- Chimera-users - RBVI Mailing Lists

improved movie tools
by Martin de Jonge 16 May '12

16 May '12

Hi, I recently published a tomographic reconstruction that was rendered using Chimera (see: http://www.pnas.org/content/107/36/15676.abstract) The movie that we were able to build using Chimera was excellent, but had to be recorded entirely in real time. That is, we had to turn on recording, manipulate the model, and turn off recording. I feel that it would be much easier if there was a nice interface to sequencing functionality. In this (as I imagine it) a sequence of particular views could be stored, and times specified for smooth transition from one element in the sequence ('view') to the next. These views could even be stored as saved sessions (if that helps with implementation). Please let me know if this functionality is already possible and (if so) please send me a sample! I note that my licence has expired; but when I try to renew it I run into problems with the server. Looking forward to your reply, Martin de Jonge Senior Scientist - XFM Australian Synchrotron p: (03) 8540 4195 | f: (03) 8540 4200 | m: 0488 338 594 800 Blackburn Road, Clayton, Victoria 3168 <br>This message and any attachments may contain proprietary or confidential information. If you are not the intended recipient or you received the message in error, you must not use, copy or distribute the message. Please notify the sender immediately and destroy the original message. Thank you.

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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 >

1 0

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

2 2

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!

2 2

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

3 5

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

3 2

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

2 1

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

3 3

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

3 4

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

2 1

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.

3 2

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

2 1

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

3 2

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

2 1

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

2 1

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

3 4

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

2 1

Merge the protein sequences of two different chains
by Hsih-Te Yang 05 Apr '12

05 Apr '12

Dear all: I am a new beginner of Chemira software package. By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence. How can I do? Thanks for any kind help further. Hsih-Te

2 4

Solvate models
by Nikolay Igorovich Rodionov 05 Apr '12

05 Apr '12

Hi all, I was wondering if some could explain to me the differences between the water models available under the solvate option. * POL3BOX - POL3 water model * SPCBOX - SPC/E water model * SPCFWBOX - SPC/Fw water model * QSPCFWBOX - qSPC/Fw water model * TIP3PBOX - TIP3P water model * TIP3PFBOX - TIP3P/F water model * TIP4PBOX - TIP4P water model * TIP4PEWBOX - TIP4P/Ew water model Thank you all in advance, Nikolay Rodionov

2 1

Coloring distance labels
by George Tzotzos 05 Apr '12

05 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

2 2

Coloring distance labels
by George Tzotzos 05 Apr '12

05 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

1 0

color by RMSD
by Thomas Evangelidis 04 Apr '12

04 Apr '12

Dear UCSF Chimera users and developers, Is it possible to color a pair of structures representing different stages of the thermodynamic cycle of a protein by the RMSD, without aligning them? thanks in advance, Thomas

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Re: [Chimera-users] [Chimera] #10638: heme not included in morph trajectory
by Elaine Meng 04 Apr '12

04 Apr '12

Hi Francesco, There is some progress... in the newest daily build (Apr 4) I can run the commands below to successfully show a morph of 1hho and 2hhb that includes heme and iron. 1hho only has two chains, so it is necessary to delete C,D from 2hhb before morphing. To include heme and iron, it is necessary to delete all the other het residues that may be different between the structures. I hope this helps, Elaine Here between "----" are contents of Chimera command file, which you could save as plain text file named something.cmd and open in Chimera to execute the commands. Lines starting with # are just comments/explanation and don't do anything. ------------- open 2hhb open 1hho # # delete 2hhb chains C,D # delete #0:.c-d # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose the structures; I used "mm" with defaults but it could be # done with options, or MatchMaker GUI, or "match" command, # or manually with mouse # mm #0 #1 # # create morph trajectory which will be model #2 # morph start #0 frames 25 morph interpolate #1 frames 25 morph movie ~modeldisp #0,1 --------------------- Then I tried to get fancy and make a tetramer of 1hho so that the morph could be from tetramer to tetramer. However, then only the heme/iron from A and B were included, not from C and D. I don't know why, because they are all in the input structures!! Here is that script in case it might be useful: --------------------- open 2hhb open 1hho # # make 1hho tetramer; #1 is original, #2 additional copy # sym #1 # # combine #1,2 dimers into tetramer model #3, close #1,2 # combine #1,2 name 1hho-tetra newchainids true close true # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose #0 and #3 # mm #0 #3 # # create morph trajectory which will be model #1 # morph start #0 frames 25 morph interpolate #3 frames 25 morph movie ~modeldisp #0,3 ---------------------

