From goddard at cgl.ucsf.edu Mon Jul 2 10:28:02 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 02 Jul 2007 10:28:02 -0700 Subject: [Chimera-users] Fixing MSMS crash Message-ID: <468935A2.7010008@cgl.ucsf.edu> P. Qian sent me a PDB model that caused Chimera to crash when calculating an MSMS surface (menu Actions / Surface / show). He got it not to crash by shifting the coordinates of all atoms (by moving and saving the PDB with "use untransformed coordinates" turned off, and reloading that file). This is a little nicer than changing atom radii as we've advised in the past. Not sure how often a simple shift (or rotation) avoids the crash though. Tom From goddard at cgl.ucsf.edu Tue Jul 3 09:49:46 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 03 Jul 2007 09:49:46 -0700 Subject: [Chimera-users] seg faults In-Reply-To: <468A5CFE.5050005@virginia.edu> References: <468A5CFE.5050005@virginia.edu> Message-ID: <468A7E2A.30908@cgl.ucsf.edu> Edward Egelman wrote: > Hi, > I have a question about very complicated chimera sessions (20 or so > large PDB files, 10 or so large brix volumes). We will sometimes get a > segmentation fault and the session will close. This is on a 32-bit > linux machine with 2GB memory (our only system with stereo display). > If we move to a 64-bit machine with more memory, will we be less > likely to crash? Or is this due to some internal memory limitations in > chimera itself? A second question is whether you have any experience > (or know of others who have) using fast nvidia stereo boards (such as > the Quadro FX3500) to accelerate display operations in chimera. > Regards, > Ed > -- Hi Ed, There are only two Chimera crash situations that I understand and are frequently reported. Computing molecular surfaces of PDB models (menu entry Actions / Surface / show) crashes for many large PDB models. If the surface calculation gives an error but does not crash it has usually corrupted memory and Chimera will crash later. The solvent excluded surface code comes from Michel Sanner and is very complex (~20000 lines of C code). We have been working on a replacement for it for over a year but it is not yet ready. The second type of crash is caused by graphics driver bugs. These are common, more so on higher-end graphics cards where Chimera takes advantage of OpenGL features that are used by few applications, also more common on laptops. Here are some of the graphics driver problems observed in Chimera. http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html#cards I have never had Chimera crash when I am working with large PDB models and maps (using Mac systems with 1-2 Gb memory), but that is probably because I only work with a few models and maps at a time, and for short sessions. It could be that memory allocation failures cause crashes in these situations. I am doubtful that using the 64-bit Linux Chimera will help. Using the 32-bit Linux Chimera on a 64-bit machine almost certainly will not help because the 32-bit address space can only access 4 Gb of memory and segments of that address space are already used by shared libraries and program stack -- so you probably only have 2 Gb of usable space. With 2 Gbytes of physical memory you probably have at least 4 Gb of virtual memory, so the 32-bit address space is the main limitation. Chimera catches memory allocation failures for large allocations (e.g. opening a new map) and those do not cause a crash. It is only when a small allocation that is not checked fails that a crash might happen. The difference in speed rendering surfaces between say a Quadro FX 3400 and an ATI Radeon Pro 9800 (in my 3 year old desktop computer) is about a factor of 4. That is about the speed up to expect between a card that is a couple years old and the latest graphics card. Benchmark scores using Chimera for different cards are on the web http://www.cgl.ucsf.edu/chimera/benchmarks.html although there are few numbers for the latest cards. For volume surfaces look at the Surface column of the table. The score is the grid size of a triangulated cube that can be rendered at 10 frames per second. Since the number of triangles increases as the square of the size you should look at the *square* of the ratio of scores between cards to gauge the increase in speed expected for a fixed size volume. Tom From goddard at cgl.ucsf.edu Tue Jul 3 11:57:58 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 03 Jul 2007 11:57:58 -0700 Subject: [Chimera-users] POVray shininess In-Reply-To: <468A9591.90009@virginia.edu> References: <468A9591.90009@virginia.edu> Message-ID: <468A9C36.7000703@cgl.ucsf.edu> Edward Egelman wrote: > Hi, > The new POV rendering is very nice, but suffers from one problem > that I do not see how to fix. Is there any way to control the surface > properties (reflectivity, "shininess", etc.)? I only see the standard > brightness and transparency for the "save as" feature. > Regards, > Ed Hi Ed, You can control the shininess of surfaces in Chimera using menu entry Tools / Viewing Controls / Shininess. The shininess you set is exported to POVray when you save a raytraced image. The POVray appearance doesn't exactly match the Chimera graphics window appearance so you may need some trial-and-error experimentation to get the desired shininess in the POVray output. Tom From piacono at gmail.com Tue Jul 3 12:11:35 2007 From: piacono at gmail.com (Pasquale Iacono) Date: Tue, 3 Jul 2007 15:11:35 -0400 Subject: [Chimera-users] Using mol2 files Message-ID: <35926c660707031211o1145444cxc19ddbd4e63e809d@mail.gmail.com> Hi I imported a .mol2 file from Gaussian to Chimera because I want to run an amber minimization with a better parameter set. However, the mol2 files are not like pdb files and do not come with atom types for amber calculations. Is there anyway to (auto?)assign amber atom types to the atoms in my file so your program can run a calculation? Thank you. -Pasquale Iacono, B.S. Ithaca.College -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jul 3 15:30:12 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 3 Jul 2007 15:30:12 -0700 Subject: [Chimera-users] Using mol2 files In-Reply-To: <35926c660707031211o1145444cxc19ddbd4e63e809d@mail.gmail.com> References: <35926c660707031211o1145444cxc19ddbd4e63e809d@mail.gmail.com> Message-ID: Hi Pasquale, The "Minimize Structure" tool and "minimize" command will automatically take care of this issue for many structures. The charge addition step (same as using the "Add Charge" tool) uses Antechamber to both calculate the partial atomic charges and assign types to atoms in nonstandard residues. In fact, PDB files don't have atom types either. But if there are only standard residues (standard, unmodified amino acids, nucleic acids, and water), the atom types and charges are simply looked up in the Amber parm files. Again, this is automatically done by Chimera. For more information on atom type and parameter assignment, see http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html Nonstandard residues get "gaff" types intended for use with Amber, as mentioned in that page (there is also a literature reference). After they are assigned, you can see what the types are by custom-labeling those atoms with the gaffType attribute, for example for a residue named GLC with the following commands: labelopt info gaffType label :glc So, minimizing in Chimera may already work for your structure. Not everything can be handled, however - the MMTK/Amber99 parameter set includes many but not all metal ions, and Antechamber is not meant to handle inorganic molecules or metal complexes. In such cases you may need to use a different program. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at 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 Jul 3, 2007, at 12:11 PM, Pasquale Iacono wrote: > Hi I imported a .mol2 file from Gaussian to Chimera because I want > to run an amber minimization with a better parameter set. However, > the mol2 files are not like pdb files and do not come with atom > types for amber calculations. Is there anyway to (auto?)assign > amber atom types to the atoms in my file so your program can run a > calculation? Thank you. > -Pasquale Iacono, B.S. > Ithaca.College From pett at cgl.ucsf.edu Fri Jul 6 11:00:15 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 6 Jul 2007 11:00:15 -0700 Subject: [Chimera-users] Using mol2 files Message-ID: <3CF2E98B-3F91-4D3C-B280-FC0732C87509@cgl.ucsf.edu> Hi Pasquale, If your structure all got put into a single residue named UNK, that typically means that your file was missing the @SUBSTRUCTURE section (http://www.tripos.com/mol2/mol2_format33.html#1370). There is an entry in our bug database (#3518) for better handling of files with missing @SUBSTRUCTURE sections. I will add your name to that report so you'll know when it gets fixed. For now, you will have to edit your file and add an @SUBSTRUCTURE section "by hand". --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From ganzx001 at umn.edu Fri Jul 6 10:21:22 2007 From: ganzx001 at umn.edu (Eric Ganz) Date: Fri, 6 Jul 2007 12:21:22 -0500 Subject: [Chimera-users] Custom presets Message-ID: <001301c7bff2$13f7db70$3be79250$@edu> Is there a way to create new presets for molecule views? We want to apply the attributes of one molecule to subsequent molecules. Is there an easy way to do this? Our second question is how to set half-bond mode off for our views. From meng at cgl.ucsf.edu Fri Jul 6 14:24:54 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 6 Jul 2007 14:24:54 -0700 Subject: [Chimera-users] Custom presets In-Reply-To: <001301c7bff2$13f7db70$3be79250$@edu> References: <001301c7bff2$13f7db70$3be79250$@edu> Message-ID: Hi Eric, Easy question first... I can think of three ways to turn off halfbond mode: - open the Model Panel (under Favorites), choose the models of interest in the left side, choose "attributes" on the right. In the model attributes panel, expand the "Component Bond Attributes" section, turn "halfbond mode" to "off" - select one or more bonds of interest, click the button on the lower right corner of the Chimera window that says what it selected (opens the Selection Inspector). In the Selection Inspector, go the bond section if you aren't there already, turn "halfbond mode" to "off" - use the command "bondcolor" (which also specifies a particular color for the bond) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bondcolor.html The Presets are pretty new, and currently there is no friendly way (without Python programming) to make your own presets. We plan to add this in the future. There is also no friendly way to transfer one molecule's attribute settings to another. However, there are some related things that may help: - the Preferences include a New Molecules section in which you can specify some display attributes of newly opened molecules. However, the options are not complete, i.e. not all attributes you might want are controllable there. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% 20Molecules - if you have a series of commands that set the attributes, you can save them to a command file (or create a command file from scratch in a text editor). Opening the command file will execute all the commands. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ indexcommand.html#cmdfile - you can alias a long command or multiple semicolon-separated commands to a short string that is much easier to type. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html If you have specific suggestions or ideas, don't hesitate to share more information about your situation. We can factor them in to our plans. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at 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 Jul 6, 2007, at 10:21 AM, Eric Ganz wrote: > Is there a way to create new presets for molecule views? > > We want to apply the attributes of one molecule to subsequent > molecules. Is > there an easy way to do this? > > Our second question is how to set half-bond mode off for our views. From seewindow at yahoo.com.cn Sun Jul 8 02:48:02 2007 From: seewindow at yahoo.com.cn (=?gb2312?q?=C3=F7=20=C3=F7?=) Date: Sun, 8 Jul 2007 17:48:02 +0800 (CST) Subject: [Chimera-users] chimera question Message-ID: <153992.93742.qm@web92007.mail.cnb.yahoo.com> Dear sir: I download the software UCSF chimera(version: chimera-0.2422-win32.exe). the I setup it in my computer(Windows XP). I want to use it to open my pdb file and the VIPERdb file. But I always could not open them. It always says that: Error reading C:\Documents and Settings\ft\1K3V.pdb: typeerror: argument 1 should be a str( see reply log for python traceback info). Then I want to ask for you help. How can I open the pdb file and VIPERdb file correctly? please read the appendix Thank you. Qiting Harbin veterinary research institute --------------------------------- Mp3???-??????? -------------- next part -------------- An HTML attachment was scrubbed... URL: From seewindow at yahoo.com.cn Sun Jul 8 02:48:42 2007 From: seewindow at yahoo.com.cn (=?gb2312?q?=C3=F7=20=C3=F7?=) Date: Sun, 8 Jul 2007 17:48:42 +0800 (CST) Subject: [Chimera-users] chimera question Message-ID: <134556.28271.qm@web92009.mail.cnb.yahoo.com> Dear sir: I download the software UCSF chimera(version: chimera-0.2422-win32.exe). the I setup it in my computer(Windows XP). I want to use it to open my pdb file and the VIPERdb file. But I always could not open them. It always says that: Error reading C:\Documents and Settings\ft\1K3V.pdb: typeerror: argument 1 should be a str( see reply log for python traceback info). Then I want to ask for you help. How can I open the pdb file and VIPERdb file correctly? please read the appendix Thank you. Qiting Harbin veterinary research institute --------------------------------- Mp3???-??????? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1.JPG Type: image/pjpeg Size: 44975 bytes Desc: 3399445583-1.JPG URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2.JPG Type: image/pjpeg Size: 28843 bytes Desc: 2012883945-2.JPG URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3.JPG Type: image/pjpeg Size: 36320 bytes Desc: 352678225-3.JPG URL: From trh30 at cam.ac.uk Sun Jul 8 10:33:58 2007 From: trh30 at cam.ac.uk (Tim Howes) Date: Sun, 8 Jul 2007 13:33:58 -0400 Subject: [Chimera-users] chimera question In-Reply-To: <134556.28271.qm@web92009.mail.cnb.yahoo.com> References: <134556.28271.qm@web92009.mail.cnb.yahoo.com> Message-ID: Dear Qiting, I suspect it cannot handle the Chinese characters in the directory name. Try moving the file to a directory with no non-standard characters. -Tim On 7/8/07, ? ? wrote: > > Dear sir: > I download the software UCSF chimera(version: chimera-0.2422-win32.exe). > the I setup it in my computer(Windows XP). I want to use it to open my pdb > file and the VIPERdb file. But I always could not open them. It always says > that: Error reading C:\Documents and Settings\ft\1K3V.pdb: typeerror: > argument 1 should be a str( see reply log for python traceback info). Then > I want to ask for you help. How can I open the pdb file and VIPERdb file > correctly? > please read the appendix > Thank you. > Qiting > Harbin veterinary research institute > > ------------------------------ > Mp3???-??????? > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bala at igib.res.in Mon Jul 9 06:50:42 2007 From: bala at igib.res.in (bala) Date: Mon, 9 Jul 2007 19:20:42 +0530 Subject: [Chimera-users] occupancy calculation Message-ID: <91F147390CA53D44BFADECB36C489D1302695D@n1ex> Hello, 1) I want to calculate the occupancy of water around few base pairs in a RNA duplex. I had one query while i was going through the "calculate atomic occupancy" documentation. "For example, cations or water hydrogens may tend to occupy space around a negatively charged solute group" In the options give for this particular calculation, nowhere there is an option to select whether i am interested in WATER or ION occupany. How then chimera calculates the occupancy. 