- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Hydrodynamic radius
by Tom Goddard 14 Oct '09

14 Oct '09

Hi Sudheer, I don't know if the theoretical hydrodynamic radius Rhyd defined on the wikipedia page http://en.wikipedia.org/wiki/Hydrodynamic_radius is a good approximation to the Stokes' radius. The Stokes' radius depends on both shape and hydration details. I've added a request for this calculation in Chimera to our feature request page (item 220). http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests This is much more specialized than typical Chimera features and I would not expect it to be implemented any time soon. If you wished to implement it I could probably show you how to get out of Chimera a list of grid points within a displayed contour level that would be the input to the calculation. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Hydrodynamic radius From: Sudheer To: goddard(a)cgl.ucsf.edu Date: 10/14/09 2:03 PM > Hi Tom, > > Im interested in the optical properties of a protein. Yes, "the > hydrodynamic radius for a uniform solid bounded by a contour surface > of your map would be useful". Yes, Stocks radius. Actually I'm running > Dynamic light Scattering experiment to find the variation in the size > distribution of a protein with change in Temperature. (I mean im > trying to find at what temperature the protein forms monomer and > dimer...!) I already have Cryo-EM map of the dimer and so just thought > of comparing the Hydrodynamic radius between the cryo-map and the DLS > result. > > I hope you got my interest in finding the Hydrodynamic radius of my > protein. > > Thank you very much for your help, > Sudheer. > > > Date: Wed, 14 Oct 2009 13:54:03 -0700 > > From: goddard > > To: Sudheer > > CC: chimera-users(a)cgl.ucsf.edu > > Subject: Re: [Chimera-users] Hydrodynamic radius > > > > Hi Sudheer, > > > > Chimera isn't able to compute hydrodynamic radius of maps or > > molecules. Are you primarily interested in diffusion properties or > > optical properties of your structure? Do you think the hydrodynamic > > radius for a uniform solid bounded by a contour surface of your map > > would be useful? Do you mean Stokes' radius or the R_H defined on the > > wikipedia page? > > > > http://en.wikipedia.org/wiki/Hydrodynamic_radius > > > > The latter looks like a pretty simple calculation. > > > > Tom > > > > -------- Original Message -------- > > Subject: [Chimera-users] Hydrodynamic radius > > From: Sudheer > > To: chimera users > > Date: 10/14/09 1:05 PM > > > Hi, > > > > > > Can I measure the Hydrodynamic radius a Cryo-EM density map using > Chimera? > > > > > > Thank you, > > > Sudheer Molugu. > > > > ------------------------------------------------------------------------

1 0

Hydrodynamic radius
by skmolugu＠miners.utep.edu 14 Oct '09

14 Oct '09

Hi, Can I measure the Hydrodynamic radius a Cryo-EM density map using Chimera? Thank you, Sudheer Molugu.

2 1

Running Chimera on Ubuntu
by Claudio Saracini 12 Oct '09

12 Oct '09

Hello, I installed Chimera on my MacBook Pro with Unix OS (Ubuntu). When I try to run the program from the bash I get: Bash: Chimera: Command not found I'm a newbie of Linux. I guess I forgot to do something after having installed Chimera. I would appreciate your help. Claudio *************************************************** Claudio Saracini Kenneth D. Karlin Research Group Department of Chemistry The Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218 E-Mail: claudio.saracini(a)jhu.edu Group Website: http://www.jhu.edu/~chem/karlin/ ****************************************************

2 1

Protein secondary structure
by Beale, John 08 Oct '09

08 Oct '09

I realize that this is probably simple, but I haven't been able to work this problem out. Is there a way to read a single pdb file into Chimera and then have the program show me what amino acid sequences of the protein are alpha helices, what are beta sheets, and what are 3,10 helices, etc? Thanks! John John M. Beale, Ph,D, Associate Professor of Medicinal Chemistry St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

2 1

Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

2 1

Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

1 0

Re: [Chimera-users] Displaying Surface For Selected Residues
by Eric Pettersen 07 Oct '09

07 Oct '09

On Oct 7, 2009, at 4:33 PM, Thiruvarangan Ramaraj wrote: > Thanks Eric, but just to follow up on the surf sel command, > > It displays the surface for the selected residues, > > does it assign solvent-excluded and solvent-accessible surface areas > per atom and residue to attributes named areaSES and areaSAS to the > selected residues or to the whole protein?. > > after I do "surf sel" I have select:/areaSAS > 50 , looks like it > selects for the whole protein. Shouldn't it show only for the > selected surface region. > Hi Thiru, Surfaces are computed for the entirety of the molecule (that the surface covers), not just the residues you display the surface on. So therefore other residues also got areaSAS/SES attributes. To get what you want I think you need: sel :/areaSAS > 50 & @/surfaceDisplay --Eric > Thanks > > -Thiru > > --- On Wed, 10/7/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: Displaying Surface For Selected Residues > To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> > Date: Wednesday, October 7, 2009, 5:14 PM > > Yes, most commands work on everything if you don't specify what to > work on. For instance "color red" colors everything red whereas > "color red sel" colors the selection red. > > --Eric > > On Oct 7, 2009, at 4:09 PM, Thiruvarangan Ramaraj wrote: > >> Worked fine, Thanks, Eric >> >> -Thiru >> >> --- On Wed, 10/7/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >> >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> Subject: Re: Displaying Surface For Selected Residues >> To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> >> Date: Wednesday, October 7, 2009, 5:04 PM >> >> "surface sel" >> >> --Eric >> >> On Oct 7, 2009, at 4:03 PM, Thiruvarangan Ramaraj wrote: >> >>> Hi Eric, >>> >>> I have a protein with a few residues selected, and I wanted to >>> show surface only on the selected residues, when I go to Actions - >>> Surface -Show , it shows surface only for the selected residues, >>> but when I use the command surface on the command line it shows >>> the surface for the entire protein. Is there a command line >>> option to show surface only for the selected residues on the >>> protein. >>> >>> Thanks >>> >>> Thiru >>> >>> --- On Thu, 10/1/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >>> >>> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >>> Subject: Re: [Chimera-users] Solvent Accessible Surface Area >>> To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> >>> Cc: "UCSF Chimera Mailing List" <chimera-users(a)cgl.ucsf.edu> >>> Date: Thursday, October 1, 2009, 3:38 PM >>> >>> Oops, spotted a bug in the script. This line: >>> >>> out = open(os.path.expanduser("~/out", "w")) >>> >>> should be: >>> >>> out = open(os.path.expanduser("~/out"), "w") >>> >>> --Eric >>> >>> >>> >> >> > >

