From 1234dndd at hanmail.net Mon May 2 02:23:33 2011 From: 1234dndd at hanmail.net (=?utf-8?B?7Jyk7ZmN66+8?=) Date: Mon, 02 May 2011 18:23:33 +0900 (KST) Subject: [Chimera-users] building large size polymer Message-ID: <20110502182333.HM.P000000000LCxHQ@1234dndd.wwl1277.hanmail.net> An HTML attachment was scrubbed... URL: From nayakpreetam at gmail.com Mon May 2 05:15:40 2011 From: nayakpreetam at gmail.com (preetam nayak) Date: Mon, 2 May 2011 17:45:40 +0530 Subject: [Chimera-users] kindly help Message-ID: Respected sir, I am using chimera for the first time.I just want to ask that after successfully removing all clashes/contacts in my pdb file using commandline arguement selectively,I am unable to save this modified pdb file even after trying many a times.Everytime I am saving my pdb file after modifications,the changes are not at all saved and again when I am opening the pdb file ,it is showing the same clashes/contacts.Sir,please help by providing the required steps as to how to save the changes one has made in the pdb file. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon May 2 09:44:55 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 May 2011 09:44:55 -0700 Subject: [Chimera-users] changing and saving structure In-Reply-To: References: Message-ID: <2E2D6AFB-25A0-44FC-BF2E-7C74F01B3BB1@cgl.ucsf.edu> Dear Preetam, My best guess is that you have not really changed the structure to remove clashes. If you use the command ~findclash to remove clashes, that means only to remove the lines showing the clashes. It does not change the structure. To change the structure so that it does not have clashes would require other actions that really change the coordinates, such as rotating bonds yourself, moving molecules or chains relative to one another, or performing energy-minimization. When you save the PDB file, it will include any changes in coordinates you have made. See this discussion on "modifying and saving data" in Chimera, and its links: The "structure analysis and comparison" tutorial also includes some clash detection and bond rotation: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 2, 2011, at 5:15 AM, preetam nayak wrote: > Respected sir, > I am using chimera for the first time.I just want to ask that after successfully removing all clashes/contacts in my pdb file using commandline arguement selectively,I am unable to save this modified pdb file even after trying many a times.Everytime I am saving my pdb file after modifications,the changes are not at all saved and again when I am opening the pdb file ,it is showing the same clashes/contacts.Sir,please help by providing the required steps as to how to save the changes one has made in the pdb file. From meng at cgl.ucsf.edu Mon May 2 13:56:41 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 May 2011 13:56:41 -0700 Subject: [Chimera-users] building large size polymer In-Reply-To: <20110502182333.HM.P000000000LCxHQ@1234dndd.wwl1277.hanmail.net> References: <20110502182333.HM.P000000000LCxHQ@1234dndd.wwl1277.hanmail.net> Message-ID: <88713D3C-C1DF-4E74-BE9B-4A6269095723@cgl.ucsf.edu> Hi Hongmin, Sorry, there is no general polymer-building feature, only for chains of amino acids (Tools... Structure Editing... Build Structure, Start Structure tab, "peptide sequence"). If you have a monomer (or small multimer) of your polymer and know the symmetry operations needed to place additional copies of that structure, you could use the command "sym." However, it may be difficult to figure out the proper helical or translational symmetry parameters. Also, these copies would not be bonded to each other. To bond the copies you would have to first put all of them in one model (see command "combine") and then use several "bond" commands, which you would probably want to generate by a script. So, it might be possible with Chimera, but not very convenient, so you may want to do polymer-building in another program if possible. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 2, 2011, at 2:23 AM, ??? wrote: > Hello I am a student of Korea.(Yonsei Univ) > > I am working on molecular dynamic and use your program for making Mol2 files. > > And now I have tried to make large size polymer that has many monomer. > > I usually use SMILES string for constructing structure. > > In this case, but I could not put the all SMILES strings for constructing. > > Because I have to connet almost 100 monomers. > > Is there a specific fuction or tool for the problem? > > I really appreciate your work. > > Sincerely. > > - Hongmin > From t.burgoyne at ucl.ac.uk Wed May 4 03:40:26 2011 From: t.burgoyne at ucl.ac.uk (Thomas Burgoyne) Date: Wed, 4 May 2011 11:40:26 +0100 Subject: [Chimera-users] Using Chimera to look at confocal data Message-ID: <002501cc0a47$ae3c87a0$0ab596e0$@ucl.ac.uk> Hi, I've been using Chimera for a few years now to look at electron tomography data and I have to say I think the software is absolutely superb. Recently I have started looking at 3D-confocal data and I discovered with a bit of work I can open the data using chimera. I open each colour channel as a separate image stack which works quite nicely. The only problem I encounter is when viewing the data using solid rendering only one channel is visible. Is there a way to view three image stacks at the same time using the solid rendering? Thanks, Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattia.rocco at istge.it Wed May 4 07:44:29 2011 From: mattia.rocco at istge.it (Mattia Rocco) Date: Wed, 04 May 2011 16:44:29 +0200 Subject: [Chimera-users] imgCIF files Message-ID: <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> To the developers of Chimera: is there any intention of implementing the uploading of imgCIF density maps files? Such files can be generated by RasMol starting from either atomic structures or low-resolution bead models (e.g. SAXS-derived models). Conversely, it would be nice if density maps could be generated within Chimera... Best - Mattia Dr. Mattia Rocco Biopolimeri e Proteomica Istituto Nazionale per la Ricerca sul Cancro (IST) c/o Centro per le Biotecnologie Avanzate (CBA) IST c/o CBA, Largo Rosanna Benzi 10 I-16132 Genova, Italy Phone: +39-0105737-310 Fax: +39-0105737-325 e-mail: mattia.rocco at istge.it ATTENZIONE. Il presente messaggio ed i suoi allegati devono intendersi ad uso esclusivo dei suoi destinatari e sono confidenziali. Persone diverse dal destinatario, anche ai sensi del D.Lgs. n. 196/2003 , non debbono prendere visione dei contenuti, copiare od inoltrare l'e-mail a terzi. Se ricevete questo messaggio per errore, Vi preghiamo di cancellarlo, di distruggerne ogni copia e di informarci immediatamente. La mail non ? un protocollo sicuro, pertanto IST declina ogni responsabilit? in caso di intercettazione o modifiche del presente messaggio. WARNING. This message and any attachments is intended solely for the use of the intended addressees and is confidential. Any unauthorized review, use, disclosure or distribution is prohibited. If you receive this message in error, please delete it, destroy all copies and immediately notify us. Mail is not a secure protocol, therefore IST will not be liable for interception or amendment of this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed May 4 09:32:13 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 4 May 2011 09:32:13 -0700 Subject: [Chimera-users] imgCIF files In-Reply-To: <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> References: <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> Message-ID: Dear Mattia, You can make a density map from atomic structures (or their parts) in Chimera using the "molmap" command: For example, commands: open 2gbp molmap ligand 4.5 molmap protein 5 ... would make a map of resolution 4.5 for the ligand part of the structure (glucose) and another map of resolution 5 for the protein part of the structure. You could also specify the whole structure, particular chains, etc. If the SAXS model was in the form of a PDB file with the beads as "atoms," perhaps you could use a similar procedure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 4, 2011, at 7:44 AM, Mattia Rocco wrote: > > To the developers of Chimera: is there any intention of implementing the uploading of imgCIF density maps files? Such files can be generated by RasMol starting from either atomic structures or low-resolution bead models (e.g. SAXS-derived models). > > Conversely, it would be nice if density maps could be generated within Chimera... > > Best - Mattia > From chiendarret at gmail.com Wed May 4 10:05:31 2011 From: chiendarret at gmail.com (Francesco Pietra) Date: Wed, 4 May 2011 19:05:31 +0200 Subject: [Chimera-users] partial failure in addH BUG? Message-ID: Hello: i had partial failure in addH to a natural product. H at a quaternary, chiral C was not added in spite of repeated attempts. All Hs were added by my favorite drawer (for organic compounds); however, this changes the coordinates, which is not what I want. I solved the issue by transferring the chimera pdb output to vmd, adding the missing H with Molefacture. On the other hand, Molefacture, if asked to add all Hs, resulted in incorrect stereochemistry at -O-CH3 and some -C-CH3 (inverted umbrella, which could not be reversed). francesco pietra From goddard at sonic.net Wed May 4 10:31:41 2011 From: goddard at sonic.net (Tom Goddard) Date: Wed, 04 May 2011 10:31:41 -0700 Subject: [Chimera-users] imgCIF files In-Reply-To: <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> References: <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> Message-ID: <4DC18D7D.6050003@sonic.net> Hi Mattia, I put imgCIF support on the Chimera feature request list http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests I don't expect it is likely to get done for several reasons. From what I read on the web imgCIF was developed for recording 2-d x-ray diffraction spot data. Chimera cannot do anything with that kind of data. In 2007 there was some work done to make it handle 3-dimensional density maps and it was included in RasMol for that purpose. There was also some talk of a PyMol plug-in to read the 3-d imgCIF maps but I don't know if anything came of that. It looks like this format is not used by most map display programs. RasMol also uses CCP4 which Chimera reads, as does almost every other map display program. And as Elaine pointed out, Chimera can directly create maps from atomic models. New volume data formats are easy to support in Chimera with Python code. If someone wants to provide and imgCIF reader/writer in Python I could put it into Chimera if the code is well written. Tom > is there any intention of implementing the uploading of imgCIF density > maps files? Such files can be generated by RasMol starting from either > atomic structures or low-resolution bead models (e.g. SAXS-derived > models). > > Conversely, it would be nice if density maps could be generated within > Chimera... From pett at cgl.ucsf.edu Wed May 4 10:43:48 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 4 May 2011 10:43:48 -0700 Subject: [Chimera-users] partial failure in addH BUG? In-Reply-To: References: Message-ID: On May 4, 2011, at 10:05 AM, Francesco Pietra wrote: > Hello: > i had partial failure in addH to a natural product. H at a quaternary, > chiral C was not added in spite of repeated attempts. Hi Francesco, My guess is that Chimera does not believe that the problem carbon is sp3, which Chimera decides based on the carbon's bond geometry. You can see what atom type Chimera assigned to that carbon by selecting it and then doing Actions->Label->IDATM type. An sp3 carbon would be "C3". An sp2 carbon would be "C2". A full table of atom types is here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/idatm.html You can force Chimera to believe the carbon is sp3 by selecting it and then using this command: setattr a idatmType C3 sel It would also probably be helpful if you used Help->Report A Bug to submit a bug report on this problem, attaching the structure file. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu > > All Hs were added by my favorite drawer (for organic compounds); > however, this changes the coordinates, which is not what I want. > > I solved the issue by transferring the chimera pdb output to vmd, > adding the missing H with Molefacture. > > On the other hand, Molefacture, if asked to add all Hs, resulted in > incorrect stereochemistry at -O-CH3 and some -C-CH3 (inverted > umbrella, which could not be reversed). > > francesco pietra > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed May 4 11:06:31 2011 From: goddard at sonic.net (Tom Goddard) Date: Wed, 04 May 2011 11:06:31 -0700 Subject: [Chimera-users] Using Chimera to look at confocal data In-Reply-To: <002501cc0a47$ae3c87a0$0ab596e0$@ucl.ac.uk> References: <002501cc0a47$ae3c87a0$0ab596e0$@ucl.ac.uk> Message-ID: <4DC195A7.7060308@sonic.net> Hi Tom, Chimera solid style volume rendering doesn't handle multi-channel images. It doesn't know how to blend the colors from the different channels. Chimera used to do this but I removed the code in 2008 because it was too complicated. If you use a really old version of Chimera it could work, although I think the only way to open a multi-channel data set was to use Priism format. I removed that code because supporting multiple channels was too complex so it made it hard to improve the code for single channel volume data (electron microscopy) which is by far the most common use in Chimera. Here is one trick that will let you blend multiple channels for a single displayed plane (attached image is an example). If you have two channels with Chimera model id numbers #0 and #1, then shift the origin of one volume so it is slightly in front of the other, for instance, set the "origin index" to "0 0 -1" for volume #1 using the Features / Coordinates tab of the volume dialog. Then make the volume in front very transparent (Features / Brightness and Transparency). Chimera renders the volumes in id number order and after it draws one solid style volume you won't see anything for a later one drawn behind (or at the same depth) as the first. But if you put it slightly in front it will be shown. This only works for a single plane unless you shift the second volume so the whole thing is in front of the first volume. If you do that you'll want to use orthographic projection (Tools / Viewing Controls / Camera) otherwise the volumes won't even superimpose due to perspective. While the above hack might be ok for making an image, I'd say Chimera is simply not useful for multi-channel volume data if you need solid-style rendering (which you most always do for noisy data). Multi-channel with surface style works. Tom > Hi, > > I've been using Chimera for a few years now to look at electron > tomography data and I have to say I think the software is absolutely > superb. Recently I have started looking at 3D-confocal data and I > discovered with a bit of work I can open the data using chimera. I > open each colour channel as a separate image stack which works quite > nicely. The only problem I encounter is when viewing the data using > solid rendering only one channel is visible. Is there a way to view > three image stacks at the same time using the solid rendering? > > Thanks, > > Tom > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: blend.jpg Type: image/jpeg Size: 35580 bytes Desc: not available URL: From Charles.Greenberg at ucsf.edu Wed May 4 11:51:30 2011 From: Charles.Greenberg at ucsf.edu (Charles Greenberg) Date: Wed, 4 May 2011 11:51:30 -0700 Subject: [Chimera-users] pause during morph conformations Message-ID: <3515C78E-591A-406F-94A2-3DD177F15E12@ucsf.edu> I have a 3-state structure and I'm currently using morph conformations to interpolate between them. This works very nicely, but I'd like the output movie to pause for half a second (a few frames) during each of the three key states. Anyone know how to do this? I know you can add behaviors during particular frames, but I don't know how to make it pause. Thanks! --Charles From meng at cgl.ucsf.edu Wed May 4 12:51:08 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 4 May 2011 12:51:08 -0700 Subject: [Chimera-users] pause during morph conformations In-Reply-To: <3515C78E-591A-406F-94A2-3DD177F15E12@ucsf.edu> References: <3515C78E-591A-406F-94A2-3DD177F15E12@ucsf.edu> Message-ID: <2240CE49-374A-49E4-A842-803DFAD25D5D@cgl.ucsf.edu> Hi Charles, It can be done with commands. First you would create the morph trajectory, then use a Chimera command script (just open a plain text file containing the commands) of the general form: movie record [options] coordset 1,20 #3; wait 20 wait 10 coordset 21,40 #3; wait 20 wait 10 coordset 41,60 #3; wait 20 movie stop movie encode [options] where [options] is not meant literally but would give your desired movie settings, and you would also change other things depending on which model is your trajectory and which frames cover the transitions, and how long you would like the pauses to be. I would also recommend saving the session with your morph trajectory in the desired orientation so you can revisit it later and easily re-make the movie with any needed variations. There is an example command file showing a similar procedure... the "trmovie" example includes morphing and uses coordset to play parts of the trajectory and does other stuff between the uses of coordset (it actually does the morph creation too, but it may be easier for you to do that part beforehand): ... and the resulting movie is in the Animation Gallery, currently third on this page: More info on movies and movie-related commands: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 4, 2011, at 11:51 AM, Charles Greenberg wrote: > I have a 3-state structure and I'm currently using morph conformations > to interpolate between them. This works very nicely, but I'd like the > output movie to pause for half a second (a few frames) during each of > the three key states. Anyone know how to do this? I know you can add > behaviors during particular frames, but I don't know how to make it > pause. Thanks! > --Charles From meng at cgl.ucsf.edu Wed May 4 12:57:28 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 4 May 2011 12:57:28 -0700 Subject: [Chimera-users] pause during morph conformations In-Reply-To: <2240CE49-374A-49E4-A842-803DFAD25D5D@cgl.ucsf.edu> References: <3515C78E-591A-406F-94A2-3DD177F15E12@ucsf.edu> <2240CE49-374A-49E4-A842-803DFAD25D5D@cgl.ucsf.edu> Message-ID: Sigh, the coordset commands in my previous reply are not quite right, you would put the model number before the frames. Sorry about that. However, the commands are all correct within the "trmovie" example command file discussed in that message. Elaine On May 4, 2011, at 12:51 PM, Elaine Meng wrote: > Hi Charles, > It can be done with commands. First you would create the morph trajectory, then use a Chimera command script (just open a plain text file containing the commands) of the general form: > > movie record [options] > coordset 1,20 #3; wait 20 > wait 10 > coordset 21,40 #3; wait 20 > wait 10 > coordset 41,60 #3; wait 20 > movie stop > movie encode [options] > > where [options] is not meant literally but would give your desired movie settings, and you would also change other things depending on which model is your trajectory and which frames cover the transitions, and how long you would like the pauses to be. I would also recommend saving the session with your morph trajectory in the desired orientation so you can revisit it later and easily re-make the movie with any needed variations. > > There is an example command file showing a similar procedure... > the "trmovie" example includes morphing and uses coordset to play parts of the trajectory and does other stuff between the uses of coordset (it actually does the morph creation too, but it may be easier for you to do that part beforehand): > > > ... and the resulting movie is in the Animation Gallery, currently third on this page: > > > More info on movies and movie-related commands: > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On May 4, 2011, at 11:51 AM, Charles Greenberg wrote: > >> I have a 3-state structure and I'm currently using morph conformations >> to interpolate between them. This works very nicely, but I'd like the >> output movie to pause for half a second (a few frames) during each of >> the three key states. Anyone know how to do this? I know you can add >> behaviors during particular frames, but I don't know how to make it >> pause. Thanks! >> --Charles > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Wed May 4 13:07:30 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 4 May 2011 13:07:30 -0700 Subject: [Chimera-users] pause during morph conformations In-Reply-To: References: <3515C78E-591A-406F-94A2-3DD177F15E12@ucsf.edu> <2240CE49-374A-49E4-A842-803DFAD25D5D@cgl.ucsf.edu> Message-ID: Hi Charles, Alternatively, you can also do this with the graphical interface. Just add each conformation twice when you are adding conformations. Then, choose the second conformation in the final list you've made (i.e. the second copy of your first conformation) and change "interpolation steps" to 15 (for a half-second pause). Then choose the third state and change the interpolation steps to however many you want when it's moving. Then choose the fourth state and use 15 again, etc. I notice that the final list of conformations wants you to click in with the mouse to change which one you're working on -- the up/down arrows keys seem to change the conformation chosen but don't update the rest of the interface, so beware of that. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 4, 2011, at 12:57 PM, Elaine Meng wrote: > Sigh, the coordset commands in my previous reply are not quite > right, you would put the model number before the frames. Sorry > about that. However, the commands are all correct within the > "trmovie" example command file discussed in that message. > Elaine > > On May 4, 2011, at 12:51 PM, Elaine Meng wrote: > >> Hi Charles, >> It can be done with commands. First you would create the morph >> trajectory, then use a Chimera command script (just open a plain >> text file containing the commands) of the general form: >> >> movie record [options] >> coordset 1,20 #3; wait 20 >> wait 10 >> coordset 21,40 #3; wait 20 >> wait 10 >> coordset 41,60 #3; wait 20 >> movie stop >> movie encode [options] >> >> where [options] is not meant literally but would give your desired >> movie settings, and you would also change other things depending on >> which model is your trajectory and which frames cover the >> transitions, and how long you would like the pauses to be. I would >> also recommend saving the session with your morph trajectory in the >> desired orientation so you can revisit it later and easily re-make >> the movie with any needed variations. >> >> There is an example command file showing a similar procedure... >> the "trmovie" example includes morphing and uses coordset to play >> parts of the trajectory and does other stuff between the uses of >> coordset (it actually does the morph creation too, but it may be >> easier for you to do that part beforehand): >> > movies.html#examples> >> >> ... and the resulting movie is in the Animation Gallery, currently >> third on this page: >> >> >> More info on movies and movie-related commands: >> >> > > >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On May 4, 2011, at 11:51 AM, Charles Greenberg wrote: >> >>> I have a 3-state structure and I'm currently using morph >>> conformations >>> to interpolate between them. This works very nicely, but I'd like >>> the >>> output movie to pause for half a second (a few frames) during each >>> of >>> the three key states. Anyone know how to do this? I know you can >>> add >>> behaviors during particular frames, but I don't know how to make it >>> pause. Thanks! >>> --Charles >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From george.f.feldman at gmail.com Wed May 4 10:44:27 2011 From: george.f.feldman at gmail.com (George Feldman) Date: Wed, 4 May 2011 13:44:27 -0400 Subject: [Chimera-users] solvent exposed charged resides Message-ID: Hello Chimera community, I am rather new to Chimera, but in general familiar with PyMol. I switched to Chimera for the added functionality and general "free-ness," and so far I like it, but I'm having difficulty getting started. What I really need to do is identify the solvent exposed (SAS) residues that are charged. In particular I would like to identify exposed lysines, arginines, glutamic acids, and aspartic acids. All I need to do is identify and count them, is there a way to do this without slowly going over the entire molecular surface? Please bear in mind that I am capable of typing in commands, but I am no programmer. If it is too complex, I will simply, and sadly, have to do it manually. My fear with the manual approach is that I will miss something or miss-classify it. Your advise and help is greatly appreciated. PS. I've tried to do Render by Attribute -> areaSAS, but that doesn't seem to be working for me even after I tell it to calculate the surface. I'm not sure what I'm doing wrong if this is the approach that I am supposed to be taking. Best regards, George -------------- next part -------------- An HTML attachment was scrubbed... URL: From mattia.rocco at istge.it Wed May 4 14:03:09 2011 From: mattia.rocco at istge.it (Mattia Rocco) Date: Wed, 04 May 2011 