '12

On May 3, 2012, at 8:05 AM, Sumitro Harjanto wrote: > Hi Elaine, > I used to use CHIMERA 1.5 to generate some molecular images. and I was able to show a "hint of shadow" of ribbon behind a semitransparent molecular surface. but I realised that I can no longer do that from Chimera 1.6 onwards. I have tried fiddling with the new "single layer transparency" value, but either option did not provide me with the visual effect that I could previously get in chimera 1.5. when I turned off the single layer transparency, the molecular surface became very messy with multiple shades and the color is visibly darker. but If I leave it on, the semi-transparent ribbon was not displayed at all. is there anyway that I can achieve a similar effect in Chimera 1.6? i.e if you're wondering what effect I am talking about here is an example: http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/n… > Thanks, Elaine! > Cheers, > Sumitro Hi Sumitro! In Chimera 1.5 each surface could have its own single-layer transparency. Thus you could still have multiple transparent layers overall, but only the top layer of each surface. I'm guessing the image is something like that (I don't have permission to view it). In Chimera 1.6 the choices are only either a single layer of transparency, or all transparent layers. In Chimera 1.5 if you turn off single-layer transparency for each surface, the result is the same as in Chimera 1.6 if you turn off global single-layer transparency. However, I realize that does not help, since you don't want to show all layers (it's often ugly, as you describe). I don't know if there is any way to get exactly what you had before, but in 1.6 I suggest trying this: use single-layer transparency (which is the default), make only the surface transparent, keep the ribbon opaque. If you want the ribbon to be less bold, try making it a pastel color. I am not involved in the graphics programming -- I CC'd the list since the other developers may have suggestions (and other users might find the discussion informative). 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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Partial Charge and Electrostatic Potential Maps
by Nikolay Igorovich Rodionov 10 May '12

10 May '12

Hi Everyone, I was wondering if there is a way to create a maps of partial charge and electrostatic potential that I could then overlay on top of a similar structure. The biological assembly I am working with is too large for good surface calculations so I would like to overlay these maps on the surface of a condensed structure that only includes the regions I am concentrating on. Thank you, Nikolay Rodionov

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Recording actions
by Nikolay Igorovich Rodionov 10 May '12

10 May '12

Hi all, Is there any way to get a read out of all of the operations I have performed within a session? I know of the command history option but that only record the commands I have entered in the command line. I would like to be able to record my command line and non-command line actions, in the order they occurred. Thank you, Nikolay Rodionov

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Writing image to a file using Chimera python script
by Dan Cohen 10 May '12

10 May '12

Hello all, Is there a python interface for exporting images to a file in the UCSF Chimera. I understand I can use runCommand("copy") or runCommand("export"). Is there a python class for doing such commands? Thank you, Dany

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Re: [Chimera-users] [chimera-dev] Dividing a model into seperate models - one for each chain
by Tom Goddard 09 May '12

09 May '12

Hi Mateusz, The "split #0" command produces separate models for each chain. They are numbered #0.1, #0.2, #0.3, ... with the same primary id number (0) and different secondary id numbers. You can use these two-part id numbers in any Chimera command (e.g. color blue #0.2), or you can refer to all the models using #0. There is currently not a way to change the id numbers of models. Tom > Hello, > > Is there a command / a way to split a model into seperate models (one > for each chain)? I know there is the "split" command, but it divides > the model into submodels. > > Mateusz >

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keyboard accelerator "es" doesn't not work after open the command box
by Weimin Wu 09 May '12

09 May '12

A command box was open to input a sym command to generate 60 copies of a pdb structure on the virus capsid surface. Does anybody know how to close this command box? because the keyboard accelerator "es" always goes to command line instead of erasing the density I specified. It is really annoying. Weimin

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Add-H to water O
by Francesco Pietra 09 May '12

09 May '12

Is it possible with CHIMERA to add-H selectively to O atoms to get H-bonded water molecules? I used REDUCE to add-H (-build flag) but was unable to get H2O from O atoms, although het database is in place. What I am trying to get is a reasonable H-bonded water for a highly hydrated protein, before submitting to MD to actually see h-bonding. thanks francesco pietra

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hydrogen bonds in Chimera
by Beale, John 09 May '12

