From hsosa at aecom.yu.edu Mon Jun 1 14:31:44 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Mon, 01 Jun 2009 17:31:44 -0400 Subject: [Chimera-users] ribbon transparency Message-ID: <4A2448C0.1060601@aecom.yu.edu> Hi, Is there a command to control the transparency of a ribbon representation or the whole model ?. I'm trying to fade in an out a molecule (in ribbon + wire atom representation) in movie. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From goddard at cgl.ucsf.edu Mon Jun 1 17:03:01 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 01 Jun 2009 17:03:01 -0700 Subject: [Chimera-users] ribbon transparency In-Reply-To: <4A2448C0.1060601@aecom.yu.edu> References: <4A2448C0.1060601@aecom.yu.edu> Message-ID: <4A246C35.5010304@cgl.ucsf.edu> Hi Hernando, There are two ways to go about this. One is to use the color command http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html say 20 times in a script to gradually increase the transparency to 1. You can specify the color as 4 values r,g,b,a in Chimera 1.4 daily builds (but not in 1.3). A second approach is to download a plugin called "Animation Commands" from the Chimera Experimental Features web page (near the bottom): http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Installing this gives you the "transition" command which can fade transparency. http://www.cgl.ucsf.edu/chimera/experimental/transition/transition.html Tom hsosa at aecom.yu.edu wrote: > Hi, > > Is there a command to control the transparency of a ribbon > representation or the whole model ?. > I'm trying to fade in an out a molecule (in ribbon + wire atom > representation) in movie. > > Thanks > > Hernando > From pett at cgl.ucsf.edu Mon Jun 1 17:15:17 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 1 Jun 2009 17:15:17 -0700 Subject: [Chimera-users] ribbon transparency In-Reply-To: <4A246C35.5010304@cgl.ucsf.edu> References: <4A2448C0.1060601@aecom.yu.edu> <4A246C35.5010304@cgl.ucsf.edu> Message-ID: <0BB2861E-BCAC-4F28-8998-35DD32D662DE@cgl.ucsf.edu> On Jun 1, 2009, at 5:03 PM, Thomas Goddard wrote: > There are two ways to go about this. One is to use the color > command > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html > > say 20 times in a script to gradually increase the transparency to 1. > You can specify the color as 4 values r,g,b,a in Chimera 1.4 daily > builds (but not in 1.3). A similar approach that does work in the 1.3 release is to color your ribbons with a color you defined with the 'colordef' command. You can then keep redefining the color to change its transparency and the ribbons will change accordingly. --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsosa at aecom.yu.edu Tue Jun 2 12:23:31 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Tue, 02 Jun 2009 15:23:31 -0400 Subject: [Chimera-users] ribbon transparency In-Reply-To: <4A246C35.5010304@cgl.ucsf.edu> References: <4A2448C0.1060601@aecom.yu.edu> <4A246C35.5010304@cgl.ucsf.edu> Message-ID: <4A257C33.4000300@aecom.yu.edu> I tried the "transition" command, it works but it seems very slow. Each frame transition takes a very long time to occur. I guess after recording it would be OK. Thanks Hernando Thomas Goddard wrote: > Hi Hernando, > > There are two ways to go about this. One is to use the color command > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html > > say 20 times in a script to gradually increase the transparency to 1. > You can specify the color as 4 values r,g,b,a in Chimera 1.4 daily > builds (but not in 1.3). A second approach is to download a plugin > called "Animation Commands" from the Chimera Experimental Features web > page (near the bottom): > > http://www.cgl.ucsf.edu/chimera/experimental/experimental.html > > Installing this gives you the "transition" command which can fade > transparency. > > http://www.cgl.ucsf.edu/chimera/experimental/transition/transition.html > > > Tom > > > hsosa at aecom.yu.edu wrote: >> Hi, >> >> Is there a command to control the transparency of a ribbon >> representation or the whole model ?. >> I'm trying to fade in an out a molecule (in ribbon + wire atom >> representation) in movie. >> >> Thanks >> >> Hernando >> > > -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From emailanindito at yahoo.co.in Tue Jun 2 23:22:36 2009 From: emailanindito at yahoo.co.in (Anindito Sen) Date: Wed, 3 Jun 2009 11:52:36 +0530 (IST) Subject: [Chimera-users] Deleting parts of secondary structures Message-ID: <453740.59774.qm@web94903.mail.in2.yahoo.com> Dear All I have a Chimera session in which I have 6 sets of PDB files (ribbon representation) showing variability in the structures. However I wish to display only few of the subunits. Questions are: 1. How do I delete undesired subunits from all the chains on the command line 2. How do I select particular residues from specific chains (not all the 6).. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 -------------- next part -------------- An HTML attachment was scrubbed... URL: From abeer.shokeer at biorg.uu.se Wed Jun 3 03:56:17 2009 From: abeer.shokeer at biorg.uu.se (Abeer Shokeer) Date: Wed, 03 Jun 2009 12:56:17 +0200 Subject: [Chimera-users] Residues that interact with active site Message-ID: <20090603125617.z2uoe75eogk0k8k8@webmail5.uu.se> Hello I have a model structure of my protein and I would like to determine which residues that could take part in active site. Can I do that with Chimera? Thanks for your help Abeer From tanja.schulz-gasch at roche.com Tue Jun 2 23:56:19 2009 From: tanja.schulz-gasch at roche.com (Schulz-Gasch, Tanja) Date: Wed, 3 Jun 2009 08:56:19 +0200 Subject: [Chimera-users] movie making Message-ID: Hi there, I used Chimera so far only for making pictures. Now I am doing the first movie steps. I want to combine features like hide, show, rock,... with the MD Movie module to show a morph between different protein conformations. How can this be done? The movie should start with the display part (using hide, show, rock,...) followed by the morphing. However, when using the MD movie module the morph starts at frame 1. 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 Email: tanja.schulz-gasch at 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." -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Jun 3 09:17:30 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 3 Jun 2009 09:17:30 -0700 Subject: [Chimera-users] Deleting parts of secondary structures In-Reply-To: <453740.59774.qm@web94903.mail.in2.yahoo.com> References: <453740.59774.qm@web94903.mail.in2.yahoo.com> Message-ID: <895613A7-FE07-416C-9C8A-2E539BE970A2@cgl.ucsf.edu> Dear Andy, There is a "language" for specifying atoms, residues, chains, models in commands. For example: delete #0:10-20.a,12.b,40.b (delete residues 10-20 in chain A and residues 12 and 40 in chain B, all in model 0) ~ribbon #0:312-456 (hide ribbon for residues 312-456 in all chains of model 0) ~disp :.a (undisplay atoms/bonds for chain A in all models) There are many fancier things you can do, including distance zones, etc., and it is all documented: There are also some examples of command-line specifications on the second page of the Quick Ref: Another more graphical possibility is to show the sequences of the various chains (Favorites... Sequence) and select parts of those, then use the Actions menu to delete atoms/bonds, or hide atoms/bonds, or hide ribbons. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 2, 2009, at 11:22 PM, Anindito Sen wrote: > Dear All > I have a Chimera session in which I have 6 sets of PDB files > (ribbon representation) showing variability in the structures. > However I wish to display only few of the subunits. Questions are: > > 1. How do I delete undesired subunits from all the chains on the > command line > > 2. How do I select particular residues from specific chains (not > all the 6). > Thanks > Andy From meng at cgl.ucsf.edu Wed Jun 3 09:38:01 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 3 Jun 2009 09:38:01 -0700 Subject: [Chimera-users] Residues that interact with active site In-Reply-To: <20090603125617.z2uoe75eogk0k8k8@webmail5.uu.se> References: <20090603125617.z2uoe75eogk0k8k8@webmail5.uu.se> Message-ID: <48683FC4-7E49-4EFC-9CB4-A9A989E5EACD@cgl.ucsf.edu> Hello Abeer, If there is some ligand bound or modeled into the site, you can certainly use Chimera to identify the residues that contact the ligand and/or form H-bonds with it. This is done, for example, in the Structure Analysis and Comparison tutorial using the "Find Clashes/Contacts" and "FindHBond" tools: If you only have the protein and no knowledge of where the active site is, however, Chimera does not predict the location of the active site. There are many, many Web servers that try to predict active sites or important residues given a structure, but I do not have a list of these, sorry. A couple of relevant Web servers that have a connection to Chimera are: (1) CASTp - finds pockets, often the largest is the active site (if you get results e-mailed to you, you can view them in Chimera) (2) ConSurf - finds related sequences, makes sequence alignment, shows residue conservation by coloring the structure; often the highly conserved residues are functionally important (one option is to show results in Chimera) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 3, 2009, at 3:56 AM, Abeer Shokeer wrote: > Hello > I have a model structure of my protein and I would like to determine > which residues that could take part in active site. Can I do that with > Chimera? > Thanks for your help > Abeer From meng at cgl.ucsf.edu Wed Jun 3 11:53:40 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 3 Jun 2009 11:53:40 -0700 Subject: [Chimera-users] movie making In-Reply-To: References: Message-ID: <14E37A04-A1DD-44EF-831A-9B17F880629C@cgl.ucsf.edu> Hi Tanja, I will describe a method that can be used in the current release (1.3) and then another newer method for which you need a recent daily build. The newer method should be easier, so maybe skip to read that first! OLDER METHOD: In the past I have done this by using a Chimera command script for the part before the morph. That script must specify the directory and naming pattern for the image files. For example, # session littlepmm2.py - movie segment before morphing movie record directory /tmp/meng pattern elaine-* supersample 2 rock y 2 68; wait wait 10 sc 1.01 20; move y -0.15 20 movie stop That only saves several images without encoding a movie. You could either create the morph before or after running the first script; if that model is not supposed to be shown in the first part of the movie, you could hide it using the Model Panel or modeldisplay command before running the script. Then I set up the display as desired for the morphing part, in my case hiding the other models, showing the morph trajectory model, and changing the 2D labels. Then using MD Movie "File... Record Movie" I would record that part. The important thing is to use the SAME directory and naming pattern as in the first part. Following the example above, you would enter the following in the "Additional recording options" area: directory /tmp/meng pattern elaine-* (the supersampling, if you wanted it, would be specified elsewhere in the dialog). Then it knows to add the additional frames to the pre- existing ones instead of starting over at 1. You could have another script after the morphing part if you wanted. If so, it would be necessary to use another option when recording the morphing part. In the MD Movie "File... Record Movie" dialog, you would put in the "Additional encoding options" area: resetMode none because this tool will always encode the movie, and you would need to prevent it from then deleting the images if the morphing were not the last part. If you had another script, it would also need to specify the same image directory and naming pattern, of course. NEWER METHOD: Although I have not gone through the full process myself, I believe it is now possible to use just a single script, where the morph- playing part could be accomplished with the "coordset" command: Then you don't have to worry about specifying the image file directory and naming pattern, or making sure the images are kept when a movie is encoded at some intermediate step. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 2, 2009, at 11:56 PM, Schulz-Gasch, Tanja wrote: > Hi there, I used Chimera so far only for making pictures. Now I am > doing the first movie steps. I want to combine features like > > hide, show, rock,... with the MD Movie module to show a morph > between different protein conformations. How can this be done? > > The movie should start with the display part (using hide, show, > rock,...) followed by the morphing. However, when using the MD movie > > module the morph starts at frame 1. > > Thanks, Tanja From pett at cgl.ucsf.edu Wed Jun 3 12:07:04 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 3 Jun 2009 12:07:04 -0700 Subject: [Chimera-users] movie making In-Reply-To: References: Message-ID: <9E6930C3-7764-45A3-AC38-5A9A6E9CB45E@cgl.ucsf.edu> Hi Tanja, If you want to show motions other than the morph itself you do have to abandon the MD Movie interface and write a command script. Also, you have to use a daily build since the 1.3 release doesn't include the command needed to play through the morph trajectory ("coordset"). There is a summary of Chimera's movie-making features here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html and a movie-making tutorial from a class we recently gave here: http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html Reading through those will give you a firm footing for creating your own movie. Nonetheless, just to give you some idea what your script might look like, here's an example (which assumes you've already created the morph as model 0): # setup the scene ~disp solvent # hide waters rib # show ribbons ribrepr smooth # nice ribbons, that is :-) # record the movie movie record supersample 3 # start recording frames rock y 2 68; wait # rock about the y axis for 68 frames (approximately one full cycle); wait for the rock to finish coordset #0 1, # play through morph movie stop # stop recording frames movie encode output ~/morph.mov bitrate 10000 # encode the movie as Quicktime with high quality, less compression --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 2, 2009, at 11:56 PM, Schulz-Gasch, Tanja wrote: > Hi there, I used Chimera so far only for making pictures. Now I am > doing the first movie steps. I want to combine features like > hide, show, rock,... with the MD Movie module to show a morph > between different protein conformations. How can this be done? > The movie should start with the display part (using hide, show, > rock,...) followed by the morphing. However, when using the MD movie > module the morph starts at frame 1. > > Thanks, Tanja > > __________________________________________ > > Dr. Tanja Schulz-Gasch -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Jun 3 12:13:13 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 3 Jun 2009 12:13:13 -0700 Subject: [Chimera-users] movie making In-Reply-To: <9E6930C3-7764-45A3-AC38-5A9A6E9CB45E@cgl.ucsf.edu> References: <9E6930C3-7764-45A3-AC38-5A9A6E9CB45E@cgl.ucsf.edu> Message-ID: On Jun 3, 2009, at 12:07 PM, Eric Pettersen wrote: > # setup the scene > ~disp solvent # hide waters > rib # show ribbons > ribrepr smooth # nice ribbons, that is :-) > # record the movie > movie record supersample 3 # start recording frames > rock y 2 68; wait # rock about the y axis for 68 frames > (approximately one full cycle); wait for the rock to finish > coordset #0 1, # play through morph > movie stop # stop recording frames > movie encode output ~/morph.mov bitrate 10000 # encode the movie as > Quicktime with high quality, less compression Actually, you can't have all those trailing '#' comments -- strip them! --Eric From pedro.al at fenhi.uh.cu Wed Jun 3 13:12:31 2009 From: pedro.al at fenhi.uh.cu (Yasser Almeida Hernandez) Date: Wed, 03 Jun 2009 16:12:31 -0400 Subject: [Chimera-users] Displaying surface residues... Message-ID: <20090603161231.39ga7vdmckwss0ok@correo.fenhi.uh.cu> Hi all... I want to know if its possible display surface residues via python script. The idea is import the chimera module inside the script, and it receive (the script), the pdb file to analyze. The script is to run in a classical bash terminal... Thanks.. ---------------------------------------------------------------- Correo FENHI From D.Kovalskyy at enamine.net Thu Jun 4 02:37:23 2009 From: D.Kovalskyy at enamine.net (Dmytro Kovalskyy) Date: Thu, 4 Jun 2009 12:37:23 +0300 Subject: [Chimera-users] chimera on GM945 Message-ID: <200906041237.23592.D.Kovalskyy@enamine.net> Hi there, I experience porblems with chimera running on Lenovo X60t in Linux. graphics: intel GM945 I have two installations on the notebook: WinXP and Linux (ALT Linux 4.1.1). Chimera's benchmark under Windows returns preety nice values (see http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, pre-pre last line, Lenovo ThinkPad X60 Tablet 6363WDP). However under linux I can not get even something reasonable to post Surf - 1 Mesh - 26 Contouring 149 Solid 1 Recoloring 5 Is it natural or due to some bugs in Linux drivers/X/kernel? Thanks in advance Dima -- ----------------------------------------------------- Dmytro Kovalskyy, PhD D.Kovalskyy at enamine.net Molecular Modelling Group Leader tel.: +38 044 537 32 18 Enamine ltd. fax : +38 044 537 32 53 23, Matrosova str. 01103 Kiev, Ukraine From gregc at cgl.ucsf.edu Thu Jun 4 08:42:06 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Thu, 4 Jun 2009 08:42:06 -0700 Subject: [Chimera-users] chimera on GM945 In-Reply-To: <200906041237.23592.D.Kovalskyy@enamine.net> References: <200906041237.23592.D.Kovalskyy@enamine.net> Message-ID: The chimera daily build has workarounds for bugs in some of the newer Linux distributions, so you should try the daily build first. Linux's OpenGL drivers, other than those directly from ATI and NVidia, are undergoing rapid evolution right now to improve performance, and that is especially true for the Intel drivers. Unfortunately, the changes affect many packages, i.e., the X server, Mesa, libdri, and others, so easiest solution for most people is to switch which Linux distribution they are using until they find one that works. We have not done much testing of Linux on computers with motherboard graphics. Fedora 10 should work. I've heard that Unbuntu 9.04 does not work (will be investigating that soon), but Ubuntu 8.10 should work. If you find a good distribution for your computer, please let us know. Greg Couch UCSF Computer Graphics Lab On Thu, 4 Jun 2009, Dmytro Kovalskyy wrote: > Hi there, > > I experience porblems with chimera running on Lenovo X60t in Linux. > graphics: intel GM945 > > I have two installations on the notebook: WinXP and Linux (ALT Linux 4.1.1). > > Chimera's benchmark under Windows returns preety nice values (see > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, pre-pre last line, > Lenovo ThinkPad X60 Tablet 6363WDP). > However under linux I can not get even something reasonable to post > Surf - 1 > Mesh - 26 > Contouring 149 > Solid 1 > Recoloring 5 > > Is it natural or due to some bugs in Linux drivers/X/kernel? > > Thanks in advance > > Dima From goddard at cgl.ucsf.edu Thu Jun 4 11:06:57 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 04 Jun 2009 11:06:57 -0700 Subject: [Chimera-users] chimera on GM945 In-Reply-To: <200906041237.23592.D.Kovalskyy@enamine.net> References: <200906041237.23592.D.Kovalskyy@enamine.net> Message-ID: <4A280D41.8080508@cgl.ucsf.edu> Hi Dima, As Greg mentioned the problem is the poor state of Intel graphics drivers on Linux. I'd try a Chimera 1.4 daily build as he suggests. If that does not help you might be able to improve the slow surface and mesh rendering by turning off use of OpenGL vertex buffer objects using the Chimera debug graphics dialog. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html You would start Chimera with "chimera --debug-opengl" and switch of vertex buffer objects in the dialog that appears. Tom Dmytro Kovalskyy wrote: > Hi there, > > I experience porblems with chimera running on Lenovo X60t in Linux. > graphics: intel GM945 > > I have two installations on the notebook: WinXP and Linux (ALT Linux 4.1.1). > > Chimera's benchmark under Windows returns preety nice values (see > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, pre-pre last line, > Lenovo ThinkPad X60 Tablet 6363WDP). > However under linux I can not get even something reasonable to post > Surf - 1 > Mesh - 26 > Contouring 149 > Solid 1 > Recoloring 5 > > Is it natural or due to some bugs in Linux drivers/X/kernel? > > Thanks in advance > > Dima > From goddard at cgl.ucsf.edu Thu Jun 4 11:38:50 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 04 Jun 2009 11:38:50 -0700 Subject: [Chimera-users] Displaying surface residues... In-Reply-To: <20090603161231.39ga7vdmckwss0ok@correo.fenhi.uh.cu> References: <20090603161231.39ga7vdmckwss0ok@correo.fenhi.uh.cu> Message-ID: <4A2814BA.3050301@cgl.ucsf.edu> Hi Yasser, You could run Chimera from a terminal chimera --nogui somemodel.pdb surfres.cmd where the --nogui tells Chimera not to display any windows, the first file is the PDB file you want to analyze and surfres.cmd is a script of Chimera commands as follows (from Elaine Meng) surf main ~surf # the following to ignore any interior bubbles and enclosed cavities setattr s allComponents false # the following could use a different cutoff, or areaSES instead of areaSAS show :/areaSAS>10 # then do whatever the person wanted, save image or save file of those residues If you need Python code for then analysis part of the script you can instead use a script file surfres.py that would look like: from chimera import runCommand as r r('surf main') r('~surf') r('setattr s allComponents false') r('show :/areaSAS>10') ... additional Python code to do analysis. Some things like saving images don't work with the --nogui option. Chimera needs to make windows for some things to work. Your concept of having a Python script that imports Chimera is a nice idea but unfortunately you are stuck using the Python that is included with Chimera. Even the slightest different version of Chimera tends to have some problems with the 40 third-party Python packages that Chimera makes use of. The above instructions are the simple way to go. Tom Yasser Almeida Hernandez wrote: > Hi all... > I want to know if its possible display surface residues via python > script. The idea is import the chimera module inside the script, and > it receive (the script), the pdb file to analyze. The script is to run > in a classical bash terminal... > > Thanks.. > > ---------------------------------------------------------------- > Correo FENHI > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Fri Jun 5 10:25:44 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 05 Jun 2009 10:25:44 -0700 Subject: [Chimera-users] Displaying surface residues... In-Reply-To: <4A2814BA.3050301@cgl.ucsf.edu> References: <20090603161231.39ga7vdmckwss0ok@correo.fenhi.uh.cu> <4A2814BA.3050301@cgl.ucsf.edu> Message-ID: <4A295518.4090203@cgl.ucsf.edu> Hi Yasser, Forgot to mention that setting surface attributes ("setattr s ...") is in Chimera 1.4 but not 1.3. If you want to use that you need to get a Chimera 1.4 daily build: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom -------- Original Message -------- Subject: Re: [Chimera-users] Displaying surface residues... From: Yasser Almeida Hernandez To: Thomas Goddard Date: 6/5/09 7:46 AM > Hi... > When i run the commands in terminal, graphical and python ways i get > the same error: > "Attribute level must be [a]tom, [r]esidue, [m]olecule, [p]seudobond, > or [g]roup" > > What that's mean...? > > I get this massage when i run the "setattr s allComponents false" > command... > > Thanks > From bala.biophysics at gmail.com Sun Jun 7 23:43:09 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Mon, 8 Jun 2009 08:43:09 +0200 Subject: [Chimera-users] loading chimera Message-ID: <288df32a0906072343n70060a25u3dfbf84743ebdb9b@mail.gmail.com> Friends, I installed chimera 1.4 ( build 27677) build in Fedora 10. The installation was successful but when i run chimera, chimera opens with the following message. ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: ignored. In addition, when i try to capture a high resolution image (300 dpi), chimera closed itself with following message. X Error of failed request: GLXBadPbuffer Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) Serial number of failed request: 75435 Current serial number in output stream: 75437 Locking assertion failure. Backtrace: #0 /usr/lib/libxcb-xlib.so.0 [0x19e767] #1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0x19e90e] #2 /usr/lib/libX11.so.6 [0xb690e9] #3 /usr/lib/nvidia/libGL.so.1 [0x6536ffd] Kindly write me what is going wrong. Thanks, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From kshatresh at gmail.com Mon Jun 8 07:42:22 2009 From: kshatresh at gmail.com (Kshatresh Dutta Dubey) Date: Mon, 8 Jun 2009 20:12:22 +0530 Subject: [Chimera-users] Segementation Fault Message-ID: <91d4c6ac0906080742h2bcae273h92096eb5f0727cdd@mail.gmail.com> Respected Sir, I am using chimera since five months. It was running without any error. But today when i am starting chimera it is giving error like segmentation fault. Kindely help me for this problem. Thanks in advance. Kshatresh Dutta dubey -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jun 8 09:36:11 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 8 Jun 2009 09:36:11 -0700 Subject: [Chimera-users] Segementation Fault In-Reply-To: <91d4c6ac0906080742h2bcae273h92096eb5f0727cdd@mail.gmail.com> References: <91d4c6ac0906080742h2bcae273h92096eb5f0727cdd@mail.gmail.com> Message-ID: <9883B42E-EBA7-4CAD-B4F3-146A207475AD@cgl.ucsf.edu> Dear Kshatresh, It is not enough information. We would need to know what kind of computer and what version of Chimera you were using, and if relevant, what input file. Also, it is not clear whether the failure was when you got a new version of Chimera or if it was the same one you were using for five months. I recommend sending bug reports to chimera-bugs at cgl.ucsf.edu (instead of chimera-users at cgl.ucsf.edu ). In most cases you could use "Help... Report a Bug" in the Chimera menu, but when Chimera doesn't start you could instead send mail directly. Make sure to include enough information and your e-mail address, otherwise it will not be possible to help you. Thanks, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 8, 2009, at 7:42 AM, Kshatresh Dutta Dubey wrote: > Respected Sir, > I am using chimera since five months. It was running without any > error. But today when i am starting chimera it is giving error like > segmentation fault. Kindely help me for this problem. > Thanks in advance. > Kshatresh Dutta dubey From gregc at cgl.ucsf.edu Mon Jun 8 10:36:35 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 8 Jun 2009 10:36:35 -0700 (PDT) Subject: [Chimera-users] loading chimera In-Reply-To: <288df32a0906072343n70060a25u3dfbf84743ebdb9b@mail.gmail.com> References: <288df32a0906072343n70060a25u3dfbf84743ebdb9b@mail.gmail.com> Message-ID: Please use chimera's Report a Bug dialog to submit this bug. It will tell me more about your system and what graphics driver you have installed so I will have a better chance of reproducing the bug. That said, I see that the backtrace says that /usr/lib/nvidia/libGL.so.1 was involved. That file is not part of the NVidia driver from www.nvidia.com, so I'm guessing you must have the open source version. If you switch to NVidia's version, then it should work. But before you switch, please submit the bug report so I'll know which driver is buggy. If you are stuck with the current graphics driver, you can workaround the bug by starting chimera with the --debug-opengl option and disabling Pbuffers. Thank you and good luck, Greg On Mon, 8 Jun 2009, Bala subramanian wrote: > Friends, > > I installed chimera 1.4 ( build 27677) build in Fedora 10. The installation > was successful but when i run chimera, chimera opens with the following > message. > > ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: > ignored. > ERROR: ld.so: object 'libGL.so' from LD_PRELOAD cannot be preloaded: > ignored. > > > In addition, when i try to capture a high resolution image (300 dpi), > chimera closed itself with following message. > > X Error of failed request: GLXBadPbuffer > Major opcode of failed request: 143 (GLX) > Minor opcode of failed request: 28 (X_GLXDestroyPbuffer) > Serial number of failed request: 75435 > Current serial number in output stream: 75437 > Locking assertion failure. Backtrace: > #0 /usr/lib/libxcb-xlib.so.0 [0x19e767] > #1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0x19e90e] > #2 /usr/lib/libX11.so.6 [0xb690e9] > #3 /usr/lib/nvidia/libGL.so.1 [0x6536ffd] > > Kindly write me what is going wrong. > > Thanks, > Bala From tanja.schulz-gasch at roche.com Tue Jun 9 12:55:45 2009 From: tanja.schulz-gasch at roche.com (Schulz-Gasch, Tanja) Date: Tue, 9 Jun 2009 21:55:45 +0200 Subject: [Chimera-users] movie making In-Reply-To: <14E37A04-A1DD-44EF-831A-9B17F880629C@cgl.ucsf.edu> References: <14E37A04-A1DD-44EF-831A-9B17F880629C@cgl.ucsf.edu> Message-ID: Thanks a lot, this helps getting started with movie making. Best, Tanja -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Wednesday, June 03, 2009 20:54 To: Schulz-Gasch, Tanja {PRCB~Basel} Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] movie making Hi Tanja, I will describe a method that can be used in the current release (1.3) and then another newer method for which you need a recent daily build. The newer method should be easier, so maybe skip to read that first! OLDER METHOD: In the past I have done this by using a Chimera command script for the part before the morph. That script must specify the directory and naming pattern for the image files. For example, # session littlepmm2.py - movie segment before morphing movie record directory /tmp/meng pattern elaine-* supersample 2 rock y 2 68; wait wait 10 sc 1.01 20; move y -0.15 20 movie stop That only saves several images without encoding a movie. You could either create the morph before or after running the first script; if that model is not supposed to be shown in the first part of the movie, you could hide it using the Model Panel or modeldisplay command before running the script. Then I set up the display as desired for the morphing part, in my case hiding the other models, showing the morph trajectory model, and changing the 2D labels. Then using MD Movie "File... Record Movie" I would record that part. The important thing is to use the SAME directory and naming pattern as in the first part. Following the example above, you would enter the following in the "Additional recording options" area: directory /tmp/meng pattern elaine-* (the supersampling, if you wanted it, would be specified elsewhere in the dialog). Then it knows to add the additional frames to the pre- existing ones instead of starting over at 1. You could have another script after the morphing part if you wanted. If so, it would be necessary to use another option when recording the morphing part. In the MD Movie "File... Record Movie" dialog, you would put in the "Additional encoding options" area: resetMode none because this tool will always encode the movie, and you would need to prevent it from then deleting the images if the morphing were not the last part. If you had another script, it would also need to specify the same image directory and naming pattern, of course. NEWER METHOD: Although I have not gone through the full process myself, I believe it is now possible to use just a single script, where the morph- playing part could be accomplished with the "coordset" command: Then you don't have to worry about specifying the image file directory and naming pattern, or making sure the images are kept when a movie is encoded at some intermediate step. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 2, 2009, at 11:56 PM, Schulz-Gasch, Tanja wrote: > Hi there, I used Chimera so far only for making pictures. Now I am > doing the first movie steps. I want to combine features like > > hide, show, rock,... with the MD Movie module to show a morph > between different protein conformations. How can this be done? > > The movie should start with the display part (using hide, show, > rock,...) followed by the morphing. However, when using the MD movie > > module the morph starts at frame 1. > > Thanks, Tanja From jparmache at lmb.uni-muenchen.de Tue Jun 9 16:15:16 2009 From: jparmache at lmb.uni-muenchen.de (Jean-Paul Armache) Date: Wed, 10 Jun 2009 01:15:16 +0200 Subject: [Chimera-users] map saving Message-ID: <4A2EED04.5070007@lmb.uni-muenchen.de> hello, i would like to ask you a question concerning map manipulations. sometimes i need to manually fit a map into another map, but when saving the map in the new position, it doesn't retain the coordinates. it simply overlays with the original, unmoved maps. is there something i need to do in order to save it in the new position afore hand ? best regards, jean-paul armache From goddard at cgl.ucsf.edu Tue Jun 9 17:31:45 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 09 Jun 2009 17:31:45 -0700 Subject: [Chimera-users] map saving In-Reply-To: <4A2EED04.5070007@lmb.uni-muenchen.de> References: <4A2EED04.5070007@lmb.uni-muenchen.de> Message-ID: <4A2EFEF1.9090905@cgl.ucsf.edu> Hi Jean-Paul, The map file formats don't allow for a rotation, so to write a map in a rotated orientation you need to interpolate the map on a rotated grid. Here's a description of how to do that: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-January/002238.html Tom -------- Original Message -------- Subject: [Chimera-users] map saving From: Jean-Paul Armache To: chimera-users at cgl.ucsf.edu Date: 6/9/09 4:15 PM > hello, > > i would like to ask you a question concerning map manipulations. > sometimes i need to manually fit a map into another map, > but when saving the map in the new position, it doesn't retain the > coordinates. it simply overlays with the original, unmoved > maps. is there something i need to do in order to save it in the new > position afore hand ? > > best regards, > > jean-paul armache > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From eric_choi89 at berkeley.edu Thu Jun 11 11:11:45 2009 From: eric_choi89 at berkeley.edu (Eric J. Choi) Date: Thu, 11 Jun 2009 11:11:45 -0700 (PDT) Subject: [Chimera-users] Morphing Code Request! Message-ID: <51857.169.230.226.177.1244743905.squirrel@calmail.berkeley.edu> Hello, chimera-users, Hi, my name is Eric Choi and currently I am interning at the Ren Lab at mission bay for Dr. Ren. For one of my assignments, I was to make a video of a conformation change of PPAR-GAMMA, from open to closed structure with the addition of a ligand. Upon trying to make this happen, I realized that I need the morphing python code(I believe it is) to be able to complete this step. This is what the movie making tutorial told me in the part "Ligand Flying into Unbound Conformation". If I could get the command to make the morph(python code) that would be great. Thank you! -Eric Choi From meng at cgl.ucsf.edu Thu Jun 11 13:15:10 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 11 Jun 2009 13:15:10 -0700 Subject: [Chimera-users] Morphing Code Request! In-Reply-To: <51857.169.230.226.177.1244743905.squirrel@calmail.berkeley.edu> References: <51857.169.230.226.177.1244743905.squirrel@calmail.berkeley.edu> Message-ID: <15D35DE5-CA42-4694-A2F5-928A86A9F974@cgl.ucsf.edu> Hi Eric, Now there is a "morph" command to create the morph trajectory and a "coordset" command to play the trajectory. The "morph" command is available in version 1.3 (Dec 2008) and newer, and the "coordset" command is available in recent daily builds: The online tutorial you are viewing is from last summer. There is a newer online tutorial on movie-making that uses the commands mentioned above (scroll down to the very end and click link to "1m51.cmd" to see the contents of that command file): I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 11, 2009, at 11:11 AM, Eric J. Choi wrote: > Hello, chimera-users, > > Hi, my name is Eric Choi and currently I am interning at the Ren Lab > at > mission bay for Dr. Ren. For one of my assignments, I was to make a > video > of a conformation change of PPAR-GAMMA, from open to closed > structure with > the addition of a ligand. Upon trying to make this happen, I > realized that > I need the morphing python code(I believe it is) to be able to > complete > this step. This is what the movie making tutorial told me in the part > "Ligand Flying into Unbound Conformation". If I could get the > command to > make the morph(python code) that would be great. Thank you! > > -Eric Choi From jeandidier.marechal at gmail.com Fri Jun 12 02:53:33 2009 From: jeandidier.marechal at gmail.com (=?iso-8859-1?Q?Dr._Jean-Didier_Mar=E9chal?=) Date: Fri, 12 Jun 2009 11:53:33 +0200 Subject: [Chimera-users] Minimize and solvate with a zinc ion Message-ID: <4a32259f.0a04d00a.7071.071b@mx.google.com> Dear all, I want to solvate then minimize (few steps) a structure with a zinc (Zn2+) ion. >From what I saw in the manual, zinc parameters are available in the actual version of the amber force field in chimera. However, I am stuck with troubles. When I solvate I have the following message: Could not determine charges for pre-existing solvent from added solvent for: Zn Zn What do I do wrong? All the best, JD *************************************************** Dr. Jean-Didier Mar?chal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Qu?mica F?sica Departament de Qu?mica Universitat Aut?noma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal at uab.es -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Fri Jun 12 11:14:04 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 12 Jun 2009 11:14:04 -0700 Subject: [Chimera-users] Minimize and solvate with a zinc ion In-Reply-To: <4a32259f.0a04d00a.7071.071b@mx.google.com> References: <4a32259f.0a04d00a.7071.071b@mx.google.com> Message-ID: Hi JD, You can basically ignore that warning and continue on. The Solvate tool is still a little rough around the edges. If you have existing ions/solvent when you run Solvate, it looks at the charges Amber gave to the added ions/solvent and tries to transfer those to the pre-existing ions/solvent. Since you didn't add any zinc ions (naturally), it couldn't -- so it popped up that panel saying so. No real issue for you. I've now changed the code to suppress the panel if the "pre-existing ions" are not alkali metals or halides. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 12, 2009, at 2:53 AM, Dr. Jean-Didier Mar?chal wrote: > Dear all, > > I want to solvate then minimize (few steps) a structure with a zinc > (Zn2+) ion. > From what I saw in the manual, zinc parameters are available in the > actual version of the amber force field in chimera. However, I am > stuck with troubles. When I solvate I have the following message: > Could not determine charges for pre-existing solvent from added > solvent for: Zn Zn > What do I do wrong? > > All the best, > JD -------------- next part -------------- An HTML attachment was scrubbed... URL: From richard.marhoefer at sp.intervet.com Mon Jun 15 08:40:54 2009 From: richard.marhoefer at sp.intervet.com (Marhoefer, R (Richard)) Date: Mon, 15 Jun 2009 17:40:54 +0200 Subject: [Chimera-users] controling multiscale models from command script Message-ID: <15BDC38CF17D784784B874C2634A3CA202ED695F@inbn223.d50.intra> Dear Chimera Users, for the production of a movie file I like to control some attributes of a multiscale model e.g. the style and the surface transparency through a Chimera command file. Unfortunately I couldn't find many commands allowing to do so in the documentation. How could that be done? Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer at sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Gesch?ftsf?hrer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From goddard at cgl.ucsf.edu Tue Jun 16 21:52:52 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 16 Jun 2009 21:52:52 -0700 Subject: [Chimera-users] controling multiscale models from command script In-Reply-To: <15BDC38CF17D784784B874C2634A3CA202ED695F@inbn223.d50.intra> References: <15BDC38CF17D784784B874C2634A3CA202ED695F@inbn223.d50.intra> Message-ID: <4A3876A4.1050007@cgl.ucsf.edu> Hi Richard, There is no command equivalent of the multiscale dialog, and other other Chimera commands don't know anything about the multiscale surfaces (none can even change the color or transparency as far as I know). Maybe the way to go is to not use multiscale, and instead make a PDB file with all the molecule copies (can use multiscale to do that) then use the "molmap" command to create surfaces for the desired chains, and the "volume" command to change colors, and other commands to show/hide ribbons and surfaces as needed. This approach should work for a tetramer, but if you have a virus with 60-fold icosahedral it will be unwieldy because every chain will need separate molmap commands to create the surfaces. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html If that isn't practical it is possible to use Python code to do the things the Multiscale dialog does. Tom -------- Original Message -------- Subject: [Chimera-users] controling multiscale models from command script From: Marhoefer, R (Richard) To: chimera-users at cgl.ucsf.edu Date: 6/15/09 8:40 AM > Dear Chimera Users, > > for the production of a movie file I like to control some attributes of a multiscale model e.g. the style and the surface transparency through a Chimera command file. Unfortunately I couldn't find many commands allowing to do so in the documentation. How could that be done? > > Kind regards, > Richard > > > Dr. Richard Marhoefer > Senior Scientist BioChemInformatics > Intervet Innovation GmbH > Zur Propstei > 55270 Schwabenheim, Germany > > E-Mail: richard.marhoefer at sp.intervet.com > Phone: +49 (6130) 948 204 > Fax: +49 (6130) 948 517 > Mobile: +49 175 723 081 4 > Home http://www.intervet.com > > Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Gesch?ftsf?hrer: Dr. Peter Schmid > > -------------------------------------- > This message and any attachments are solely for the intended recipient. > > If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited > > > > -- please immediately and permanently delete. > -------------------------------------- > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From Alexander.Gawronski at nrc-cnrc.gc.ca Thu Jun 18 07:02:31 2009 From: Alexander.Gawronski at nrc-cnrc.gc.ca (Gawronski, Alexander) Date: Thu, 18 Jun 2009 10:02:31 -0400 Subject: [Chimera-users] Electrostatics Message-ID: Hello, I'm a student at Carleton University and I need to create meshes with electrostatic coloring for all the proteins in the pdb. I need a way of automating this process with scripts but I can't figure out how. Is this possible to do this through command line? How do I call chimera commands from a script? Any help would be greatly appreciated! Thanks, Alex Gawronski -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Thu Jun 18 11:28:08 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 18 Jun 2009 11:28:08 -0700 Subject: [Chimera-users] Fade in/out a surface for movie making In-Reply-To: <4A3876A4.1050007@cgl.ucsf.edu> References: <15BDC38CF17D784784B874C2634A3CA202ED695F@inbn223.d50.intra> <4A3876A4.1050007@cgl.ucsf.edu> Message-ID: <4A3A8738.3060600@cgl.ucsf.edu> Hi Richard, Just yesterday I made the surftransparency command take an optional "frames" argument so you can fade in or out a surface over a specified number of frames. This may be of use to you. Before we would sometimes use twenty surftransp commands in a row in a script to gradually change the transparency. Now a command like surft 100 #2 50 will fade out surface model #2 to full (100%) transparency over 50 frames. To use that you'll need to get a Chimera 1.4 daily build. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Good luck with movie making. We're trying to make this easier in Chimera but have a long ways to go. Tom Tom Goddard wrote: > Hi Richard, > > There is no command equivalent of the multiscale dialog, and other > other Chimera commands don't know anything about the multiscale surfaces > (none can even change the color or transparency as far as I know). > > Maybe the way to go is to not use multiscale, and instead make a PDB > file with all the molecule copies (can use multiscale to do that) then > use the "molmap" command to create surfaces for the desired chains, and > the "volume" command to change colors, and other commands to show/hide > ribbons and surfaces as needed. This approach should work for a > tetramer, but if you have a virus with 60-fold icosahedral it will be > unwieldy because every chain will need separate molmap commands to > create the surfaces. > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html > > If that isn't practical it is possible to use Python code to do the > things the Multiscale dialog does. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] controling multiscale models from command script > From: Marhoefer, R (Richard) > To: chimera-users at cgl.ucsf.edu > Date: 6/15/09 8:40 AM >> Dear Chimera Users, >> >> for the production of a movie file I like to control some attributes of a multiscale model e.g. the style and the surface transparency through a Chimera command file. Unfortunately I couldn't find many commands allowing to do so in the documentation. How could that be done? >> >> Kind regards, >> Richard >> >> >> Dr. Richard Marhoefer >> Senior Scientist BioChemInformatics >> Intervet Innovation GmbH >> Zur Propstei >> 55270 Schwabenheim, Germany >> >> E-Mail: richard.marhoefer at sp.intervet.com >> Phone: +49 (6130) 948 204 >> Fax: +49 (6130) 948 517 >> Mobile: +49 175 723 081 4 >> Home http://www.intervet.com >> >> Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Gesch?ftsf?hrer: Dr. Peter Schmid >> >> -------------------------------------- >> This message and any attachments are solely for the intended recipient. >> >> If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited >> >> >> >> -- please immediately and permanently delete. >> -------------------------------------- >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > _______________________________________________ > 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 Thu Jun 18 11:50:29 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 18 Jun 2009 11:50:29 -0700 Subject: [Chimera-users] Electrostatics In-Reply-To: References: Message-ID: <9F693BF6-D975-4EFE-95BF-AF9528CFB571@cgl.ucsf.edu> Hi Alex, In theory this is doable. In practice, this will not work for some of structures in the PDB until our next release. This is because the MSMS surfacing library that we're currently using will fail for a small fraction of the structures in the PDB. Of course, a "small fraction" of the entire PDB is still probably hundreds of structures. Our next release (1.4) will include a new surfacing library that will be more stable -- though it might not be as fast as MSMS. My best guesstimate of when the 1.4 release will be available is September, though there's a slight chance it could be earlier. Do you intend to compute electrostatics using some Poisson-Boltzmann solver? If so, then doing that for the entire PDB seems like a Herculean task. Certainly Chimera can show the output once you've computed it, but it won't be much help in automating the computation. An alternative is that the current daily build includes the Coulombic Surface Coloring tool, which unsurprisingly performs the somewhat cruder coulombic electrostatics computation for a structure and then colors a surface appropriately. Although Poisson-Boltzmann is a more accurate computation it has been our experience that qualitatively the results are quite similar. You can see an informal comparison here: http://tinyurl.com/mzopva There is no command line version of Coulombic Surface Coloring, so you would have to use the Python API. Given a surface, RGBA values, and corresponding potential values, something like: from ESP import colorESP colorESP(surf, rgbas, potVals) and to get a surface object (assuming exactly one is open): import chimera, _surface surf = chimera.openModels.list(modelTypes=[_surface.SurfaceModel])[0] As to how to call Chimera commands from a Python script: from chimera import runCommand runCommand("surf") To run a Python script without bringing up the Chimera GUI, look at the --nogui and --script arguments documented here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html Further questions should probably be sent to the chimera-dev mailing list rather than the chimera-users list. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 18, 2009, at 7:02 AM, Gawronski, Alexander wrote: > Hello, > > I?m a student at Carleton University and I need to create meshes > with electrostatic coloring for all the proteins in the pdb. I need > a way of automating this process with scripts but I can?t figure out > how. Is this possible to do this through command line? How do I call > chimera commands from a script? > > Any help would be greatly appreciated! > > Thanks, > Alex Gawronski > _______________________________________________ > 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 marlovits at imp.ac.at Thu Jun 18 10:16:24 2009 From: marlovits at imp.ac.at (Thomas C. Marlovits) Date: Thu, 18 Jun 2009 19:16:24 +0200 Subject: [Chimera-users] 3D mouse - connexion Message-ID: <598A1EFE-24BC-4033-9C79-0546EB9161BF@imp.ac.at> Hi, the Chimera documentation indicates that the 3D mouse from Connexion (Space navigator) is supported. I have just asked the company, but they didn't know anything about Chimera. I am wondering, whether you have some good experience using it, or whether you have an alternative mouse model that would work nicely together with Chimera. Tx -Thomas Here is the link at your documentation site: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#otherinput ------------------------------------------------------------------------------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits at imp.univie.ac.at -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Jun 18 12:46:40 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 18 Jun 2009 12:46:40 -0700 Subject: [Chimera-users] 3D mouse - connexion In-Reply-To: <598A1EFE-24BC-4033-9C79-0546EB9161BF@imp.ac.at> References: <598A1EFE-24BC-4033-9C79-0546EB9161BF@imp.ac.at> Message-ID: Hi Thomas, We have a Space Navigator and have been using it (well, mostly Tom Goddard has been using it, but the rest of us have tried it). There is a video of Tom using this device -- see the bottom section of this page: and our group has tried some other things such as head tracking and force feedback, see Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 18, 2009, at 10:16 AM, Thomas C. Marlovits wrote: > Hi, > > the Chimera documentation indicates that the 3D mouse from Connexion > (Space navigator) is supported. I have just asked the company, but > they didn't know anything about Chimera. I am wondering, whether > you have some good experience using it, or whether you have an > alternative mouse model that would work nicely together with Chimera. > > Tx > -Thomas > > Here is the link at your documentation site: >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#otherinput From goddard at cgl.ucsf.edu Thu Jun 18 12:53:58 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 18 Jun 2009 12:53:58 -0700 Subject: [Chimera-users] 3D mouse - connexion In-Reply-To: <598A1EFE-24BC-4033-9C79-0546EB9161BF@imp.ac.at> References: <598A1EFE-24BC-4033-9C79-0546EB9161BF@imp.ac.at> Message-ID: <4A3A9B56.9060402@cgl.ucsf.edu> Hi Thomas, We have a TechNote evaluating the space navigator. http://www.cgl.ucsf.edu/Outreach/technotes/spacenavigator.html The basic conclusion is that it has some utility but that having a third input device beyond the keyboard and mouse and only 2 hands is irksome. Tom Thomas C. Marlovits wrote: > Hi, > > the Chimera documentation indicates that the 3D mouse from Connexion > (Space navigator) is supported. I have just asked the company, but they > didn't know anything about Chimera. I am wondering, whether you have > some good experience using it, or whether you have an alternative mouse > model that would work nicely together with Chimera. > > Tx > -Thomas > > Here is the link at your documentation site: >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#otherinput > > > ------------------------------------------------------------------------------- > > Thomas C. Marlovits, PhD, M.A.S. > Research Group Leader > > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) > > Dr. Bohr-Gasse 3 > Room IMBA/6.02 > A-1030 Vienna > Austria, Europe > > fone: (++43-1) 79044-4630 > fax: (++43-1) 79044-4401 > email: marlovits at imp.univie.ac.at > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From nils.becker at ens-lyon.fr Thu Jun 18 13:03:19 2009 From: nils.becker at ens-lyon.fr (Nils Becker) Date: Thu, 18 Jun 2009 22:03:19 +0200 Subject: [Chimera-users] 3D mouse - connexion Message-ID: <4A3A9D87.7010608@ens-lyon.fr> Hi Thomas, I'm also using it (recently, on a daily basis, on Mac OS X). It works very nicely, and it's cheap. Also, try the keyboard shortcuts na, nz etc... cheers, Nils From sette at uniroma2.it Sat Jun 20 02:42:34 2009 From: sette at uniroma2.it (sette at uniroma2.it) Date: Sat, 20 Jun 2009 11:42:34 +0200 Subject: [Chimera-users] Electrostatics In-Reply-To: <9F693BF6-D975-4EFE-95BF-AF9528CFB571@cgl.ucsf.edu> References: <9F693BF6-D975-4EFE-95BF-AF9528CFB571@cgl.ucsf.edu> Message-ID: <20090620114234.44281br9mbqy30ga@webmail.uniroma2.it> Hi, do you think it is possible in future versions of Chimera to read the results of APBS calculation for electrostatic properties? Thanks, Marco Def. Quota "Eric Pettersen" : > Hi Alex, > In theory this is doable. In practice, this will not work for some > of structures in the PDB until our next release. This is because > the MSMS surfacing library that we're currently using will fail for > a small fraction of the structures in the PDB. Of course, a "small > fraction" of the entire PDB is still probably hundreds of > structures. Our next release (1.4) will include a new surfacing > library that will be more stable -- though it might not be as fast > as MSMS. My best guesstimate of when the 1.4 release will be > available is September, though there's a slight chance it could be > earlier. > Do you intend to compute electrostatics using some > Poisson-Boltzmann solver? If so, then doing that for the entire > PDB seems like a Herculean task. Certainly Chimera can show the > output once you've computed it, but it won't be much help in > automating the computation. An alternative is that the current > daily build includes the Coulombic Surface Coloring tool, which > unsurprisingly performs the somewhat cruder coulombic > electrostatics computation for a structure and then colors a > surface appropriately. Although Poisson-Boltzmann is a more > accurate computation it has been our experience that qualitatively > the results are quite similar. You can see an informal comparison > here: http://tinyurl.com/mzopva > There is no command line version of Coulombic Surface Coloring, so > you would have to use the Python API. Given a surface, RGBA values, > and corresponding potential values, something like: > > from ESP import colorESP > colorESP(surf, rgbas, potVals) > > and to get a surface object (assuming exactly one is open): > > import chimera, _surface > surf = chimera.openModels.list(modelTypes=[_surface.SurfaceModel])[0] > > As to how to call Chimera commands from a Python script: > > from chimera import runCommand > runCommand("surf") > > To run a Python script without bringing up the Chimera GUI, look at > the --nogui and --script arguments documented here: > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html > > Further questions should probably be sent to the chimera-dev > mailing list rather than the chimera-users list. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Jun 18, 2009, at 7:02 AM, Gawronski, Alexander wrote: > >> Hello, >> >> I?m a student at Carleton University and I need to create meshes >> with electrostatic coloring for all the proteins in the pdb. I need >> a way of automating this process with scripts but I can?t figure >> out how. Is this possible to do this through command line? How do >> I call chimera commands from a script? >> >> Any help would be greatly appreciated! >> >> Thanks, >> Alex Gawronski >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette at uniroma2.it e-mail: m77it at yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From miguel.ortiz-lombardia at afmb.univ-mrs.fr Sat Jun 20 04:46:12 2009 From: miguel.ortiz-lombardia at afmb.univ-mrs.fr (Miguel Ortiz Lombardia) Date: Sat, 20 Jun 2009 13:46:12 +0200 Subject: [Chimera-users] Electrostatics In-Reply-To: <20090620114234.44281br9mbqy30ga@webmail.uniroma2.it> References: <9F693BF6-D975-4EFE-95BF-AF9528CFB571@cgl.ucsf.edu> <20090620114234.44281br9mbqy30ga@webmail.uniroma2.it> Message-ID: <3BF8D43B-33FA-423F-A3E5-3A6E83AF14D0@afmb.univ-mrs.fr> Hi Marco, It is already possible, Chimera can read the open dx files generated by APBS. You can represent them with the Volume Viewer and/or map them on surfaces. In the latter case, it is preferable to use solvent accessible surfaces and not molecular surfaces and to use lower thresholds (such as 2 kT/e, equivalent to ~ 50 mV at 298 K ) to avoid a bias towards local features. Of course, this depends on the purpose of your representation. While it is not possible with the current implementation of Chimera surfaces (MSMS) to produce solvent accessible surfaces, it can be approximated by adding 1.4 A to all van der Waals radii ( vdwdefine +1.4) and then set the probe radius to its minimum allowed value ( it should be 0 A, because you included the probe in the previous command, but at the moment it must be 0.5 A ) It will be great to have solvent accessible surfaces in the next 1.4 release of chimera :-) Best, Miguel Le 20 juin 09 ? 11:42, sette at uniroma2.it a ?crit : > > Hi, > > do you think it is possible in future versions of Chimera to read the > results of APBS calculation for electrostatic properties? > > Thanks, > Marco > > > Def. Quota "Eric Pettersen" : > >> Hi Alex, >> In theory this is doable. In practice, this will not work for some >> of structures in the PDB until our next release. This is because >> the MSMS surfacing library that we're currently using will fail for >> a small fraction of the structures in the PDB. Of course, a "small >> fraction" of the entire PDB is still probably hundreds of >> structures. Our next release (1.4) will include a new surfacing >> library that will be more stable -- though it might not be as fast >> as MSMS. My best guesstimate of when the 1.4 release will be >> available is September, though there's a slight chance it could be >> earlier. >> Do you intend to compute electrostatics using some >> Poisson-Boltzmann solver? If so, then doing that for the entire >> PDB seems like a Herculean task. Certainly Chimera can show the >> output once you've computed it, but it won't be much help in >> automating the computation. An alternative is that the current >> daily build includes the Coulombic Surface Coloring tool, which >> unsurprisingly performs the somewhat cruder coulombic >> electrostatics computation for a structure and then colors a >> surface appropriately. Although Poisson-Boltzmann is a more >> accurate computation it has been our experience that qualitatively >> the results are quite similar. You can see an informal comparison >> here: http://tinyurl.com/mzopva >> There is no command line version of Coulombic Surface Coloring, so >> you would have to use the Python API. Given a surface, RGBA values, >> and corresponding potential values, something like: >> >> from ESP import colorESP >> colorESP(surf, rgbas, potVals) >> >> and to get a surface object (assuming exactly one is open): >> >> import chimera, _surface >> surf = chimera.openModels.list(modelTypes=[_surface.SurfaceModel])[0] >> >> As to how to call Chimera commands from a Python script: >> >> from chimera import runCommand >> runCommand("surf") >> >> To run a Python script without bringing up the Chimera GUI, look at >> the --nogui and --script arguments documented here: >> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html >> >> Further questions should probably be sent to the chimera-dev >> mailing list rather than the chimera-users list. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> On Jun 18, 2009, at 7:02 AM, Gawronski, Alexander wrote: >> >>> Hello, >>> >>> I?m a student at Carleton University and I need to create meshes >>> with electrostatic coloring for all the proteins in the pdb. I need >>> a way of automating this process with scripts but I can?t figure >>> out how. Is this possible to do this through command line? How do >>> I call chimera commands from a script? >>> >>> Any help would be greatly appreciated! >>> >>> Thanks, >>> Alex Gawronski >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > > > Dr.Marco Sette, Ph.D. > > Department of Chemical Sciences and Technology > University of Rome, "Tor Vergata" > via della Ricerca Scientifica, 00133, Rome, Italy > e-mail: sette at uniroma2.it > e-mail: m77it at yahoo.it > Tel.: +39-0672594424 > Fax: +39-0672594328 > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > -- Miguel Ortiz Lombard?a Architecture et Fonction des Macromol?cules Biologiques (UMR6098) CNRS, Universit?s d'Aix-Marseille I & II Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1916 bytes Desc: not available URL: From pedro.al at fenhi.uh.cu Mon Jun 22 10:10:43 2009 From: pedro.al at fenhi.uh.cu (Yasser Almeida Hernandez) Date: Mon, 22 Jun 2009 13:10:43 -0400 Subject: [Chimera-users] Getting Delphi Message-ID: <20090622131043.tcjroq0kw88g4444@correo.fenhi.uh.cu> Hi all... Where can i download the Delphi executable to run in Chimera...? Thanks ---------------------------------------------------------------- Correo FENHI From meng at cgl.ucsf.edu Mon Jun 22 10:45:40 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 22 Jun 2009 10:45:40 -0700 Subject: [Chimera-users] Getting Delphi In-Reply-To: <20090622131043.tcjroq0kw88g4444@correo.fenhi.uh.cu> References: <20090622131043.tcjroq0kw88g4444@correo.fenhi.uh.cu> Message-ID: Hello, DelPhi can be downloaded from the Honig lab Web site. There is a link to that site from several places in the Chimera documentation, but I include it here for your convenience: Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 22, 2009, at 10:10 AM, Yasser Almeida Hernandez wrote: > Hi all... > > > Where can i download the Delphi executable to run in Chimera...? > > Thanks > > ---------------------------------------------------------------- > Correo FENHI From goddard at cgl.ucsf.edu Mon Jun 22 13:45:54 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 22 Jun 2009 13:45:54 -0700 Subject: [Chimera-users] New surface coloring command Message-ID: <4A3FED82.4080001@cgl.ucsf.edu> I added a Chimera command "scolor" that can color surfaces radially or according to volume data values such as electrostatic potential. This command is the equivalent of the Surface Color dialog. A few examples: scolor #0 geometry cylindrical colors the surface by distance from a cylinder axis (default z-axis) with default coloring red-white-blue ranging from minimum to maximum surface radius. scolor #0 geom radial cmap 100,gray:150,blue:200,purple colors radially with colors gray,blue,purple at radii of 100,150,200. scolor #0 volume #1 cmap -10,red:0,white:10,blue colors surface #0 using volume data #1 with colors red,white,blue for volume data values -10,0,10. Here's a summary of the full command syntax. Detailed documentation will be available in the manual before the next Chimera release. scolor [volume ] [gradient ] [geometry radial|cylindrical|height] [color ] [center |] [axis x|y|z||] [coordinateSystem ] [cmap ::...|rainbow|gray|redblue|cyanmaroon] [cmapRange |full] [reverseColors true|false] [colorOutsideVolume ] [autoUpdate true|false] [capOnly true|false] [perPixel true|false] Tom From I.moustafa at psu.edu Mon Jun 22 15:53:10 2009 From: I.moustafa at psu.edu (Ibrahim Moustafa) Date: Mon, 22 Jun 2009 18:53:10 -0400 Subject: [Chimera-users] Saving image and rendering Message-ID: Dear Chimera team, Recently, I have some trouble saving images with POV-RAY option ?true?. The process of rendering is too slow (both on the mac and windows version). To give the feeling of how slow: rendering an image with 1700 lines takes 7 hrs (with quality 9 in pov-ray options) and 2 hrs (quality 5). I used to get the images rendered much faster than that (with older versions; however, I?m not exactly sure of when I started to see such a slow rendering behavior). There is another related problem but only with the windows version: If I want to save an image, with depth cue, using the fast mode (POV-RAY false), the image output lacks any depth used in the model, with poor quality and darker than it should be. Somehow, the camera orientation is messed. In addition, the depth cue will be no longer available for the rest of the session (I have to restart over again). To get the depth cue I want, I need to turn the POV-RAY option ?true?....but then too slow to create a good figure. I?d appreciate any comment or explanation from Chimera people; and what is the best way to overcome this problem? P.S. I have the PPC version for the MAC running OSX 10.4; the PC running Windows XP. Many thanks in advance for your help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kay_jay at earthlink.net Mon Jun 22 16:26:12 2009 From: kay_jay at earthlink.net (Kenward Vaughan) Date: Mon, 22 Jun 2009 16:26:12 -0700 Subject: [Chimera-users] Saving image and rendering In-Reply-To: References: Message-ID: <1245713172.5852.15.camel@hpotter.vaughan.home> On Mon, 2009-06-22 at 18:53 -0400, Ibrahim Moustafa wrote: > Dear Chimera team, > > Recently, I have some trouble saving images with POV-RAY option > ?true?. The process of rendering is too slow (both on the mac and > windows version). > To give the feeling of how slow: rendering an image with 1700 lines > takes 7 hrs (with quality 9 in pov-ray options) and 2 hrs (quality 5). > I used to get the images rendered much faster than that (with older > versions; however, I?m not exactly sure of when I started to see such > a slow rendering behavior). ... I have seen the same behavior. I want to create some images for posters in my lab, but the time has gone up roughly 7 to 10 fold for images at the same settings as before. An additional problem is that 2D label letters are not properly rendered, with the result looking like the letters have lost their tops, being sliced off at a slanting angle. There is scattered "debris" as well in the images. Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca From pett at cgl.ucsf.edu Tue Jun 23 10:24:23 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 23 Jun 2009 10:24:23 -0700 Subject: [Chimera-users] Saving image and rendering In-Reply-To: References: Message-ID: On Jun 22, 2009, at 3:53 PM, Ibrahim Moustafa wrote: > Dear Chimera team, > > Recently, I have some trouble saving images with POV-RAY option > ?true?. The process of rendering is too slow (both on the mac and > windows version). > To give the feeling of how slow: rendering an image with 1700 lines > takes 7 hrs (with quality 9 in pov-ray options) and 2 hrs (quality > 5). I used to get the images rendered much faster than that (with > older versions; however, I?m not exactly sure of when I started to > see such a slow rendering behavior). I'm guessing you're using transparent surfaces. We've made improvements in the fidelity of translation of transparent colors between Chimera and POV-Ray since the 1.3 release. In 1.3, the transparent colors were much darker than they appeared in Chimera. This change increases the rendering time because the amount of supersampling that POV-ray performs depends on how much color variation there is in the image and the new scheme provides a lot more variation than its uniformly dark predecessor. One example I tried produced slightly more than a factor of two in rendering times between the 1.3 version and the current daily build. Now, if you're rendering such a high-resolution image you don't really need as much effort expended on each individual pixel as you do for a smaller image. I find that if I increase the "Antialias threshold" POV-Ray option from 0.3 to 1.0 then I get an almost unchanged image in approximately the same time as as the 1.3 version required. You might even be able to go higher than that and still get a good image. > There is another related problem but only with the windows > version: If I want to save an image, with depth cue, using the fast > mode (POV-RAY false), the image output lacks any depth used in the > model, with poor quality and darker than it should be. Somehow, the > camera orientation is messed. In addition, the depth cue will be no > longer available for the rest of the session (I have to restart over > again). To get the depth cue I want, I need to turn the POV-RAY > option ?true?....but then too slow to create a good figure. I understand that Greg (who works on this code) recently made some depth-cueing related bug fixes. Please try the very latest daily build and see if you still get this problem. If you still do then please use Help->Report a Bug to send us a bug report which will automatically include detailed information about the system you're using. > I?d appreciate any comment or explanation from Chimera people; > and what is the best way to overcome this problem? An alternative to ray tracing is to turn on "glossy lighting" (from the Lighting tab of the Side View). That may look good enough for what you want and works with Chimera's non-raytraced image saving. --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Tue Jun 23 10:27:44 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 23 Jun 2009 10:27:44 -0700 Subject: [Chimera-users] Saving image and rendering In-Reply-To: <1245713172.5852.15.camel@hpotter.vaughan.home> References: <1245713172.5852.15.camel@hpotter.vaughan.home> Message-ID: <2CBE2FBA-25D0-4F44-92A3-3B1B6E65B264@cgl.ucsf.edu> On Jun 22, 2009, at 4:26 PM, Kenward Vaughan wrote: > On Mon, 2009-06-22 at 18:53 -0400, Ibrahim Moustafa wrote: >> Dear Chimera team, >> >> Recently, I have some trouble saving images with POV-RAY option >> ?true?. The process of rendering is too slow (both on the mac and >> windows version). >> To give the feeling of how slow: rendering an image with 1700 lines >> takes 7 hrs (with quality 9 in pov-ray options) and 2 hrs (quality >> 5). >> I used to get the images rendered much faster than that (with older >> versions; however, I?m not exactly sure of when I started to see such >> a slow rendering behavior). > ... > > I have seen the same behavior. I want to create some images for > posters > in my lab, but the time has gone up roughly 7 to 10 fold for images at > the same settings as before. As per my recent mail to Ibrahim, try increasing the "Antialias threshold" to 1.0 or even higher. > An additional problem is that 2D label letters are not properly > rendered, with the result looking like the letters have lost their > tops, > being sliced off at a slanting angle. There is scattered "debris" as > well in the images. I have not seen this behavior. 2D labels look fine in the images I rendered. Does this happen on just one machine? Please use the "Report a Bug" menu item to send in a bug report so that we can find out the details of the system you're using. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From I.moustafa at psu.edu Tue Jun 23 12:26:34 2009 From: I.moustafa at psu.edu (Ibrahim Moustafa) Date: Tue, 23 Jun 2009 15:26:34 -0400 Subject: [Chimera-users] Saving image and rendering In-Reply-To: Message-ID: Thanks Eric for the reply. Actually, I?m not using transparent surfaces. The image I tried to make is a normal cartoon model. For the ?glossy lighting? option: the button with the default ?normal? is inactive. How to turn it on? I could not figure it out. Thanks, Ibrahim On 6/23/09 1:24 PM, "Eric Pettersen" wrote: > On Jun 22, 2009, at 3:53 PM, Ibrahim Moustafa wrote: > >> Dear Chimera team, >> >> Recently, I have some trouble saving images with POV-RAY option ?true?. >> The process of rendering is too slow (both on the mac and windows version). >> To give the feeling of how slow: rendering an image with 1700 lines takes 7 >> hrs (with quality 9 in pov-ray options) and 2 hrs (quality 5). I used to get >> the images rendered much faster than that (with older versions; however, I?m >> not exactly sure of when I started to see such a slow rendering behavior). > > I'm guessing you're using transparent surfaces. We've made improvements in > the fidelity of translation of transparent colors between Chimera and POV-Ray > since the 1.3 release. In 1.3, the transparent colors were much darker than > they appeared in Chimera. This change increases the rendering time because > the amount of supersampling that POV-ray performs depends on how much color > variation there is in the image and the new scheme provides a lot more > variation than its uniformly dark predecessor. One example I tried produced > slightly more than a factor of two in rendering times between the 1.3 version > and the current daily build. > > Now, if you're rendering such a high-resolution image you don't really need as > much effort expended on each individual pixel as you do for a smaller image. > I find that if I increase the "Antialias threshold" POV-Ray option from 0.3 to > 1.0 then I get an almost unchanged image in approximately the same time as as > the 1.3 version required. You might even be able to go higher than that and > still get a good image. > >> There is another related problem but only with the windows version: If I >> want to save an image, with depth cue, using the fast mode (POV-RAY false), >> the image output lacks any depth used in the model, with poor quality and >> darker than it should be. Somehow, the camera orientation is messed. In >> addition, the depth cue will be no longer available for the rest of the >> session (I have to restart over again). To get the depth cue I want, I need >> to turn the POV-RAY option ?true?....but then too slow to create a good >> figure. > > I understand that Greg (who works on this code) recently made some > depth-cueing related bug fixes. Please try the very latest daily build and > see if you still get this problem. If you still do then please use > Help->Report a Bug to send us a bug report which will automatically include > detailed information about the system you're using. > >> I?d appreciate any comment or explanation from Chimera people; and what is >> the best way to overcome this problem? > > An alternative to ray tracing is to turn on "glossy lighting" (from the > Lighting tab of the Side View). That may look good enough for what you want > and works with Chimera's non-raytraced image saving. > > --Eric > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Tue Jun 23 13:23:52 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 23 Jun 2009 13:23:52 -0700 Subject: [Chimera-users] Saving image and rendering In-Reply-To: References: Message-ID: <4A4139D8.7020501@cgl.ucsf.edu> Hi Ibrahim, The glossy lighting quality setting is not available if your OpenGL driver and graphics card does not support shaders. Most graphics cards from the past few years support pixel and vertex shaders but older ones may not. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Saving image and rendering From: Ibrahim Moustafa To: Eric Pettersen Date: 6/23/09 12:26 PM > Thanks Eric for the reply. > > Actually, I?m not using transparent surfaces. The image I tried to > make is a normal cartoon model. > > For the ?glossy lighting? option: the button with the default ?normal? > is inactive. How to turn it on? I could not figure it out. > > Thanks, > Ibrahim > > > On 6/23/09 1:24 PM, "Eric Pettersen" wrote: > > On Jun 22, 2009, at 3:53 PM, Ibrahim Moustafa wrote: > > Dear Chimera team, > > Recently, I have some trouble saving images with POV-RAY > option ?true?. The process of rendering is too slow (both on > the mac and windows version). > To give the feeling of how slow: rendering an image with 1700 > lines takes 7 hrs (with quality 9 in pov-ray options) and 2 > hrs (quality 5). I used to get the images rendered much faster > than that (with older versions; however, I?m not exactly sure > of when I started to see such a slow rendering behavior). > > > I'm guessing you're using transparent surfaces. We've made > improvements in the fidelity of translation of transparent colors > between Chimera and POV-Ray since the 1.3 release. In 1.3, the > transparent colors were much darker than they appeared in Chimera. > This change increases the rendering time because the amount of > supersampling that POV-ray performs depends on how much color > variation there is in the image and the new scheme provides a lot > more variation than its uniformly dark predecessor. One example I > tried produced slightly more than a factor of two in rendering > times between the 1.3 version and the current daily build. > > Now, if you're rendering such a high-resolution image you don't > really need as much effort expended on each individual pixel as > you do for a smaller image. I find that if I increase the > "Antialias threshold" POV-Ray option from 0.3 to 1.0 then I get an > almost unchanged image in approximately the same time as as the > 1.3 version required. You might even be able to go higher than > that and still get a good image. > > There is another related problem but only with the windows > version: If I want to save an image, with depth cue, using the > fast mode (POV-RAY false), the image output lacks any depth > used in the model, with poor quality and darker than it should > be. Somehow, the camera orientation is messed. In addition, > the depth cue will be no longer available for the rest of the > session (I have to restart over again). To get the depth cue I > want, I need to turn the POV-RAY option ?true?....but then too > slow to create a good figure. > > > I understand that Greg (who works on this code) recently made some > depth-cueing related bug fixes. Please try the very latest daily > build and see if you still get this problem. If you still do then > please use Help->Report a Bug to send us a bug report which will > automatically include detailed information about the system you're > using. > > I?d appreciate any comment or explanation from Chimera people; > and what is the best way to overcome this problem? > > > An alternative to ray tracing is to turn on "glossy lighting" > (from the Lighting tab of the Side View). That may look good > enough for what you want and works with Chimera's non-raytraced > image saving. > > --Eric > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Tue Jun 23 16:19:50 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 23 Jun 2009 16:19:50 -0700 Subject: [Chimera-users] Surface Creation In-Reply-To: <580593.67454.qm@web53904.mail.re2.yahoo.com> References: <580593.67454.qm@web53904.mail.re2.yahoo.com> Message-ID: On Jun 23, 2009, at 2:25 PM, Thiruvarangan Ramaraj wrote: > Hi, > > I tried to create two surfaces, one for the Antibody and one for the > Antigen for an Antibody-Antigen complex (1A14.pdb). I am able to > create two surfaces as two models in one session. But when I try to > save this session it gives me an warning > "Cannot save surfaces without associated structure. > Surface will not be saved." This happens when you close the structure that a surface is based on. Sessions don't store vertex/triangle information for surfaces (which would be voluminous) but instead just the parameters that were used to generate the surface -- and the surface is regenerated when the session is restored. But if the underlying structure is gone then that won't work. > Then when I try to open the saved session there is only surface that > I could see. > > Is there any way that I could have both surfaces saved in one session. > > Any help would be greatly appreciated. Well, obviously one approach is to not close the underlying structure. FYI, you can get separate surfaces on the antigen/antibody without using multiple copies of the structure. You need to get the antigen and antibody into separate "surface categories" (as described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/msms.html ). Here is a sequence of commands (Favorites->Command Line) that gets the antigen (chain N) into its own surface category named "antigen" and then surfaces both the antigen and antibody: surfcat antigen :.n; surf antigen; surf --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu From fglaser at technion.ac.il Wed Jun 24 07:28:14 2009 From: fglaser at technion.ac.il (Fabian Glaser) Date: Wed, 24 Jun 2009 17:28:14 +0300 Subject: [Chimera-users] high quality pictures for publication Message-ID: <4A4237FE.9040806@technion.ac.il> Hi all, I am trying to produce high quality figures for publication with chimera, and despite I am working some time with it, I am not quite satisfied with the result I get. I don't know if I can send figures to this list, just as example I send these two. They are fine, but they are not gorgeus as I would like. I don't know they are produced with and without the pov-ray in linux, with 300 dpi, etc. Could somebody try to help me how to improve them? Thanks a lot in advance, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser at tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396 -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 1673609 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image2.png Type: image/png Size: 1971863 bytes Desc: not available URL: From meng at cgl.ucsf.edu Wed Jun 24 12:47:06 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 24 Jun 2009 12:47:06 -0700 Subject: [Chimera-users] high quality pictures for publication In-Reply-To: <4A4237FE.9040806@technion.ac.il> References: <4A4237FE.9040806@technion.ac.il> Message-ID: <23FFAD3A-39D7-41A5-B5BE-89C67C794741@cgl.ucsf.edu> Dear Fabian, For publication images, to some extent different people will prefer different things. I will describe what I think is important, but keep in mind others may have artistic differences! The User's Guide includes a more comprehensive "image tips" page, also available by clicking the Tips button on the image-saving dialog: It seems like many people think POV-Ray is always the fancier/better option, whereas the Chimera rendering without raytracing only has the advantage of being faster. I disagree. For my own presentation/ publication images, I always use the Chimera rendering as I can get much better results that way. This may be due in part to my lack of expertise with POV-Ray, but it is also because there are options only available with the Chimera rendering, and because the shadows from raytracing tend to add to the complexity of an image and make it harder to understand. Of course, the faster turnaround and somewhat more WYSIWYG nature of the Chimera rendering also helps in making nicer images. Most of the Chimera images in the gallery and all currently in the feature highlights page were made directly in Chimera, without raytracing. For images primarily containing opaque molecular surfaces, I would use Chimera (non-raytraced) rendering with settings: white background, increase molecular surface vertex density to 10, turn off depth cueing, turn on sihouette edges, and either use glossy lighting, or if that is not available on your computer, increase the shininess and brightness parameters. ** If you simply use the publication preset #1 or #2 (see Preset menu) it will do all of the above for you! ** Example image from using publication preset #1 is attached at the bottom of this message. Just now, I also made a page with more images showing the settings being changed individually: However, let's say you have decided to use raytracing because you want shadows. My suggestions for raytracing surfaces would be: (a) increase molecular surface vertex density to make the surface smoother (b) if white background, make the surface some other color (silhouette edges would better demarcate the boundary, but they are not available with raytracing) (c) for faster rendering increase the POV-Ray Option "antialias threshold" from the default of 0.3 to at least 0.5, but 1.0 or even higher may still look as good and be much faster (d) if shadows are too dark, try decreasing the "key-to-fill" ratio in Lighting. Your shadows look much darker than what I got when raytracing today with the default ratio of 2.0. The default used to be higher, but that was a long time ago (changed before production release 1.2540 July 2008). (e) if shadows are in the wrong place, try moving the "key" light position in Lighting The latter two as well as quick shadow location previewing are mentioned in the raytracing page: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html -------------- next part -------------- A non-text attachment was scrubbed... Name: presetpub1.png Type: image/png Size: 110779 bytes Desc: not available URL: -------------- next part -------------- From goddard at cgl.ucsf.edu Wed Jun 24 15:05:20 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 24 Jun 2009 15:05:20 -0700 Subject: [Chimera-users] high quality pictures for publication In-Reply-To: <23FFAD3A-39D7-41A5-B5BE-89C67C794741@cgl.ucsf.edu> References: <4A4237FE.9040806@technion.ac.il> <23FFAD3A-39D7-41A5-B5BE-89C67C794741@cgl.ucsf.edu> Message-ID: <4A42A320.10802@cgl.ucsf.edu> Hi Elaine, I agree with your advice. I seldom use raytracing to produce publication images. I do always use glossy lighting. Glossy lighting is not enabled by the publication presets as far as I know. It has to be turned on separately in the Lighting panel (Tools / Viewing Controls / Lighting). Tom Elaine Meng wrote: > Dear Fabian, > For publication images, to some extent different people will prefer > different things. I will describe what I think is important, but keep > in mind others may have artistic differences! The User's Guide includes > a more comprehensive "image tips" page, also available by clicking the > Tips button on the image-saving dialog: > > > It seems like many people think POV-Ray is always the fancier/better > option, whereas the Chimera rendering without raytracing only has the > advantage of being faster. I disagree. For my own > presentation/publication images, I always use the Chimera rendering as I > can get much better results that way. This may be due in part to my > lack of expertise with POV-Ray, but it is also because there are options > only available with the Chimera rendering, and because the shadows from > raytracing tend to add to the complexity of an image and make it harder > to understand. Of course, the faster turnaround and somewhat more > WYSIWYG nature of the Chimera rendering also helps in making nicer > images. Most of the Chimera images in the gallery and all currently in > the feature highlights page were made directly in Chimera, without > raytracing. > > > > For images primarily containing opaque molecular surfaces, I would use > Chimera (non-raytraced) rendering with settings: white background, > increase molecular surface vertex density to 10, turn off depth cueing, > turn on sihouette edges, and either use glossy lighting, or if that is > not available on your computer, increase the shininess and brightness > parameters. > > ** If you simply use the publication preset #1 or #2 (see Preset menu) > it will do all of the above for you! ** > > Example image from using publication preset #1 is attached at the bottom > of this message. Just now, I also made a page with more images showing > the settings being changed individually: > > > However, let's say you have decided to use raytracing because you want > shadows. My suggestions for raytracing surfaces would be: > > (a) increase molecular surface vertex density to make the surface smoother > (b) if white background, make the surface some other color (silhouette > edges would better demarcate the boundary, but they are not available > with raytracing) > (c) for faster rendering increase the POV-Ray Option "antialias > threshold" from the default of 0.3 to at least 0.5, but 1.0 or even > higher may still look as good and be much faster > (d) if shadows are too dark, try decreasing the "key-to-fill" ratio in > Lighting. Your shadows look much darker than what I got when raytracing > today with the default ratio of 2.0. The default used to be higher, but > that was a long time ago (changed before production release 1.2540 July > 2008). > (e) if shadows are in the wrong place, try moving the "key" light > position in Lighting > The latter two as well as quick shadow location previewing are mentioned > in the raytracing page: > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > ------------------------------------------------------------------------ > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Wed Jun 24 16:22:36 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 24 Jun 2009 16:22:36 -0700 Subject: [Chimera-users] high quality pictures for publication In-Reply-To: <4A42A320.10802@cgl.ucsf.edu> References: <4A4237FE.9040806@technion.ac.il> <23FFAD3A-39D7-41A5-B5BE-89C67C794741@cgl.ucsf.edu> <4A42A320.10802@cgl.ucsf.edu> Message-ID: <682B9C5C-81CF-4DD1-83A5-160CF87C720C@cgl.ucsf.edu> Hi, My understanding of glossy lighting vs. increased shininess/brightness: Glossy lighting, if available on your system, has the advantage of making surfaces of all kinds look smoother and shinier even at fairly low vertex density (and ribbons, spheres, sticks at fairly low subdivision quality). However, glossy lighting is not available for some proportion of users. At least in my experience, and as shown in the image comparisons here, >> you can get a just-as-nice appearance by increasing the shininess and brightness, but at the cost of also needing to increase the vertex density and subdivision quality. That increases the triangles in the scene and thus computational demands. The publication presets increase molecular surface vertex density, subdivision quality, shininess and brightness -- but they do not adjust vertex density of nonmolecular surfaces. For those other surfaces, how to smooth or if they even can be smoothed depends on how they were created (e.g. volume surfaces could be subdivided and smoothed using options in the Volume Viewer tool) and you would have to do that separately. At least for a volume surface, that is sort of like massaging the data and probably wouldn't be good to have a preset do