1 0

Re: [Chimera-users] Chimera pov-tracing question
by Tom Goddard 07 Oct '09

07 Oct '09

Hi Maya, Your mesh is transparent in the povray image (zoom in on the image and look at the mesh lines) but I guess is much less transparent than in the Chimera window. I ran some test images with the current Chimera 1.4 daily build which also showed the povray mesh looked much different (darker, thicker and less transparent) than in the Chimera window. While we have improved the match between povray images and what you see in the Chimera window it is still very bad. Dozens of messages on the chimera-users mailing list relate to the poor quality of Chimera Povray images. http://www.google.com/search?hl=en&q=povray+site%3Awww.cgl.ucsf.edu%2Fpiper… As suggested in the following message, with these poor quality povray results a better presentation can almost always be obtained by not using povray: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004030.html Attached are 5 test images showing some of the problems. 1mwm chain A, molmap 6 angstroms. test.png - povray transparent mesh 0.24, appears very dark test2.png - povray transparent mesh 0.04, black specks all over the mesh test4.png - povray transparent surface 0.24, ugly multilayer mosaic test5.png - no povray, transparent surf 0.24, glossy lighting, silhouette edges test6.png - no povray, same as test5 but mesh. Tom -------- Original Message -------- Subject: Chimera pov-tracing question From: maya shcushan To: 'Thomas Goddard' Date: 10/7/09 9:59 AM > > Dear Dr Goddard, > > > > You previously assisted me with other problems with Chimera, so now I > am asking your help again. > > I have a density map and a structure mapped on it. I showed the map as > transparent mesh, and tried to pov-ray the image. However, the picture > came up with the map not transparent (attached). Do you have any idea > how to resolve this issue, making the map transparent in the image as > it is in the main window > > > > Thanks, > > Best, > > *Maya Schushan* > > Department of Biochemistry > > George S. Wise Faculty of Life Sciences > Tel Aviv University >

2 1

Movies in Chimera
by Anindito Sen 07 Oct '09

07 Oct '09

Dear All These questions may have been answered in the past ( and I must have missed it)- 1. I have 3 movies (.mov) made in Chimera. I want to add them all together to make a single movie. How can I do that? 2. How can I build a movie where I "zoom"-inside a crystal structure or an EM density map showing the regions of interest. Thank you Andy Dr. Anindito Sen (Ph.D)

2 1

(no subject)
by Cathy Lawson 06 Oct '09

06 Oct '09

Dear Chimera Team, I have been using Chimera fairly intensively in recent days with good success. Just wanted to pass along a short list of features I wish were available. (maybe some are already available in Chimera or there are workarounds but I haven't been able to figure them out...). I'm using the current production release (1.3) mac osx (X11). (1) A way "close" the command line at the bottom of the view window (among other reasons why one might want to do this, I can't figure out how to get accelerator shortcuts to work after the command line is open). (2) An "undo" button for "fit in map" (restore model to position before fit) (3) Fine tuning of the "preset" views -- interactive (ribbons) is something I use frequently but I'd prefer a white background. (4) It is great to have the down and up arrow to narrow and broaden selection, would be great if a final down arrow would lead to clearing the selection. cheers, Cathy ********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson(a)rutgers.edu http://roma.rutgers.edu **********************************

4 4

Re: [Chimera-users] SAS values for single atoms and residues
by Elaine Meng 06 Oct '09

06 Oct '09

Hi Dave, It is not clear to me what you did to list values in the Reply Log. After you display surface to create those surface area attributes, then start "Render by Attribute" (for example, from under Tools... Depiction) and in that dialog, choose "File... Save Attributes." In the resulting file-save dialog you can specify not only which attribute you want to save, but there is a checkbox "Restrict save to current selection" that you will want to activate before saving the file. For example, you could select all the LYS and then this would be used to write a file listing the areaSAS of each of those residues. Alternatively you could select all the :lys@nz and then write the areas of the selected atoms. 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 Oct 6, 2009, at 9:23 AM, David Chenoweth wrote: > Hi Elaine, > > I'm trying to calculate the solvent accessible surface area for > several lysine residues in a protein to evaluate which are most > likely to be free on the surface for functionalization. My thought > was to just calculate the SAS area and rank order them. When I > select just the primary amine of all the lysine residues and go to > the reply log I get several numbers in a row under SAS and I'm not > sure which are correct. These numbers don't seem to change if I > select different residues so I'm not sure how to get the SAS values > just for my lysine amines. > > Thanks, > Dave

2 1

SAS values for single atoms and residues
by David Chenoweth 06 Oct '09

06 Oct '09

Hi Elaine, I'm trying to calculate the solvent accessible surface area for several lysine residues in a protein to evaluate which are most likely to be free on the surface for functionalization. My thought was to just calculate the SAS area and rank order them. When I select just the primary amine of all the lysine residues and go to the reply log I get several numbers in a row under SAS and I'm not sure which are correct. These numbers don't seem to change if I select different residues so I'm not sure how to get the SAS values just for my lysine amines. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

1 0

citation
by Abeer Shokeer 06 Oct '09

06 Oct '09

Hello I have used Chimera to prepare very nice figure in my manuscript and I would like to cite the Chimera. which reference that should be cited? Best wishes Abeer

2 1

python scripting for multiscale model
by Pat Weinkam 05 Oct '09

05 Oct '09

Hi, I am a new postdoc with Andrej Sali. I am looking to use the multiscale model tool to recreate a 3x3x3 set of unit cells around my pdb file. I can use the GUI to do this just fine but I would like to incorporate this into a python script. Is such a thing available? It would be greatly appreciated. Thanks! Pat