2)I presume that chimera calculates the occupany of say water as follows, if i select a residue, it puts the residue in a grid and calculated the density of water molecule in the grid points in frame. Is this the way it calculates the occupancy. I am not getting how i should differentiate occupancy and density. thanks, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jul 9 10:03:01 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Jul 2007 10:03:01 -0700 Subject: [Chimera-users] occupancy calculation In-Reply-To: <91F147390CA53D44BFADECB36C489D1302695D@n1ex> References: <91F147390CA53D44BFADECB36C489D1302695D@n1ex> Message-ID: Hi Bala, It counts the times the atom(s) appear in the 3D grid cells over the specified trajectory frames. It is not average density, but the total count in each cell over multiple frames, and the number is not divided by the volume of the cell. Typically to get a nice map at the end, you would use a small grid spacing so that there would not be more than one water or ion (or whatever atoms you choose, see below) in a given grid cell in a given frame. As described in the documentation, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ movie.html#occupancy there are two separate selection steps: (1) select the atoms to hold steady, then choose "Actions... Hold selection steady" from the MD Movie menu. This step is optional, for example, your trajectory might already be processed to hold certain atoms in place. (2) select the atoms for which occupancy (density, whatever) should be computed. This is where you would select solvent, ions, whatever. There are many ways to select: Select menu, picking from screen and arrow keys, or commands, for example: select solvent select ions Then you run the occupancy calculation. I hope this clears things up, Elaine p.s. there are examples of occupancy calculation in Part 2 of the "Trajectory and Ensemble Analysis" tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2 On Jul 9, 2007, at 6:50 AM, bala wrote: > Hello, > 1) I want to calculate the occupancy of water around few base pairs > in a RNA duplex. I had one query while i was going through the > "calculate atomic occupancy" documentation. > > "For example, cations or water hydrogens may tend to occupy space > around a negatively charged solute group" > > In the options give for this particular calculation, nowhere there > is an option to select whether i am interested in WATER or ION > occupany. How then chimera calculates the occupancy. > > 2)I presume that chimera calculates the occupany of say water as > follows, if i select a residue, it puts the residue in a grid and > calculated the density of water molecule in the grid points in > frame. Is this the way it calculates the occupancy. > > I am not getting how i should differentiate occupancy and density. > thanks, > Bala From triffo at rice.edu Mon Jul 9 12:18:46 2007 From: triffo at rice.edu (William Jeffrey Triffo) Date: Mon, 09 Jul 2007 12:18:46 -0700 Subject: [Chimera-users] clobbered chimera, can't start from fresh install (help) Message-ID: <46928A16.4080307@rice.edu> hello, I changed some of the preferences for the IDLE shell, which produced errors that would not allow IDLE to run (tried to remap a couple of keys). This problem persisted when restarting Chimera. so, I deleted that install (Mac OS X) and re-installed the most recent release, but still produced the errors, and cannot launch IDLE. I went ahead and deleted the files in ~/.chimera, but the errors still occur. Are there any other user-specific files that I can delete that might be causing the problem? I am assuming this is the case, because even a fresh install has the same problem. I submitted a bug report about the IDLE preferences issue I experienced, but am hoping a simple fix might allow me to launch IDLE again. thanks, -Jeff From triffo at rice.edu Mon Jul 9 12:29:41 2007 From: triffo at rice.edu (William Jeffrey Triffo) Date: Mon, 09 Jul 2007 12:29:41 -0700 Subject: [Chimera-users] clobbered chimera, can't start from fresh install (help) In-Reply-To: <46928A16.4080307@rice.edu> References: <46928A16.4080307@rice.edu> Message-ID: <46928CA5.0@rice.edu> please disregard this email, Eric just told me about the .idlerc config file. thanks, -Jeff William Jeffrey Triffo wrote: > hello, > > I changed some of the preferences for the IDLE shell, which produced > errors that would not allow IDLE to run (tried to remap a couple of > keys). This problem persisted when restarting Chimera. > > so, I deleted that install (Mac OS X) and re-installed the most recent > release, but still produced the errors, and cannot launch IDLE. I went > ahead and deleted the files in ~/.chimera, but the errors still occur. > > Are there any other user-specific files that I can delete that might be > causing the problem? I am assuming this is the case, because even a > fresh install has the same problem. > > I submitted a bug report about the IDLE preferences issue I experienced, > but am hoping a simple fix might allow me to launch IDLE again. > > thanks, > > -Jeff > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > From pett at cgl.ucsf.edu Mon Jul 9 13:15:26 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 9 Jul 2007 13:15:26 -0700 Subject: [Chimera-users] pdb-l: Selecting phytols in Chimera? In-Reply-To: References: Message-ID: <3BE7A6B9-9D11-469A-BEFE-F7E243070272@cgl.ucsf.edu> On Jul 9, 2007, at 6:39 AM, Morgan Ryan wrote: > Is it possible to write a selection string that will select all the > phytol substituents in a model? I'm looking at photosystem II. I > would like to select all the phytol side chains of the many > chlorophyll molecules and hide them, so that only the porphyrin-like > chlorin ring structures are visible. Can that be done? Thanks! Morgan Hi Morgan, I think the only direct way is to use the command line (Favorites- >Command Line). This command should do it: ~disp :cla at c=; disp :cla at c?a,c?b,c?c,c?d It undisplays all the carbons in the chlorophyll (:cla at c=) and then redisplays the carbons involved in the porphyrin ring (all of which have 3-letter names that end in A-D). You might want to consider posing Chimera-specific questions to the Chimera users mailing list (chimera-users at cgl.ucsf.edu) since there will be more people able to answer there. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu From meng at cgl.ucsf.edu Mon Jul 9 14:12:36 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Jul 2007 14:12:36 -0700 Subject: [Chimera-users] pdb-l: Selecting phytols in Chimera? In-Reply-To: <3BE7A6B9-9D11-469A-BEFE-F7E243070272@cgl.ucsf.edu> References: <3BE7A6B9-9D11-469A-BEFE-F7E243070272@cgl.ucsf.edu> Message-ID: <1D8F4C6A-B464-4919-BF08-3F3243B3C96F@cgl.ucsf.edu> Hi Morgan, More generally, to figure out Chimera selection strings for atoms in unusual residues, display an example of that residue and label its atoms to see their names. Then, using the names to specify, you can either (1) display the whole residue and then undisplay certain atoms or (2) undisplay the whole residue and then display certain atoms (as in Eric's example). You may be able to incorporate partial wild cards (? for single character, = for completion). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#wildcards Another way to see the names that will be used in remediated PDB files is to look up that residue in the chemical components dictionary. In structure 2axt, there are many chlorophyll A residues (CLA). To see its atom names, you could look at the PDB's component definition, http://remediation.wwpdb.org/pyapps/ldHandler.py?query=CLA http://remediation.wwpdb.org/data/C/CLA/CLA_D3L1.gif or you could use the following commands in Chimera open 2axt color byhet show :1.het focus la :1.het It looks like the phytol moiety of CLA is C1-C20. If I were working repeatedly with this structure, I'd probably use the "alias" command to alias the phytol selection string to something short and easy to type, for example alias phytol :cla at c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,c 18,c19,c20 (add/subtract atom names as desired). A range (c1-c20) will not work because names are treated as characters rather than numbers. After using that alias command, you can simply use "phytol" as the command- line specifier, for example ~disp phytol For subsequent use, you could put the alias in a command file (simply a text file containing one or more commands). Opening a command file executes its commands, and you can even designate it as a startup file to be automatically executed when the command line is first started. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ indexcommand.html#cmdfile http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Midas Of course, this approach depends on a consistent set of atom names being used in the various structures you use, which it should be in the remediated PDB files. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at 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 Jul 9, 2007, at 1:15 PM, Eric Pettersen wrote: > On Jul 9, 2007, at 6:39 AM, Morgan Ryan wrote: > >> Is it possible to write a selection string that will select all the >> phytol substituents in a model? I'm looking at photosystem II. I >> would like to select all the phytol side chains of the many >> chlorophyll molecules and hide them, so that only the porphyrin-like >> chlorin ring structures are visible. Can that be done? Thanks! Morgan > > Hi Morgan, > I think the only direct way is to use the command line (Favorites- >> Command Line). This command should do it: > > ~disp :cla at c=; disp :cla at c?a,c?b,c?c,c?d > > It undisplays all the carbons in the chlorophyll (:cla at c=) and then > redisplays the carbons involved in the porphyrin ring (all of which > have 3-letter names that end in A-D). > You might want to consider posing Chimera-specific questions to the > Chimera users mailing list (chimera-users at cgl.ucsf.edu) since there > will be more people able to answer there. > > --Eric > Eric Pettersen > UCSF Computer Graphics Lab > pett at cgl.ucsf.edu > http://www.cgl.ucsf.edu From meng at cgl.ucsf.edu Mon Jul 9 14:36:33 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Jul 2007 14:36:33 -0700 Subject: [Chimera-users] pdb-l: Selecting phytols in Chimera? In-Reply-To: <1D8F4C6A-B464-4919-BF08-3F3243B3C96F@cgl.ucsf.edu> References: <3BE7A6B9-9D11-469A-BEFE-F7E243070272@cgl.ucsf.edu> <1D8F4C6A-B464-4919-BF08-3F3243B3C96F@cgl.ucsf.edu> Message-ID: The following Chimera command is supposed to be all one line (unfortunately, mail message processing splits it up): > alias > phytol :cla at c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17 > ,c > 18,c19,c20 From aczader at yahoo.com Tue Jul 10 14:51:25 2007 From: aczader at yahoo.com (Arkadiusz Czader) Date: Tue, 10 Jul 2007 14:51:25 -0700 (PDT) Subject: [Chimera-users] Chimera and Debian Message-ID: <317768.20209.qm@web56103.mail.re3.yahoo.com> Hi, I have a problem running 32 bit linux version of Chimera on Debian64. When I run it, it complains about some libraries. Below I pasted what I get when I type chimera in a terminal window arek at teton:~$ chimera Traceback (most recent call last): File "/home/arek/progs/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "/home/arek/progs/chimera/share/chimeraInit.py", line 231, in init import chimera File "/home/arek/progs/chimera/lib/python2.4/site-packages/PIL/__init__.py", l ine 15, in ? ImportError: libGL.so.1: cannot open shared object file: No such file or directory The library libGL.so.1 is only in /usr/lib. Should it be in a different place? Any help appreciated. cheers, Arek ____________________________________________________ | | __ __ | | Arkadiusz Czader | | | _| | __ | | Department of Chemistry | | | | | | | | | | University of Houston | | | | | | | | | | Houston, TX 77204-5003 | | | | |_|_| | | | Phone: (713)-743-5101 | \ \_| ___ | | | E-mail: aczader at uh.edu | \___| |/ | | | | | | | | | | | | |__| |__| | |____________________________|_______________________| ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ From gregc at cgl.ucsf.edu Tue Jul 10 15:11:45 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 10 Jul 2007 15:11:45 -0700 (PDT) Subject: [Chimera-users] Chimera and Debian In-Reply-To: <317768.20209.qm@web56103.mail.re3.yahoo.com> References: <317768.20209.qm@web56103.mail.re3.yahoo.com> Message-ID: On Tue, 10 Jul 2007, Arkadiusz Czader wrote: > Hi, > > I have a problem running 32 bit linux version of > Chimera on Debian64. When I run it, it complains about > some libraries. Below I pasted what I get when I type > chimera in a terminal window > > > arek at teton:~$ chimera > > Traceback (most recent call last): > File "/home/arek/progs/chimera/share/__main__.py", > line 59, in ? > value = chimeraInit.init(sys.argv) > File > "/home/arek/progs/chimera/share/chimeraInit.py", line > 231, in init > import chimera > File > "/home/arek/progs/chimera/lib/python2.4/site-packages/PIL/__init__.py", > l ine 15, in ? > > ImportError: libGL.so.1: cannot open shared object > file: No such file or directory > > The library libGL.so.1 is only in /usr/lib. Should it > be in a different place? > Any help appreciated. > > cheers, > Arek /usr/lib is the right place. Run "ldd /usr/lib/libGL.so.1", and if you see "not found" in the output, then one of the libraries libGL is linked against is missing which will cause it to fail to load. You can also use the strace program to figure out what went wrong. If you email me the ldd output and the voluminous strace output ("strace chimera 2>&1 > strace-output.txt"), I should be able to pinpoint why your Debian system has problems. Greg Couch UCSF Computer Graphics Lab From best at biochem.mpg.de Tue Jul 10 16:40:14 2007 From: best at biochem.mpg.de (Christoph Best) Date: Wed, 11 Jul 2007 01:40:14 +0200 Subject: [Chimera-users] Chimera and Debian In-Reply-To: <317768.20209.qm@web56103.mail.re3.yahoo.com> References: <317768.20209.qm@web56103.mail.re3.yahoo.com> Message-ID: <18068.6366.893375.11213@random.tigertiger.de> Hi, Arkadiusz Czader writes: > I have a problem running 32 bit linux version of > Chimera on Debian64. When I run it, it complains about > some libraries. Below I pasted what I get when I type > chimera in a terminal window have you made sure that the ia32-libs package is installed? It contains the 32-bit libraries on Debian (everything else would be 64-bits on a pure Debian-amd64 system). You can check using ldconfig -p | grep libGL\\. and then you should see some lines like this libGL.so.1 (libc6,x86-64) => /usr/lib/libGL.so.1 libGL.so.1 (libc6) => /usr/lib32/libGL.so.1 (Replace x86-64 by IA-64 if you have an Itanium system). The second one is the 32-bit library, which should go in /usr/lib32. -Christoph -- | Christoph Best http://www.rzg.mpg.de/~cbest | Max-Planck-Institut fuer Biochemie, Munich, Germany +49-89-8578 2634 From aczader at yahoo.com Wed Jul 11 09:53:21 2007 From: aczader at yahoo.com (Arkadiusz Czader) Date: Wed, 11 Jul 2007 09:53:21 -0700 (PDT) Subject: [Chimera-users] Chimera and Debian In-Reply-To: <18068.6366.893375.11213@random.tigertiger.de> Message-ID: <619930.41994.qm@web56105.mail.re3.yahoo.com> Hi, Thank you Christoph and Greg for help. I naively assumed that 32 bit applications work smoothly on 64 bit systems (probably because I used SUSE before). Anyway, after installing the ia32-libs package chimera runs without any problems. Thanks again. Regards, Arek Christoph Best wrote: Hi, Arkadiusz Czader writes: > I have a problem running 32 bit linux version of > Chimera on Debian64. When I run it, it complains about > some libraries. Below I pasted what I get when I type > chimera in a terminal window have you made sure that the ia32-libs package is installed? It contains the 32-bit libraries on Debian (everything else would be 64-bits on a pure Debian-amd64 system). You can check using ldconfig -p | grep libGL\\. and then you should see some lines like this libGL.so.1 (libc6,x86-64) => /usr/lib/libGL.so.1 libGL.so.1 (libc6) => /usr/lib32/libGL.so.1 (Replace x86-64 by IA-64 if you have an Itanium system). The second one is the 32-bit library, which should go in /usr/lib32. -Christoph -- | Christoph Best http://www.rzg.mpg.de/~cbest | Max-Planck-Institut fuer Biochemie, Munich, Germany +49-89-8578 2634 ____________________________________________________ | | __ __ | | Arkadiusz Czader | | | _| | __ | | Department of Chemistry | | | | | | | | | | University of Houston | | | | | | | | | | Houston, TX 77204-5003 | | | | |_|_| | | | Phone: (713)-743-5101 | \ \_| ___ | | | E-mail: aczader at uh.edu | \___| |/ | | | | | | | | | | | | |__| |__| | |____________________________|_______________________| --------------------------------- Don't be flakey. Get Yahoo! Mail for Mobile and always stay connected to friends. -------------- next part -------------- An HTML attachment was scrubbed... URL: From menetret at bu.edu Wed Jul 11 12:57:40 2007 From: menetret at bu.edu (jean-francois menetret) Date: Wed, 11 Jul 2007 15:57:40 -0400 (EDT) Subject: [Chimera-users] memory usage Message-ID: It seems that Chimera is not releasing memory easily on our linux PC. Is this a know problem for Chimera ? Jean-Fran?ois M?n?tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret at bu.edu Mailing address: 715 Albany Street From meng at cgl.ucsf.edu Wed Jul 11 13:52:54 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Jul 2007 13:52:54 -0700 Subject: [Chimera-users] Using mol2 files In-Reply-To: <2014FD36-D4C3-48C6-A897-B040D6DDC25C@cgl.ucsf.edu> References: <35926c660707031211o1145444cxc19ddbd4e63e809d@mail.gmail.com> <35926c660707060854j45f27341v90d826b89685f557@mail.gmail.com> <92A5C4B8-253C-464E-A1C4-7E3C417B7661@cgl.ucsf.edu> <2014FD36-D4C3-48C6-A897-B040D6DDC25C@cgl.ucsf.edu> Message-ID: <5EB1D7E2-F6A3-4B8C-BF81-8682AB24ADFE@cgl.ucsf.edu> Hi Pasquale, As Eric figured out, your mol2 file does not contain substructure information. For the structure to be read by Chimera as a series of residues, there would need to be residue information in each line in the @ATOM section and then a corresponding @SUBSTRUCTURE section at the bottom. You would have to edit that information into your file. Otherwise, the structure appears as one big residue. Mol2 format description: http://www.tripos.com/mol2/mol2_format8.html ATOM section - need substructure ID and name (residue number and name) for each atom http://www.tripos.com/mol2/mol2_format33.html#1370 SUBSTRUCTURE section - more information on those substructures (residues) To get an example mol2 file, open a PDB file of a protein in Chimera, add hydrogens if you want those in your example, and then write it out as Mol2 (File... Save Mol2...) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at 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 Jul 6, 2007, at 10:57 AM, Eric Pettersen wrote: > Hi Pasquale, > If your structure all got put into a single residue named UNK, > that typically means that your file was missing the @SUBSTRUCTURE > section (http://www.tripos.com/mol2/mol2_format33.html#1370). > There is an entry in our bug database (#3518) for better handling > of files with missing @SUBSTRUCTURE sections. I will add your name > to that report so you'll know when it gets fixed. For now, you > will have to edit your file and add an @SUBSTRUCTURE section "by > hand". > > --Eric >> >> On Jul 6, 2007, at 8:54 AM, Pasquale Iacono wrote: >> >>> Hey Elaine, >>> My structure is currently being labeled as one big residue >>> (UNK) and when I minimize it it says it does not recognize the >>> residue, so it seems like the calculation program is using >>> residue parameters and not those for specific atoms. Also, my >>> structure contains a Zn(II) metal center and I was wondering if >>> the parm files would detect it as such if it actually used the >>> atom types. I attached my mol2 file so you can check it out. Thanks >>> -Pasquale Iacono From gregc at cgl.ucsf.edu Wed Jul 11 13:56:07 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 11 Jul 2007 13:56:07 -0700 (PDT) Subject: [Chimera-users] memory usage In-Reply-To: References: Message-ID: On Wed, 11 Jul 2007, jean-francois menetret wrote: > It seems that Chimera is not releasing memory easily on our linux PC. > Is this a know problem for Chimera ? That is normal UNIX behavior. Once virtual memory is assigned to a process, it isn't unassigned (released) until the process dies. Internally, chimera is releasing the memory, so it's not leaking memory on Linux anymore than any other platform (there might be no leaks, but I can't say for sure). To get a better of idea of chimera's memory use, you should check the RSS (Resident Set Size) instead of the SZ (swap size) or VSZ (virtual memory size). The RSS number lags the actual amoumt of memory that chimera is using because the system won't page out memory unless another process needs it, but it is much closer to chimera's actual memory use. So if you run: ps -o pid,rss,sz,vsz,user,args You'll see that the RSS value is smaller than the SZ value which is smaller than the VSZ value. If the process didn't use any shared libraries then the SZ and VSZ values would be the same. Hope this helps, Greg Couch UCSF Computer Graphics LabA From meng at cgl.ucsf.edu Wed Jul 11 18:33:55 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Jul 2007 18:33:55 -0700 Subject: [Chimera-users] Using mol2 files In-Reply-To: <5EB1D7E2-F6A3-4B8C-BF81-8682AB24ADFE@cgl.ucsf.edu> References: <35926c660707031211o1145444cxc19ddbd4e63e809d@mail.gmail.com> <35926c660707060854j45f27341v90d826b89685f557@mail.gmail.com> <92A5C4B8-253C-464E-A1C4-7E3C417B7661@cgl.ucsf.edu> <2014FD36-D4C3-48C6-A897-B040D6DDC25C@cgl.ucsf.edu> <5EB1D7E2-F6A3-4B8C-BF81-8682AB24ADFE@cgl.ucsf.edu> Message-ID: Hi Pasquale, Eric just reminded me of a further problem (sorry): the need for standard atom names. Chimera relies on the stereotypical atom and residue names to recognize standard amino acid and nucleotide residues and assign them Amber parameters for minimization, as described here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html#parameters I believe these stereotypical names originated with the PDB, but are also used in mol2 files generated by programs such as SYBYL. This atom/residue naming issue will affect ribbon display (which relies on backbone atom names) and Amber parameter assignment (for minimization). However, Chimera atom type assignment, hydrogen addition, H-bond and clash detection, etc. do not require the use of standard atom and residue names. Elaine On Jul 11, 2007, at 1:52 PM, Elaine Meng wrote: > Hi Pasquale, > As Eric figured out, your mol2 file does not contain substructure > information. For the structure to be read by Chimera as a series > of residues, there would need to be residue information in each > line in the @ATOM section and then a corresponding > @SUBSTRUCTURE section at the bottom. You would have to > edit that information into your file. Otherwise, the structure > appears as one big residue. From mgretes at interchange.ubc.ca Fri Jul 13 05:08:38 2007 From: mgretes at interchange.ubc.ca (Mike Gretes) Date: Fri, 13 Jul 2007 08:08:38 -0400 Subject: [Chimera-users] ValueError: More than 2 coplanar positions specified! Message-ID: <57FE184C-8418-4E86-86F0-35BA7E855D17@interchange.ubc.ca> Hello, When trying to calculate hydrogen bonding between two molecules, I get the error: "ValueError: More than 2 coplanar positions specified!" I have successfully calculated h-bonding between two other similar molecules, so I'm not sure what the problem is (I have no alternate conformations or anything weird in the PDB files I don't think... is there anything that usually triggers this error?) thanks! mike ___________________ Michael Gretes PhD Candidate (Structural Biology) Senior Graduate Trainee, Michael Smith Foundation for Health Research NCJ Strynadka Laboratory Dept. of Biochemistry, University of British Columbia Life Sciences Center, 2350 Health Sciences Mall Vancouver, BC Canada V6T 1Z3 phone 604 822 7729 fax 604 822 5227 ____________________ From mailman-bounces at cgl.ucsf.edu Wed Jul 11 09:49:04 2007 From: mailman-bounces at cgl.ucsf.edu (mailman-bounces at cgl.ucsf.edu) Date: Wed, 11 Jul 2007 09:49:04 -0700 Subject: [Chimera-users] Forward of moderated message Message-ID: An embedded message was scrubbed... From: =?gb2312?q?=C3=F7=20=C3=F7?