- Chimera-users - RBVI Mailing Lists

MemoryError restoring session
by Eric Pettersen 07 May '08

07 May '08

Christian Rickert wrote: > At the university, I saved a huge project of mine containing a > density map and multiple (!) rigid-body fitted pdbs. > Although this system is a 32-bit Kubuntu 8.04 only (4 Gig of RAM > installed), I observed the same problems with my 64-bit SUSE 10.3 > (4 Gig of RAM installed as well) at work. > > Creating this project took me two days in total, so I really would > appreciate any suggestions from you ... Hi Christian, It's possible that your shell is imposing a limit on memory use by a single process. Before starting Chimera, remove the memory limit of your shell by typing: csh-type shell: unlimit sh-type shell: ulimit -v unlimited Let me know if this helps or not. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to use hbonds spec
by Miguel Ortiz-Lombardía 07 May '08

07 May '08

Hello, I'm trying to follow hydrogen bonds in a trajectory from amber. To do so, I would like to run a 'per frame' script with something like: hbonds spec :100 selRestrict cross relax false However, this fails because apparently no atoms are selected. This fails as well: hbonds spec #0:100 selRestrict cross relax false I can only see the hydrogen bonds if insert a select :100 before the hbonds command. I wouldn't like to see the green 'aura' of the selection, that's why I would like to make the selection within the hbonds command. I'm probably missing something, but cannot figure out what. Thank you! Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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Tile structure request
by Eduardo Sanz-Garcia 06 May '08

06 May '08

I noticed that the tile structure option arranges the models logically when there are 5 or less models opened. When there are 6 or more, the arrangement is a little bit chaotic, the models are not placed sequentially. Could this option be improved so the sequence is more logical? Thank you very much. Chimera is great!! PS: I am used to work with EM models, I don't know if the previously described behaviour also applies to atomic coordinates models.

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solvent-accessible surface area
by Elaine Meng 06 May '08

06 May '08

Dear Jose, Prof. Ferrin forwarded your question to me. Our program Chimera, the successor to MidasPlus, can calculate the solvent-accessible surface area. It is available for download for Windows, Mac OSX, Linux and other platforms. The features I will mention are relatively new, so you would need to get a recent version such as the May 1 snapshot: http://www.cgl.ucsf.edu/chimera/download.html#snapshots You would first load the structure in Chimera (File... Open for a local file, File... Fetch by ID to get it directly from the PDB). Then there are a couple of different approaches you could take. (1) simply show a molecular surface in Chimera (Actions... Surface... show) or command "surface". The total will be reported in the Reply Log (under Favorites in the menu). You can use the solvent- accessible value or solvent-excluded as you prefer. The difference is explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces Besides the total, the values per atom and per residue are assigned as "attributes" named areaSAS and areaSES for solvent-accessible and solvent-excluded, respectively. You can see a histogram of the values by opening "Render by Attribute" (under Tools... Depiction), and you can write out the values to a file by choosing File... Save Attributes from that dialog's menu. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render The Render dialog can be set to show the values for "atoms" or "residues" (simply the sum over the atoms in each residue). What it writes out are the atom (or residue) specifiers and the value for each, not a grid. (2) instead of doing the calculation in Chimera, you can send the coordinates to a web server with the tool "Area/Volume from Web" (under Tools... Surface/Binding Analysis). There are various options for what you want to calculate. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html Again you get the values assigned as attributes (but this time atoms only) and can view and save them in the same way as described for #1 above. The help links above are part of the User's Guide, which is also accessible from the Help menu of Chimera, once you have downloaded it (Help... User's Guide, Search Documentation, Tutorials). If you still have trouble you can send questions to chimera-users(a)cgl.ucsf.edu 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 On May 5, 2008, at 4:52 PM, Tom Ferrin wrote: > ------- Forwarded Message > > Date: Wed, 30 Apr 2008 17:20:27 -0400 > From: Jose Gascon <jose.gascon(a)uconn.edu> > To: tef(a)cgl.ucsf.edu > Subject: midasplus > > Dear Prof. Ferrin > > I am an Assistant Professor in the Chemistry Department at UConn, I am > interested in calculating the solvent accessible area of a protein. I > looked up on the internet and found that the program midasplus is > suppose to do that. The links seem to be outdated and I was not been > able to find the program. I assume that midasplus has probably evolved > to other programs such as chimera. I understand that you were involved > in the development of this program. > > At the end, given a pdb input file, I am just interested in > obtaining a > grid of x,y,z coordinates representing the SAS. > Do you know if there is such a program? Is DMS, from midasplus, still > available somewhere? > > Thanks for your help. > > Sincerely, > > Jose A. Gascon > > > -- > Jose A. Gascon - Assistant Professor > 55 North Eagleville Rd. > Department of Chemistry > University of Connecticut - (860) 486-0591 > Storrs, CT 06269 > http://gascon.chem.uconn.edu > > ------- End of Forwarded Message >