2 1

mouse selection not working
by lorenzo 05 Oct '09

05 Oct '09

Hi everybody, I just installed chimera-1.3-linux.exe on an atom netbook. The OS is ubuntu 9.04. My problem is that the mouse selection tool does not work. To complete the scenario I add a few details 1) I don't have the green outline and setting Fill mode for selection highlighting in Preferences does not work around the problem (probably just a screen setting problem). 2) Other forms of selections work. For example by Select -> Chemistry -> Element -> H and then by Actions -> Atoms/Bonds -> Delete I can delete hydrogens. 3) I cannot delete anything that I select by ctrl + mouse left button. 4) libgl1-mesa-glx and libgl1-mesa-dri are installed. Thanks for your attention Lorenzo Bongini

2 3

CA-only shown as ribbons
by Andrei Neamtu 05 Oct '09

05 Oct '09

Hello, Just a quick question: I have downloaded the latest daily build of CHIMERA and I want to make a ribbon picture only fom the alpha-Carbon trace. On the site it is said in the Appearance and Image-Saving section that "CA-only and P-only structures can be shown as ribbons and worms " I tried but didn't succeded . Does anybody know what are the steps in displayng such a structure? Andrei

3 2

comparing protein structures
by Beale, John 03 Oct '09

03 Oct '09

Hello, I am trying to compare a protein structure generated through molecular dynamics to a reference structure that is the starting pdb file. I was using MATCHMAKER. I get the rms value and the residue matches, but when I do this I don't get the overlaid reference and MD structure in the viewing window. Can someone tell me what I need to do to get the overlaid structures? Thanks! John

2 1

Saving ligand and protein as a single PDB
by Nancy 03 Oct '09

03 Oct '09

Hello, I am planning to run a docking simulation in a different program, and I need to have a "reference ligand" included in the PDB file. The particular PDB I am working on does not have a ligand included. So I am trying to position one using Chimera. I started with the protein file and a ligand file (ligand is in .mol2 format). I loaded both into Chimera, and I correctly positioned the ligand relative to the PDB. I then saved both using File -> Save PDB... I choose to save the file relative to the protein, and I select "save multiple models: in a single file". However, when I load the file into the docking program, it does not show the ligand. Additionally, there are a few structural errors in the output PDB file. Please advise. Thanks, Nancy

2 3

zone command
by Francesco Pietra 02 Oct '09

02 Oct '09

Hi: I prepared with the zone command a model (#0) of a protein partly immersed into a hydrated lipidic bilayer (cut-and-paste from the two models from the zone command). Now I would like to solvate with water the part of protein which protrudes out of the bilayer. Water is single-point (coarse-grain simulations) indicated in model #0 as ATOM 2724 W W 2060 45.420 3.750 23.380 1.00 0.00 W and in the pdb file of the water block (model #1) to be added ATOM 27558 W W 5018 84.320 142.862 11.262 1.00 0.00 Once model #0 and model #1 are superimposed, clearly the zone command does not distinguish W from the two models. How could the zone command be made working now? I renamed W to WAT in model #1 but the zone command does not recognizes WAT under such circumstances. Not yet found a way out, which should be simple. Thanks for suggestions. (solvating model #0 with programs from the MD suite also solvates what it should not; this is why I am trying with CHIMERA) francesco pietra

2 2

3D-glassen
by Thomas Classen 02 Oct '09

02 Oct '09

Dear colleaques; I want to use 3D-glasses of nVidia for the sequential stereo view in chimera. Are there any experiences with that system in combination with chimera? Or are there some problems with that kind of technology known? Wanted hardware - nVidia GF 3D Vision 3D-Glasses -nVidia graphicboard; GTX285 Series min. 1024MB Additional hardware: - Intel 2 Duo Quad Prozessor; Q9650; boxed - 8GB DDR2 RAM PC1066 Thanks for your help from germany Tom

2 1

licensing
by Schulz-Gasch, Tanja 02 Oct '09

02 Oct '09

Hi there, I have a single-user license for Chimera at Roche. Meanwhile others are interested in using Chimera as well. Could you please send me an update on licensing scemes and costs? Thanks, Tanja __________________________________________ Dr. Tanja Schulz-Gasch F. Hoffmann-La Roche Ltd Pharmaceuticals Division PRCBLM Bldg. 92/2.10D CH-4070 Basel Switzerland Tel. +41(0)61 68 88309 Fax. +41(0)61 68 86459 http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html <http://compchem.bas.roche.com:8080/schulzt2/PICS_DB/index.html> Email: tanja.schulz-gasch(a)roche.com "The information transmitted in this message is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you receive this message in error, please contact the sender and delete the material from any computer."

1 0

segmentation fault
by Francesco Pietra 01 Oct '09

01 Oct '09

Hi: On Debian Linux i386 squeeze I had the X system broken while attempting to install the gnome cd burner "brasero". I purged everything about that bad code, installed and reconfigured the X system, however something is still broken. Attempts at launching CHIMERA returned "segmentation fault". That also sitting in the directory where chimera is installed ( /usr/local/chimera/bin). As I had an old version, I reinstalled chimera-1.3-linux.exe, while that did not solve the above problem. I do not remember where to put the hands in such cases. Thankful for reminding me about that. francesco@deb32:~$ gcc --version gcc (Debian 4.3.4-2) 4.3.4 francesco pietra

3 4

Re: [Chimera-users] Solvent Accessible Surface Area
by Elaine Meng 01 Oct '09

01 Oct '09

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am using Chimera for identifying the surface residues. > > I select areaSAS > 0.05 square angstroms, is this same as saying > areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq > angstroms have these been switched some how or are they curiously > the same in the following statement? > > I just need some help in understanding. > Thank You > Sincerely > -Thiru Ramaraj Hi Thiru, In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms. Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state. See for example the GetArea server, which gives "Ratio(%)": <http://curie.utmb.edu/area_man.html> However, what Chimera reports is just the surface area of the atom or residue in your structure. To choose surface residues, I'd probably use a bigger cutoff, say select :/areaSAS>10 but it depends on what you are going to do with the results. You can try different values and see what looks reasonable. 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

4 7

Transparent Spheres
by Waight, Andrew 30 Sep '09

30 Sep '09

Hello everyone again. I apologize for a potentially embarassing question but is it possible to display sidechains as transparent spheres with solid stick representation inside. Seeing as I also can't find an image in the Chimera gallery where it is represented as such, I am wondering if it is possible to individually color (and set opacity) on spheres. I am also aware that vdw will create dots of varying density, but is it alternatively possible to display vdw as solid surface with opacity. Thanks to all for your patience. Drew ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 26
by vamsi krishna 30 Sep '09