= Subject: chimera question Date: Sun, 8 Jul 2007 19:14:43 +0800 (CST) Size: 154546 URL: From pett at cgl.ucsf.edu Fri Jul 13 11:03:17 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 13 Jul 2007 11:03:17 -0700 Subject: [Chimera-users] Forward of moderated message In-Reply-To: References: Message-ID: <91A1E424-BE60-4048-BFA0-7134A8D81AEC@cgl.ucsf.edu> Oops, didn't see the date embedded inside this message when I approved it. Sorry! Please ignore. --Eric On Jul 11, 2007, at 9:49 AM, mailman-bounces at cgl.ucsf.edu wrote: > > From: ? ? > Date: July 8, 2007 4:14:43 AM PDT > To: mailman at cgl.ucsf.edu > Subject: chimera question > > > Dear sir: > I download the software UCSF chimera(version: chimera-0.2422- > win32.exe). the I setup it in my computer(Windows XP). I want to > use it to open my pdb file and the VIPERdb file. But I always could > not open them. It always says that: Error reading C:\Documents and > Settings\ft\1K3V.pdb: typeerror: argument 1 should be a str( see > reply log for python traceback info). Then I want to ask for you > help. How can I open the pdb file and VIPERdb file correctly? > please read the appendix > Thank you. > Qiting > Harbin veterinary research > institute > > ????????3.5G???20M??? > <1.JPG> > <2.JPG> > <3.JPG> > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Fri Jul 13 11:20:40 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 13 Jul 2007 11:20:40 -0700 Subject: [Chimera-users] ValueError: More than 2 coplanar positions specified! In-Reply-To: <57FE184C-8418-4E86-86F0-35BA7E855D17@interchange.ubc.ca> References: <57FE184C-8418-4E86-86F0-35BA7E855D17@interchange.ubc.ca> Message-ID: Hi Mike, That error typically means that either there are bad bonds in the molecule (which could be the fault of Chimera or a problem with the input) or that a non-sp2 atom has been wrongly assigned an sp2 type (usually Chimera's fault alone). Could you provide the structure that elicits the error so that I can investigate? Thanks. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Jul 13, 2007, at 5:08 AM, Mike Gretes wrote: > Hello, > > When trying to calculate hydrogen bonding between two molecules, I > get the error: > > "ValueError: More than 2 coplanar positions specified!" > > I have successfully calculated h-bonding between two other similar > molecules, so I'm not sure what the problem is (I have no alternate > conformations or anything weird in the PDB files I don't think... is > there anything that usually triggers this error?) > > thanks! > > mike > > > ___________________ > > Michael Gretes > PhD Candidate (Structural Biology) > Senior Graduate Trainee, Michael Smith Foundation for Health Research > NCJ Strynadka Laboratory > Dept. of Biochemistry, University of British Columbia > Life Sciences Center, 2350 Health Sciences Mall > Vancouver, BC Canada V6T 1Z3 > phone 604 822 7729 > fax 604 822 5227 > ____________________ > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jul 16 09:28:14 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Jul 2007 09:28:14 -0700 Subject: [Chimera-users] Using mol2 files In-Reply-To: <35926c660707160759s3fab5081k67d8f14f29767af9@mail.gmail.com> References: <35926c660707031211o1145444cxc19ddbd4e63e809d@mail.gmail.com> <35926c660707060854j45f27341v90d826b89685f557@mail.gmail.com> <92A5C4B8-253C-464E-A1C4-7E3C417B7661@cgl.ucsf.edu> <35926c660707061319h148ec66fx6eee205383ab40e@mail.gmail.com> <35926c660707111254j550e855bq9fd516e9efb0278d@mail.gmail.com> <5B9DB28E-2E69-44FA-8E9D-DA1894FE5F0E@cgl.ucsf.edu> <35926c660707160759s3fab5081k67d8f14f29767af9@mail.gmail.com> Message-ID: <8688F987-37A1-4B4A-BB04-C1794B206DF3@cgl.ucsf.edu> Hi Pasquale, You can definitely open multiple PDB files and move them independently. By default everything will move together, which might even be what you want. However, if you don't want them to move together, you can freeze any structure in place ("deactivate" it), move the other(s), and then "activate" the first structure again if you want it to be movable. There are several ways to control activation/deactivation; probably the easiest is to open the Model Panel (Favorites... Model Panel). Then just uncheck/check the box in the Active column to freeze/ unfreeze a model. We use the word model to mean the contents of a structure file (PDB, Mol2, etc.), so if you read in two separate PDB files, there would be two models listed in the Model Panel. Alternative ways of controlling activation/deactivation are with the little checkboxes under the Command Line and using the command "select". You would still be able to minimize multiple models as a single system by choosing all of them in the "Minimize Structure" dialog. Elaine ----- Elaine C. Meng, Ph.D. meng at 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 Jul 16, 2007, at 7:59 AM, Pasquale Iacono wrote: > well in order to make the dimer i used two separate pdb files and > imported them both into the same gaussian gjf file. then i imported > that file as a mol2 file into chimera, so unless i can manipulate > separate pdb files in chimera then that would be great but i cannot > figure out how to move separate pieces of my dimer. > > On 7/15/07, Elaine Meng wrote: Hi Pasquale, > I had one long-shot possibility for getting the correct atom and > residue names - did you start with a PDB file before the guassian > calculations? If so, that file may have had the correct atom and > residue names. If that starting file had all the same atoms > (including hydrogens) and the order of the atoms is exactly the same > in that gaussian output, you could simply replace (probably with a > script) the coordinates in each line of the starting PDB file with > those from the gaussian output. That would only work if the order is > exactly the same, however. > > Otherwise it would be extremely tedious to figure out which > coordinates go with which atom/res/number. > Best, > Elaine From rking at uri.edu Tue Jul 17 06:26:28 2007 From: rking at uri.edu (Roberta King) Date: Tue, 17 Jul 2007 09:26:28 -0400 Subject: [Chimera-users] presets criteria Message-ID: <000301c7c876$161b4310$16208083@RKD420> Hello, I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within "Interactive 1:setup ribbons" preset for determining which residue side chains are depicted as sticks in the binding pocket? This is a useful shortcut, but I would like to understand the specific criteria. Thank you very much, Roberta ******************************** Roberta S. King, Ph.D. Associate Professor Department of Biomedical and Pharmaceutical Sciences College of Pharmacy University of Rhode Island http://www.uri.edu/pharmacy/faculty/king -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Jul 17 11:12:40 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 17 Jul 2007 11:12:40 -0700 Subject: [Chimera-users] presets criteria In-Reply-To: <000301c7c876$161b4310$16208083@RKD420> References: <000301c7c876$161b4310$16208083@RKD420> Message-ID: <2A2C9898-74CD-47B0-8D66-4E6B933F6F86@cgl.ucsf.edu> Hi Roberta, That preset will depict residues with non-backbone atoms within 3.5 angstroms of: a metal-ion-only residue; a residue classified as ligand (that classification explained here: http://www.cgl.ucsf.edu/ chimera/docs/UsersGuide/midas/surface.html#surfcats). Also, residues involved in a metal-coordination complex will be depicted, though usually that is also covered by the first criteria above. Nucleic acid side chains are always depicted. The idea was to quickly get to a view that would be relatively easy to understand yet still useful for analysis. This was my best first approximation. I'm open to suggestions for improvements. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Jul 17, 2007, at 6:26 AM, Roberta King wrote: > Hello, > > > > I have upgraded to Chimera 12417 with the new presets for > visualization. What are the criteria within ?Interactive 1:setup > ribbons? preset for determining which residue side chains are > depicted as sticks in the binding pocket? > > > > This is a useful shortcut, but I would like to understand the > specific criteria. > > > > Thank you very much, > > Roberta > > > > ******************************** > > Roberta S. King, Ph.D. > > Associate Professor > > Department of Biomedical and Pharmaceutical Sciences > > College of Pharmacy > > University of Rhode Island > > http://www.uri.edu/pharmacy/faculty/king > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Tue Jul 17 12:11:43 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 17 Jul 2007 12:11:43 -0700 Subject: [Chimera-users] Reading a data set from a text file In-Reply-To: <707DECCF-2528-407A-9B25-3F6B2F334EE2@mail.nih.gov> References: <97D9F35E-3A95-43E0-B1E5-3BD4C83F550A@mail.nih.gov> <7D52D40B-61D0-48AE-87AA-3CBE3F8B45A4@mail.nih.gov> <46853B58.9090009@cgl.ucsf.edu> <707DECCF-2528-407A-9B25-3F6B2F334EE2@mail.nih.gov> Message-ID: <469D146F.3080201@cgl.ucsf.edu> Hi Kyaw, I see what you've done and see that you have a set of (x,y,z) coordinates. But I'm not sure what you want or what these coordinates represent. To make a surface out of a set of points you need to know which points are next to each other. In Chimera you need a set of points, and a set of triangles, each triangle defined by 3 integer indices into the set of points that give the triangle vertices. If you can define the set of triangles I can tell you how to make the surface. Tom Kyaw Zeyar Myint wrote: > Hello Tom, > I apologize for not being able to respond to you earlier. The > set of view vectors that I want to make surface out of it are in (x, y, > z) coordinates. > > So far, I've done a quick and 'rough' way of using these vectors for > display. What I did in chimera was that I wrote a mini plugin which > makes a .bild > file with a > set of cylinders, given a set of vectors. > Each cylinder is centered at origin (0,0,0) and drawn according > to the vector (which is from my set of view vectors). So if the V(x,y,z) > has (0.0523, 0.0000, 0.9986), then the cylinder is drawn by: > /.cylinder 0 0 0 0.0523 0.0000 0.9986 0.03 / in .bild file. > Then .bild file is fed into chimera and then a set of cylinders > is displayed. In a sense, each cylinder represents each view vector in > the set. But this is just a quick solution. > If you can share some ideas of how to better do this, please let > me know. I'd really appreciate your help. > > Thanks a lot! > Kyaw > (P.S: I've attached .bild file which you can display in chimera and see > what inside using a text editor.) > > ------------------------------------------------------------------------ > > > On Jun 29, 2007, at 1:03 PM, Tom Goddard wrote: > >> Hi Kyaw, >> >> I'm not sure I understand what type of data you want to display in >> Chimera. Is it a list of density values, or is it a list of x, y, and >> z coordinates? If it is density values in text rather than binary, >> you could reformat it into XPLOR format >> >> http://www.scripps.edu/rc/softwaredocs/msi/xplor981/formats.html >> >> which can be read into Chimera. >> >> Tom > From triffo at rice.edu Tue Jul 17 16:18:55 2007 From: triffo at rice.edu (triffo at rice.edu) Date: Tue, 17 Jul 2007 18:18:55 -0500 Subject: [Chimera-users] Reading a data set from a text file In-Reply-To: <469D146F.3080201@cgl.ucsf.edu> References: <97D9F35E-3A95-43E0-B1E5-3BD4C83F550A@mail.nih.gov> <7D52D40B-61D0-48AE-87AA-3CBE3F8B45A4@mail.nih.gov> <46853B58.9090009@cgl.ucsf.edu> <707DECCF-2528-407A-9B25-3F6B2F334EE2@mail.nih.gov> <469D146F.3080201@cgl.ucsf.edu> Message-ID: <1184714335.469d4e5f48e28@webmail.mail.rice.edu> if you don't have connectivity defined already (your set of triangles), I think VTK (and other free packages out there) will derive the connectivity for you, if you assume that all points lie on the surface - (Delaunay tessellation/triangulation). Matlab also has this, if you have access. These algorithms will often give you back the points with a convention defining the surface normal, which may be important. -Jeff Quoting Thomas Goddard : > Hi Kyaw, > > I see what you've done and see that you have a set of (x,y,z) > coordinates. But I'm not sure what you want or what these coordinates > represent. > > To make a surface out of a set of points you need to know which > points are next to each other. In Chimera you need a set of points, and > a set of triangles, each triangle defined by 3 integer indices into the > set of points that give the triangle vertices. If you can define the > set of triangles I can tell you how to make the surface. > > Tom > > > Kyaw Zeyar Myint wrote: > > Hello Tom, > > I apologize for not being able to respond to you earlier. The > > set of view vectors that I want to make surface out of it are in (x, y, > > z) coordinates. > > > > So far, I've done a quick and 'rough' way of using these vectors for > > display. What I did in chimera was that I wrote a mini plugin which > > makes a .bild > > file with a > > set of cylinders, given a set of vectors. > > Each cylinder is centered at origin (0,0,0) and drawn according > > to the vector (which is from my set of view vectors). So if the V(x,y,z) > > has (0.0523, 0.0000, 0.9986), then the cylinder is drawn by: > > /.cylinder 0 0 0 0.0523 0.0000 0.9986 0.03 / in .bild file. > > Then .bild file is fed into chimera and then a set of cylinders > > is displayed. In a sense, each cylinder represents each view vector in > > the set. But this is just a quick solution. > > If you can share some ideas of how to better do this, please let > > me know. I'd really appreciate your help. > > > > Thanks a lot! > > Kyaw > > (P.S: I've attached .bild file which you can display in chimera and see > > what inside using a text editor.) > > > > ------------------------------------------------------------------------ > > > > > > On Jun 29, 2007, at 1:03 PM, Tom Goddard wrote: > > > >> Hi Kyaw, > >> > >> I'm not sure I understand what type of data you want to display in > >> Chimera. Is it a list of density values, or is it a list of x, y, and > >> z coordinates? If it is density values in text rather than binary, > >> you could reformat it into XPLOR format > >> > >> http://www.scripps.edu/rc/softwaredocs/msi/xplor981/formats.html > >> > >> which can be read into Chimera. > >> > >> Tom > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > From j0walr01 at louisville.edu Sat Jul 21 20:12:55 2007 From: j0walr01 at louisville.edu (Jason M Walraven) Date: Sat, 21 Jul 2007 23:12:55 -0400 Subject: [Chimera-users] Windows Vista Message-ID: <46A292F6.2B58.0052.0@gwise.louisville.edu> I just installed the latest version of Chimera on my Windows Vista operating system (home basic). Everything seems to work perfectly, except that the colors appear to be messed up. The colors appear darker than on my previous computer (with Windows XP). Has anyone else had this problem? All colors in all other programs are normal on my computer except for in Chimera. I assume it is a compatibility issue, but I don't know enough about it to say that for sure. jw -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Mon Jul 23 10:54:03 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 23 Jul 2007 10:54:03 -0700 (PDT) Subject: [Chimera-users] Windows Vista In-Reply-To: <46A292F6.2B58.0052.0@gwise.louisville.edu> References: <46A292F6.2B58.0052.0@gwise.louisville.edu> Message-ID: On Sat, 21 Jul 2007, Jason M Walraven wrote: > I just installed the latest version of Chimera on my Windows Vista > operating system (home basic). Everything seems to work perfectly, > except that the colors appear to be messed up. The colors appear darker > than on my previous computer (with Windows XP). Has anyone else had > this problem? All colors in all other programs are normal on my > computer except for in Chimera. I assume it is a compatibility issue, > but I don't know enough about it to say that for sure. We have seen that bug on Vista when you're using the default graphics driver. To fix it, you need to install the appropriate graphics driver for your graphics card or the integrated graphics on the motherboard. If you have an older computer, there might not be Vista graphics drivers for your setup, so your only option is to buy a ~$40 graphics card and install the driver. Good luck, Greg Couch UCSF Computer Graphics Lab From meng at cgl.ucsf.edu Wed Jul 25 09:11:30 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 25 Jul 2007 09:11:30 -0700 Subject: [Chimera-users] Fwd: CCL: hydroxide for dock References: <-id#3ma-34794-070725105103-29764-xG+9ooz9j38bBiBSkQkbOA@server.ccl.net> Message-ID: <7ADEDD83-88C2-4C49-B39D-0080D66F4ED7@cgl.ucsf.edu> Begin forwarded message: > From: "Yubo Fan yubofan|-|mail.chem.tamu.edu" chemistry at ccl.net> > Date: July 25, 2007 7:50:36 AM PDT > Subject: CCL: hydroxide for dock > Reply-To: "CCL Subscribers" > > Hi, everyone, > I'm preparing structures with Chimera for docking with Dock6. There > is a Zn-coordinating hydroxide that I want to keep in the > structure. When I prepare dock files, Chimera always treat it as a > water. Is there any way to define it as a hydroxide in Chimera? > Thanks, > Yubo > ============================================================ > Dr. Yubo Fan Email: yubofan_+_mail.chem.tamu.edu > Department of Chemistry Tel: 1-979-845-5237 > Texas A&M University > College Station, TX 77843 > ============================================================ Dear Yubo, I could answer more precisely if I could see the file, but without seeing it, I recommend: (a) looking at the residue name of the hydroxide in the text of the file. Is it WAT or HOH? If so, you could edit it to a different name, say XOH or HOM. (b) then, run Dock Prep in Chimera including hydrogen addition and all the steps before that (but don't assign charges or write the Mol2 file). (c) check the structure; if hydrogen is added where you didn't want it, simply delete it. For example, Ctrl-click to select an atom and use "Actions... Atoms/Bonds... delete" in the menu to delete it. The protonation states are intended to be reasonable at physiological pH, but if a group is expected to have a perturbed pKa (for example, in an active site or near an ion), it is a good idea to check it and manually add/delete hydrogens as needed. ( more details in http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html ) (d) run Dock Prep again with only the steps AFTER hydrogen addition (charge assignment and Mol2 file output) turned on. If it asks for the net charge of XOH (or whatever you named it), indicate -1. (e) that procedure will use Antechamber to calculate the partial charges on the hydroxide O and H. If, however, you already know the charges you want to use for these atoms, you can edit the charge values in the output Mol2 file. In that case you wouldn't even have to go through all these steps, but could simply also delete the extra hydrogen from the Mol2 file, if you can figure out which line it is! I just realized this last point, so it wasn't in my original reply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at 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 From jbeale at stlcop.edu Sun Jul 29 08:12:21 2007 From: jbeale at stlcop.edu (Beale, John) Date: Sun, 29 Jul 2007 10:12:21 -0500 Subject: [Chimera-users] Chimera on Linux Message-ID: I have been using Chimera on a Linux-equipped laptop for a long time. All that I had to do to get the software working was to download the appropriate version of Chimera and click on the executable. I am trying to install Chimera on a new Linux workstation. I downloaded the program for Linux, but when I try to run the executable I get a message that says that the software downloaded is for MS-DOS and not Linux, and I am unable to install Chimera. Has anyone run into this problem, and is there a fix for it? John Beale From conrad at cgl.ucsf.edu Mon Jul 30 10:35:11 2007 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Mon, 30 Jul 2007 10:35:11 -0700 Subject: [Chimera-users] CSB 2007 Molecular Visualization tutorial Message-ID: <46AE214F.6050102@cgl.ucsf.edu> Scooter Morris and Conrad Huang will be giving an introductory molecular visualization tutorial using Chimera on August 13 at CSB 2007 (the Conference on Computational Systems Bioinformatics) in San Diego. Interested folks can visit http://www.lifesciencessociety.org/CSB2007/index07.html for more information on CSB 2007. The tutorial abstract is attached below. An Introduction to Molecular Visualization Tutorial at the Computational Systems Bioinformatics (CSB) conference (AM2) University of California, San Diego August 13, 2007 Abstract Projects such as Structural Genomics are providing increasing numbers of experimental protein and protein-complex structures. Furthermore, increasing numbers of theoretical models are being predicted from primary sequence. Biologists have an increasing need to understand and communicate the structures, functions and relationships between these protein and protein-complex structures. As a result, molecular visualization is becoming an important tool for the presentation and communication of the results of biological experiments and research. This tutorial will provide a basic foundation for the understanding of molecular structures through use of visualization tools. Attendees will learn the basics of molecular visualization and will be provided an overview of available tools and techniques for visualization, analysis and modeling of protein structure. To make these concepts more concrete, attendees will be shown the academic program UCSF Chimera in more detail, and receive instruction in its features and use. The field of structural biology is still changing, and new techniques are continually being developed. Attendees will be shown how they can add new analysis techniques and their own data to the visualization. Outline: 1. Introduction to Molecular Visualization 2. Available Tools 3. Using UCSF Chimera 4. Scenarios of use 5. Extending Chimera From gregc at cgl.ucsf.edu Mon Jul 30 11:17:54 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 30 Jul 2007 11:17:54 -0700 (PDT) Subject: [Chimera-users] Chimera on Linux In-Reply-To: References: Message-ID: On Sun, 29 Jul 2007, Beale, John wrote: > I have been using Chimera on a Linux-equipped laptop for a long time. > All that I had to do to get the software working was to download the > appropriate version of Chimera and click on the executable. I am trying > to install Chimera on a new Linux workstation. I downloaded the program > for Linux, but when I try to run the executable I get a message that > says that the software downloaded is for MS-DOS and not Linux, and I am > unable to install Chimera. Has anyone run into this problem, and is > there a fix for it? Did you change the version on linux on your laptop? The exact steps needed to install chimera can vary between distributions and versions of linux. For instance, the MS-DOS warning is because the installer has a .exe suffix. But not all linux systems give that warning. I am surpised you were ever able to click on the chimera installer on linux and have it install. When the installer is downloaded, it is typically not executable, so you need to startup a terminal window, cd to the directory with the chimera installer, then chmod +x chimera-VERSION-linux.exe, and then run it. (FYI, even if you used the GUI to change the installer to be executable, it would still fail when clicked on because it needs the terminal window to asked questions in.) Greg Couch UCSF Computer Graphics Lab From pett at cgl.ucsf.edu Mon Jul 30 11:27:32 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 30 Jul 2007 11:27:32 -0700 Subject: [Chimera-users] Chimera on Linux In-Reply-To: References: Message-ID: <71097644-CDDC-4196-B1D6-AD33A9E859D9@cgl.ucsf.edu> On Jul 29, 2007, at 8:12 AM, Beale, John wrote: > I have been using Chimera on a Linux-equipped laptop for a long > time. All that I had to do to get the software working was to > download the appropriate version of Chimera and click on the > executable. I am trying to install Chimera on a new Linux > workstation. I downloaded the program for Linux, but when I try to > run the executable I get a message that says that the software > downloaded is for MS-DOS and not Linux, and I am unable to install > Chimera. Has anyone run into this problem, and is there a fix for it? Hi John, The basic problem is that some Linux desktop managers are "smart" enough to "know" that files that end in .exe are Windows executables, even when they are not. Possible solutions are outlined in the answer to question #2 in this mail: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-April/001496.html --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu