- Chimera-users - RBVI Mailing Lists

distance measurements
by Bala subramanian 19 Feb '10

19 Feb '10

Friends, Greetings. I have 5Aromatic residues and 4 aliphatic residues in a loop. I want to calculate the CA distance between between each of Aromatic with the CA of each of the aliphatic residues in a single command. Can i do it in some fancy way. I have tried distance command but it takes exactly two atoms. Any example script would be of great help to me. Thank you, Bala

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Density map in Chimera
by Pancera, Marie (NIH/VRC) [C] 17 Feb '10

17 Feb '10

Hi, I opened an electron density map in chimera. For some reason it is forming a box and I am not quite sure how to get the density outside of the box (to cover symmetry molecules etc...) Thanks for helping me with that. Best regards, Marie

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copyright permission
by M P Williamson 17 Feb '10

17 Feb '10

Hi folks. I am getting near to the end of writing a book called How Proteins Work (to be published by Garland, hopefully this fall). I would like to include a figure showing anisotropic B factors for a protein, and the best image I have come across is of heme on your website, http://www.cgl.ucsf.edu/chimera/feature_highlights/ellipsoids.png I would like to include this image in the book. Could you let me know if there are copyright restrictions on the image, and how you would like me to refer to it? Thanks Mike Williamson

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help
by Giuseppe Falini 17 Feb '10

17 Feb '10

Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe

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writing a trajectory to multiple pdbs
by Dan Gurnon 16 Feb '10

16 Feb '10

Hi everyone, How would one write a trajectory read into MD Movie to a series of pdb files instead of one large file? I don't see a suitable option specified for the "write" command, and for "Save PDB" it seems the option of multiple files is only available when multiple models are selected. Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Hydrogen Atoms
by Elaine Meng 16 Feb '10

16 Feb '10

On Feb 14, 2010, at 11:31 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am working on calculating the Solvent accessible Surface Area on > the antigen interaction region. I am confused about adding/removing > hydrogen's, my question is will there be a change in SASA if you > have or not have hydrogen's atoms added. > Thank You. > -Thiru > Hi Thiru, Yes, it will be different with and without hydrogen, because the molecule is treated as a set of spheres where each atom is a sphere. There will be more small bumps on the surface when there are hydrogens. Also, the radii of the other atoms may change because there are different defaults for structures with and without hydrogens, as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> I think surface area calculations are usually done on structures without hydrogens. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html P.S. you may want to use "measure buriedArea" (or maybe you are already doing that): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedAr… >

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reference for saving pdb
by Samuel Coulbourn Flores 12 Feb '10

12 Feb '10

Hi Guys, I'm having what I am sure is a trivial problem. When I save my PDB coordinates, I am asked what the reference is, and choose a density map. But when I read those coordinates back in, they are translated/rotated from where they should be and no longer match the density map. Can you tell me what is the correct procedure for setting the reference? Thanks Sam

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Row interleaved stereo and Zalman monitors under Linux
by David Bhella 12 Feb '10

12 Feb '10

Hello again! I have just installed a Zalman M220W monitor on one of our workstations under OpenSuse 11.1, after a small amount of fiddling to get it working with dual head mode it seems to be behaving. In Amira it gives beautiful 3D, although the assignment of left and right eye views seems fairly random, as Amira has the option to reverse left and right eye views this is not a problem. In Chimera however with row interleaved stereo I seem to always get the views the wrong way around. It took me a while to work out why it didnt seem to be giving good depth and it was quite disconcerting to look at while viewing cryoEM 3D reconstructions, however with a pdb file it was quite obvious that my right eye was getting the left eye view. There only seems to be the option of reversing the views for sequential stereo however.... I would be grateful if anyone could advise me on how I can fix this. Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Skype: d.bhella Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html

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Shadows
by David Bhella 12 Feb '10

12 Feb '10

Hi, I just updated my Chimera installation to 1.4.1 (Mac OSX aqua), and I noticed that for some reason shadows are not so nicely rendered in standard 3x3 super-sampled output. They look very blocky, much as they always have done in the viewer. In version 1.4 I always got very nice shadows when I saved an image. I am trying to save images of an isosurface view of a 3D reconstruction. Is there a setting I need to adjust to get high quality shadows back again? Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Skype: d.bhella Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html

