- Chimera-users - RBVI Mailing Lists

changing HIS to HIP
by Francesco Pietra 16 Dec '10

16 Dec '10

Hello: I need to change several histidine residues (both HIS and HIE, although both called HIS) to HIP. I tried manually. In case of monoprotonation at NE2: modify structure element N bonds 3 geom trigonal connect to preex atoms color by element change modified residue's name to HIP set atom names to ND1 or retain current atom names In both cases the proton attached to ND1 takes the name "H1" instead of the expected HD1. Is that error in the above procedure or chimera bug? (chimera alpha version 1.5 (build 30702) on GNU/LINUX 32bit) Addendum: is there any other method of accomplishing the task with chimera? It is rather troublesome to go through all monoprotonated histidines of this large homomer (in different chains HIS of the same number have been differently protonated by reduce). A problem with reduce (if not my misuse of reduce) is that all histidines become monoprotonated, while the experimental pH is such that all should be diprotonated. I must add that I am bound to reduce because the program that I use subsequently goes through reduce. thanks for help francesco pietra

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selection line-width
by Daniel Gurnon 15 Dec '10

15 Dec '10

Hi everyone, Two requests that would help with interactive demonstrations to large audiences: In preferences/background, the selection mode can be "fill" or "outline". Is it possible to add a line-width option for outline? I want to increase the thickness of a selection outline to make it easier for my students to see when I'm projecting an image, but I don't want to use the fill option and lose residue color information. I suspect that's an easy fix, but this one might be more difficult: Transparent surfaces are very informative when combined with underlying ribbons or stick representations of atoms. But if a residue is visible beneath a transparent surface, selecting it (via the command line) does not show the selection outline. Is it possible to make that work? Thanks, 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] [Chimera-announce] Chimera 1.5 release
by Elaine Meng 15 Dec '10

15 Dec '10

Hi Surendra, Yes, if you are doing map-in-map fitting, it calculates the correlation values, in 1.5 and also in earlier versions. You have the choice of calculating the correlation about zero or about the mean. If you are doing atoms-in-map fitting, it does not give correlation values UNLESS you turn on the "Use map simulated from atoms" option, and in that case you also need to enter a resolution value for the simulated map. If you click the Help button on the dialog it will show the manual page with more detailed explanations, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht…> 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 Dec 15, 2010, at 9:33 AM, Negi, Surendra S. wrote: > Hi Elaine, > In EM fit, Is it possible to calculate the Correlation? I am using current version 1.5 of UCSF chimera. > Thank you. > Surendra > ps: the snapshot is available at : http://img221.imageshack.us/img221/2492/screenshotpt.png

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Maximum surface areas for each amino acid
by Boaz Shaanan 15 Dec '10

15 Dec '10

Hi Elaine, The values in the table you mentioned seem to correspond to side-chain accessibility only, if I compare them to those for Gly-X-Gly peptide as in the classical paper by Miller et al. (1987), 196, 641-656. Their table can also be found in the book by Creighton: Proteins, 2nd edition, p. 142. Best regards, Boaz ----- Original Message ----- From: chimera-users-request(a)cgl.ucsf.edu Date: Tuesday, December 14, 2010 21:11 Subject: Chimera-users Digest, Vol 92, Issue 11 To: chimera-users(a)cgl.ucsf.edu > 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. Maximum surface areas for each amino acid (Tom > Goddard) 2. Center of segmentation regions (Tom Goddard) > 3. Chimera Error (Kshatresh Dutta Dubey) > 4. Re: Chimera Error (Elaine Meng) > 5. Re: Maximum surface areas for each amino acid > (Elaine Meng) > 6. 3D-Stereo. (ayassin(a)wadsworth.org) > 7. merging 3D volumes (Marlovits,Thomas) > 8. Re: merging 3D volumes (Elaine Meng) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Mon, 13 Dec 2010 18:08:11 -0800 > From: Tom Goddard <goddard(a)sonic.net> > Subject: [Chimera-users] Maximum surface areas for each amino acid > To: iropson(a)psu.edu > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4D06D18B.7040806(a)sonic.net> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Ira, > > I don't know of any table of maximal solvent > accessible surface areas > for each residue type when bounded by glycines. Maybe > someone on the > Chimera mailing list will know. > > A Chimera Python script could run through the PDB > and accumulate > per-residue surface area statistics. One trouble with that > would be > that surface calculation fails in Chimera in some percentage of > cases > (~5%) due to numerical problems. > > Tom > > > Hi Tom, > > > > Love the software. Do you have a table for calculating the > maximum > > available surface area for amino acids eg.(Gly-Xxx-Gly) so > that I can > > get a relative percentage exposed surface area from the > calculations? > > Do you know how to find one in the literature? Has anyone > written a > > program that describes the possible surface exposure for a > residue in > > a particular secondary structure and/or a particular sequence? > This > > maximal value would certainly be different depending on the > local > > sequence and structure. For example, a residue in the middle > of a > > helix would have to be shielded from the solvent by the i+4 > and i-4 > > residues, and the size of those residues would matter. > > > > Thanks, > > Ira > > > > > > On 12/10/10 2:41 PM, Tom Goddard wrote: > >> Hi Sumitro, > >> > >> I made a Chimera video tutorial showing how to > determine which > >> residues are on the surface. > >> > >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html > >> > >> Tom > >