30 Sep '09

Dear all, I am using chimera to calculate solvent accessibility of residues , may i ask you what cutoff is appropriate to identify surface residues significant for substrate binding . Thank you vamsi chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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: Solvent Accessible Surface Area (Elaine Meng) > 2. Re: Solvent Accessible Surface Area (Thiruvarangan Ramaraj) > 3. Re: Solvent Accessible Surface Area (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 Sep 2009 12:14:48 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Thiruvarangan Ramaraj <thiruvaranganr(a)yahoo.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Solvent Accessible Surface Area > Message-ID: <E24233F9-9564-4824-8D82-6D9506261ACB(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > > >> Hi Elaine, >> I am using Chimera for identifying the surface residues. >> >> I select areaSAS > 0.05 square angstroms, is this same as saying >> areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq >> angstroms have these been switched some how or are they curiously >> the same in the following statement? >> >> I just need some help in understanding. >> Thank You >> Sincerely >> -Thiru Ramaraj >> > > > Hi Thiru, > In Chimera there is no percentage (%) measurement, it is only the area > value in square angstroms. Some other programs give % exposed for a > residue, which is a ratio of the area of that residue in your > structure to the area of the same type of residue in some theoretical > unfolded state. See for example the GetArea server, which gives > "Ratio(%)": > <http://curie.utmb.edu/area_man.html> > > However, what Chimera reports is just the surface area of the atom or > residue in your structure. To choose surface residues, I'd probably > use a bigger cutoff, say > > select :/areaSAS>10 > > but it depends on what you are going to do with the results. You can > try different values and see what looks reasonable. > 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 > > > > > ------------------------------ > > Message: 2 > Date: Mon, 28 Sep 2009 13:49:00 -0700 (PDT) > From: Thiruvarangan Ramaraj <thiruvaranganr(a)yahoo.com> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Solvent Accessible Surface Area > Message-ID: <842106.2825.qm(a)web53905.mail.re2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks,? Elaine for the information. > > Also I am having problems with installing Chimera on Linux Fedora 11(32 bit version). I am able to download it and install it. When I start chimera it comes up and then crashes immediately, the only message it gives is Segmentation Fault. > > Is there anyway I could resolve this problem. > > Thank You > > -Thiru Ramaraj > > --- On Mon, 9/28/09, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Solvent Accessible Surface Area > To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Date: Monday, September 28, 2009, 1:14 PM > > On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > > >> Hi Elaine, >> I am using Chimera for identifying the surface residues. >> >> I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers? 5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement? >> >> I just need some help in understanding. >> Thank You >> Sincerely >> -Thiru Ramaraj >> > > > Hi Thiru, > In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms.? Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state.? See for example the GetArea server, which gives "Ratio(%)": > <http://curie.utmb.edu/area_man.html> > > However, what Chimera reports is just the surface area of the atom or residue in your structure.? To choose surface residues, I'd probably use a bigger cutoff, say > > select :/areaSAS>10 > > but it depends on what you are going to do with the results.? You can try different values and see what looks reasonable. > 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 > > > > > > >

2 1

Using Chimera to read SMILES string into structure
by Miriam Gochin 29 Sep '09

29 Sep '09

I have downloaded the latest build (Aug 30, 2009) and don't seem to be able to input a SMILES string. I have tried both the Utilities -> Structure Diagram and the Structure Editing -> Build Structure tool, and in both cases I can see a box to input the SMILES string, but the copy and paste mechanism won't work. I can enter text in the box, but cannot paste it in, which I need to do. Thanks for your help. Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

4 8

Zoom factor for model when first opened
by Tom Goddard 25 Sep '09

25 Sep '09

Hi Kevin, The camera settings (position, amount of zoom, angular field of view) all contribute to how much of the Chimera window is filled when you open a map. How those are initially set when you start Chimera and open a map has changed a few times over the last year or two so if you run different Chimera versions (Help / About Chimera... to check version number) you may see different initial sizes. Tom -------- Original Message -------- Subject: chimera question From: Kevin Koehntop To: goddard Date: 9/24/09 6:34 PM > Hi Tom, > > I have a quick chimera question. When I open the same EM map in two > different chimera sessions, even though the scale factor, origin, > voxel size, and isosurface threshold level are exactly the same, the > map appears much smaller in one of the windows and I can't determine > why. Is there another parameter that I need to check? Thank you > > Kevin

1 0

Re: [Chimera-users] [chimera-dev] select opt
by Eric Pettersen 23 Sep '09

23 Sep '09

On Sep 21, 2009, at 7:27 AM, Victor MuÃ±oz wrote: > I'd like to know if there's a way to select the select mode "append" > using the > command line instead of the visual interface. Hi Victor, There isn't a way to do that, but it typically isn't necessary. The "|" and "&" characters perform union and intersection operations respectively. So for example you can add all LYS residues to the current selection with: sel sel | : LYS or you could intersect the current selection with LYS residues with: sel sel & :LYS If you really need to change the mode for some reason, let me know what that reason is and maybe we can add something. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. The "|" character is a vertical bar, not a capital i, in case that's not clear in the font you're using.

2 1

Re: [Chimera-users] question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear Elaine: Thank you very much for your instruction. We'll follow your guide. Best wishes WU Xue >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: 吴雪<wuxue(a)nankai.edu.cn> >Subject: Re: [Chimera-users] question about Chimera >Date: Tue, 22 Sep 2009 11:00:11 -0700 > >Dear Wu Xue, >There are several different distance and angle cutoffs that depend on >the donor and acceptor atom types. For example, the distance and >angle cutoffs for finding a H-bond donated from hydroxyl -OH to >carbonyl =O will be different than from amine -NH3 to carbonyl =O. >The cutoff values are taken from tables in this paper: > > Three-dimensional hydrogen-bond geometry and probability >information from a crystal survey. Mills JE, Dean PM. J Comput Aided >Mol Des. 1996 Dec;10(6):607-22. > >As discussed in the FindHBond documentation, > findhbond.html#criteria> > >the criteria in this paper were based on very high resolution crystal >structures of small molecules. Typically the structures in the PDB >are not so high resolution and so the criteria are relaxed. For >example, if a strict criterion from the paper is 2.8 Angstroms >cutoff, then with 0.4 relaxation the cutoff becomes 3.2 Angstroms. >We set the default relaxation amounts to what we felt gives >reasonable results on most PDB structures. However, we made them >user-adjustable so that if you don't like them, you can change the >values to whatever you want. > >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 Sep 22, 2009, at 4:18 AM, 吴雪 wrote: > >> Dear colleague: >> I have a question about the "find hydrongen bond" in Chimera. >> The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". >> I don't understand the meaning of the parameter. 20 degree may >> means the angle bias the line,but I can't figure out what is the >> 0.04nm. >> The cutoff of the hydrogen is 0.4nm, and the angle is about 90 >> degree or some other parameters depending on the strength of the >> hydrogen bond. >> If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds >> are found. I don't know the criteria. Can you give me some advice >> so that I can follow your instruction? >> Sincerly Yours >> WU Xue > >