09 May '12

I have a model of a ligand docked in the active site of a receptor protein. I want to visualize only the hydrogen bonds between ligand and receptor- not for the entire protein. Is this possible in Chimera? John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110-1088 Office: 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 John.Beale(a)stlcop.edu<mailto:John.Beale@stlcop.edu>

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Glassy surface in Chimera
by John Squire 08 May '12

08 May '12

Hello, I am trying to show a density map as a glassy surface within which various molecular chains have been fitted. Can anyone please tell me how to produce such a glassy surface for the density map in Chimera? Thanks, John Squire Professor John M Squire, Muscle Contraction Group, School of Physiology and Pharmacology, University of Bristol, University Walk, Bristol BS8 1TD. United Kingdom. Visiting Professor Imperial College London (44) (0)1722 421734 j.squire(a)imperial.ac.uk j.m.squire(a)bristol.ac.uk -------------------------------

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NMR
by MESHAL ALMUALLIMI 07 May '12

07 May '12

Hello, How can I show only the average of my NMR solved structure? As when I fetch the PDBID 1YJR it shows all the structures aligned and I only need the average. I figured out how to eliminate as much structures as I can but I am interested in taking the average of all. Regards Meshal MS candidate Georgetown University

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Chelation of Calcium with Citrate
by Nancy 06 May '12

06 May '12

Hi All, I would like to find the stoichiometry for the chelation of a calcium ion (Ca 2+) with a citrate ion (citrate 3-), as well as the equilibrium constant or free energy of calcium-citrate complex formation. x*Ca2+ + y*citrate3- <=> z*calcium-citrate-complex (x, y, and z are the stoichiometric coefficients) Thanks in advance, Nancy

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Amber Force Field
by Forbes J. Burkowski 04 May '12

04 May '12

Hi: I have noticed that scripts can start with: import MMTK import MMTK.ForceFields from MMTK.ForceFields import Amber94ForceField We are doing some side chain packing studies that would benefit from the availablity of "easy" force field calculations. Currently, the algorithm works with useRotamers() to set two neighbouring rotamers and this is followed by a simple energy calculation to evaluate the interaction energy between the two rotamers. Right now, the energy calculation is only a bit more sophisticated than a steric collision detector. Question: Can we use some functions in the MMTK.ForceFields module to get an improved energy calculation? Any suggestions would be appreciated. Cheers, Forbes

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Re: [Chimera-users] transform coordinates of multiple volumes
by Elaine Meng 03 May '12

03 May '12

On Apr 27, 2012, at 9:26 AM, Ludovic Renault wrote: > Hi Elaine, > I have 120 or so 3d volumes (EM maps). They are all equivalent and are centered at the same position. > I would like to move each one of these 120 volumes by a specific value in terms of euler angles and shift (in pixels I assume). I can use the 'trAnsform coordinates' tool but then if I save the map, it is not saved with the new coordinates. > So > 1- How to (Or can I) save the new coordinates for each volume? > 2- Can I use command lines to automate the process for example by giving the command a text file with the specific coordinates for each volume? > > I did do the rotation with spider software, but the shifting doesn't work because the volume(s) go outside of the box. So if all the above is not doable, is it possible to increase the volumes boxe size in chimera, then I could use the shift function in spider? > > I hope I'm clear enough. > Thanks, > Ludovic Hi Ludovic, It is recommended to send Chimera questions to the chimera-users list (CC'd) -- I'm not the top expert on volumes, so others may have better answers! I think the shift in Transform Coordinates is not in pixels but in units of length. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor…> How the volume grid units map to units of length can be viewed by using Features...Coordinates in the Volume Viewer menu. Chimera has commands for translation (move) and rotation (turn) in X,Y,Z coordinate systems, but I don't know of a command to apply Euler rotations. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> About saving a transformed map: 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", for example: vop #1 resample onGrid #0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> To save the new resampled volume to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its "save" option. However, I see that "vop resample" is most pertinent for saving a map that has been fitted to another. In your case you are simply transforming the map, so it is unclear on what grid you could resample. Maybe there is some way to make a "dummy" grid in the right place. Although "vop cover" extends a map, it assumes periodicity of that map, whereas I assume you want zeroes in the expanded parts. Perhaps expanding a map with zeroes could be done using "vop add" to add a dummy zero map to your data set of interest. Sorry I couldn't give a more complete solution, 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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About resolution and origin
by Yuhong Li 03 May '12