1 0

occupancy field
by Darjan Andrejc 03 Apr '12

03 Apr '12

Hey, Is it possible to change occupancy field to 1.0 in Chimera? I need a pdb file of my protein for docking and the file needs to have an occupancy field 1.0. Thanks for the help Darjan Andrejc, Mpharm PhD student, Department of Biotechnology National institute of Chemistry, Ljubljana, Slovenia

2 2

Minimize with fixed atoms
by Hurt, Darrell (NIH/NIAID) [E] 03 Apr '12

03 Apr '12

Hi there, I'm trying to minimize a protein after mutating a residue with the Rotamers panel. I first do a Check Clashes and select the clashing atoms. Then I expand the selection using Zone to <5 A. I use these selected atoms as the non-fixed atoms and the unselected atoms as the fixed ones. When I then run the minimization with the appropriate settings, I get an RMSD of 0.000 A for each step, even though the step size is 0.02 A. Nothing moves. Same thing if I have no fixed atoms. Am I in a local minima? Is that why nothing moves? The energy is very high (from the Reply Log): Potential energy: 222274199.525130, Gradient norm: 833984762.552943 Updated 6029 atoms. RMSD: 0.000000 Finished 1 of 5 steepest descent minimization steps Any ideas? I do have some hetero atoms... Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

3 5

Re: [Chimera-users] morphing
by Elaine Meng 31 Mar '12

31 Mar '12

Hello Francesco! First make sure you are hiding the input conformations, so that you are seeing only the morph (for example, you could show Model Panel from Favorites menu, then uncheck the S(hown) boxes for everything except the morph results). I say that because if you see something not moving, it might be the original structure. As explained here, the morph should contain all of the atoms in the protein chain that are included in all of the input structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p…> Since your input structures are the same protein, if each one includes the sidechain atoms, the morph should contain all the same sidechains and they should move from one position to the other during the morph. They may not be displayed automatically, however. Try displaying all atoms (again better to hide the other structures first) to make sure of what is there. About the ion: even if the ion is in both structures, it may not be in the morph if you are using an older version of Chimera. However, there have been some fixes, and I believe if you are using Chimera 1.6 or newer, the ion should be included. The fix I'm thinking of was 6 months ago and is described here: <http://plato.cgl.ucsf.edu/trac/chimera/ticket/9886> If you try Chimera 1.6 and the suggestions above but you believe there is a bug, you could use Help... Report a Bug in the menu and describe how to reproduce the problem, attaching session file if necessary. 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 31, 2012, at 5:24 AM, Francesco Malatesta wrote: > Hello from Rome! > I'm trying to morph 2 different conformations of the same protein. I get a very very nice movie, but I can't get amino acid side chains or heteroatoms (heme iron) to move also. > Is there any way to do this? > thank you for help > Francesco

2 1

How to save VIPER transformation matrix
by snoze pa 30 Mar '12

30 Mar '12

Dear Chimera Users, Is it possible to save the coordinates after the VIPER transformation (xyz-2 fold symmetry) in Chimera. I can create a multiscale biological molecule in chimera but it is not saving the viper matrix in pdb file. Please note that this pdb is a model not the crystal structure and I am trying to save the viper matrix for this pdb. Thank you, S

4 5

Chimera is not loading properly
by Andrea Edwards 27 Mar '12

27 Mar '12

I have not used Chimera in awhile. I just downloaded the new version for Mac-OSX-64-bit and when I open it, none of the buttons on the gui are visible. There are ovals and things where there should be buttons, but not words on them. How can I fix this? attached is a screenshot. Thanks, Andrea

3 2

PDB model merging
by Nikolay Igorovich Rodionov 27 Mar '12

27 Mar '12

Hi all, I'm working on a project that requires me to merge models created through PDB BIOMT records. I have been using the copy&combine feature in the model panel to merge all of my models, and then writing a new PDB of only the combined model. I've noticed that this method deletes a large amount of information about the structure, including secondary structure records. Is there a way to merge models without losing such data? If it is relevant, I am merging 90+ models.