automatically. So another advantage of the glossy lighting is that it makes all the surfaces look smoother without changing the actual triangulation. The image comparisons page mentioned above doesn't include a comparison of with and without glossy lighting at low vertex density/ subdivision quality, but users with that feature available can try it for themselves. Elaine On Jun 24, 2009, at 3:05 PM, Thomas Goddard wrote: > Hi Elaine, > > I agree with your advice. I seldom use raytracing to produce > publication images. I do always use glossy lighting. Glossy > lighting is not enabled by the publication presets as far as I > know. It has to be turned on separately in the Lighting panel > (Tools / Viewing Controls / Lighting). > > Tom > > Elaine Meng wrote: >> Dear Fabian, >> For publication images, to some extent different people will prefer >> different things. I will describe what I think is important, but >> keep in mind others may have artistic differences! The User's >> Guide includes a more comprehensive "image tips" page, also >> available by clicking the Tips button on the image-saving dialog: >> >> It seems like many people think POV-Ray is always the fancier/ >> better option, whereas the Chimera rendering without raytracing >> only has the advantage of being faster. I disagree. For my own >> presentation/publication images, I always use the Chimera rendering >> as I can get much better results that way. This may be due in part >> to my lack of expertise with POV-Ray, but it is also because there >> are options only available with the Chimera rendering, and because >> the shadows from raytracing tend to add to the complexity of an >> image and make it harder to understand. Of course, the faster >> turnaround and somewhat more WYSIWYG nature of the Chimera >> rendering also helps in making nicer images. Most of the Chimera >> images in the gallery and all currently in the feature highlights >> page were made directly in Chimera, without raytracing. >> >> >> For images primarily containing opaque molecular surfaces, I would >> use Chimera (non-raytraced) rendering with settings: white >> background, increase molecular surface vertex density to 10, turn >> off depth cueing, turn on sihouette edges, and either use glossy >> lighting, or if that is not available on your computer, increase >> the shininess and brightness parameters. >> ** If you simply use the publication preset #1 or #2 (see Preset >> menu) it will do all of the above for you! ** >> Example image from using publication preset #1 is attached at the >> bottom of this message. Just now, I also made a page with more >> images showing the settings being changed individually: >> >> However, let's say you have decided to use raytracing because you >> want shadows. My suggestions for raytracing surfaces would be: >> (a) increase molecular surface vertex density to make the surface >> smoother >> (b) if white background, make the surface some other color >> (silhouette edges would better demarcate the boundary, but they are >> not available with raytracing) >> (c) for faster rendering increase the POV-Ray Option "antialias >> threshold" from the default of 0.3 to at least 0.5, but 1.0 or even >> higher may still look as good and be much faster >> (d) if shadows are too dark, try decreasing the "key-to-fill" ratio >> in Lighting. Your shadows look much darker than what I got when >> raytracing today with the default ratio of 2.0. The default used >> to be higher, but that was a long time ago (changed before >> production release 1.2540 July 2008). >> (e) if shadows are in the wrong place, try moving the "key" light >> position in Lighting >> The latter two as well as quick shadow location previewing are >> mentioned in the raytracing page: >> >> I hope this helps, >> Elaine From cdlau at ucsd.edu Wed Jun 24 23:41:08 2009 From: cdlau at ucsd.edu (cdlau at ucsd.edu) Date: Wed, 24 Jun 2009 23:41:08 -0700 (PDT) Subject: [Chimera-users] Sending commands via terminal Message-ID: <53271.133.1.134.198.1245912068.squirrel@acs-webmail.ucsd.edu> Hi, I was wondering if there was a simple way to send commands (such as "open 1zik" or "preset apply int 2?" ) to an already running instance of chimera. I want to be able to send this command using 1 line of command. This means that "--start ReadStdin" would not work because it allows commands to be sent indefinitely. Potentially I could write the commands in a python script and use the --send command, however I would like to avoid this if I just want to send a single command to chimera. Thanks for your help, Chris Lau From fglaser at technion.ac.il Thu Jun 25 07:05:36 2009 From: fglaser at technion.ac.il (Fabian Glaser) Date: Thu, 25 Jun 2009 17:05:36 +0300 Subject: [Chimera-users] high quality pictures for publication In-Reply-To: <4A42A320.10802@cgl.ucsf.edu> References: <4A4237FE.9040806@technion.ac.il> <23FFAD3A-39D7-41A5-B5BE-89C67C794741@cgl.ucsf.edu> <4A42A320.10802@cgl.ucsf.edu> Message-ID: <4A438430.5080501@technion.ac.il> Thanks you all for your kind and informative answer, indeed the glossy representation is very nice, I wasn't aware of it. Best regards, Fabian Thomas Goddard said the following on 06/25/2009 01:05 AM: > Hi Elaine, > > I agree with your advice. I seldom use raytracing to produce > publication images. I do always use glossy lighting. Glossy lighting > is not enabled by the publication presets as far as I know. It has to > be turned on separately in the Lighting panel (Tools / Viewing Controls > / Lighting). > > Tom > > > Elaine Meng wrote: >> Dear Fabian, >> For publication images, to some extent different people will prefer >> different things. I will describe what I think is important, but keep >> in mind others may have artistic differences! The User's Guide includes >> a more comprehensive "image tips" page, also available by clicking the >> Tips button on the image-saving dialog: >> >> >> It seems like many people think POV-Ray is always the fancier/better >> option, whereas the Chimera rendering without raytracing only has the >> advantage of being faster. I disagree. For my own >> presentation/publication images, I always use the Chimera rendering as I >> can get much better results that way. This may be due in part to my >> lack of expertise with POV-Ray, but it is also because there are options >> only available with the Chimera rendering, and because the shadows from >> raytracing tend to add to the complexity of an image and make it harder >> to understand. Of course, the faster turnaround and somewhat more >> WYSIWYG nature of the Chimera rendering also helps in making nicer >> images. Most of the Chimera images in the gallery and all currently in >> the feature highlights page were made directly in Chimera, without >> raytracing. >> >> >> >> For images primarily containing opaque molecular surfaces, I would use >> Chimera (non-raytraced) rendering with settings: white background, >> increase molecular surface vertex density to 10, turn off depth cueing, >> turn on sihouette edges, and either use glossy lighting, or if that is >> not available on your computer, increase the shininess and brightness >> parameters. >> >> ** If you simply use the publication preset #1 or #2 (see Preset menu) >> it will do all of the above for you! ** >> >> Example image from using publication preset #1 is attached at the bottom >> of this message. Just now, I also made a page with more images showing >> the settings being changed individually: >> >> >> However, let's say you have decided to use raytracing because you want >> shadows. My suggestions for raytracing surfaces would be: >> >> (a) increase molecular surface vertex density to make the surface smoother >> (b) if white background, make the surface some other color (silhouette >> edges would better demarcate the boundary, but they are not available >> with raytracing) >> (c) for faster rendering increase the POV-Ray Option "antialias >> threshold" from the default of 0.3 to at least 0.5, but 1.0 or even >> higher may still look as good and be much faster >> (d) if shadows are too dark, try decreasing the "key-to-fill" ratio in >> Lighting. Your shadows look much darker than what I got when raytracing >> today with the default ratio of 2.0. The default used to be higher, but >> that was a long time ago (changed before production release 1.2540 July >> 2008). >> (e) if shadows are in the wrong place, try moving the "key" light >> position in Lighting >> The latter two as well as quick shadow location previewing are mentioned >> in the raytracing page: >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> >> ------------------------------------------------------------------------ >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser at tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396 From goddard at cgl.ucsf.edu Thu Jun 25 11:24:13 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 25 Jun 2009 11:24:13 -0700 Subject: [Chimera-users] Sending commands via terminal In-Reply-To: <53271.133.1.134.198.1245912068.squirrel@acs-webmail.ucsd.edu> References: <53271.133.1.134.198.1245912068.squirrel@acs-webmail.ucsd.edu> Message-ID: <4A43C0CD.7060203@cgl.ucsf.edu> Hi Chris, We don't have a one step way to send a command to Chimera though I agree that would be handy. I'll add to our request list a command-line option like --send that just takes Chimera command instead of a file. For now I'm afraid the best that can be done is to use a temporary file: echo "open 1zik" > /tmp/a.cmd ; chimera --send /tmp/a.cmd Tom -------- Original Message -------- Subject: [Chimera-users] Sending commands via terminal To: chimera-users at cgl.ucsf.edu Date: 6/24/09 11:41 PM > Hi, > > I was wondering if there was a simple way to send commands (such as "open > 1zik" or "preset apply int 2?" ) to an already running instance of > chimera. I want to be able to send this command using 1 line of command. > This means that "--start ReadStdin" would not work because it allows > commands to be sent indefinitely. > > Potentially I could write the commands in a python script and use the > --send command, however I would like to avoid this if I just want to send > a single command to chimera. > > Thanks for your help, > > Chris Lau > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From bshaanan at bgu.ac.il Thu Jun 25 14:24:51 2009 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Thu, 25 Jun 2009 21:24:51 GMT Subject: [Chimera-users] where is 'glossy' In-Reply-To: References: Message-ID: Hi, I don't see 'glossy'? in the Lighting panel (Tools / Viewing Controls / Lighting) that Tom mentioned (I'm using the latest production release, XP). Is this a recent development or what am I missing ? ?????? Cheers, ??????????????????? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan? -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Jun 25 14:30:23 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 25 Jun 2009 14:30:23 -0700 Subject: [Chimera-users] where is 'glossy' In-Reply-To: References: Message-ID: Hi Boaz, It's been there a while, but was added after the last production release, so you would need to get a daily build to try it. List of what changed since production release (I know, it's getting long... see "Lighting" down in the Tool Changes section): Best, Elaine On Jun 25, 2009, at 2:24 PM, Boaz Shaanan wrote: > Hi, > I don't see 'glossy' in the Lighting panel (Tools / Viewing > Controls / Lighting) that Tom mentioned (I'm using the latest > production release, XP). Is this a recent development or what am I > missing ? > Cheers, > Boaz > From bshaanan at bgu.ac.il Thu Jun 25 14:34:04 2009 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Thu, 25 Jun 2009 21:34:04 GMT Subject: [Chimera-users] where is 'glossy' In-Reply-To: References: Message-ID: Hi Elaine, Thanks a lot. As I've produced in Chimera beautiful production quality images without using 'glossy' I think I'll live without it until the next production release. ?Cheers, ?????????? Boaz ----- Original Message ----- From: Elaine Meng Date: Friday, June 26, 2009 0:30 Subject: Re: [Chimera-users] where is 'glossy' To: Boaz Shaanan Cc: chimera-users at cgl.ucsf.edu > Hi Boaz, > It's been there a while, but was added after the last > production? > release, so you would need to get a daily build to try it. > > List of what changed since production release (I know, it's > getting? > long... see "Lighting" down in the Tool Changes section): > > > Best, > Elaine > > On Jun 25, 2009, at 2:24 PM, Boaz Shaanan wrote: > > > Hi, > > I don't see 'glossy'? in the Lighting panel (Tools / > Viewing? > > Controls / Lighting) that Tom mentioned (I'm using the > latest? > > production release, XP). Is this a recent development or what > am I? > > missing ? > >??????? Cheers, > >???????????????????? Boaz > > > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan? -------------- next part -------------- An HTML attachment was scrubbed... URL: From Berni.Paetzold at gmx.de Thu Jun 25 14:26:40 2009 From: Berni.Paetzold at gmx.de (=?iso-8859-1?Q?=22Bernhard_P=E4tzold=22?=) Date: Thu, 25 Jun 2009 23:26:40 +0200 Subject: [Chimera-users] Faster raytracing Message-ID: <20090625212640.291990@gmx.net> Hello I love Chimera and the only little bummer to me are the long rendering times for raytraced movies. I managed to get the PovRay version 3.7 which uses multiple cores running on our server. However now I am stuck and here comes my question. Is there away how I can get Chimera to use the newer Version of PovRay? Or can I somehow change my script so that I get only the .pov and .ini files for all the frames while the actual raytracing is skipped and I can do it subsequently with the newer Version? Currently the whole things has to happen on a windows system, but I hope that I'll get my ubuntu version soon up and running again, so hints and advices for both options are welcome. Thanks a lot in advance Berni -- GRATIS f?r alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 From meng at cgl.ucsf.edu Thu Jun 25 17:01:08 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 25 Jun 2009 17:01:08 -0700 Subject: [Chimera-users] Faster raytracing In-Reply-To: <20090625212640.291990@gmx.net> References: <20090625212640.291990@gmx.net> Message-ID: <384CCEB8-E209-4D12-9FA7-49AC2B80FBCA@cgl.ucsf.edu> Hi Berni, This is only a partial answer: In the POV-Ray Options section of Preferences, you can specify the location of the povray executable. You could try setting that to your newer version. It might not work (for example, if that newer version expects different input), but worth a try... let us know what happens. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 25, 2009, at 2:26 PM, Bernhard P?tzold wrote: > Hello > > I love Chimera and the only little bummer to me are the long > rendering times for raytraced movies. I managed to get the PovRay > version 3.7 which uses multiple cores running on our server. However > now I am stuck and here comes my question. > > Is there away how I can get Chimera to use the newer Version of > PovRay? Or can I somehow change my script so that I get only > the .pov and .ini files for all the frames while the actual > raytracing is skipped and I can do it subsequently with the newer > Version? > > Currently the whole things has to happen on a windows system, but I > hope that I'll get my ubuntu version soon up and running again, so > hints and advices for both options are welcome. > > Thanks a lot in advance > > Berni From goddard at cgl.ucsf.edu Thu Jun 25 17:18:12 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 25 Jun 2009 17:18:12 -0700 Subject: [Chimera-users] Faster raytracing In-Reply-To: <20090625212640.291990@gmx.net> References: <20090625212640.291990@gmx.net> Message-ID: <4A4413C4.3000906@cgl.ucsf.edu> Hi Berni, Elaine's suggestion to change the path to the povray executable in Favorites / Preferences, category POV-Ray may work if you don't need some extra command arguments to tell it to use multiple cores. A couple changes to parameters in the POV-Ray preferences pane can also speed up render frames very dramatically (3x or more). First change "Antialias threshold" from 0.3 to 1.5. That gave a 3x speed-up with almost no noticable change in edges (it removes jagged edges). Also try reducing quality from 9 to 4 or 5. See the documentation for what you would be missing by doing that: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#POV-Ray%20Options Also if you are using the Chimera 1.3 production release you might want to get a Chimera 1.4 daily build where the transparency handling by pov-ray now matches what is on-screen much better. Also if you get tonight's daily build or more recent you will not get the pov-ray progress dialogs popping up at each frame. Instead the halt button will be on the status line. Finally, you might consider some comments on the Chimera mailing list from this week which suggest that you can often make a better image without using pov-ray. Better lighting and silhouette edges are available in Chimera without pov-ray -- and the main feature of pov-ray, shadows, can be more distracting than illuminating http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004030.html Tom -------- Original Message -------- Subject: [Chimera-users] Faster raytracing From: Bernhard P?tzold To: chimera-users at cgl.ucsf.edu Date: 6/25/09 2:26 PM > Hello > > I love Chimera and the only little bummer to me are the long rendering times for raytraced movies. I managed to get the PovRay version 3.7 which uses multiple cores running on our server. However now I am stuck and here comes my question. > > Is there away how I can get Chimera to use the newer Version of PovRay? Or can I somehow change my script so that I get only the .pov and .ini files for all the frames while the actual raytracing is skipped and I can do it subsequently with the newer Version? > > Currently the whole things has to happen on a windows system, but I hope that I'll get my ubuntu version soon up and running again, so hints and advices for both options are welcome. > > Thanks a lot in advance > > Berni From punk.dervish.physics at gmail.com Sun Jun 28 19:11:08 2009 From: punk.dervish.physics at gmail.com (Dave Hassan) Date: Sun, 28 Jun 2009 19:11:08 -0700 Subject: [Chimera-users] GROMACS trajectory Message-ID: <6a3054370906281911s25d24d7cj1f67a72a72133b82@mail.gmail.com> Hi All, I'm trying to generate an MD move from a gromacs trajectory. I used tools > MD/Ensemble Analysis > MD movie in the toolbar. I then get the following error message: VERSION 4.0.5 using floats version 58? generation 17 9975 atoms DICKERSON DODECAMER in water 17 atoms 456 residues Exception in Tk callback ? Function: (type: ) ? Args: () Traceback (innermost last): ? File "/Applications/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ ??? return apply(self.func, args) ? File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 244, in command ??? getattr(s, buttonFuncName(txt))() ? File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 458, in OK ??? self.Apply() ? File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/EnsembleLoader.py", line 92, in Apply ??? self.callback) ? File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble ??? startFrame, endFrame, callback) ? File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble ??? ensemble = Gromacs(topology, trajectory, startFrame, endFrame) ? File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, in __init__ ??? self.topology = TprTopology(topology) ? File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py", line 68, in __init__ ??? self._readTopology(version) ? File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py", line 181, in _readTopology ??? for i in range(numResidues)] : list index out of range attached are the .trr and .tpr I used. Any help would be greatly appreciated. Thanks, Dave Hassan -------------- next part -------------- A non-text attachment was scrubbed... Name: Dickerson_grompp2em.tpr Type: application/octet-stream Size: 342060 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Dickerson_md_em.trr Type: application/octet-stream Size: 7189200 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon Jun 29 08:40:51 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 29 Jun 2009 08:40:51 -0700 Subject: [Chimera-users] GROMACS trajectory In-Reply-To: <6a3054370906281911s25d24d7cj1f67a72a72133b82@mail.gmail.com> References: <6a3054370906281911s25d24d7cj1f67a72a72133b82@mail.gmail.com> Message-ID: <8E4E5DAB-7091-480A-B858-35C09086D955@cgl.ucsf.edu> Dear Dave, When reporting a problem it is best to say what version of Chimera and what type of computer you are using. You can use "Help... Report a Bug" from the Chimera menu which will automatically include this information in what it sends to us. However, it is not necessary in this case since I believe the problem has been fixed. I tried your files in both 1.3 (latest production release, Dec 2008) and the current daily build. The production release gave the error, but in the daily build, MD Movie read the files successfully. Probably there were some cases that were not handled in the earlier version that have now been fixed. Daily builds: I recommend keeping your production release in addition to one or more daily builds... just give them different names or put them in different places. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 28, 2009, at 7:11 PM, Dave Hassan wrote: > Hi All, > > I'm trying to generate an MD move from a gromacs trajectory. I used > tools > MD/Ensemble Analysis > MD movie in the toolbar. I then get the > following error message: > > VERSION 4.0.5 > using floats > version 58 generation 17 > 9975 atoms > DICKERSON DODECAMER in water > 17 atoms > 456 residues > Exception in Tk callback From pett at cgl.ucsf.edu Mon Jun 29 10:14:29 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 29 Jun 2009 10:14:29 -0700 Subject: [Chimera-users] GROMACS trajectory In-Reply-To: <6a3054370906281911s25d24d7cj1f67a72a72133b82@mail.gmail.com> References: <6a3054370906281911s25d24d7cj1f67a72a72133b82@mail.gmail.com> Message-ID: Hi Dave, Gromacs 4 trajectories are currently only supported in the daily build. I'd like to second Elaine's suggestion to send these kind of problem reports to chimera-bugs, particularly ones with large attachments like this. I see that you did send in such a report on Friday afternoon, so I guess I also counsel patience :-) since such a report may not get turned around until the following Monday. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 28, 2009, at 7:11 PM, Dave Hassan wrote: > Hi All, > > I'm trying to generate an MD move from a gromacs trajectory. I used > tools > MD/Ensemble Analysis > MD movie in the toolbar. I then get the > following error message: > > VERSION 4.0.5 > using floats > version 58 generation 17 > 9975 atoms > DICKERSON DODECAMER in water > 17 atoms > 456 residues > Exception in Tk callback > Function: (type: ) > Args: () > Traceback (innermost last): > File "/Applications/Chimera.app/Contents/Frameworks/ > Python.framework/Versions/2.5/lib/python2.5/site-packages/Pmw/ > Pmw_1_3/lib/PmwBase.py", > line 1747, in __call__ > return apply(self.func, args) > File "/Applications/Chimera.app/Contents/Resources/share/chimera/ > baseDialog.py", > line 244, in command > getattr(s, buttonFuncName(txt))() > File "/Applications/Chimera.app/Contents/Resources/share/chimera/ > baseDialog.py", > line 458, in OK > self.Apply() > File "/Applications/Chimera.app/Contents/Resources/share/ > Trajectory/EnsembleLoader.py", > line 92, in Apply > self.callback) > File "/Applications/Chimera.app/Contents/Resources/share/ > Trajectory/formats/Gromacs/__init__.py", > line 56, in loadEnsemble > startFrame, endFrame, callback) > File "/Applications/Chimera.app/Contents/Resources/share/ > Trajectory/formats/Gromacs/__init__.py", > line 67, in loadEnsemble > ensemble = Gromacs(topology, trajectory, startFrame, endFrame) > File "/Applications/Chimera.app/Contents/Resources/share/ > Trajectory/formats/Gromacs/Gromacs.py", > line 25, in __init__ > self.topology = TprTopology(topology) > File "/Applications/Chimera.app/Contents/Resources/share/ > Trajectory/formats/Gromacs/Gromacs.py", > line 68, in __init__ > self._readTopology(version) > File "/Applications/Chimera.app/Contents/Resources/share/ > Trajectory/formats/Gromacs/Gromacs.py", > line 181, in _readTopology > for i in range(numResidues)] > : list index out of range > > attached are the .trr and .tpr I used. > > Any help would be greatly appreciated. > > Thanks, > Dave Hassan > < > Dickerson_grompp2em > .tpr > >_______________________________________________ > 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 cdlau at ucsd.edu Mon Jun 29 17:11:08 2009 From: cdlau at ucsd.edu (cdlau at ucsd.edu) Date: Mon, 29 Jun 2009 17:11:08 -0700 (PDT) Subject: [Chimera-users] modeldisp Message-ID: <56488.133.1.134.198.1246320668.squirrel@acs-webmail.ucsd.edu> Hi, I am currently using the modeldisp command on the command line to hide and view various molecules within a single mol2 file. I was wondering how I would be able to access how many total molecules there were in a single mol2 file. For example, if the mol2 file is loaded into model 0, I would be using modeldisp #0.$i etc in a large loop where $i is changing. What command can I use to return a value for the total number of molecules in the mol2 file so I can have this be the upper limit of $i? Thanks for your help, Chris From pett at cgl.ucsf.edu Mon Jun 29 17:48:58 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 29 Jun 2009 17:48:58 -0700 Subject: [Chimera-users] modeldisp In-Reply-To: <56488.133.1.134.198.1246320668.squirrel@acs-webmail.ucsd.edu> References: <56488.133.1.134.198.1246320668.squirrel@acs-webmail.ucsd.edu> Message-ID: <037E8109-DD15-47FC-935A-4D28025CD1BE@cgl.ucsf.edu> Hi Chris, I don't know how you opened your file, but if you opened it with chimera.openModels.open() then the return value is a list of models from that file, so... models = chimera.openModels.open("myfile.mol2") for i in range(len(models)): ... though perhaps more direct would be: models = chimera.openModels.open("myfile.mol2") for m in models: m.display = False for i, m in enumerate(models): ... setup stuff m.display = True ... more stuff m.display = False --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 29, 2009, at 5:11 PM, cdlau at ucsd.edu wrote: > Hi, > > I am currently using the modeldisp command on the command line to > hide and > view various molecules within a single mol2 file. I was wondering > how I > would be able to access how many total molecules there were in a > single > mol2 file. For example, if the mol2 file is loaded into model 0, I > would > be using > > modeldisp #0.$i > > etc in a large loop where $i is changing. What command can I use to > return a value for the total number of molecules in the mol2 file so > I can > have this be the upper limit of $i? > > Thanks for your help, > > Chris > _______________________________________________ > 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 efunit at yahoo.it Tue Jun 30 07:55:07 2009 From: efunit at yahoo.it (Michele Lunelli) Date: Tue, 30 Jun 2009 16:55:07 +0200 Subject: [Chimera-users] standalone programs for processing volume data Message-ID: <4A4A274B.30008@yahoo.it> Dear all, I want to use the program combine.py to subtract two delphi potential maps. I have the most recent stable version of Chimera installed in /usr/local/chimera. Following the documentation, I set the PYTHONPATH variable with setenv PYTHONPATH /usr/local/chimera/share then I try to run the program with /usr/local/chimera/bin/python2.5 /usr/local/chimera/share/VolumeProcessing/combine.py but the result is always: Traceback (most recent call last): File "/usr/local/chimera/share/VolumeProcessing/combine.py", line 12, in from VolumeData import Grid_Data File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 10, in # File "CHIMERA/share/VolumeData/opendialog.py", line 70, in File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 72, in File "/usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py", line 15, in ImportError: No module named _chimera How can I overcome this problem? Thanks in advance, Michele From meng at cgl.ucsf.edu Tue Jun 30 09:41:31 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 30 Jun 2009 09:41:31 -0700 Subject: [Chimera-users] standalone programs for processing volume data In-Reply-To: <4A4A274B.30008@yahoo.it> References: <4A4A274B.30008@yahoo.it> Message-ID: <07976B69-F99A-4367-9D0B-F1A2CFD76C8D@cgl.ucsf.edu> Dear Michele, You can now subtract maps using the command "vop": Be aware that this subtraction requires the grids of the two maps to be the same (same numbers of points and in the same locations), so you might need to use the "vop" resample option first, if that is not already true. I believe the "vop" resampling and subtraction options have been available for a while, since version 1.2540 (Jul 2008). We have been planning to remove the standalone processing programs as the same features become available elsewhere in Chimera, and perhaps they are currently broken. 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 http://www.cgl.ucsf.edu/home/meng/index.html On Jun 30, 2009, at 7:55 AM, Michele Lunelli wrote: > Dear all, > I want to use the program combine.py to subtract two delphi > potential maps. > I have the most recent stable version of Chimera installed in /usr/ > local/chimera. > Following the documentation, I set the PYTHONPATH variable with > > setenv PYTHONPATH /usr/local/chimera/share > > then I try to run the program with > > /usr/local/chimera/bin/python2.5 /usr/local/chimera/share/ > VolumeProcessing/combine.py > > but the result is always: > > Traceback (most recent call last): > File "/usr/local/chimera/share/VolumeProcessing/combine.py", line > 12, in > from VolumeData import Grid_Data > File "/usr/local/chimera/lib/python2.5/site-packages/PIL/ > __init__.py", line 10, in > # > File "CHIMERA/share/VolumeData/opendialog.py", line 70, in > File "/usr/local/chimera/lib/python2.5/site-packages/PIL/ > __init__.py", line 72, in > > File "/usr/local/chimera/lib/python2.5/site-packages/PIL/ > __init__.py", line 15, in > > ImportError: No module named _chimera > > How can I overcome this problem? > > > Thanks in advance, > Michele > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users