February 2010 - Chimera-users - RBVI Mailing Lists

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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Chimera-users February 2010