23:03:09 +0200 Subject: [Chimera-users] imgCIF files In-Reply-To: <4DC18D7D.6050003@sonic.net> References: <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> Message-ID: <5.1.1.6.0.20110504225345.02d20a48@quipo.it> Hi Tom, many thanks also to you for another fast and very informative answer! I didn't know that RasMol could read ccp4 maps, but at the moment it will not save a generated map in that format. I have recently contacted the RasMol developers, and Dr. Bernstein wrote back to me that he will make a save in ccp4 format option available, so in the end the circle will be hopefully closed... ;-) Best wishes - Mattia At 10.31 04/05/2011 -0700, Tom Goddard wrote: >Hi Mattia, > > I put imgCIF support on the Chimera feature request list > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests > >I don't expect it is likely to get done for several reasons. From what I >read on the web imgCIF was developed for recording 2-d x-ray diffraction >spot data. Chimera cannot do anything with that kind of data. In 2007 >there was some work done to make it handle 3-dimensional density maps and >it was included in RasMol for that purpose. There was also some talk of a >PyMol plug-in to read the 3-d imgCIF maps but I don't know if anything >came of that. It looks like this format is not used by most map display >programs. RasMol also uses CCP4 which Chimera reads, as does almost every >other map display program. And as Elaine pointed out, Chimera can >directly create maps from atomic models. > > New volume data formats are easy to support in Chimera with Python > code. If someone wants to provide and imgCIF reader/writer in Python I > could put it into Chimera if the code is well written. > > Tom > >>is there any intention of implementing the uploading of imgCIF density >>maps files? Such files can be generated by RasMol starting from either >>atomic structures or low-resolution bead models (e.g. SAXS-derived models). >> >>Conversely, it would be nice if density maps could be generated within >>Chimera... > > > From meng at cgl.ucsf.edu Wed May 4 15:20:02 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 4 May 2011 15:20:02 -0700 Subject: [Chimera-users] solvent exposed charged resides In-Reply-To: References: Message-ID: Hi George, Welcome to Chimera! Don't worry, I'm not a programmer either. There is a video tutorial that covers some of what I describe below, I can't tell from your description what might be going wrong, but yes the basic procedure would be to show a surface (which you could then hide, the important part is showing it at some point), and then choose residues of the desired types that have surface area greater than some cutoff. For example, open PDB 2gbp, show surface with Actions... Surface... show (or command "surface"). As soon as you create the surface, atoms and residues will be assigned attributes named areaSES and areaSAS containing their solvent-excluded and solvent-accessible surface areas. The solvent-excluded surface is what Chimera displays, but both are calculated, as discussed here: These values will include surface area from interior bubbles. If you don't want interior bubbles to be included, next enter the command: setattr s allComponents false Then, so you will be able to see what you are selecting, hide the surface and show all atoms, for example with commands: ~surf ~ribbon disp Then, experiment with different cutoffs of surface area to classify a residue as solvent-exposed or not. Don't worry about the residue type for now. You could do this interactively using Select by Attribute (menu: Select... By Attribute Value, set level to "residues" instead of "atoms" and attribute to "areaSAS" or "areaSES" as preferred), or with commands such as: sel :/areaSAS>50 I'd probably use something like 40 or 50, but it depends on your goal, so go with whatever cutoff you find selects the residues you expect. Then you can unselect residues that are not of the desired type, for example with command: ~sel ~:glu,asp,lys,arg,his (unselect residues that are NOT the ones named). The names/numbers of the remaining selected residues can be written out to a file with "Actions... Write List" in the menu, or the command "writesel". Render by Attribute or command "rangecolor" would be used if you wanted to show the surface area values with colors. If you wanted to write out the area values along with the residues, you would use "File... Save Attributes" from the menu of the dialog of Render/Select by Attribute. There is an option to save only the values for the current selection. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 4, 2011, at 10:44 AM, George Feldman wrote: > Hello Chimera community, > > I am rather new to Chimera, but in general familiar with PyMol. I switched to Chimera for the added functionality and general "free-ness," and so far I like it, but I'm having difficulty getting started. What I really need to do is identify the solvent exposed (SAS) residues that are charged. In particular I would like to identify exposed lysines, arginines, glutamic acids, and aspartic acids. All I need to do is identify and count them, is there a way to do this without slowly going over the entire molecular surface? Please bear in mind that I am capable of typing in commands, but I am no programmer. If it is too complex, I will simply, and sadly, have to do it manually. My fear with the manual approach is that I will miss something or miss-classify it. Your advise and help is greatly appreciated. > > PS. I've tried to do Render by Attribute -> areaSAS, but that doesn't seem to be working for me even after I tell it to calculate the surface. I'm not sure what I'm doing wrong if this is the approach that I am supposed to be taking. > > Best regards, > George From goddard at sonic.net Wed May 4 17:30:30 2011 From: goddard at sonic.net (Tom Goddard) Date: Wed, 04 May 2011 17:30:30 -0700 Subject: [Chimera-users] imgCIF files In-Reply-To: <5.1.1.6.0.20110504224722.02d1f008@quipo.it> References: <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> <5.1.1.6.0.20110504163106.02eafe28@mail.istge.priv> <5.1.1.6.0.20110504224722.02d1f008@quipo.it> Message-ID: <4DC1EFA6.3050409@sonic.net> HI Mattia, Chimera can save MRC2000 format which is nearly identical to CCP4 format. Any software that reads CCP4 will likely read the MRC output from Chimera as CCP4, but the origin of the map is specified differently. The MRC format allows a floating point origin specification which is not part of the CCP4 format and Chimera uses that. So alignment of the Chimera written MRC and atomic models may not work right in other software. A basic problem with CCP4 is that the origin has to lie on a crystallographic lattice point, which isn't so good for electron microscopy or maps from non-crystal sources. Chimera doesn't know about a SAXS bead radius in PDB header remarks. Also Chimera may try some heuristics to connect up the beads as if they were actual atoms. You'll have to try and see. You can adjust the sphere radius for the beads by selecting them and using Selection Inspector (green button in lower right of main Chimera window) or a command setattr a radius 5 #0 For making a simulated map with the Chimera "molmap" command the atom radius is not used. It simply adds 3-dimensional Gaussians centered at each atom. The Gaussian width is calculated by the resolution value used in the molmap command molmap #0 8 See the documentation for details. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html Tom > > Dear Elaine, > > thanks for your very fast and informative answer! I missed that option > in the list of Chimera commands. I will try it out tomorrow (I'm at > home now...). Perhaps it would be nice to add it to one of the > pull-down menus (in the Volume options?). Is there a way then to save > the map, say in ccp4 format? > > As for the SAXS file, yes, for instance the DAMMIN/DAMMIF-generated > files are in PDB format. But will Chimera read in the correct radius > for the beads, which is stored in the file header? (or is there a way > to externally enter the radius?). > > Thanks again - Mattia > > At 09.32 04/05/2011 -0700, Elaine Meng wrote: >> Dear Mattia, >> You can make a density map from atomic structures (or their parts) in >> Chimera using the "molmap" command: >> >> >> >> For example, commands: >> >> open 2gbp >> molmap ligand 4.5 >> molmap protein 5 >> >> ... would make a map of resolution 4.5 for the ligand part of the >> structure (glucose) and another map of resolution 5 for the protein >> part of the structure. You could also specify the whole structure, >> particular chains, etc. >> >> If the SAXS model was in the form of a PDB file with the beads as >> "atoms," perhaps you could use a similar procedure. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On May 4, 2011, at 7:44 AM, Mattia Rocco wrote: >> > >> > To the developers of Chimera: is there any intention of implementing >> the uploading of imgCIF density maps files? Such files can be >> generated by RasMol starting from either atomic structures or >> low-resolution bead models (e.g. SAXS-derived models). >> > >> > Conversely, it would be nice if density maps could be generated >> within Chimera... >> > >> > Best - Mattia >> > > From 1234dndd at hanmail.net Thu May 5 07:39:52 2011 From: 1234dndd at hanmail.net (=?utf-8?B?7Jyk7ZmN66+8?=) Date: Thu, 05 May 2011 23:39:52 +0900 (KST) Subject: [Chimera-users] building large size polymer Message-ID: <20110505233952.HM.P000000000LCxI5@1234dndd.wwl1277.hanmail.net> An HTML attachment was scrubbed... URL: From t.burgoyne05 at imperial.ac.uk Sun May 8 08:45:44 2011 From: t.burgoyne05 at imperial.ac.uk (Burgoyne, Thomas) Date: Sun, 8 May 2011 16:45:44 +0100 Subject: [Chimera-users] Morphing volumes Message-ID: Hi, I have two 3D-EM volumes that I wish to use the morph option for. I can align the two maps in chimera by hand so that they sit well together but the problem is I want to be able to create a morph video from the maps new positions. When I use the morph option it only allows me to create a morph from the original set starting positions of each volume. Is there a way to get around this? I would be very thankful for any help or guidance. Tom From hemeteam at wsu.edu Mon May 9 10:23:47 2011 From: hemeteam at wsu.edu (Satterlee, James D) Date: Mon, 9 May 2011 10:23:47 -0700 Subject: [Chimera-users] System Compatiblility Message-ID: Hello, I've not yet downloaded or used Chimera, but I am contemplating it. I am looking for Windows System compatibility information for the various newer versions of Chimera. To me it wasn't obvious on the Chimera home site. I do not use Window's 7 and I'm wondering which version might be most trouble-free for a Windows XP version with all service packs installed. Thanks, Jim Satterlee James D. Satterlee Professor of Chemistry Washington State University Pullman, WA 99164-4630 hemeteam at wsu.edu 509.335.8620 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Tue May 10 11:49:57 2011 From: goddard at sonic.net (Tom Goddard) Date: Tue, 10 May 2011 11:49:57 -0700 Subject: [Chimera-users] Morphing volumes In-Reply-To: References: Message-ID: <4DC988D5.3030807@sonic.net> Hi Tom, The morph tool just linearly interpolates between the grid points in the two maps. So it doesn't use a new alignment of the maps that you did before morphing. To make that work you should interpolate one of the maps on the grid of the other map after you've made the alignment. Then you can morph between the two maps which are now defined on the same grid. To do that interpolation use the vop (volume operation command): vop resample #1 ongrid #0 This command makes a new copy of map #0 interpolating on the grid of map #1. Another issue that may arise is that the map density values are scaled differently. You can apply a scale factor in the Morph Map options panel to correct that. Here's a video tutorial that demonstrates the alignment, interpolation, and scale factor http://www.cgl.ucsf.edu/chimera/videodoc/MorphAlign Tom > Hi, > > I have two 3D-EM volumes that I wish to use the morph option for. I can align the two maps in chimera by hand so that they sit well together but the problem is I want to be able to create a morph video from the maps new positions. When I use the morph option it only allows me to create a morph from the original set starting positions of each volume. Is there a way to get around this? I would be very thankful for any help or guidance. > > Tom > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From zhouming2 at mail.nih.gov Tue May 10 12:18:42 2011 From: zhouming2 at mail.nih.gov (Zhou, Ming (NIH/NCI) [C]) Date: Tue, 10 May 2011 15:18:42 -0400 Subject: [Chimera-users] color side chain only Message-ID: <794DFDD3C128EF44AC49ADC58FD0090C030EC3AF01@NIHMLBX10.nih.gov> Hello, this is Ming Zhou at NCI-Frederick, Maryland. I am trying to use Chimera to make some ribbon structure figures. I am wondering how I can display only side chain (without backbone) for a specific residue. Usually, if I display the residue, select the residue at the Atom specifier and color it. The color would be partially on the ribbon structure too since the backbone of that residue is on the ribbon. How do I avoid coloring backbone, only color the side chain? Thank you very much. Ming -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue May 10 14:52:03 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 10 May 2011 14:52:03 -0700 Subject: [Chimera-users] color side chain only In-Reply-To: <794DFDD3C128EF44AC49ADC58FD0090C030EC3AF01@NIHMLBX10.nih.gov> References: <794DFDD3C128EF44AC49ADC58FD0090C030EC3AF01@NIHMLBX10.nih.gov> Message-ID: <0B5DE1B5-1FD5-4565-B6B2-34967FA0FA5C@cgl.ucsf.edu> Hi Ming! If you are using the color command, you would include ",a" right after the color name, no spaces, to color the atoms but not ribbons, surfaces, labels, etc.. For example: color hot pink,a :45.a,55.a,13.b .... would color the atoms only of residues 45 and 55 in chain A and 13 in chain B If you are using the Actions menu, you would open the Color Actions dialog (Actions... Color... all options...) and in the right-hand side set Coloring applies to "atoms/bonds" instead of "all of the above." Clicking to choose a color will then color only the atoms/bonds of the selected residues. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 10, 2011, at 12:18 PM, Zhou, Ming (NIH/NCI) [C] wrote: > Hello, this is Ming Zhou at NCI-Frederick, Maryland. I am trying to use Chimera to make some ribbon structure figures. I am wondering how I can display only side chain (without backbone) for a specific residue. > Usually, if I display the residue, select the residue at the Atom specifier and color it. The color would be partially on the ribbon structure too since the backbone of that residue is on the ribbon. How do I avoid coloring backbone, only color the side chain? > Thank you very much. > Ming From ryonitta at m.u-tokyo.ac.jp Tue May 10 19:42:32 2011 From: ryonitta at m.u-tokyo.ac.jp (=?iso-2022-jp?B?GyRCP05FRBsoQiAbJEJOPBsoQg==?=) Date: Wed, 11 May 2011 11:42:32 +0900 Subject: [Chimera-users] R-factor In-Reply-To: <6DB1449E-0D9D-4B03-9B34-5CA66DB451E2@m.u-tokyo.ac.jp> References: <6DB1449E-0D9D-4B03-9B34-5CA66DB451E2@m.u-tokyo.ac.jp> Message-ID: <9284C2A4-3130-48C3-A409-56FEFB99F301@m.u-tokyo.ac.jp> Hi, Chimera staffs To evaluate the validity of fitting of the atomic model with the EM map, can I calculate the real-space R factor with chimera? Ryo From goddard at sonic.net Wed May 11 09:39:21 2011 From: goddard at sonic.net (Tom Goddard) Date: Wed, 11 May 2011 09:39:21 -0700 Subject: [Chimera-users] R-factor In-Reply-To: <9284C2A4-3130-48C3-A409-56FEFB99F301@m.u-tokyo.ac.jp> References: <6DB1449E-0D9D-4B03-9B34-5CA66DB451E2@m.u-tokyo.ac.jp> <9284C2A4-3130-48C3-A409-56FEFB99F301@m.u-tokyo.ac.jp> Message-ID: <4DCABBB9.2070901@sonic.net> Hi Ryo, Chimera does not calculate the real-space R-factor. The real space R-factor defined for crystallographic maps in Branden C. and Jones A., Nature 343 687-689 (1990) is RSRF = sum(|d_o - d_c|) / sum(|d_o + d_c|) where d_o is the observed (experimental) density d_c is the calculated density from the atomic model. and the sum is over grid points in the d_c map, probably using d_o interpolated values at those exact same points. They also compute RSRF per-residue and I'm not clear what grid points they use in that case -- maybe just the atom center positions. This has some immediate problems when applied to EM maps and fit models. First you need the observed and calculated density maps to have the same normalization. If the experimental density values range from -5000 to 10000 and the calculated ones from 0.001 to 0.01 then obviously you get nonsense. The next problem is that the experimental density values from single-particle EM reconstructions are often negative in parts of the map. You can see from the formula above that can cause havoc. If experimental density at just one grid point is close to being the negative of the calculated density it will make a huge contribution to RSRF. X-ray maps also have many negative density values, but their magnitudes seem to be less. The idea behind RSRF is to judge the fit by looking at the size of difference map values d_o - d_c relative to the size of the values in the observed and calculated maps. The standard cross-correlation coefficient does something very similar and does it better I think. Here's how. Consider the sum of the squares of the residuals over all the grid points and normalize by the sums of squares of the densities in the experimental and calculated maps E = sum((d_o - d_c)**2) / (sqrt(sum(d_o**2)) * sqrt(sum(d_c**2))) This has the same problem described above that the maps may have different normalizations. So put a scale factor f in front of the calculated map d_c E = sum((d_o - f*d_c)**2) / (sqrt(sum(d_o**2)) * sqrt(sum((f*d_c)**2))) and choose the scale factor f so that E is minimized. In other words, we scale the calculated map to minimize the error between experimental and calculated maps. It is easy to show that f = sqrt(sum(d_o**2)) / sqrt(sum(d_c**2)) and then E = 2 * ( 1 - CCC ) where CCC = sum(d_o * d_c) / (sqrt(sum(d_o**2)) * sqrt(sum(d_c**2))) is just the normal cross-correlation coefficient (without mean values being subtracted). So the standard cross-correlation coefficient is a direct and sensible measure of residual error. If you can give me a sound reason why another measure of residual error is useful, I'll be happy to add it to Chimera. Tom > Hi, Chimera staffs > > To evaluate the validity of fitting of the atomic model with the EM map, can I calculate the real-space R factor with chimera? > > Ryo > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From zhouming2 at mail.nih.gov Wed May 11 05:43:58 2011 From: zhouming2 at mail.nih.gov (Zhou, Ming (NIH/NCI) [C]) Date: Wed, 11 May 2011 08:43:58 -0400 Subject: [Chimera-users] color side chain only In-Reply-To: <0B5DE1B5-1FD5-4565-B6B2-34967FA0FA5C@cgl.ucsf.edu> References: <794DFDD3C128EF44AC49ADC58FD0090C030EC3AF01@NIHMLBX10.nih.gov> <0B5DE1B5-1FD5-4565-B6B2-34967FA0FA5C@cgl.ucsf.edu> Message-ID: <794DFDD3C128EF44AC49ADC58FD0090C030EC3AF2C@NIHMLBX10.nih.gov> Thanks, Elaine, I got it. Ming -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Tuesday, May 10, 2011 5:52 PM To: Zhou, Ming (NIH/NCI) [C] Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] color side chain only Hi Ming! If you are using the color command, you would include ",a" right after the color name, no spaces, to color the atoms but not ribbons, surfaces, labels, etc.. For example: color hot pink,a :45.a,55.a,13.b .... would color the atoms only of residues 45 and 55 in chain A and 13 in chain B If you are using the Actions menu, you would open the Color Actions dialog (Actions... Color... all options...) and in the right-hand side set Coloring applies to "atoms/bonds" instead of "all of the above." Clicking to choose a color will then color only the atoms/bonds of the selected residues. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 10, 2011, at 12:18 PM, Zhou, Ming (NIH/NCI) [C] wrote: > Hello, this is Ming Zhou at NCI-Frederick, Maryland. I am trying to use Chimera to make some ribbon structure figures. I am wondering how I can display only side chain (without backbone) for a specific residue. > Usually, if I display the residue, select the residue at the Atom specifier and color it. The color would be partially on the ribbon structure too since the backbone of that residue is on the ribbon. How do I avoid coloring backbone, only color the side chain? > Thank you very much. > Ming From gregc at cgl.ucsf.edu Wed May 11 10:39:10 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 11 May 2011 10:39:10 -0700 Subject: [Chimera-users] System Compatiblility In-Reply-To: References: Message-ID: <4DCAC9BE.5000905@cgl.ucsf.edu> In the Notes column for the Microsoft Windows platform on the Chimera download web page, it says: "Runs on Windows XP, Vista, and 7." And for the 64-bit version, it only says: "Runs on Windows 7." So any (32-bit) Microsoft Windows version of Chimera will work. The most trouble free version should be the latest version, the 1.5.3 release candidate. HTH, Greg On 05/09/2011 10:23 AM, Satterlee, James D wrote: > > Hello, > > I've not yet downloaded or used Chimera, but I am contemplating it. I > am looking for Windows System compatibility information for the > various newer versions of Chimera. To me it wasn't obvious on the > Chimera home site. > > I do not use Window's 7 and I'm wondering which version might be most > trouble-free for a Windows XP version with all service packs installed. > > Thanks, > > Jim Satterlee > > James D. Satterlee > > Professor of Chemistry > > WashingtonState University > > Pullman, WA 99164-4630 > > hemeteam at wsu.edu > > 509.335.8620 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From uzma05 at gmail.com Wed May 11 15:11:59 2011 From: uzma05 at gmail.com (uzma saqib) Date: Wed, 11 May 2011 17:11:59 -0500 Subject: [Chimera-users] constructing a dimer Message-ID: Hello, I want to totally freeze the movement of one protein (which is a homology model) and open another molecule of the same protein, which I want to keep movable, so that I can make a dimer out of this at my chosen place on the first protein molecule. Plz help . thanks uzma -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed May 11 15:59:48 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 May 2011 15:59:48 -0700 Subject: [Chimera-users] constructing a dimer In-Reply-To: References: Message-ID: <3F4FC5DC-119B-4A38-B93D-49E0F6D859F8@cgl.ucsf.edu> Hi Uzma, Open the same file twice. You can control the activation state of each structure (whether it is movable or not) in several ways: - checking/unchecking the "A" (Active) boxes in the Model Panel (under Favorites in the menu) - checking/unchecking the boxes below the Command Line (also under Favorites in the menu) - with the "select" command, e.g. ~select 0 select 0 to freeze/unfreeze model 0. Generally the first structure you open is model 0, the next is model 1, etc. There are also function buttons in the right side of the Model Panel that control model activation. See also this previous post about making dimers: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 11, 2011, at 3:11 PM, uzma saqib wrote: > Hello, > I want to totally freeze the movement of one protein (which is a homology model) and open another molecule of the same protein, which I want to keep movable, so that I can make a dimer out of this at my chosen place on the first protein molecule. > Plz help . > thanks > uzma From ryonitta at m.u-tokyo.ac.jp Wed May 11 18:27:23 2011 From: ryonitta at m.u-tokyo.ac.jp (=?iso-2022-jp?B?GyRCP05FRBsoQiAbJEJOPBsoQg==?