1 0

.sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera
by Xarana 22 Sep '09

22 Sep '09

Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this inner surface with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie

4 5

question about Chimera
by 吴雪 22 Sep '09

22 Sep '09

Dear colleague: I have a question about the "find hydrongen bond" in Chimera. The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". I don't understand the meaning of the parameter. 20 degree may means the angle bias the line,but I can't figure out what is the 0.04nm. The cutoff of the hydrogen is 0.4nm, and the angle is about 90 degree or some other parameters depending on the strength of the hydrogen bond. If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds are found. I don't know the criteria. Can you give me some advice so that I can follow your instruction? Sincerly Yours WU Xue

2 1

Write out phi/psi angles
by David Belnap 21 Sep '09

21 Sep '09

I've read on the archived lists that Chimera does not have a Ramachandran plot viewer. I found phi/psi angles by selecting "Actions", "Inspect", then inspecting "Residue". Can I output the phi/ psi angles to a text file? If so, how do I write out that information? Thanks. David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David.Belnap(a)byu.edu ============================================

2 1

Zooming and orthographic projection mode
by James Conway 21 Sep '09

21 Sep '09

I am struggling a bit and would be interested in any pointers from the knowledgeable folk here. It seems that I cannot use the mouse to get arbitrarily close to a surface in orthographic mode, but I can in perspective mode. In orthographic mode (Viewing -> Camera -> Projection) if I try to zoom in, the camera instead moves in until the front surface clips, but without much actually zooming. (True for the different "Center of Rotation" methods). In the Viewing -> Side View panel, the width of the field is represented by red lines that I cannot control but which I really want to move close together. According to the help for the Viewing -> Camera panel: horizontal field of view (allowed range 1.0-179.0°) - how much perspective is used; does not affect the orthographic projection. The vertical field of view will change along with the horizontal field of view, but their exact relationship depends on the aspect ratio of the graphics window. In fact, with the nightly builds of 1.4 this parameter *does* affect the orthographic projection, and does zoom in (or out) without clipping. Is there an updated explanation of how this works, and if it has changed since 1.3 as I seem to find? Am I looking in the wrong place for help on nightly builds? Thanks, James Conway

5 5

Fit MAP to MODEL
by Michael Schmid 21 Sep '09

21 Sep '09

HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.

3 4

select many atoms by serial number
by Stefano Meliga 21 Sep '09

21 Sep '09

Hello, I use a clustering algorithm to find partitions of proteins. The output is the list of node indexes belonging to each cluster. I would like to plot the clusters in different colours. I successfully managed to select one atom in the graphical interface using: Select > Atom Specifier and typing @\serialNumber=n Nevertheless, I need to select many atoms from a list of serial numbers, what can I do? Cheers, Stefano

2 1

measurements to planes
by Elaine Meng 18 Sep '09

18 Sep '09

Hi Serge, Dave, Jim, et al., In recent daily builds of Chimera, you can now define planes and measure distances and angles to these objects. The planes are shown as disks, and you can perform plane-plane, axis-plane, and atom-plane measurements, in addition to the axis-axis and atom-axis measurements we had earlier. The tool formerly known as Axes is now "Axes/Planes," and we anticipate it will eventually include centroids. The updated documentation isn't there today but should show up tomorrow at <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > and the interface is mostly self-explanatory anyway. Each of you had asked about planes at some point (possibly a while ago), in case you are wondering why I addressed this message to you. 8-) Enjoy! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Cannot open pdb files with older versions of Chimera
by Hiroshi Nikaido 17 Sep '09

17 Sep '09

Hello, I sometimes have to use older versions of Chimera (1.2350 or 1.2422) because the more recent versions refuse to calculate surfaces for my protein. They used to work fine in my old computer running windows xp, but with my new computer (still running xp) an attempt to try any pdb files on my hard disk produces an error message (TypeError: argument 1 should be a str.). How could this problem be fixed? Your help will be greatly appreciated. Hiroshi

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 16
by Gaël McGill 16 Sep '09