3 5

Trajectory analysis: hbond
by George Tzotzos 26 Mar '12

26 Mar '12

I'm wondering if there's a way to determine hbond formation during a trajectory in a similar way to the way the Plot distances tool in MD Movie/Analysis works. Or dumb values to a file. Many thanks in advance for any suggestions Regards George

3 4

Re: [Chimera-users] Electrostatic Potential using APBS .dx file
by Tom Goddard 26 Mar '12

26 Mar '12

Hi Soca, Sounds like you are doing everything right. That makes me suspect that something is wrong with your APBS file -- like all the potential values are zero. To see what the distribution of the potential values are, open the APBS file and then use menu Tools / Volume Data / Volume Viewer, and click on the histogram (empty rectangle in the middle of the volume dialog). That will show a histogram of the potential values. You can move the vertical bar on the histogram to see what the potential value is at that position. Check if -5 to 5 is a reasonable range. Tom > Hello, > > I have been attempting to generate a electrostatic surface map in > chimera using an external potential file generated from APBS (.dx). > > I understand that Chimera has an internal surface calculation protocol > via Coulombic Surface Coloring, however, I would like to use the > Electrostatic Surface Coloring. > > However, when I open my molecule (PDB), show surfaces, and choose its > MSMS main surface to color by electrostatic potential using the .dx > file, the surface map is not the red, white, blue that I have set in > my parameterts under Surface color. Everything turns to grey. My other > parameters include: > > red -5, white 0, blue 5. Colors 3. Palette Red-Blue. Surface offset 1.4. > > I feel as though I am missing something trivia that would allow me to > generate the surface image I want, however I am lost after may > searches for advice through the forums and tutorials. > > Please let me know what I am missing. > > Thanks > > Soca > > -- > Ardian Soca Wibowo, Ph.D. > Postdoctoral Associate > Dann Research Group > Department of Chemistry > Indiana University

1 1

Dimethyl Sulfoxide Electromagnetic Absorbance
by Nancy 25 Mar '12

25 Mar '12

Hi All, I would greatly appreciate it if anyone could provide a reference or information on the electromagnetic absorbance characteristics of dimethyl sulfoxide, especially in the region of 800-1400nm. Thank you, Nancy

1 1

RMSD plot
by lecan 23 Mar '12

23 Mar '12

Hi everybody. I am interested in plotting RMSD values vs time from molecular dynamics. Is there a way to extract the RMSD values from a the RMSD map in the analysis tool of MD movie. Or maybe exists another way to do this with Chimera. Thank you in advance Luis L.

2 1

how to measure the volume of the active site
by Thomas Evangelidis 23 Mar '12

23 Mar '12

Dear UCSF Chimera developers, I am interested in measuring the volume of the active site of a kinase. I have searched through the documentation and the only thing I found was how to measure the enclosed volume of a surface object. Is it possible to do what I want with UCSF Chimera? Could you please point me towards the relevant commands? Thanks in advance for any help. 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/

2 1

Multi-PDB fitting question
by Tom Goddard 21 Mar '12

21 Mar '12

> Dear Tom, > > ... > Currently we are trying to use a lot of PDBs (hundreds!) to fit one > density map and trying to find out the best fitted PDB, and we found > that fitting the PDBs one by one manually was very time-consuming and > low-efficiency. So we are wondering that if there is any advanced way > or batch file that can speedup this process? > > Thank you so much and we are looking forward your reply. > > Best Regards, > Lei > Hi Lei, Ok, I added a new "eachModel" option to the Chimera fitmap command so that one command can independently fit many molecules in the same map. For example, fit #1-50 #0 resolution 13.5 eachModel true listFits true will fit PDB models with id numbers 1 to 50 into map with id #0 and list the fits in a dialog. Each of the fits is done independently (no account for clashes between molecules). Details on each fit are given in the Reply Log dialog (menu Favorites / Reply Log). This will be in tonight's Chimera daily builds (run at midnight) if they succeed: http://www.cgl.ucsf.edu/chimera/download.html#daily Here is the fitmap command documentation which will be updated later this week or next week. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html You will probably find that you can't open hundreds of PDB molecules in Chimera because it takes too much memory. But you can fit them in a few batches if this happens. Tom

1 0

disulfides: naive question
by George Tzotzos 21 Mar '12

21 Mar '12

Apologies for the earlier message. I need to clarify. Loading the topology and trajectory files onto Chimera and selecting functional group/disulfides shows the bonds throughout the trajectory. The problem I have is that I don't see the bonds in pdb files that I've generated from the topology files. Thanks again George

2 4

disulfides: naive question
by George Tzotzos 20 Mar '12

20 Mar '12

I've built a number of disulfide bonds in Amber topology files. From these, I've generated pdb files. When I load them in Chimera and do Select/Chemistry/Functional group/disulfed, I fail to see the selected residues and/or the bonds between them. Obviously, I'm doing something wrong. Any help would be greatly appreciated Regards George

1 0

depicting secondary structure elements
by Jordi Querol Audi 20 Mar '12

20 Mar '12

Dear Chimera developers, I would like to show a fitting of a pdb into my EM reconstruction but instead of displaying helices and b-sheets I would prefer to use cylinders or tubes. Is there any way to display a pdb this way? Thank you so much in advance, Jordi

3 2

smoothMD.py
by Anne Bowen 19 Mar '12

19 Mar '12

Hello, I would like to smooth an MD trajectory using the script " smoothMD.py" mentioned here (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-September/006797.html) I can't access the attachment. Could someone send it to me? Thanks! Anne

2 1

Chimera Modeller interface trouble
by Karel Berka 16 Mar '12

16 Mar '12

Dear all, I have a strange problem with Chimera 1.6.1 Modeller (9.10) interface - when I tried to prepare a model based on template 3DDQ (CDK2 kinase), it showed that Modeller locally is running: 0%, but it stayed on this value. When I checked Task list, I have found that although it is still "running", the result was "progress: finished" with no protein model produced. I dwelwed more and I later found that Modeller script was prepared, but Modeller was unable to start due to the misspelling between sequence used for the template (probably from SEQRES) and sequence calculated from template structure. When I deleted residues that Modeller was unable to find in the structure, I was able to build the models. As for the web homology modelling interface - I was also unable to get model from Opal server, probably for the same reason. What to repair in Chimera to get Modeller interface running? because otherwise it seems like homology modelling is not working at all, which is not true. Best wishes Karel "Krápník" Berka P.S.: I have tried both Win64 and Debian64 binaries of Chimera 1.6.1. **************************************************************** RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.berka(a)upol.cz ****************************************************************

2 1

Calculating partial charges of a charged ligand
by Christos Deligkaris 16 Mar '12

16 Mar '12

Dear Chimera users, I have a charged ligand (formal charge of +2) and I have tried using Chimera to calculate the partial charges of that molecule. Even though Chimera predicts correctly that the net charge is +2, after calculating the partial charges (using the Gasteiger method) I see that the sum of all partial charges is zero. Changing the net charge of the molecule seems to have no effect on the calculation of the partial charges. It also seems that the Gasteiger website does not offer the service of calculating the partial charges any more... ( http://www2.chemie.uni-erlangen.de/services/petra/smiles.html) Do you have any suggestions on how to calculate the Gasteiger charges so that the net charge on my molecule is +2? Thank you for your help, -- Christos

2 1

Match structures and density maps
by Sam Meyer 16 Mar '12

16 Mar '12

Good morning, I have two density maps, which I want to align for comparison. They are associated to 2 different PDB structures that I can use as references. I want to match the two PDB structures, and use the rotation/translation matrix of this alignment to move the density map as well. Is that possible ? Thanks Sam Meyer

2 1

1.6.1 release out
by Eric Pettersen 14 Mar '12

14 Mar '12

Hi all, We have put out a 1.6.1 release which, along with some minor fixes, corrects these problems: - Graphics would be corrupted or chimera would crash on recent versions of Linux, e.g., Ubuntu 11.10 and Fedora 16 - Planes (of Axes/Planes/Centroids tool) failed to start - Inappropriate "file types" (e.g. PDB ID) included in the file-type list of the main File→Open dialog - Very old sessions (pre-2006) would not restore on 64-bit Windows Please download 1.6.1 if these problems are affecting you. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

plz ans the ques
by rashmi gupta 12 Mar '12

12 Mar '12

Sir, I am working on insilico metabolomic and genomic study of edible cyanobacteria. What plan should i do to accomplish my goal. -- Rashmi research scholar School of Biomedical Engineering IT BHU

1 0

resolution for volume fitting
by Bala subramanian 07 Mar '12

07 Mar '12

Friends, I am a newbie to fitting molecular structures on a volume map. I would appreciate if someone could suggest me some guidelines to choose an optimal resolution of the map before fitting. Thanks, Bala -- C. Balasubramanian

3 4

Increasing the mesh thickness in Chimera Volume Viewer
by Pradeep Pallan 07 Mar '12

07 Mar '12

Hi, I wanted to know whether there is an option to increase the mesh thickness in Chimera? I have loaded the map in Volume Viewer, but do not know how to increase the thickness of the mesh. Thanks for your help, Pradeep -- -------------------------------------------------------------------

2 2

Linux and Chimera 1.6
by Greg Couch 07 Mar '12

07 Mar '12

If you have are running a recent version of Linux, for example, Ubuntu 11.10 or Fedora 16, then you should wait for Chimera 1.6.1 before updating or use a daily build. -- Greg

2 1

Re: [Chimera-users] [Dock-fans] Help with antechamber
by Scott Brozell 07 Mar '12

07 Mar '12

Hi, On Tue, Mar 06, 2012 at 08:04:51PM -0500, Brad Ridder wrote: > Thanks for the responses, but I am still stuck on antechamber. > > We are holding off on this python scripting; that was the plan before, but > I want to make sure I can get the individual components working properly > before I go to the effort of writing a python script to do dock prepping. > > I cannot get either the DOCK-supplied version of antechamber or the > CHIMERA-supplied version of antechamber to work correctly. ==== dock > First, I tried the DOCK distribution again. $AMBERHOME was not defined. I > used: > > *$DOCK_HOME/bin/antechamber -i $PDBFILES/3GLR.pdb -fi pdb -o > $DESKTOP/3GLRcharged.mol2 -fo mol2 -c bcc* > > This returns the error: > * > Total number of electrons: 0; net charge: 0 > > Running: $DOCK_HOME/bin/mopac.sh > Error: unable to find mopac charges in mopac.out > * It is possible that antechamber is working and that mopac really fails. Did you look in mopac.out ? Are you really trying to run antechamber on 3glr, which is a protein ? antechamber is not the way to assign charges to a protein. Read the AmberTools manual http://ambermd.org/doc11/AmberTools.pdf Here is one way to test your dock's antechamber: cd dock6/install/test/amber_score_181l make ../../../bin/antechamber -s 2 -i lig.1.mol2 -fi mol2 -o lig.1.gaff.mol2 -fo mol2 -nc 0 -c bcc This last command should emit: ... Running: $DOCK_HOME/bin/mopac.sh Running: .../dock6/bin/am1bcc -i ... ... > I then repeated this later with $AMBERHOME defined to $CHIMERA/bin/amber11, > which gives the new error message: > > *Total number of electrons: 0; net charge: 0 > > Running: $AMBERHOME/bin/divcon > sh: > /home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/divcon: > not found > Error: cannot run "$AMBERHOME/bin/divcon" of bcc() in charge.c properly, > exit* This approach - using dock's antechamber with amberhome defined to be inside chimera - is not a good one. However, you might get it to work: It is very likely that sqm, not divcon, is the qm program that should be invoked. So get help to look for the option to force sqm usage: antechamber -h ... -df am1-bcc flag, 2 - use sqm(default); 0 - use mopac ... is probably what you'll find; if so then add -df 2 to your antechamber command line. > Now, a few questions/reflections: > > 1. As per the first error message, why is mopac.out causing trouble? Is > this a file I am supposed to make? mopac.out is the output of the mopac qm program which antechamber invokes and then processes to make am1-bcc charges. > 2. As per the second error message, I have no idea what "divcon" is, or > what it is needed for. There is no divcon file that comes with the CHIMERA > amber11 directory, nor is there any divcon file in the AmberTools amber11 > directory I have on my Desktop. divcon is another qm program. ==== chimera > I then tried the version of antechamber with the CHIMERA distribution. > First I typed: > > *$CHIMERA/bin/amber11/bin/antechamber* > > And antechamber said "AMBERHOME is not set!" > > So, I set $AMBERHOME to be $CHIMERA/bin/amber11. Then I used > > *$CHIMERA/bin/amber11/bin/antechamber -i $PDBFILES/3GLR.pdb -fi pdb -o > $DESKTOP/3GLRcharged.mol2 -fo mol2 -c bcc* > > The Terminal then spams: > > *Warning: detected more than 10 Residue sequence numbers; > this may be a large multiple residue PDB file; > large multiple residue PDB files are not supported. > Continuing, but problems may be encountered.* > > And then finally stops with > > *Segmentation fault* This warning was absent in early versions of antechamber. And it likely right on target. mopac (above) probably failed because you are really trying to run antechamber on 3glr. antechamber is not the way to assign charges to a protein. > So, in short, I am utterly bamboozled. Obviously, antechamber can handle > "large multiple residue PDB files", since the Dock Prep tutorial used the > AM1-BCC charge model on the large 1ABE.pdb protein, and it worked fine. Why > is it not working for me? No, the receptor charges were assigned using residue matching. See step 1 of http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecule… and the chimera dockprep docs: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecontrib.html "Charges for standard residues ... are taken from Amber (details)." Read the force field chapter of the AmberTools manual and references therein for even more details. scott > On Wed, Feb 29, 2012 at 10:30 PM, Scott Brozell <sbrozell(a)rci.rutgers.edu>wrote: > > Here's another similar ligand prep script: > > http://mailman.docking.org/pipermail/dock-fans/2011-December/002591.html > > While it is a good pedagogical exercise to prep once manually, > > scripting is the only practical approach for lots of ligands. > > > > As far as running antechamber, be careful and be specific about which > > one you run: > > If you are manually running Dock's antechamber then define DOCK_HOME. > > Do not define AMBERHOME. > > See > > http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#Error%20from%20amberize_ligand > > ; > > > > If you are manually running Chimera's antechamber then DOCK_HOME > > is irrelevant but AMBERHOME may be relevant. > > ( I have not manually run Chimera's antechamber, so my advice may be > > wrong. ) > > > > Also note that Dock's antechamber is circa 2006 with some key subsequent > > bugfixes. Chimera's antechamber is much more recent. > > Dock's antechamber uses mopac for qm; > > Chimera's antechamber uses sqm for qm; > > (http://ambermd.org/#AmberTools) > > I have found mopac to be more robust than sqm. > > Your mileage may vary. > > > > scott > > > > On Wed, Feb 29, 2012 at 04:08:22PM -0800, Eric Pettersen wrote: > > > This previous posting to the dock-fans list seems to be more directly > > > pertinent: > > > > > > http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html > > > > > > On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote: > > > >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. > > > > > > > >-----Original Message----- > > > >From: Brad Ridder <clustro(a)gmail.com> > > > >To: dock-fans <dock-fans(a)docking.org> > > > > > > > >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?

2 1

Surface charge density!
by IONEL , ALINA ELENA 06 Mar '12

06 Mar '12

Hi, My name is Alina Ionel and I am PhD student. I have a pseudoatomic model (in pdb format) for a capsid protein. I did a representation of the electrostatic potential in Chimera with the option “Coulombic Surface Coloring” for a hexamer, for example. The unit of this potential are in Kcal/mol*e and the surface is colored in a range of values -10 to 10 Kcal/mol*e. I want to know the surface charge density for this hexamer (in C/m2). I need the value. Can you help me, please? Thank you, Alina

3 3

Atom distances
by Kyle Morris 05 Mar '12

05 Mar '12

Hi, Is there a way in chimera to search a PDB (or any structure file..) for a particular distance and report back in text or visually between what atoms this occurs, i.e. query whether a structure contains atoms spaced at between 5.5-5.6 Å and which ones? Thanks in advance for your help, appreciate it! Kyle

3 2

how to show backbone carbonyl oxygen
by james09 pruza 03 Mar '12

03 Mar '12

Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James

2 5

How to show the electron density of just selected residues? Thanks
by Pingyang Liu 02 Mar '12

02 Mar '12

Hi, How to show the electron density of just selected residues? Thanks I followed the Chimera tutorial, but still the electron density of the whole protein was displayed. Another question: what does the convexity of a protein structure tell? I did not find much information about convexity online. Thanks a lot. Best, Andy --

2 2

segmentation fault
by nauton lionel 02 Mar '12

02 Mar '12

Hello I send this Email, because I can't used chimera-1.6 for linux 64 bits ( 2-29-2012 version) it crash with this comment "segmentation fault", everytime I tried to load pdb or mol2 files. and I don't have this problem with chimera-1.6rc for linux-32 bits or chimera-1.6( 2-29-2012 version) and chimera-1.5.3 for linux 64bits works well on the same PC I used fedora 16... regards

2 1

Chimera 1.6 officially released
by Eric Pettersen 02 Mar '12

02 Mar '12

Hello everybody, A new production release of UCSF Chimera (version 1.6) is available: <http://www.cgl.ucsf.edu/chimera/download.html> Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). This will be the last Chimera release supporting Mac PowerPC platforms and OS X 10.5 (Leopard). New features include a Rapid Access interface to frequently used data and tools, new ribbon spline options, improved transparency rendering, new fetch type: Uniprot protein sequence and annotations, and several options for fitting atomic structures into density maps: global search, iterative sequential fitting, symmetric fitting, etc. More details are given below; see release notes for the full list: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html> Graphics, Depiction: * new spline options for ribbon closer to backbone atom positions * new initial model colors, pastel rather than saturated * improved transparency rendering (global single-layer on by default) * 3D labels drawn on top by default * fancy backgrounds: images from files, color gradients from Palette Editor * options for cleaner pocket/tunnel surface display (see "sop" command) Structure Analysis and Modeling: * AddH allows specifying less common states of Asp, Glu, Lys, Cys * FindHBond can label H-bonds with distances * Blast Protein shows more info for PDB hits (ligands, resolution, etc.) * Build Structure improvements for joining peptides, swapping substituents * tools to change chain IDs, renumber residues * minimization: - can be conjugate gradient (previously steepest descent only) - parts of structures can be ignored * distance and angle plotting for trajectories * Cage Builder tool for generating polyhedral cage models <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebu… > * interface to MultiFit web service (simultaneous rigid fitting of multiple structures to density, developed by the Sali Lab, UCSF) * "fitmap" command: - global search with random initial placement - iterative sequential fitting - symmetric fitting * "measure" command options: - map symmetry - surface contact area - center of mass User Interface and I/O: * Rapid Access interface to frequently used data and tools shown at startup, can be hidden/shown at any time by clicking the lightning-bolt icon <http://www.cgl.ucsf.edu/chimera/1.6/docs/UsersGuide/rapid.html> * caching fetched data is turned on by default * scaling with mouse/touchpad scrolling can be turned off (Mouse prefs) * Model Panel: - group/ungroup function, such as for NMR ensembles - functions reorganized into favorites/all * new input types: SPHGEN spheres, Maestro/Glide docking output (ViewDock) * WebGL export (experimental feature) Sequence-related: * new fetch type UniProt: protein sequence and feature annotations * Multalign Viewer: - UniProt features can be mapped onto already open sequences - Region Browser improvements for handling feature annotation regions - calculation of region overall RMSD - interface to Modeller homology modeling allows including water, other HET Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] reading SMILES description into Chimera
by Elaine Meng 01 Mar '12

01 Mar '12

Hi Boaz, You can just use the command line, for example: open smiles:CC1=CC=C(C=C1)S(=O)(=O)[O-] I'm thinking it may be a mistake that SMILES shows up as a file type in the "Open File" dialog. The only other place I can think of is in Build Structure (under Tools... Structure Editing), where the Start Structure section includes a SMILES option. In that case you would just type or paste in the SMILES string in the indicated field. 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 1, 2012, at 7:08 AM, Boaz Shaanan wrote: > Hi, > > I'm trying to read a small molecule for which I have a SMILES description into Chimera. I selected 'smiles' from the input options but it's not clear to me how to proceed. Do I have to generate a text file with the smiles description in it? do I paste the smiles description in the file name line? or what? > > Thanks for your help. > > 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 > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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how to copy partial charges from a .mol2 file to another
by Thomas Evangelidis 29 Feb '12

29 Feb '12

Dear Chimera community, Is there any straight forward way to copy the partial charges from one .mol2 file to another? 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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partial conservation coloring
by Eric Pettersen 28 Feb '12

28 Feb '12

Jill Voreis wrote: > I'm trying to use chimera to show conservation maps. Using pdb files > that I fetch from the database using the pdb id number and > alignments created in clustal that contain the sequence of the pdb > file, I select render by conservation. For some reason, the > conservation colors only go onto my model when it's in ribbon form. > When I try to show the surface representation or use spheres so that > I can use commans to show the SAS, the colors of my model do not > match the conservation model but rather are stuck on some sort of > coloring scheme related to the compounds that are there. The > majority of the map looks brown, like the default color before > rendering by conservation. If you could help me, I'd really > appreciate it! Hi Jill, There are a few possibilities here, though it's impossible to be certain what the problem without access to a concrete example. My best guess is that much of the surface region of your protein is poorly conserved and those areas have columns where the rows are more than 50% gap characters. For such columns no conservation score is assigned. That means that when you use Render By Attribute with default settings, those atoms / surface parts will retain their original colors. If in Render By Attribute you use the "No-value color" color well to assign a color to such regions (perhaps gray) you will be able to tell if this is what is happening. Two other possibilities are that you don't have the "Color atom" and "Color surfaces" check boxes checked [though I image you would have noticed this!] or that your protein has multiple chains and that only one is associated with the alignment and only that one is getting colored. If none of these are "it", if you can provide me with a specific example so I can reproduce the behavior then I will investigate. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Not crossfade but coinciding bond command...
by Kevin D. Walker 28 Feb '12

28 Feb '12

I temporarily disabled a bond command and found this to be the cause of the selected bond problem I am having. I don't think crossfade has anything to do with it.

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Animate a Reacton Mechanism?
by Kevin D. Walker 28 Feb '12

28 Feb '12

I constructed a movie for the first part of a reaction mechanism (substrate docking). I would like the animated mechanism to continue as follows. The substrate donates a proton to a tyrosine residue of the enzyme, forming an intermediate. The intermediate rotates 180 (I have accomplished this part) and the proton rebounds to the intermediate forming a new product, which is released. I can animate the product release -- it's the reverse of substrate docking. The part of the animation I cannot envisage is how to smoothly show or morph the bond transitions (bond breaking and making) during the reaction progression. IAny advice on whether Chimera or other ancillary software can do this is appreciated.

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using CalcAttr from a Python script
by Roger L. Chang 28 Feb '12

28 Feb '12

Hi, 1) I need to get residue.areaSES for two separate selections (all polar amino acids and all nonpolar amino acids). I have successfully generated a list of residue.areaSES using the GUI simply by selecting the residues of interest and then using the attribute calculator typing "residue.areaSES" in the formula box of the Attribute Calculator, which outputs the list to the Reply Log. This is the data that I need, but I need to get it for >2000 PDB structures and would like to automate this analysis through a Python script. I am somewhat new to Python and Chimera and don't yet know all the ins and outs yet. I dug through the code and found a method "getResidueAttr" in the "ResidueDataWrapper" class from "CalcAttr". This seems to be what I need, but I don't know the proper syntax to call it from my Python script. Could someone please provide an example? 2) I would like to sum the residue.areaSES values once I have them. I tried "sum(residue.areaSES)" in the formula box of the Attribute Calculator in the GUI, but this returns the error "Formula evaluation error: expecting vector argument in function". I'm not sure again on the proper syntax to use "sum()" in the Attribute Calculator. If I knew how to generate/save the residue.areaSES data from the command line, I could just parse the saved file and sum the values in Python. How can Attribute Calculator formulas be used from the command line, and if they can't, how can I save the residue.areaSES data to file from a Python script? Thanks in advance, Roger -- Roger L. Chang Graduate Student Bioinformatics and Systems Biology Graduate Program University of California, San Diego

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Coloring molmap surfaces
by Tom Goddard 24 Feb '12

24 Feb '12

> Greetings Tom > > How can color the molmap surface of certain atoms/residues. > > Many Thanks, Vijay > Hi Vijay, Use the Color Zone dialog to color a molmap surface to match nearby atom colors (menu Tools / Volume Data / Color Zone). You select the atoms you want to use for color (e.g. menu Select / Select All) choose a distance range from those atoms to color in the Color Zone dialog and press the Color button. In Chimera 1.6 (release candidate available on the web) or daily builds there is a command version of color zone. For example scolor #0 zone @ca range 5 says to color molmap surface #0 to match C-alpha atom colors within a distance of 5 Angstroms. To avoid jagged edges in the coloring you should use the molmap gridSpacing option to specify a grid size about 1/5 to 1/10 the map resolution. The default value is 1/3 of map resolution making a fairly coarse surface mesh. Colors are only assigned to the mesh vertices, so a fine mesh is needed for smooth boundaries between different color regions. Tom

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batch peptide builder
by Xiao-Ping Zhang 23 Feb '12

23 Feb '12

Dear Chimera developers, I would like to generate some peptides from a protein sequence. The peptide builder in Chimera is a very nice application. I wonder if there is a stand alone script which I can use to generate series peptides from the command line. Thank you for your help. Xiao-Ping Zhang

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Drawing arrows without using .bild file
by Victor Muñoz 21 Feb '12

21 Feb '12

Dear all, I'm trying to make a script that draws an arrow on every atom and every frame during a trajectory using the MD movie. Right now, the script creates a .bild file to draw the arrows, but it is not a very good approach since it is creating a new file for every frame of the trajectory. I was wondering if there's a way to do the same thing without having to create the .bild file. I already checked the "shape" command but you can´t use it to draw an arrow. Maybe I should make a combination between a cylinder and a rectangle to draw an arrow? Is there any other easy way to do that? Thanks in advance. Kind regards, --

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bug
by Eifler, Jay Q. (UMKC-Student) 21 Feb '12

21 Feb '12

Whew, too much work to get you guys a message. The bug report form was lengthy. Anyway, can't join models in your latest 1.6 version but 1.5 whatever is fine. Should have never updated.

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(no subject)
by Valia Dimitrova 21 Feb '12

21 Feb '12

Hi, I am PhD student, and I am working with program Gaussian, I want ask you some questions. I want to make maps with electrostatic potential, I saw that with this program may be make very beautiful pictures. What type of files I have to have, so I can do these pictures? I have ".fchk" files and ".cube" files. May I use them to make this? I will be very appreciated if some one can help me. thank you in advance Valia Nikolova

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how to find
by Bishwajit Das 18 Feb '12

18 Feb '12

suppose i want so select ARG 188 and TRP 144 and also want to see the distance between them ....how i do this in chimera..please help me. -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* * --

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