=) Date: Thu, 12 May 2011 10:27:23 +0900 Subject: [Chimera-users] R-factor In-Reply-To: <4DCABBB9.2070901@sonic.net> References: <6DB1449E-0D9D-4B03-9B34-5CA66DB451E2@m.u-tokyo.ac.jp> <9284C2A4-3130-48C3-A409-56FEFB99F301@m.u-tokyo.ac.jp> <4DCABBB9.2070901@sonic.net> Message-ID: <6574FA9D-0FBE-425E-AAE8-3AF8C3ACE27B@m.u-tokyo.ac.jp> Hi Tom, Thank you for your quick response. As you suggested, CCC is very efficient to minimize the squares of residuals. Simple rigid body fitting works well with the evaluation by CCC. Recent improvement of the resolution of EM map has allowed us to further refine the fitted atomic model (crystal structure) by dividing it into the several domains or flexible MD fitting. Now I have tried to fit the crystal structure to the EM map, but simple rigid body fitting of 1monomer does not work well. So I divided the monomer into four sub-domains which seem to fit better with the increasing cross-correlation. However, the four domain-fitting fit really better than rigid body monomer fitting? Because increasing the number of parameters must decrease the squares of residuals, the fitting with four parameters (four domain-fitting) must have the lower squares of residuals than that with one parameters (rigid body monomer fitting). I think, therefore, in this type of model fitting, some other criteria or correction might be needed to avoid the over-fitting of the model. (ex. Rfree in crystallography; AIC (Akaike's Information Criterion)...) Do you have any opinion about that? Ryo On 2011/05/12, at 1:39, Tom Goddard wrote: > Hi Ryo, > > Chimera does not calculate the real-space R-factor. The real space R-factor defined for crystallographic maps in > > Branden C. and Jones A., Nature 343 687-689 (1990) > > is > > RSRF = sum(|d_o - d_c|) / sum(|d_o + d_c|) > > where > > d_o is the observed (experimental) density > d_c is the calculated density from the atomic model. > > and the sum is over grid points in the d_c map, probably using d_o interpolated values at those exact same points. They also compute RSRF per-residue and I'm not clear what grid points they use in that case -- maybe just the atom center positions. > > This has some immediate problems when applied to EM maps and fit models. First you need the observed and calculated density maps to have the same normalization. If the experimental density values range from -5000 to 10000 and the calculated ones from 0.001 to 0.01 then obviously you get nonsense. The next problem is that the experimental density values from single-particle EM reconstructions are often negative in parts of the map. You can see from the formula above that can cause havoc. If experimental density at just one grid point is close to being the negative of the calculated density it will make a huge contribution to RSRF. X-ray maps also have many negative density values, but their magnitudes seem to be less. > > The idea behind RSRF is to judge the fit by looking at the size of difference map values d_o - d_c relative to the size of the values in the observed and calculated maps. The standard cross-correlation coefficient does something very similar and does it better I think. Here's how. Consider the sum of the squares of the residuals over all the grid points and normalize by the sums of squares of the densities in the experimental and calculated maps > > E = sum((d_o - d_c)**2) / (sqrt(sum(d_o**2)) * sqrt(sum(d_c**2))) > > This has the same problem described above that the maps may have different normalizations. So put a scale factor f in front of the calculated map d_c > > E = sum((d_o - f*d_c)**2) / (sqrt(sum(d_o**2)) * sqrt(sum((f*d_c)**2))) > > and choose the scale factor f so that E is minimized. In other words, we scale the calculated map to minimize the error between experimental and calculated maps. It is easy to show that > > f = sqrt(sum(d_o**2)) / sqrt(sum(d_c**2)) > > and then > > E = 2 * ( 1 - CCC ) > > where > > CCC = sum(d_o * d_c) / (sqrt(sum(d_o**2)) * sqrt(sum(d_c**2))) > > is just the normal cross-correlation coefficient (without mean values being subtracted). > > So the standard cross-correlation coefficient is a direct and sensible measure of residual error. > > If you can give me a sound reason why another measure of residual error is useful, I'll be happy to add it to Chimera. > > Tom > > >> Hi, Chimera staffs >> >> To evaluate the validity of fitting of the atomic model with the EM map, can I calculate the real-space R factor with chimera? >> >> Ryo >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > From goddard at sonic.net Wed May 11 19:10:25 2011 From: goddard at sonic.net (Tom Goddard) Date: Wed, 11 May 2011 19:10:25 -0700 Subject: [Chimera-users] How to show an icosahedral cage In-Reply-To: <02b801cc1043$e6355590$b2a000b0$@sinica.edu.tw> References: <02b801cc1043$e6355590$b2a000b0$@sinica.edu.tw> Message-ID: <4DCB4191.9030100@sonic.net> Hi Yen-Chywan, The Chimera "hkcage" command makes a cage of pentagons and hexagons to show virus symmetry. For example, open emdbID:1058 hkcage 1 1 radius 170 orient 222r linewidth 4 color blue The hkcage command has options for the lattice parameters for your virus, its radius, what icosahedral coordinate system is being used. Here's the documentation. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscage The meshmol command can make the edges of the cage cylinders instead of lines. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html The HHMI virus viewer Chimera tool is not part of the standard Chimera distribution. It was made for a CD distributed by the Howard Hughes Medical Institute http://wwwtest.cgl.ucsf.edu/Outreach/ViralOutbreak/index.html http://www.hhmi.org/catalog/main?action=product&itemId=366 We don't distribute it separately. Tom > Dear Tom, > > I attend Scripps cryoEM workshop before and meet you there. > > Attach please find a screen capture of a virus. But there is a > icosahedra cage. My question is how to display that cage with my virus > volume? > > I did find it in HHMI virus viewer demo movie. But where can download > this viewer? > > Thanks > > Yen-Chywan > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cage1058.jpg Type: image/jpeg Size: 25096 bytes Desc: not available URL: From goddard at sonic.net Wed May 11 19:56:29 2011 From: goddard at sonic.net (Tom Goddard) Date: Wed, 11 May 2011 19:56:29 -0700 Subject: [Chimera-users] How to show an icosahedral cage In-Reply-To: <4DCB4191.9030100@sonic.net> References: <02b801cc1043$e6355590$b2a000b0$@sinica.edu.tw> <4DCB4191.9030100@sonic.net> Message-ID: <4DCB4C5D.90203@sonic.net> Hi Yen-Chywan, To show a simple icosahedral cage with 12 triangles use the "shape" command. shape icos radius 170 orient 222r mesh true divisions 1 color blue linewidth 4 Here's documentation http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/shape.html#icosahedron Tom > Dear Tom, > > If you look at the attach figure carefully, you will find it is not > hkcage. In the figure it connect all the 5 fold vertex. How can we > generate it? > > Yen-Chywan > Hi Yen-Chywan, > > The Chimera "hkcage" command makes a cage of pentagons and hexagons > to show virus symmetry. For example, > > open emdbID:1058 > hkcage 1 1 radius 170 orient 222r linewidth 4 color blue > > The hkcage command has options for the lattice parameters for your > virus, its radius, what icosahedral coordinate system is being used. > Here's the documentation. > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscage > > The meshmol command can make the edges of the cage cylinders instead > of lines. > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html > > The HHMI virus viewer Chimera tool is not part of the standard Chimera > distribution. It was made for a CD distributed by the Howard Hughes > Medical Institute > > http://wwwtest.cgl.ucsf.edu/Outreach/ViralOutbreak/index.html > http://www.hhmi.org/catalog/main?action=product&itemId=366 > > We don't distribute it separately. > > Tom > >> Dear Tom, >> >> I attend Scripps cryoEM workshop before and meet you there. >> >> Attach please find a screen capture of a virus. But there is a >> icosahedra cage. My question is how to display that cage with my >> virus volume? >> >> I did find it in HHMI virus viewer demo movie. But where can download >> this viewer? >> >> Thanks >> >> Yen-Chywan >> > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: icage1058.jpg Type: image/jpeg Size: 28029 bytes Desc: not available URL: From cheung at lmb.uni-muenchen.de Thu May 12 08:54:41 2011 From: cheung at lmb.uni-muenchen.de (Alan Cheung) Date: Thu, 12 May 2011 17:54:41 +0200 Subject: [Chimera-users] Pseudobonds disappearing during morphing movie Message-ID: Hi there - i'm scripting a complex movie and am having problems with pseudobonds during morphing. Script is pasted at the end. Part of the movie contains a morph between two structures, both of which are missing the same amino acid segment. Loading the two structures show the pseudobond for the missing residues and the resulting morph also contains the same pseudobond. I've been changing the thickness of the pseudobond with : setattr g lineWidth 8 and while the two static structures and the morph in the chimera window have a thicker pseudobond, the resulting movie (encoded to .mov) does not. Am i doing something wrong? Alan p.s. incidentally, when morphing by script, if one includes "nogui true" with the "morph movie" command, pseudobonds aren't kept in the morph at all. A bug? p.p.s. can someone explain to me the difference between "setattr g" and "setattr p"? I've read the manual but i don't understand why only the former seems to work for me. ## movie script open model1.pdb open model2.pdb morph start #0 frames 50 name morph1 method linear morph interpolate #1 name morph1 morph movie name morph1 coordset #2 1,1 setattr g lineWidth 8 ~modeldisplay # movie record supersample 3 directory ~/TEMP/ modeldisplay #2 coordset #2 1,51 ; wait 51 movie stop movie encode output morph1.mov From maznar at merlin.ffn.ub.es Thu May 12 05:32:44 2011 From: maznar at merlin.ffn.ub.es (maznar) Date: Thu, 12 May 2011 14:32:44 +0200 Subject: [Chimera-users] shape factor Message-ID: Hello, We are using Chimera to classify viruses. We use pdb files from viper. We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it? Thank you. From meng at cgl.ucsf.edu Thu May 12 09:25:09 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 12 May 2011 09:25:09 -0700 Subject: [Chimera-users] Pseudobonds disappearing during morphing movie In-Reply-To: References: Message-ID: Hi Alan, I haven't tried the whole script yet (can you send me the PDB files? I'll keep them private, i.e. only for the development group here if you send them just to me) but will try to address the low-hanging fruit in your set of questions: (A) lines thinner in saved movie. In general, lines such as silhouette edges and pseudobonds may turn out thinner in saved images and movies when you are doing "supersampling," which initially saves a larger image and samples it down to the final requested size. You can check if this is the issue by using File... Save Image to save a single image -- the dialog should report the maximum achievable linewidth given the requested size and amount of supersampling. The reason is that there is an upper limit to how fat your computer can draw the lines (at least via the method used by Chimera). If you have 2x2 supersampling, for example, Chimera will try to make the lines twice as fat in the initial larger image, but may run into this upper limit. Then when the image is sampled down to the final size, the lines may not be as thick as they appear in the interactive display. You could try using lower supersampling. Also make sure you are using a recent version (1.5.3 candidate or 1.6) because there was a lines-too-thin-in-images bug a couple of months ago. (B) setattr "p" vs. "g" -- this is because some attributes are for individual pseudobonds (p) and some attributes are defined for whole pseudobond groups (g). Individual pseudobonds don't have a linewidth attribute, it is set at the group level. All the pseudobonds in that group (for example, hydrogen bonds) would get the same linewidth and it is not possible to make different ones in the same group have different widths. If you are looking at the Selection Inspector or some other attributes inspector, it will show you which attributes are for individual pseudobonds and which are for groups. The balloon help will give the attribute name and allowed values. I will try to look at your other issues and get back to you, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 12, 2011, at 8:54 AM, Alan Cheung wrote: > Hi there - i'm scripting a complex movie and am having problems with > pseudobonds during morphing. Script is pasted at the end. > > Part of the movie contains a morph between two structures, both of > which are missing the same amino acid segment. Loading the two > structures show the pseudobond for the missing residues and the > resulting morph also contains the same pseudobond. > > I've been changing the thickness of the pseudobond with : > > setattr g lineWidth 8 > > and while the two static structures and the morph in the chimera > window have a thicker pseudobond, the resulting movie (encoded to > .mov) does not. Am i doing something wrong? > > Alan > > p.s. incidentally, when morphing by script, if one includes "nogui > true" with the "morph movie" command, pseudobonds aren't kept in the > morph at all. A bug? > p.p.s. can someone explain to me the difference between "setattr g" > and "setattr p"? I've read the manual but i don't understand why only > the former seems to work for me. > > ## movie script > > open model1.pdb > open model2.pdb > morph start #0 frames 50 name morph1 method linear > morph interpolate #1 name morph1 > morph movie name morph1 > coordset #2 1,1 > setattr g lineWidth 8 > ~modeldisplay # > > movie record supersample 3 directory ~/TEMP/ > modeldisplay #2 > coordset #2 1,51 ; wait 51 > movie stop > movie encode output morph1.mov From goddard at sonic.net Thu May 12 09:31:25 2011 From: goddard at sonic.net (Tom Goddard) Date: Thu, 12 May 2011 09:31:25 -0700 Subject: [Chimera-users] shape factor In-Reply-To: References: Message-ID: <4DCC0B5D.6060304@sonic.net> I don't understand what you want to do. Here is an example of using the hkcage command http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscage You will want to add a radius option (e.g. radius 330 for 330 Angstrom radius cage) to that example and you will need to figure out the h and k lattice parameters. Chimera cannot figure out the h,k values you need. I usually try a few values by hand and visually determine the correct values. When you say "shape factor" I guess you probably mean "sphere factor", the Chimera term for the radial interpolation factor (0 to 1) between a flat faced icosahedron and a sphere. Chimera has no way to automatically determine that value. I sometimes judge that by eye using the Icosahedron Surface dialog, menu entry Tools / Higher-Order Structure / Icosahedron Surface That dialog has sliders to adjust the radius of the icosahedron and the "sphere factor" so you can interactively try different values. It would be nice if Chimera could automatically determine the icosahedral coordinate system, outer radius, and best sphere factor, but currently that is only done by eye. Tom > > Hello, > > We are using Chimera to classify viruses. We use pdb files from viper. > > We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it? > > Thank you. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Thu May 12 10:22:34 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 12 May 2011 10:22:34 -0700 Subject: [Chimera-users] Pseudobonds disappearing during morphing movie In-Reply-To: References: Message-ID: <87B693F5-BD4D-4B88-AFE9-3F01C6A70FFA@cgl.ucsf.edu> Hi Alan, Never mind about the PDBs, I made up my own by deleting parts of the structures in my favorite morph test case. I think I answered all of your issues except for the pseudobonds completely disappearing with "morph movie nogui true" -- I did reproduce that problem, and it seems like a bug, albeit mysterious. I'll file a report about that one, but in the meanwhile I hope you will be able to manage without using that option. One minor thing is that I generally recommend adding a few more wait frames to the recording after the morph plays, to avoid any "motion blur" effect at the end you might get as a result of encoding. I didn't see much of that effect in my test case proteins using your script, however. It may be because the morph is spread out over 50 frames so there is less differences between adjacent frames, but I was also using different PDBs than you. Best, Elaine On May 12, 2011, at 9:25 AM, Elaine Meng wrote: > Hi Alan, > I haven't tried the whole script yet (can you send me the PDB files? I'll keep them private, i.e. only for the development group here if you send them just to me) but will try to address the low-hanging fruit in your set of questions: > > (A) lines thinner in saved movie. In general, lines such as silhouette edges and pseudobonds may turn out thinner in saved images and movies when you are doing "supersampling," which initially saves a larger image and samples it down to the final requested size. You can check if this is the issue by using File... Save Image to save a single image -- the dialog should report the maximum achievable linewidth given the requested size and amount of supersampling. The reason is that there is an upper limit to how fat your computer can draw the lines (at least via the method used by Chimera). If you have 2x2 supersampling, for example, Chimera will try to make the lines twice as fat in the initial larger image, but may run into this upper limit. Then when the image is sampled down to the final size, the lines may not be as thick as they appear in the interactive display. You could try using lower supersampling. Also make sure you are using a recent version (1.5.3 candidate ! > or 1.6) because there was a lines-too-thin-in-images bug a couple of months ago. > > (B) setattr "p" vs. "g" -- this is because some attributes are for individual pseudobonds (p) and some attributes are defined for whole pseudobond groups (g). Individual pseudobonds don't have a linewidth attribute, it is set at the group level. All the pseudobonds in that group (for example, hydrogen bonds) would get the same linewidth and it is not possible to make different ones in the same group have different widths. If you are looking at the Selection Inspector or some other attributes inspector, it will show you which attributes are for individual pseudobonds and which are for groups. The balloon help will give the attribute name and allowed values. > > > I will try to look at your other issues and get back to you, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On May 12, 2011, at 8:54 AM, Alan Cheung wrote: > >> Hi there - i'm scripting a complex movie and am having problems with >> pseudobonds during morphing. Script is pasted at the end. >> >> Part of the movie contains a morph between two structures, both of >> which are missing the same amino acid segment. Loading the two >> structures show the pseudobond for the missing residues and the >> resulting morph also contains the same pseudobond. >> >> I've been changing the thickness of the pseudobond with : >> >> setattr g lineWidth 8 >> >> and while the two static structures and the morph in the chimera >> window have a thicker pseudobond, the resulting movie (encoded to >> .mov) does not. Am i doing something wrong? >> >> Alan >> >> p.s. incidentally, when morphing by script, if one includes "nogui >> true" with the "morph movie" command, pseudobonds aren't kept in the >> morph at all. A bug? >> p.p.s. can someone explain to me the difference between "setattr g" >> and "setattr p"? I've read the manual but i don't understand why only >> the former seems to work for me. >> >> ## movie script >> >> open model1.pdb >> open model2.pdb >> morph start #0 frames 50 name morph1 method linear >> morph interpolate #1 name morph1 >> morph movie name morph1 >> coordset #2 1,1 >> setattr g lineWidth 8 >> ~modeldisplay # >> >> movie record supersample 3 directory ~/TEMP/ >> modeldisplay #2 >> coordset #2 1,51 ; wait 51 >> movie stop >> movie encode output morph1.mov > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Thu May 12 10:29:45 2011 From: goddard at sonic.net (Tom Goddard) Date: Thu, 12 May 2011 10:29:45 -0700 Subject: [Chimera-users] R-factor In-Reply-To: <6574FA9D-0FBE-425E-AAE8-3AF8C3ACE27B@m.u-tokyo.ac.jp> References: <6DB1449E-0D9D-4B03-9B34-5CA66DB451E2@m.u-tokyo.ac.jp> <9284C2A4-3130-48C3-A409-56FEFB99F301@m.u-tokyo.ac.jp> <4DCABBB9.2070901@sonic.net> <6574FA9D-0FBE-425E-AAE8-3AF8C3ACE27B@m.u-tokyo.ac.jp> Message-ID: <4DCC1909.4080603@sonic.net> Hi Ryo, Adding more parameters to your atomic model will improve the fit to the map, but it may give an answer further from the truth. I don't have suggestions about how to evaluate this. At a crude level if my map only has N bits of information I probably should not fit with more than N bits of parameters. Perhaps there is a way to evaluate that. But I don't think it is the major source of getting a wrong model. I suspect the main problem is that the parameters you choose (e.g. your 4 domains) may be bad parameters -- the molecule doesn't really have the flexibility defined by those parameters. Tom > Hi Tom, > > Thank you for your quick response. > As you suggested, CCC is very efficient to minimize the squares of residuals. > Simple rigid body fitting works well with the evaluation by CCC. > > Recent improvement of the resolution of EM map has allowed us to further refine the fitted atomic model (crystal structure) by dividing it into the several domains or flexible MD fitting. > Now I have tried to fit the crystal structure to the EM map, but simple rigid body fitting of 1monomer does not work well. So I divided the monomer into four sub-domains which seem to fit better with the increasing cross-correlation. > However, the four domain-fitting fit really better than rigid body monomer fitting? > Because increasing the number of parameters must decrease the squares of residuals, the fitting with four parameters (four domain-fitting) must have the lower squares of residuals than that with one parameters (rigid body monomer fitting). > I think, therefore, in this type of model fitting, some other criteria or correction might be needed to avoid the over-fitting of the model. (ex. Rfree in crystallography; AIC (Akaike's Information Criterion)...) > > Do you have any opinion about that? > > Ryo > > On 2011/05/12, at 1:39, Tom Goddard wrote: > >> Hi Ryo, >> >> Chimera does not calculate the real-space R-factor. The real space R-factor defined for crystallographic maps in >> >> Branden C. and Jones A., Nature 343 687-689 (1990) >> >> is >> >> RSRF = sum(|d_o - d_c|) / sum(|d_o + d_c|) >> >> where >> >> d_o is the observed (experimental) density >> d_c is the calculated density from the atomic model. >> >> and the sum is over grid points in the d_c map, probably using d_o interpolated values at those exact same points. They also compute RSRF per-residue and I'm not clear what grid points they use in that case -- maybe just the atom center positions. >> >> This has some immediate problems when applied to EM maps and fit models. First you need the observed and calculated density maps to have the same normalization. If the experimental density values range from -5000 to 10000 and the calculated ones from 0.001 to 0.01 then obviously you get nonsense. The next problem is that the experimental density values from single-particle EM reconstructions are often negative in parts of the map. You can see from the formula above that can cause havoc. If experimental density at just one grid point is close to being the negative of the calculated density it will make a huge contribution to RSRF. X-ray maps also have many negative density values, but their magnitudes seem to be less. >> >> The idea behind RSRF is to judge the fit by looking at the size of difference map values d_o - d_c relative to the size of the values in the observed and calculated maps. The standard cross-correlation coefficient does something very similar and does it better I think. Here's how. Consider the sum of the squares of the residuals over all the grid points and normalize by the sums of squares of the densities in the experimental and calculated maps >> >> E = sum((d_o - d_c)**2) / (sqrt(sum(d_o**2)) * sqrt(sum(d_c**2))) >> >> This has the same problem described above that the maps may have different normalizations. So put a scale factor f in front of the calculated map d_c >> >> E = sum((d_o - f*d_c)**2) / (sqrt(sum(d_o**2)) * sqrt(sum((f*d_c)**2))) >> >> and choose the scale factor f so that E is minimized. In other words, we scale the calculated map to minimize the error between experimental and calculated maps. It is easy to show that >> >> f = sqrt(sum(d_o**2)) / sqrt(sum(d_c**2)) >> >> and then >> >> E = 2 * ( 1 - CCC ) >> >> where >> >> CCC = sum(d_o * d_c) / (sqrt(sum(d_o**2)) * sqrt(sum(d_c**2))) >> >> is just the normal cross-correlation coefficient (without mean values being subtracted). >> >> So the standard cross-correlation coefficient is a direct and sensible measure of residual error. >> >> If you can give me a sound reason why another measure of residual error is useful, I'll be happy to add it to Chimera. >> >> Tom >> >> >>> Hi, Chimera staffs >>> >>> To evaluate the validity of fitting of the atomic model with the EM map, can I calculate the real-space R factor with chimera? >>> >>> Ryo >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Thu May 12 11:44:58 2011 From: goddard at sonic.net (Tom Goddard) Date: Thu, 12 May 2011 11:44:58 -0700 Subject: [Chimera-users] shape factor In-Reply-To: References: Message-ID: <4DCC2AAA.8080004@sonic.net> Here is a video showing how to display an icosahedral cage for a virus density map using the hkcage command. http://www.cgl.ucsf.edu/chimera/videodoc/cage/ Tom > > Hello, > > We are using Chimera to classify viruses. We use pdb files from viper. > > We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it? > > Thank you. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From ryonitta at m.u-tokyo.ac.jp Thu May 12 18:19:09 2011 From: ryonitta at m.u-tokyo.ac.jp (=?iso-2022-jp?B?GyRCP05FRBsoQiAbJEJOPBsoQg==?