16 Sep '09

Hi Andrew, You might try contacting Monica Zoppe (in Pisa, Italy) - she has experience importing PDB data into Blender. Here is her site: http://www.scivis.ifc.cnr.it/ Her e-mail: Monica Zoppè <mzoppe(a)ifc.cnr.it> Hope this is helpful, -Gael. ------------------------- Gaël McGill, Ph.D. Director of Molecular Visualization Center for Molecular & Cellular Dynamics Harvard Medical School www.molecularmovies.org President & CEO Digizyme, Inc. P.O. Box 1921 Brookline, MA 02446-1921 (617) 232-7676 (phone) (617) 232-5623 (fax) mcgill(a)digizyme.com www.digizyme.com On 9/16/09 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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: Exporting from Chimera to Blender - basic questions. > (Tom Goddard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Sep 2009 23:03:03 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Exporting from Chimera to Blender - basic > questions. > To: "Waight, Andrew" <Andrew.Waight(a)med.nyu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4AB07F97.6080108(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Andrew, > > Chimera exports the surface vertex and individual atom and ribbon > residue colors in the X3D and VRML output. If you raytrace a scene > with Chimera File / Save Image... it first exports X3D and then converts > that X3D to input for POVray which does get all the colors right. So I > think your question calls for some expertise with Blender, to find out > what color information it can handle when importing those files. I > don't know anything about Blender. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] Exporting from Chimera to Blender - basic > questions. > From: Waight, Andrew <Andrew.Waight(a)med.nyu.edu> > To: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > Date: 9/15/09 10:31 AM >> Hello all, >> >> I have recently solved the structure of a novel membrane protein, and >> have been using chimera quite a bit for my figures and analysis. In my free >> time I have been playing around with the 3D animation package Blender which I >> must say is a total blast, and makes fantastic movies and animations. However >> exporting from Chimera to Blender is a little tricky, in that when using >> VRML2 or X3D formats while the actual 3D "mesh vertices" import quite well, >> the colors are not imported, and imported items such as cartoon helices seem >> to have totally random materials assigned to nonsensical segments (instead of >> materials assigned by chain for example) . Ideally I would like to perform >> and export the coloring operations using chimera because it's obviously an >> order of magnitude easier to select residues, chains and monomers with >> chimera. Or at least have the grouping of objects imported correctly. This is >> really just for fun so I'd thought I'd ask if anyone here has any experienc! > e ! >> with importing Chimera models into Blender. Of course I have no idea how >> VRML2 actually works. Thanks all. >> >> Andrew Waight >> Wang Lab >> Skirball Institute of Biomedical Sciences >> NYU School of Medicine >> >> P.S. Extra Credit: Does anyone have any idea how to export the calculated >> electrostatic surface into UV mapping for a Blender Object (the surface mesh >> obviously)? >> >> ------------------------------------------------------------ >> This email message, including any attachments, is for the sole use of the >> intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. Any >> unauthorized review, use, disclosure, or distribution is prohibited. If you >> have received this email in error please notify the sender by return email >> and delete the original message. Please note, the recipient should check this >> email and any attachments for the presence of viruses. The organization >> accepts no liability for any damage caused by any virus transmitted by this >> email. >> ================================= >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 77, Issue 16 > *********************************************

1 0

RMSD supports symmetry?
by Kevin Wu 11 Sep '09

11 Sep '09

Hi all, I'm wondering if the RMSD function in Chimera will correctly calculate RMSD when two molecules are compared. For example, if a benzene ring is flipped, will the RMSD stay the same? Furthermore, how does Chimera do this comparison? Thanks! Kevin

2 2

Zalman 3D
by Miles Pufall 11 Sep '09

11 Sep '09

Hi Guys - I got a Zalman 3D - it's pretty cool with Coot and Pymol. Your site says the row-interleaved stereo view under camera will work with this monitor, but I wasn't having much success. Do you have some more detailed instructions for this particular monitor? I can drop by and visit with it, or you can come see me if you's like. Thanks! Miles in Yamamoto Lab S574 Genentech Hall

5 4

Re: [Chimera-users] [chimera-dev] suggestion for feature addition to chimera
by Eric Pettersen 09 Sep '09

09 Sep '09

On Sep 4, 2009, at 5:09 PM, Rocco Varela wrote: > Hello, > > I have a small suggestion for an additional feature for Chimera that > I think would be useful. I often look at structures of multiple > small molecules, some artificial and some real, and I noticed > something interesting with the way Chimera writes mol2 files. > > Here is Scenario 1: > > 1) I open a mol2 file that contains multiple molecules flagged as > "separate" MOLECULEs. > > 2) I save the loaded file as mol2 and select "a single file > [combined @MOLECULE section]" for the "Save multiple models in" > option. > > > 3) After saving and reloading this new mol2 file that now has a > single MOLECULE section, all the "names" of the previous molecules > have been lost. (ex. s-030, s-048, s-055, etc...) Instead in the > SUBSTRUCTURE section "UNK0" is used. > > It would useful if Chimera could name the components of the new > single molecule with the proper names. I could easily write a > script to fix this after the fact but I thought it might be a useful > option for other people too? Okay, I changed the Mol2 writer to use the model name instead of the residue type under the following conditions (only): 1) Combining models into a single @MOLECULE 2) All models are a single residue 3) Model names are unique and residue types are not This change will be in tonight's build. > Scenario 2: > > 1) Same as 1 above. > 2) Now I want to save all the MOLECULEs in the file as separate mol2 > files but with the proper "names" that are listed in the original > file loaded. Currently the only option is to provide a common name > and to append the "model number". It would be nice if we were > allowed to NOT provide a common name and allow it to name all the > files according to the molecule "names" not model numbers. This seems like a reasonable enough request. I will open a ticket in our Trac database for it, with you on the recipient list so you'll know when it gets done. It's a tad more work than the preceding change because aside from adding code to support it, the interface has to be changed to allow for the option and the documentation has to be updated to describe it -- whereas the other change can sneak in under the radar. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Can you morph a ligand
by Walter Fast 09 Sep '09

09 Sep '09

Hi! Chimera is great - thanks again! I use it all the time for research and teaching. I have a quick question: We have two different product-bound structures, but when I morph between the two we loose the active site metal ions and the active-site ligands. Is there a way to include these as well? Thanks, Walt -- Walter Fast, Ph.D. Associate Professor The University of Texas at Austin College of Pharmacy The Division of Medicinal Chemistry Phone: (512) 232-4000 Fax: (512) 232-2606 Lab: (512) 471-5839 Email: WaltFast(a)mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html

2 2

Re: [Chimera-users] [chimera-dev] Suggestion: define selection name for startup chimera
by Jean Didier Pie Marechal 09 Sep '09

09 Sep '09

Hi Eric, "binding site" was an idea more than anything else but I realize from your e-mail that we don't really need. Strangely, though using @/display frequently I never thought about using it for selecting. Think I can do without the shortcut... Sorry! Cheers JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Dimecres, Setembre 9, 2009 8:46 pm Assumpte: Re: [chimera-dev] Suggestion: define selection name for startup chimera > On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote: > > > In the new builts of chimera, you have change the initial > > representation of the protein so that binding sites immediately > > appear and the rest of the protein is in ribbon (which is a > great > > idea by the way). That means that you have a automatic analysis > of > > binding site recognition. I wonder if you couldn't include a > > selection named "binding site" (or something similar), that > would > > appear as a named selection and that we could call at the early > > beginning of the session. > > Hi JD, > I could. I definitely wouldn't want to call it "binding site" > since > it includes waters and residues not necessarily involved in > binding, > not to mention the entire structure for small-molecule structures. > > It's also a misleading name for structures without ligand present - > - > since their binding sites won't be selected by it. FInally, it's > also > somewhat confusing as to what should happen if you open multiple > structures over the course of a session. > So it could be called "smart display atoms" I suppose. If some > other > users thought it'd be useful I'd do that (anyone?). In the > interim, > you can pretty easily create the selection yourself with these > commands after opening the structure: > > sel @/display; namesel smart atoms; ~sel > > You could alias that to something snappier. :-) > > --Eric > >