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movie trajectory
by Jean-Paul Armache 05 May '08

05 May '08

Hi Elaine, Eric, Thanks for the answer - I know the webpage for the movies, but it will be helpful to use the savepos command. I will let you know whether this produces the desired effect or further help will be needed. Best regards, Jean-Paul

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movie trajectory
by Jean-Paul Armache 05 May '08

05 May '08

hi all, i have a small question. would any of you know a way to set up a specific trajectory for a camera to move around the molecule? i know you can rotate the whole molecule, but the question is more related to similarity to 3ds max or maya - if you could set up a specific way the camera moves around the molecule (rotation, movement at specific point, zoom, stop, restart, further movement etc) ? maybe the question is trivial, however i haven't found a way to do it (an easy way - you can do quite a huge script with small movements - one step at a time). my question is more about path drawing and setting stop points. regards, jean-paul

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Re: [Chimera-users] transparent surfaces (fwd)
by Greg Couch 05 May '08

05 May '08

Just so everyone on the list knows. Extrapolating from what Charles said, the error was probably that MegaPOV wasn't able to include the transforms.inc file because MegaPOV wasn't configured properly to include the POV-Ray library files. And on Mac OS X, Linux, and other UNIX systems, to use the CHIMERA/bin/povray.exe program outside of chimera, you need to setup the shared library path to include CHIMERA/lib. Chimera does that setup automatically for many of the programs in CHIMERA/bin, so we should probably fix it for povray as well, but if you're going to use your own POV-Ray anyway, like the multi-threaded 3.7 beta release, then that is not an issue. - Greg ---------- Forwarded message ---------- I figured it out. In MegaPOV you need to set the library path for the render, also POVray 3.6 will not work as a standalone application in Mac OS 10.4 and higher. Charles On May 5, 2008, at 2:15 PM, Greg Couch wrote: > On Thu, 1 May 2008, Charles Midgett wrote: > >> I want to make a transparent surface in volume viewer that can be >> drawn in POVray. It appears the *.pov and *.ini files produced by >> Chimera cannot be read by other POVray renders. Is there some work >> around that will allow me to ray trace a transparent surface >> displayed by the volume viewer? >> >> Charles > > That is news to us. The chimera povray output was only tested with the > POV-Ray 3.6.1 renderer that comes with chimera. Please submit a bug report > using chimera's Help / Report a Bug dialog and include the name and version > number of the other POV-ray renderers, as well as the error message you get. > > Thank you, > > Greg Couch > UCSF Computer Graphics Lab

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Consistency of surface color
by Bui Khanh Huy 05 May '08

05 May '08

Hi all, I have a problem with color consistency on Chimera. The surface color of my model from my Windows server is different than that from my linux server. Even when I connect from home to the linux server, the color render is also different from those two above. I use the same session for all of them but the color comes out quite different on different machines. Is there anyway to avoid this inconsistency? Regards, Huy

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transparent surfaces
by Charles Midgett 05 May '08

05 May '08

I want to make a transparent surface in volume viewer that can be drawn in POVray. It appears the *.pov and *.ini files produced by Chimera cannot be read by other POVray renders. Is there some work around that will allow me to ray trace a transparent surface displayed by the volume viewer? Charles

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areaSAS_areaSES
by De Nicola, Gian 05 May '08

05 May '08

To whom it may concern I would like to calculate the areaSAS and areasSES using Chimera.This is what I do Load the structure tools Surface Binding Analysis area/volume from web I choose the type of surface I want. Click apply then Ok As an output I get " unexpected output from struc tools server" . What am I doing wrong? Regards Gian

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