03 May '12

Hi friends, Firstly, I was wondering how to know the resolution of my map since one day I opened volume viewer...tools...fit to segments. And I found that there displaying "density map resolution". So my question is whether that number is the correct resolution of my map? Secondly, in the volume viewer...corrdinates I can know the origin index, but how can I know the origin? These questions may seem to be stupid, but I just want to know. So hope to hear from you very soon! Best Wishes, Yuhong Lee

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changing map dimensions
by Elaine Meng 01 May '12

01 May '12

On Apr 30, 2012, at 6:56 PM, Yuhong Li wrote: > Hi Elaine, > Thanks for your help, now I've understood what those numbers mean. But I was wondering if you could tell me how I can change those gird points, such as change 88 66 94 to 94 94 94 or any cubic numbers ? > Best Wishes, > Yuhong Lee > Hi Yuhong, Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of directly to me. Those numbers are the size of your input data file, so I'm not sure what you mean. You can't just change the numbers arbitrarily. It is possible to make a new data set by cutting off part of the original data set. One way to do that is to use the "volume" command to save a new map file, using the "saveSubregion" option to include only part of the original map. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> However, it sounds like you want to make a new data set that is bigger than your original map. There is a "vop cover" command that will make a bigger map, but it assumes periodicity of the input map. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> If instead you wanted values of zero at the additional grid points, however, I don't know how to do that -- maybe the others have ideas. 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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Just want atom distances
by Patricia LiWang 01 May '12

01 May '12

Hello users group, I don't want anything complicated-- I just want to get some rough distances between atoms. So I go to Tools Structure Analysis Distances A window comes up with an empty table. (No instructions on how to pick atoms) A search of the Chimera documentation tells me I have to Control-leftclick to pick two atoms But no matter how often I click and click and click, it never gives me anything. I can't get even one atom to show up in the panel, let alone two. The side chains are sitting right there, getting clicked away, with nothing happening in the table. I am reading so many similar documentation pages, and apparently there is a difference between "selecting" and "picking" So I figure I'll just use the command line. But the instructions don't even bother to tell you how to use the command line to get the distance between two atoms. There is documentation on how to get distances between something and a "plane". Why do they make this so hard? Surely this is the main "simple" thing people want to do with this program. Would someone please tell me how to Pick or Select or Whatever two amino acids (any atom in them would be fine) and get a distance? Or better yet, please tell me the exact command line command I can use to get the distance between Asparate 234 carboxyl oxygen and Aspartate 295 carboxyl oxygen, both from chain "G"? Thanks! Patti ---------------------------------------------------------------------------

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Measure contact between copies of the same map
by Giovanni Cardone 30 Apr '12

30 Apr '12

Hi, I can use the tool measure contactArea on the surface models of two different maps, but I can not make it work when using it on two copies of the same map: no matter how much I move one map with respect to the other, the first surface listed in the command line will always be entirely colored in red (using offset 0). It looks like the command ignores the transformation. Is this the expected behavior? I can work around it by resampling the maps after the transformation (vop resample # onGrid #), but I liked more the idea of doing the measure without this additional step. Tested it with the latest alpha version 1.7 (build 36320). Thank you, Giovanni

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Contour mapping
by Nikolay Igorovich Rodionov 30 Apr '12

30 Apr '12

Hi all, I was wondering if anyone could help me create an accurate contour map based on surface charge. I've tried rendering my molecule by charge, then using the surface clipping, capping, and the color zone tools. However, the coloring varies based on how I orient the plane. Does anyone know a better and more accurate way to creating a contour map? Nikolay Rodionov

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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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Selecting submodels when they are density maps
by Javier Velazquez 05 Apr '12

05 Apr '12

Hi, I am interested in generating a map from a PDB with 2 chains, and color each chain differently. I can do it very easily using the graphical interface, but I couldn't figure out how to do it from the command line. Here are my commands: molmap #0:.A 7 molmap #0:.B 7 And now adding color is simple: volume #0 color red But this adds color to both maps. Is there a way to specify a submap, so I can add color separately. I am looking for something like this: volume #0:.A color red which I tried and didn't work. Thank you for your help. Javier

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