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session writing
by Jean-Paul Armache 11 Feb '10

11 Feb '10

hello, i would like to ask whether it would be possible to save sessions with relative path, instead of absolute one ? it is a bit complicated to move the sessions between different platforms with the absolute one. thank you, best, jp armache

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Re: [Chimera-users] 64-bit version of Chimera for windows
by Tom Goddard 11 Feb '10

11 Feb '10

Hi Pu, Greg Couch in our lab is working on a 64-bit version of Chimera for Windows 7. It should be available in a month or two if we don't run into overwhelming difficulties. Tom > Hi Tom, > > Do you have 64-bit version chimera for windows. Our computer manager asked me > this question. > > Happy Chinese New Year. > > Best regards > > > Pu Qian > > >

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Peptide Builder in 1.4x
by nettles 10 Feb '10

10 Feb '10

Hi All, I was very excited to download the 1.4 version of Chimera with it many improved features yesterday. However, I was surprised today when I tried to build an anti parallel beta sheet and it came out looking like an alpha helix. After experimenting around i realized all option give alpha helix. This is true for 1.4 (build 26788) and 1.4.1 (build 29977)and . The old version 1 build 2540 works fine. (It worked with a newer version I had too, but silly me overwrote that with the 1.4.x) Thought you would like to know. I appreciate your excellent software. Thanks, Jim Nettles

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measure crossing angles for axes
by Tom Duncan 09 Feb '10

09 Feb '10

I have used the "measure rotation" command to create several axes. In each case, a marker set (to show the axis) is generated that consists of 2 pseudoatoms and 1 bond. Is there a simple way to measure the crossing angle between 2 such axes? If the marker set had 3 atoms, I could probably use the Axes/Planes tools to do this. Thanks, Tom

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BCC CHARGES
by emrys.fslife.co.uk 08 Feb '10

08 Feb '10

Hi folks Is it possible(within Chimera) to get the dipole moment of low-molecular weight ligands alongside their calculated BCC atomic charges? Best wishes E.Thomas

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Chimera/VMD visualization difference
by Keith Battle 08 Feb '10

08 Feb '10

Hello Chimera team, I recently conducted a MD simulation of a 12-mer peptide adjacent to a hydroxyapatite crystal using NAMD 2.6. When I viewed the output coordinates from the simulation in pdb format using Chimera 1.4, the protein ribbon was broken and the hydrogens of certain residues were not bonded but in close proximity. All of the non-bonded hydrogens were colored purple by default. The waters of the system and the crystal looked normal. Overall, the protein looked distorted. I decided to visualize the peptide using VMD 1.8.7 and to my surprise the protein ribbon was intact with all hydrogens bonded to their respective residues. Any insight into why this difference occurred would be greatly appreciated. Best, Keith Battle Research Technician University of South Alabama

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Align the molecule
by snoze pa 08 Feb '10

08 Feb '10

Dear Chimera Users, I am wondering if it is possible to align the molecule along the X-Y or Z axis. I want to place the molecule, along a line joining N to C terminal line. Idea is to place a molecule along this line(N to C line) which is X or Y or Z axis. Thank you, S

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display comsia contour maps
by Joern Lenz 08 Feb '10

08 Feb '10

hi there, i am wondering if it is possible to display contour plots for 3d qsar (comsia) made by sybyl in chimera. any help is much appreciated, cheers, jorn

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Aligning planes with principal planes
by Dipl.-Ing. Thomas Mitterfellner 05 Feb '10

05 Feb '10

Hello! Is there a command in Chimera that turns a molecule in a way that a plane (explicitly created or just the selected atoms defining the plane) is parallel to the xy or the other principal planes? Thank you, Thomas

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SDF partial charges
by Elaine Meng 04 Feb '10