1 0

Re: [Chimera-users] [chimera-dev] Suggestion: define selection name for startup chimera
by Eric Pettersen 09 Sep '09

09 Sep '09

On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote: > In the new builts of chimera, you have change the initial > representation of the protein so that binding sites immediately > appear and the rest of the protein is in ribbon (which is a great > idea by the way). That means that you have a automatic analysis of > binding site recognition. I wonder if you couldn't include a > selection named "binding site" (or something similar), that would > appear as a named selection and that we could call at the early > beginning of the session. Hi JD, I could. I definitely wouldn't want to call it "binding site" since it includes waters and residues not necessarily involved in binding, not to mention the entire structure for small-molecule structures. It's also a misleading name for structures without ligand present -- since their binding sites won't be selected by it. FInally, it's also somewhat confusing as to what should happen if you open multiple structures over the course of a session. So it could be called "smart display atoms" I suppose. If some other users thought it'd be useful I'd do that (anyone?). In the interim, you can pretty easily create the selection yourself with these commands after opening the structure: sel @/display; namesel smart atoms; ~sel You could alias that to something snappier. :-) --Eric

1 0

label
by Bala subramanian 09 Sep '09

09 Sep '09

Friends, Is there any possiblity to move a 3D label along a particular axis in chimera 1.4. I labelled the residues of a DNA molecule using rlabel command. Some residue labels are displayed behind the base of the DNA. I tried to change the lighting also but it vain. Thanks, Bala

2 1

Problem with benzenes split across crystal unit cell
by Tom Goddard 04 Sep '09

04 Sep '09

Hi Mike, The Chimera unit cell dialog is behaving as expected in the cases where the asymmetric unit contains half of a benzene ring. First, parts of the asymmetric unit are not moved relative to other parts of the asymmetric unit, so as you observe the half benzenes in asymmetric unit copies sometimes lie outside the unit cell. All unit cell dialog just puts the center of the asymmetric unit in the unit cell box. A second problem is that a half benzene ring from one asymmetric unit will not be joined to a half benzene ring from another asymmetric unit. They will line up perfectly but Chimera does not see bonds between the two halfs so for instance, selecting aromatic rings won't pick those up. I guess the first problem could be handled by moving each connected group of atoms so its center lies in the unit cell. I think it could lead to undesired results. For example a protein with a bound ligand might have the ligand outside the unit cell causing it to be moved to some other asymmetric unit's binding site. The trouble with that is that the protein and ligand are part of one molecule model in Chimera, so now you have taken the ligand in that molecule and placed it with the protein of another copy of the molecule. That may not be what you want. Another answer to the first problem, is that I added to the unit cell dialog the ability to make multiple asymmetric unit copies to fill multiple unit cells. If you make several unit cells, then the half benzenes lying outside one unit cell do join up with the half benzenes from a different unit cell. If you were trying to make a figure and you didn't want half-benzenes floating around -- you could simply select them and delete them (Actions / Atoms / Delete). The second problem is harder. Chimera could guess that the half-benzenes should be joined since they have exactly coincident atoms. (This relies on the strange inconsistency that the half-benzenes in the PDB files you sent contain 4 atoms instead of the expected 3 atoms. So it doesn't actually represent an asymmetric unit since there is an extra atom that will be duplicated in other asymmetric units.) But Chimera can't join them because covalent bonds can't be formed between different molecule objects -- it would require making a new molecule to contain all the atoms. Creating extra molecule models to join the half benzenes is possible but weird. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard Date: 9/4/09 12:41 PM > Hi Tom, > > Thanks. It looks like the issue is mostly resolved. > > The is a problem with molecular units sitting at symmetry element in > non-primitive cells, for now I've found it in C2/c (iat03.pdb) and > Fdd2 (ta21.pdb) which I've attached. As far as I can tell this is not > unique to chimera, some programs handle this okay, many don't. You'll > see that in these two cases benzene molecules land outside of the cell > or fail to complete a pair. > > If I had to lobby for any particular ticket on your list it would be > #201. What I would add in way of description on that ticket is that > I'm not talking about using SHELX in Chimera. What I meant to say is > for Chimera to read a standard format CIF file containing the > reciprocal space transform of the real space electron density. The fft > routines to transform back to real space have been around forever and > are in most all modern languages. > > All crystallography packages can write this type of file containing > h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in > degrees). This the preferred format for sending data to the PDB. > > I'm not looking to add a bunch of "stuff" to your already huge pile > but I thought most of this was already in the public domain. After > all, nothing is impossible for the guy that doesn't have to do it. > It's all easy and straightforward, right? ;0) > > As for the issue of reading the CIF, P21/n is a very common alternate > setting of P21/c and the PDB symmetry list does not contain it. > > Thanks again!! > Cheers, > Mike > > <<< > ------------------------------------------------------------------------>>> > Dr. Michael W. Day > Director - X-ray Crystallography Lab & Molecular Observatory > California Institute of Technology > Mail Code 139-74 > Pasadena, CA 91125 > > <<< > ------------------------------------------------------------------------>>> > > On Sep 2, 2009, at 5:54 PM, Tom Goddard wrote: > > Hi Mike, > > I've fixed the unit cell dialog to handle inverting symmetries. It > was a simple change. Will be in tonight's daily builds. > > We could have Unit Cell work with CIF files but that is an > enhancement that will have to compete for time with the hundreds of > other feature requests we're looking at. My list of requests is here > > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests > > and Eric and other developer maintain their own off-line lists. So > you need to make a good case. It could be an easy task if our > third-party CIF file reader already parses the needed symmetry > operators. If it does not provide those then it could be a > significant bit of work. > > Tom > > > -------- Original Message -------- > Subject: Re: [Chimera-users] Centro-symmetric space groups > From: Michael Day > To: Thomas Goddard > Date: 9/1/09 1:19 PM >> Hi Tom, >> >> Thanks. >> >> Another option you might consider is to have the Unit Cell tool work >> also with CIF files then only coordinate transformations are needed >> as the symmetry operators are included. An advantage is that if >> someone uses a non-standard setting of a space group the symmetry >> operators are still valid for the coordinates. >> >> Thanks for all your work. All of you on the Chimera team (Elaine, >> Eric and Greg) set the bar pretty high! My hats off to you. >> >> Cheers, >> Mike >> >> <<< >> ------------------------------------------------------------------------>>> >> Dr. Michael W. Day >> Director - X-ray Crystallography Lab & Molecular Observatory >> California Institute of Technology >> Mail Code 139-74 >> Pasadena, CA 91125 >> >> <<< >> ------------------------------------------------------------------------>>> >> >> On Sep 1, 2009, at 9:27 AM, Thomas Goddard wrote: >> >> Hi Mike, >> >> Thanks for the suggestions. The coordinate transformations are >> routine. The trouble is that the Chimera Molecule C++ code takes the >> transformation matrix and orthonormalizes it to a proper rotation. >> So the inversion operator of "P -1" gets changed to inverting x and >> y axes but not the z axis. The orthonormalization is supposed to >> just fix tiny round-off transformation problems, like matrices read >> from a PDB file that have only 5 digits of precision. Really we >> should be warning if a transformation is very far from a proper rotation. >> >> I'll let you know when the problem is fixed in the daily builds. >> >> Tom >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Centro-symmetric space groups >> From: Michael Day >> To: Thomas Goddard >> Date: 8/31/09 7:54 PM >> >>> Tom, >>> Thanks again. Awesome! >>> I suspect mirrors and therefore glide planes could be an issue as >>> you don't see them in proteins. >>> I don't know what your overall strategy is for applying space group >>> operators but to avoid issues I would suggest; >>> 1) deorthogonalize into crystallographic coordinates as fractions of >>> cell edge >>> 2) apply symmetry operators in turn to the original set (x,y,z) to >>> get (x',y',z') for each operator >>> 3) calculate the centroid for each equivalent set of coordinates >>> (x',y',z') >>> 4) move centroids into unit cell as needed so they are x=0,1 y=0,1 >>> and z=0,1 >>> I suspect you already know this but it never hurts to say it. My >>> students think I overstate the basics at times but it sure helps all >>> of us get on the same page. >>> Cheers, >>> Mike >>> <<< >>> ------------------------------------------------------------------------>>> >>> Dr. Michael W. Day >>> Director - X-ray Crystallography Lab & Molecular Observatory >>> California Institute of Technology >>> Mail Code 139-74 >>> Pasadena, CA 91125 >>> > >>> <<< >>> ------------------------------------------------------------------------>>> >>> On 31 Aug, 2009, at 6:14 PM, Thomas Goddard wrote: >>>> Hi Mike, >>>> >>>> Oops. The symmetries that invert coordinates don't work in the Unit >>>> Cell tool. This is because it sets the transformation matrix >>>> (rotation and shift) for the asymmetric unit copies but it can only >>>> handle proper rotations. Chimera is generally used for proteins >>>> which are handed (not symmetric under inversion) so such space >>>> groups generally don't occur for proteins. But of course for small >>>> molecules they can. >>>> >>>> I'll fix this soon, maybe later this week. I'll have to change >>>> atom coordinates instead of setting the transform matrix for the >>>> asymmetric unit copies. >>>> >>>> Tom