=) Date: Fri, 13 May 2011 10:19:09 +0900 Subject: [Chimera-users] R-factor In-Reply-To: <4DCC1909.4080603@sonic.net> References: <6DB1449E-0D9D-4B03-9B34-5CA66DB451E2@m.u-tokyo.ac.jp> <9284C2A4-3130-48C3-A409-56FEFB99F301@m.u-tokyo.ac.jp> <4DCABBB9.2070901@sonic.net> <6574FA9D-0FBE-425E-AAE8-3AF8C3ACE27B@m.u-tokyo.ac.jp> <4DCC1909.4080603@sonic.net> Message-ID: Hi Tom, Thank you for your response. I'm sorry, I cannot get your true meaning, but If my interpretation is correct, you disallow the multi-domain fitting or flexible fitting of atomic models to the EM maps? In my case, two crystal structures were already reported and inter-domain movement between 4 sub-domains were truly observed. However, since both crystal structures could not be fitted well into my EM map, I divided them into 4 sub-domains which separately, rigidly fitted to my EM map and finally got a good fit with my EM map (fit in map tool with CCC). I fitted two type of crystal structures independently and got same results, suggesting that my model might be close to the truth. In fact, each density contributing to 15 helices which can be clearly, separately observed in my EM map fits well with the helices of atomic model. In your words, my EM map clearly separates the densities of 4 sub-domains so that my map has at least 4 bits of information. Furthermore, since my EM map clearly separates 15 densities of helices, my map has 15 bits of information in this term. Thus, we can choice the numbers of parameters from 1 to 15. 1 means rigid body fit of atomic model itself. 15 means 15 helices divided from atomic model separately, rigidly fit into EM map. My question is the fitting of models from 1 to 15 parameters can be simply evaluated by squares of residuals or CCC because increasing parameters always decreases squares of residuals? Ryo On 2011/05/13, at 2:29, Tom Goddard wrote: > Hi Ryo, > > Adding more parameters to your atomic model will improve the fit to the map, but it may give an answer further from the truth. I don't have suggestions about how to evaluate this. At a crude level if my map only has N bits of information I probably should not fit with more than N bits of parameters. Perhaps there is a way to evaluate that. But I don't think it is the major source of getting a wrong model. I suspect the main problem is that the parameters you choose (e.g. your 4 domains) may be bad parameters -- the molecule doesn't really have the flexibility defined by those parameters. > > Tom > >> Hi Tom, >> >> Thank you for your quick response. >> As you suggested, CCC is very efficient to minimize the squares of residuals. >> Simple rigid body fitting works well with the evaluation by CCC. >> >> Recent improvement of the resolution of EM map has allowed us to further refine the fitted atomic model (crystal structure) by dividing it into the several domains or flexible MD fitting. >> Now I have tried to fit the crystal structure to the EM map, but simple rigid body fitting of 1monomer does not work well. So I divided the monomer into four sub-domains which seem to fit better with the increasing cross-correlation. >> However, the four domain-fitting fit really better than rigid body monomer fitting? >> Because increasing the number of parameters must decrease the squares of residuals, the fitting with four parameters (four domain-fitting) must have the lower squares of residuals than that with one parameters (rigid body monomer fitting). >> I think, therefore, in this type of model fitting, some other criteria or correction might be needed to avoid the over-fitting of the model. (ex. Rfree in crystallography; AIC (Akaike's Information Criterion)...) >> >> Do you have any opinion about that? >> >> Ryo >> >> On 2011/05/12, at 1:39, Tom Goddard wrote: >> >>> Hi Ryo, >>> >>> Chimera does not calculate the real-space R-factor. The real space R-factor defined for crystallographic maps in >>> >>> Branden C. and Jones A., Nature 343 687-689 (1990) >>> >>> is >>> >>> RSRF = sum(|d_o - d_c|) / sum(|d_o + d_c|) >>> >>> where >>> >>> d_o is the observed (experimental) density >>> d_c is the calculated density from the atomic model. >>> >>> and the sum is over grid points in the d_c map, probably using d_o interpolated values at those exact same points. They also compute RSRF per-residue and I'm not clear what grid points they use in that case -- maybe just the atom center positions. >>> >>> This has some immediate problems when applied to EM maps and fit models. First you need the observed and calculated density maps to have the same normalization. If the experimental density values range from -5000 to 10000 and the calculated ones from 0.001 to 0.01 then obviously you get nonsense. The next problem is that the experimental density values from single-particle EM reconstructions are often negative in parts of the map. You can see from the formula above that can cause havoc. If experimental density at just one grid point is close to being the negative of the calculated density it will make a huge contribution to RSRF. X-ray maps also have many negative density values, but their magnitudes seem to be less. >>> >>> The idea behind RSRF is to judge the fit by looking at the size of difference map values d_o - d_c relative to the size of the values in the observed and calculated maps. The standard cross-correlation coefficient does something very similar and does it better I think. Here's how. Consider the sum of the squares of the residuals over all the grid points and normalize by the sums of squares of the densities in the experimental and calculated maps >>> >>> E = sum((d_o - d_c)**2) / (sqrt(sum(d_o**2)) * sqrt(sum(d_c**2))) >>> >>> This has the same problem described above that the maps may have different normalizations. So put a scale factor f in front of the calculated map d_c >>> >>> E = sum((d_o - f*d_c)**2) / (sqrt(sum(d_o**2)) * sqrt(sum((f*d_c)**2))) >>> >>> and choose the scale factor f so that E is minimized. In other words, we scale the calculated map to minimize the error between experimental and calculated maps. It is easy to show that >>> >>> f = sqrt(sum(d_o**2)) / sqrt(sum(d_c**2)) >>> >>> and then >>> >>> E = 2 * ( 1 - CCC ) >>> >>> where >>> >>> CCC = sum(d_o * d_c) / (sqrt(sum(d_o**2)) * sqrt(sum(d_c**2))) >>> >>> is just the normal cross-correlation coefficient (without mean values being subtracted). >>> >>> So the standard cross-correlation coefficient is a direct and sensible measure of residual error. >>> >>> If you can give me a sound reason why another measure of residual error is useful, I'll be happy to add it to Chimera. >>> >>> Tom >>> >>> >>>> Hi, Chimera staffs >>>> >>>> To evaluate the validity of fitting of the atomic model with the EM map, can I calculate the real-space R factor with chimera? >>>> >>>> Ryo >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users at cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > From dhirajks at gmail.com Thu May 12 19:25:35 2011 From: dhirajks at gmail.com (Dhiraj Srivastava) Date: Thu, 12 May 2011 21:25:35 -0500 Subject: [Chimera-users] rigid body rotation of subunit Message-ID: Hi I have the structure of two homologous protein. These proteins are dimeric. when I am superimposing chain A of one protein on to the chain A of other, it looks like chain B of one protein is related to chain B of other protein by rigid body rotation. How can I calculate the angle of rotation in chimera? Is there any way, I can draw a vector along beta sheet? Thank you. Dhiraj -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri May 13 10:56:50 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 13 May 2011 10:56:50 -0700 Subject: [Chimera-users] rigid body rotation of subunit In-Reply-To: References: Message-ID: <5CA2F211-BB4A-4CDF-8B93-E633D74221CC@cgl.ucsf.edu> Dear Dhiraj, With Chimera, you can define an axis or a plane from any set of atoms, and measure the angles it makes with other axes and planes. One way is with the Axes/Planes/Centroids tool (under Tools... Structure Analysis in the menu). Axes are shown with cylinders, planes with thin disks. You can also create the objects with the "define" command and measure their angles with the "angle" command. It sounds like you may be able to define the orientation of chain B using its beta sheet, which could be represented by a plane. In the Axes/Planes/Centroids tool, click Define plane... then in the main Chimera interface select the atoms you want to use to define the plane, then click OK or Apply. The details of how you would select the atoms depend on the structure, and there are usually several ways (with the Select menu, the Sequence tool, the command "select" with specific residue ranges, the mouse in the graphics window etc.) You might try using different subsets of atoms in one copy of chain B to define planes and then decide (by looking at the planes) which gives a reasonable description of the domain orientation. It might be all atoms of the beta sheet, or just the alpha-carbons, or only the central two or three strands of the sheet. Then define a plane using the same set of atoms in the other copy of B, then measure the angle between the two planes of interest by choosing the corresponding two rows in the Axes/Planes/Centroids dialog. Another way is to use the accelerator "ai" (command "ac ai"), but that requires the parts being compared to have exactly the same sequence, numbering, and chain ID, and provides less control over exactly which atoms are used in the calculation: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 12, 2011, at 7:25 PM, Dhiraj Srivastava wrote: > Hi > I have the structure of two homologous protein. These proteins are dimeric. when I am superimposing chain A of one protein on to the chain A of other, it looks like chain B of one protein is related to chain B of other protein by rigid body rotation. How can I calculate the angle of rotation in chimera? Is there any way, I can draw a vector along beta sheet? > Thank you. > Dhiraj > From goddard at sonic.net Fri May 13 12:09:05 2011 From: goddard at sonic.net (Tom Goddard) Date: Fri, 13 May 2011 12:09:05 -0700 Subject: [Chimera-users] shape factor In-Reply-To: <4DCC0B5D.6060304@sonic.net> References: <4DCC0B5D.6060304@sonic.net> Message-ID: <4DCD81D1.8020208@sonic.net> Hi Maria, If you mean you want to create a map that is all ones inside a surface, for example inside an icosahedron, I just today made the Chimera "mask" command able to do that. shape icosahedron radius 160 mask ones #0 spacing 3.5 border 20 You would need to get tonight's Chimera daily build to use the "mask ones" capability. Tom > The video has been useful for me, thank you. > > Other question: the "meshmol" command creates a molecule model from a surface, there are a command to create a map from a surface? > > Thank, Mar?a. -------- Original Message -------- Subject: Re: [Chimera-users] shape factor From: Tom Goddard Date: 5/12/11 9:31 AM > I don't understand what you want to do. Here is an example of using the > hkcage command > > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscage > > You will want to add a radius option (e.g. radius 330 for 330 Angstrom > radius cage) to that example and you will need to figure out the h and k > lattice parameters. Chimera cannot figure out the h,k values you need. > I usually try a few values by hand and visually determine the correct > values. When you say "shape factor" I guess you probably mean "sphere > factor", the Chimera term for the radial interpolation factor (0 to 1) > between a flat faced icosahedron and a sphere. Chimera has no way to > automatically determine that value. I sometimes judge that by eye using > the Icosahedron Surface dialog, menu entry > > Tools / Higher-Order Structure / Icosahedron Surface > > That dialog has sliders to adjust the radius of the icosahedron and the > "sphere factor" so you can interactively try different values. > > It would be nice if Chimera could automatically determine the > icosahedral coordinate system, outer radius, and best sphere factor, but > currently that is only done by eye. > > Tom > >> Hello, >> >> We are using Chimera to classify viruses. We use pdb files from viper. >> >> We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it? >> >> Thank you. >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Fri May 13 12:34:44 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 13 May 2011 12:34:44 -0700 Subject: [Chimera-users] Pseudobonds disappearing during morphing movie In-Reply-To: <4DCD2DAF.9060208@lmb.uni-muenchen.de> References: <87B693F5-BD4D-4B88-AFE9-3F01C6A70FFA@cgl.ucsf.edu> <4DCD2DAF.9060208@lmb.uni-muenchen.de> Message-ID: Hi Alan, Sorry, there isn't currently a command to apply residue class, only scaling (ribscale) and style (ribrepr): Some possibilities: - save session with morph already calculated and residue class applied. Your script would then restore the session, play the trajectory, and record the movie. I agree this is not as nice, since then you are saving two files instead of one, and the session file is large. You wouldn't have to wait for the morph to recalculate, however. - use a small python script to apply the residue class. Your Chimera script could open that python file, which automatically executes it. One of the other developers would have to supply the python (beyond my skill set, sorry), and that also requires having two files, albeit much smaller than a session file. In general when playing a morph