04 Feb '10

Hello, An additional follow-up to Nancy's question from Jan 31. <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004754.html > Daily builds (version 1.5) dated Feb 4 or newer will now automatically read the partial charges in 3D SDF files obtained directly from the PubChem database. <http://pubchem.ncbi.nlm.nih.gov/release3d.html> However, I wanted to caution everybody that the protonation states of the resulting molecules are not what you would expect at physiological pH. The functional groups that would generally be charged near pH 7 are neutralized, at least from the few examples that I've examined: carboxylic and other acids fully protonated rather than formally negative, aliphatic amines neutral rather than formally positive. For example, alanine is given as H2N-CH(CH3)-COOH rather than + H3N- CH(CH3)-COO - If that is the case for all of the 3D SDFs obtained directly from PubChem (Nancy, you may want to take a closer look at a sample of your structures), I would not recommend them for docking. Instead, you may want to get small molecule structures from some place that has attempted to put them in reasonable charge states, such as the ZINC database. <http://zinc.docking.org/> Best, 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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Calculating sigma level for EM map
by Thomas Goddard 04 Feb '10

04 Feb '10

Hi Andy, I don't know any convention defining the sigma value for an EM map. For x-ray maps there is a convention because the density is periodic you can just take the root-mean square density value across a whole unit cell. Note that that isn't a measure of noise level -- it's just a reproducible value describing the typical density levels across the unit cell. That isn't useful in EM maps because the value depends on how big the box is that contains the non-periodic structure. A bigger box contains more grid points outside the structure (values near zero) that make the root-mean square value (RMS) smaller. So such an RMS value isn't a reproducible measure of density values since it depends on the box size. I think when sigma is mentioned in EM papers they tend to mean the noise level. I don't know of any standard protocol for determining the noise level. If you knew the sigma level you wished to use, Chimera is still not able to display density values in sigma units. That is on our feature request list. Currently you have to take the values Chimera displays and divide by the sigma value yourself. I haven't added this capability yet because the notion of sigma does not seem to be well defined in EM work. Since Chimera map analysis is primarily used for EM, not x-ray, showing sigma units has not been a high priority. Tom -------- Original Message -------- Subject: Re: Threshold From: Anindito Sen To: Tom Goddard Date: 2/4/10 1:09 AM > Hi Tom > > I should have been more specific- my reconstruction is a EM density map > of a helical biopolymer. In that case what should be the correct > approach to calculate the threshold. Can you site any reference which > may be useful in this regard? > > Do we have the option of directly obtaining sigma value for the > threshold in Chimera ? > > Dr. Anindito Sen (Ph.D) > > --- On *Thu, 4/2/10, Tom Goddard* wrote: > > > From: Tom Goddard > Subject: Re: Threshold > To: "Anindito Sen" > Date: Thursday, 4 February, 2010, 9:29 > > Hi Andy, > > That may be right. But there are many issues. If your map is for > a crystal unit cell then that seems reasonable. In other cases > where the map is not a crystal unit cell then the RMS of the whole > map will depend on what the boundaries are of the map. For > instance, for an EM single particle reconstruction the RMS will > depend on how much padding of zeros there is, ie how big the box > is. If it is an x-ray map but not a unit cell again the RMS will > vary depending on what part of the map is taken. > > Tom > > > -------- Original Message -------- > Subject: Threshold > From: Anindito Sen > To: Tom Goddard > Date: 2/3/10 7:23 PM >> * >> >> Hi Tom >> >> I am "cropping" out high electron dense region from my >> density map to determine the volume of that region. The value of >> the Level in my Volume viewer is 438 (Range -618- 1024). The other >> factors are : >> >> f15_volume035.brix: mean = 23.123, SD = 137.14, RMS = 139.07 >> >> Therefore following your email, can I say, threshold is 438/139.07 >> = 3.1s >> >> Thanks for your help. >> >> Best Wishes >> >> Andy >> >> >> >> Tom Goddard* >> /Tue May 20 15:54:10 PDT 2008/ >> ------------------------------------------------------------------------ >> Hi Dave, >> >> Chimera can report the mean, standard deviation and root mean square >> map value using menu entry >> >> Tools / Volume Data / Volume Mean, SD, RMS >> >> The values using whatever normalization the map file has. If you divide >> the threshold level you set in the volume dialog by the RMS value you >> will get a sigma value. Actually I'm not sure if that is correct -- >> depends on the definition of sigma. Maybe you have to take the volume >> dialog number, subtract the mean and divide by the SD. The reported SD >> and RMS differ only in that the SD is the standard deviation of the map >> about the mean while the RMS is the standard deviation about 0. >> >> Allowing the volume dialog to show the sigma values directly is on our >> requested features list (item 88) but has not yet been implemented. >> >> http://www.cgl.ucsf.edu/chimera/plans.html >> >> Tom >> >> >> David Chenoweth wrote: >> >/ Hi! >> />/ >> />/ Can you please let me know if there is a way to report or set the >> />/ sigma value for an electron density map from a high resolution crystal >> />/ structure. I am using a ccp4 FWT.map and DELFWT.map file for >> />/ structures <1.2 angstrom resolution. Can I somehow find the sigma >> />/ value that corresponds to the Level setting in the Volume viewer? >> />/ >> />/ Thanks, >> />/ Dave Chenoweth >> />/ >> / >> >> ------------------------------------------------------------------------