2 2

Computing xray density from structure factors
by Tom Goddard 04 Sep '09

04 Sep '09

Hi Mike, If it is just a matter of computing a Fourier transform that is easy. Chimera already has libraries that does that. The trouble will be parsing the CIF file. Chimera reads molecular structure CIF and mmCIF files using a third party library called mmLib. I don't know if mmLib will read the structure factors. If you send me an example CIF file with structure factors I'll give it a try. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard Date: 9/4/09 12:41 PM > Hi Tom, > > ... > > If I had to lobby for any particular ticket on your list it would be > #201. What I would add in way of description on that ticket is that > I'm not talking about using SHELX in Chimera. What I meant to say is > for Chimera to read a standard format CIF file containing the > reciprocal space transform of the real space electron density. The fft > routines to transform back to real space have been around forever and > are in most all modern languages. > > All crystallography packages can write this type of file containing > h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase angle in > degrees). This the preferred format for sending data to the PDB. > > I'm not looking to add a bunch of "stuff" to your already huge pile > but I thought most of this was already in the public domain. After > all, nothing is impossible for the guy that doesn't have to do it. > It's all easy and straightforward, right? ;0) > > As for the issue of reading the CIF, P21/n is a very common alternate > setting of P21/c and the PDB symmetry list does not contain it. > > Thanks again!! > Cheers, > Mike > > <<< > ------------------------------------------------------------------------>>> > Dr. Michael W. Day > Director - X-ray Crystallography Lab & Molecular Observatory > California Institute of Technology > Mail Code 139-74 > Pasadena, CA 91125 > > <<< > ------------------------------------------------------------------------>>>

2 1

hydrogen bond representation
by Bala subramanian 04 Sep '09

04 Sep '09

Friends, Is there any way to represent hydrogen bonds as dotted lines instead of a solid line in Chimera. Sometimes hbond analysis in chimera shows same atom to be involved in two hydrogen bonds, why is it so ? Thanks, Bala

2 1

2D projections
by Ana Luiza 03 Sep '09

03 Sep '09

Hi, Is it possible to build 2D projections from a 3D surface in Chimera? Thanks, Ana Luiza.

3 3

wglMakeCurrent failed
by Stefano Marzi 03 Sep '09

03 Sep '09

Hi, With the new production releases, from 1.2540 to the very last one 1.4_b28596, for windows, I am keeping getting the wglMakeCurrent failure. This happens when I try to make a movie. I have searched in the Chimera-user mailing list archive but I have found only a thread by Greg Couch saying that this bug has been fixed already one year ago, September 2008. Could anyone please help me with that? Thank you, Best Stefano Marzi

2 1