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delete named selection
by S. Shunmugasundararaj 14 Dec '10

14 Dec '10

Hi, How do I delete the "Named selection" from the chimera file? I could not get the info from the archive or by searching the web. Thanks in advance Raj

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3D-Stereo.
by ayassin＠wadsworth.org 14 Dec '10

14 Dec '10

Hello, Will the sequential stereo work with the Nvidia 3D vision kit available with the Toshiba 3DV series laptops? if not, What would be the best option for sequential stereo? Thank You. Aymen Yassin. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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merging 3D volumes
by Marlovits,Thomas 14 Dec '10

14 Dec '10

Hi, I was wondering, whether a 3D map can be placed into a box with a user defined number or x/y/z planes ? Ideally, I would like to place several 3D maps into boxes of the same dimensions and would like then to merge all maps into one 3D map file. Is this possible ? Tx for your fast answer, Best, -Thomas Thomas C Marlovits Research Group Leader marlovits(a)imp.ac.at

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Chimera Error
by Kshatresh Dutta Dubey 14 Dec '10

14 Dec '10

Dear All, When i am trying to assign partial charge on a molecule, it is giving error something like this- AttributeError: '_chimera.Atom' object has no attribute 'gaffType' File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py", line 289, in writeMol2 atomType = atom.gaffType I am using chimera 1.5 on linux 64-bit Kindly help to resolve this problem Thanks in advance kshatresh

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Maximum surface areas for each amino acid
by Tom Goddard 14 Dec '10

14 Dec '10

Hi Ira, I don't know of any table of maximal solvent accessible surface areas for each residue type when bounded by glycines. Maybe someone on the Chimera mailing list will know. A Chimera Python script could run through the PDB and accumulate per-residue surface area statistics. One trouble with that would be that surface calculation fails in Chimera in some percentage of cases (~5%) due to numerical problems. Tom > Hi Tom, > > Love the software. Do you have a table for calculating the maximum > available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can > get a relative percentage exposed surface area from the calculations? > Do you know how to find one in the literature? Has anyone written a > program that describes the possible surface exposure for a residue in > a particular secondary structure and/or a particular sequence? This > maximal value would certainly be different depending on the local > sequence and structure. For example, a residue in the middle of a > helix would have to be shielded from the solvent by the i+4 and i-4 > residues, and the size of those residues would matter. > > Thanks, > Ira > > > On 12/10/10 2:41 PM, Tom Goddard wrote: >> Hi Sumitro, >> >> I made a Chimera video tutorial showing how to determine which >> residues are on the surface. >> >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html >> >> Tom

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Center of segmentation regions
by Tom Goddard 13 Dec '10

13 Dec '10

Hi Tyler, The Chimera Segger segmentation tool currently doesn't report the geometric center of segmentation regions or the principal axes. I've attached a Python script that will do that. Select the regions in Chimera then open the script (File / Open). The results will appear in the reply log (menu Favorites / Reply Log). The results are in physical coordinates (taking account of volume grid spacing), not grid index units. Tom > Dr. Meng, > > I am using Segger in Chimera and displaying the principal axes for > some of my segmentations. I am wondering if there is a way to find > the XYZ coordinates of the origin of the principal axes for each of my > segments. Is there a way to put the coordinates for these axes in a > text file? > > Thank you, > > Tyler Steele >

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