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Smooth Surface
by sudheer molugu 03 Feb '10

03 Feb '10

Hi, I've installed the latest chimera version. I wanted take pov-ray pictures of a cryo-EM map. I would greatly appreciate if you can help me in make the map surface smooth. I couldn't find the option for smooth surface. Thank you, Sudheer.

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Mac 64-bit Chimera for large data sets
by Tom Goddard 02 Feb '10

02 Feb '10

A 64-bit Mac Chimera daily build is now available for Mac OS 10.6. It will not run on Mac OS 10.5. http://www.cgl.ucsf.edu/chimera/download.html#daily If you work with EM maps larger than 1 Gbyte or molecular models of several hundred thousand atoms the larger addressable memory in the 64-bit version will help avoid out-of-memory errors and crashes. The 32-bit Mac Chimera versions can only address 4 Gbytes of memory and because libraries, stack and other uses of memory the practical working data size limit for 32-bit versions of Chimera is about 1 Gbyte. You should have more than 4 Gbytes of memory installed in order to benefit from the 64-bit version. The 64-bit Mac Chimera is in early testing so will have more bugs than usual. I've tested the 64-bit Mac Chimera running Gaussian filtering on a 2048 by 2048 by 800 map requiring about 3.2 Gbytes for the floating point result and 0.8 Gbytes for the original map. This worked correctly (took about 3 minutes on a machine with 6 Gbytes of memory) but failed with 32-bit Mac Chimera. We are also working on a 64-bit Windows Chimera that will work with Windows 7. This may be available within a month if no serious obstacles are encountered. A 64-bit Linux Chimera has been available for a few years. Tom

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alter volume data with python
by Michael Zimmermann 02 Feb '10

02 Feb '10

Dear Chimera users, I cannot find a way to search the chimera-users archive, so I appologize if this has been asked already. I wish to alter some volume data in specific ways; delete (zero out) all volume values that do not meet certain density criteria. The following code modifies the matrix values, but I can't figure out how to update the map that is being displayed in the volume viewer. I would like to be able to do something like: opened[0].full_matrix = H Then I would only see the swath that I "selected" with the following code. # ------------------------------------------------------------------------ source = '1R0A_antigen_6A_8s_0.425f_inv.mrc' opened = chimera.openModels.open(source) em = opened[0] H = em.full_matrix() s = H.shape for k in range(0,s[2]-1): for i in range(0,s[0]-1): for j in range(0,s[1]-1): if(H[i,j,k] >= -.28) and (H[i,j,k] <= -0.001): H[i,j,k] = H[i,j,k]+1 else: H[i,j,k] = 0 # ------------------------------------------------------------------------ Thank you, -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University

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SDF Partial Charges
by Nancy 01 Feb '10

01 Feb '10

Hello, I am performing protein-ligand docking simulations, and the preferred ligand input file format is Mol2. I obtained some of my ligand structures from PubChem in SDF format, and I noticed that the SDF files contain partial charges ("PUBCHEM_MMFF94_PARTIAL_CHARGES"). Is there a way to preserve the charges in Chimera when converting to Mol2 file format? Thanks in advance. Nancy

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Converting SDF to Mol2: Errors
by Nancy 01 Feb '10

01 Feb '10

Hi All, When I convert an SDF file to Mol2 format using UCSF Chimera, I noticed that some valence errors were introduced. I can correct these errors for individual molecules, but doing so for large sets becomes cumbersome; is there any solution to this problem? Thanks in advance. Nancy

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