with ribbons that show secondary structure, consider whether you need to recalculate the secondary structure assignments with "ksdssp" at each frame. To execute a set of commands at each frame, one would use the "perframe" command in combination with "alias": For example, your script could contain something like: alias ^redefine ksdssp #2 perframe redefine movie record coordset #2 1,21; wait 21; ~perframe I hadn't used ksdssp/perframe in my examples since (perhaps fortuitously) the secondary structure didn't change that much. If you are just displaying a tube or licorice which doesn't show secondary structure with different widths, it doesn't matter, however. You're right that the shape tube surface will not automatically morph along with the structures, but it might work to destroy/recreate it at each coordinate frame using "perframe". Interesting idea... I haven't tried it, though! I hope this helps, Elaine On May 13, 2011, at 6:10 AM, Alan Cheung wrote: > Thanks Elaine! Yes, the reported thickness was 3.333 (pixels?) and that seems to match the width of the pseudobond i see on the video. The width isn't too bad, and i can live with it. > > Thanks for the explanations and tip too. > > One last question : can I apply a saved residue class (from the ribbon style editor) via a command? I'm morphing a mixture of ribbon and side chain atoms and (for a leucine residue) the CA-CB bond is unrealistically long, but seems ok if i remove the orientation atom (O) from the residue class. I saw the "shape tube" feature in the documentation that draws a tube through CA atoms, but i guessed it's not morphable (and might also not include my precious pseudobond ;) ) > > Many thanks again for the quick replies! > > Alan > > On 12/05/2011 19:22, Elaine Meng wrote: >> Hi Alan, >> Never mind about the PDBs, I made up my own by deleting parts of the structures in my favorite morph test case. >> >> I think I answered all of your issues except for the pseudobonds completely disappearing with "morph movie nogui true" -- I did reproduce that problem, and it seems like a bug, albeit mysterious. I'll file a report about that one, but in the meanwhile I hope you will be able to manage without using that option. >> >> One minor thing is that I generally recommend adding a few more wait frames to the recording after the morph plays, to avoid any "motion blur" effect at the end you might get as a result of encoding. I didn't see much of that effect in my test case proteins using your script, however. It may be because the morph is spread out over 50 frames so there is less differences between adjacent frames, but I was also using different PDBs than you. >> Best, >> Elaine >> >> On May 12, 2011, at 9:25 AM, Elaine Meng wrote: >> >>> Hi Alan, >>> I haven't tried the whole script yet (can you send me the PDB files? I'll keep them private, i.e. only for the development group here if you send them just to me) but will try to address the low-hanging fruit in your set of questions: >>> >>> (A) lines thinner in saved movie. In general, lines such as silhouette edges and pseudobonds may turn out thinner in saved images and movies when you are doing "supersampling," which initially saves a larger image and samples it down to the final requested size. You can check if this is the issue by using File... Save Image to save a single image -- the dialog should report the maximum achievable linewidth given the requested size and amount of supersampling. The reason is that there is an upper limit to how fat your computer can draw the lines (at least via the method used by Chimera). If you have 2x2 supersampling, for example, Chimera will try to make the lines twice as fat in the initial larger image, but may run into this upper limit. Then when the image is sampled down to the final size, the lines may not be as thick as they appear in the interactive display. You could try using lower supersampling. Also make sure you are using a recent version (1.5.3 candida > te ! >>> or 1.6) because there was a lines-too-thin-in-images bug a couple of months ago. >>> >>> (B) setattr "p" vs. "g" -- this is because some attributes are for individual pseudobonds (p) and some attributes are defined for whole pseudobond groups (g). Individual pseudobonds don't have a linewidth attribute, it is set at the group level. All the pseudobonds in that group (for example, hydrogen bonds) would get the same linewidth and it is not possible to make different ones in the same group have different widths. If you are looking at the Selection Inspector or some other attributes inspector, it will show you which attributes are for individual pseudobonds and which are for groups. The balloon help will give the attribute name and allowed values. >>> >>> >>> I will try to look at your other issues and get back to you, >>> Elaine >>> ---------- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> On May 12, 2011, at 8:54 AM, Alan Cheung wrote: >>> >>>> Hi there - i'm scripting a complex movie and am having problems with >>>> pseudobonds during morphing. Script is pasted at the end. >>>> >>>> Part of the movie contains a morph between two structures, both of >>>> which are missing the same amino acid segment. Loading the two >>>> structures show the pseudobond for the missing residues and the >>>> resulting morph also contains the same pseudobond. >>>> >>>> I've been changing the thickness of the pseudobond with : >>>> >>>> setattr g lineWidth 8 >>>> >>>> and while the two static structures and the morph in the chimera >>>> window have a thicker pseudobond, the resulting movie (encoded to >>>> .mov) does not. Am i doing something wrong? >>>> >>>> Alan >>>> >>>> p.s. incidentally, when morphing by script, if one includes "nogui >>>> true" with the "morph movie" command, pseudobonds aren't kept in the >>>> morph at all. A bug? >>>> p.p.s. can someone explain to me the difference between "setattr g" >>>> and "setattr p"? I've read the manual but i don't understand why only >>>> the former seems to work for me. >>>> >>>> ## movie script >>>> >>>> open model1.pdb >>>> open model2.pdb >>>> morph start #0 frames 50 name morph1 method linear >>>> morph interpolate #1 name morph1 >>>> morph movie name morph1 >>>> coordset #2 1,1 >>>> setattr g lineWidth 8 >>>> ~modeldisplay # >>>> >>>> movie record supersample 3 directory ~/TEMP/ >>>> modeldisplay #2 >>>> coordset #2 1,51 ; wait 51 >>>> movie stop >>>> movie encode output morph1.mov >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > -- > Alan Cheung > Gene Center > Ludwig-Maximilians-University > Feodor-Lynen-Str. 25 > 81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76999 > E-mail: cheung at lmb.uni-muenchen.de From goddard at sonic.net Fri May 13 13:08:35 2011 From: goddard at sonic.net (Tom Goddard) Date: Fri, 13 May 2011 13:08:35 -0700 Subject: [Chimera-users] rigid body rotation of subunit In-Reply-To: References: Message-ID: <4DCD8FC3.9080408@sonic.net> Hi Dhiraj, You can measure domain rotation using the MatchMaker tool to make the needed alignments, and the "measure rotation" command. Here's a video showing the procedure for HIV capsid protein. http://www.cgl.ucsf.edu/chimera/videodoc/AlignDomains Tom > Hi > I have the structure of two homologous protein. These proteins are > dimeric. when I am superimposing chain A of one protein on to the > chain A of other, it looks like chain B of one protein is related to > chain B of other protein by rigid body rotation. How can I calculate > the angle of rotation in chimera? Is there any way, I can draw a > vector along beta sheet? > > Thank you. > Dhiraj > From danielgurnon at depauw.edu Sun May 15 10:56:44 2011 From: danielgurnon at depauw.edu (Daniel Gurnon) Date: Sun, 15 May 2011 13:56:44 -0400 Subject: [Chimera-users] labeling residues Message-ID: Hi all, A student of mine wants to make a wire sculpture of a protein, and I'm thinking of ways Chimera could make the task easier. Ideally, I would create a script that would display any protein in wire-form, with residue positions clearly and unobtrusively labeled. I'd like to use the command line to display a backbone as a licorice ribbon with residue numbers and 1-letter codes at the alpha carbon of each residue. so starting out, I would use: ribscale licorice; ribbackbone; rlabel @ca; But instead of "ALA 24.B", I want "A 24". Though I can get what I want using the Actions menu, I can't find a way to create custom rlabels via the command line. Is there a way to do this? If possible, I would also like to position each label near the spot on the ribbon closest to the alpha carbon (the "primary atom"). I can see how to do this with the molecule attributes panel, but I'm having difficulty setting the placement through the command line. And while I'm at it...is there a way to color a spot on the ribbon closest to the alpha carbon a different color than the rest of the ribbon? Thanks for the help! Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon at depauw.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 101845 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon May 16 09:55:06 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 May 2011 09:55:06 -0700 Subject: [Chimera-users] labeling residues In-Reply-To: References: Message-ID: Hi Dan, You'd probably also want to undisplay atoms/bonds, so something like ~disp; ribbon; ribsc licorice (A) label positioning. You could either use residue labels with "primary atom" positioning or atom labels at CA showing residue info, i.e. : rlabel; setattr m residueLabelPos 2 - OR - disp @ca; labelopt info residue; la @ca (the balloon help on the attributes panel gives the attribute name and its allowed values for use with "setattr," and "m" indicates it is an attribute of molecule models). Even though you might expect "centroid" residue label positioning to be the same as "primary atom" when only the CA is displayed, it is different because the latter includes an offset. (B) custom label content. I don't think it can be done with Chimera commands, but the Chimera command file could open a python snippet. Somebody else would need to give the exact code for what you describe, but this previous message gives something similar for custom residue labeling: (C) color ribbon near CA. I believe you can only color the segment representing the whole residue. I don't think there is any way to color a shorter segment of ribbon than that. An alternative, however, is to abandon ribbons entirely and make a tubular surface that follows the path of the backbone instead. This allows coloring a narrow band of tube and has the added advantage of following the true locations of the atoms instead of making a smooth interpolation like the ribbon. More details here: ... but briefly, something like: ~ribbon; rainbow shape tube :.a at ca radius 0.35 bandLength 2 modelId 1 ... where I just used rainbow to color the invisible alpha-carbons so you can see the colored bands on the resulting tube. The above only makes a tube for chain a (:.a). If there are multiple chains, you'd want to do them separately, or else the tube would connect the end of one to the beginning of the next. modelId is the model number for the resulting output surface. To label alpha-carbons, you would need to display them along with the tube but turn off auto-chaining so that Chimera won't draw straight lines between them: disp @ca; setattr m autochain 0 So, if you went with the tube approach your overall script could be something like open 4hhb ~ribbon; show @ca; setattr m autochain 0 rlabel; setattr m residueLabelPos 2 # open python file for custom labeling, not incl here # color alpha-carbons as you like: rainbow shape tube :.a at ca radius 0.35 bandLength 2 modelId 1 shape tube :.b at ca radius 0.35 bandLength 2 modelId 2 shape tube :.c at ca radius 0.35 bandLength 2 modelId 3 shape tube :.d at ca radius 0.35 bandLength 2 modelId 4 Image attached. You may want to take a look at the tube options and try different values: 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: tube.png Type: image/png Size: 62031 bytes Desc: not available URL: -------------- next part -------------- On May 15, 2011, at 10:56 AM, Daniel Gurnon wrote: > Hi all, > A student of mine wants to make a wire sculpture of a protein, and I'm thinking of ways Chimera could make the task easier. Ideally, I would create a script that would display any protein in wire-form, with residue positions clearly and unobtrusively labeled. > > I'd like to use the command line to display a backbone as a licorice ribbon with residue numbers and 1-letter codes at the alpha carbon of each residue. > so starting out, I would use: > ribscale licorice; ribbackbone; rlabel @ca; > > But instead of "ALA 24.B", I want "A 24". Though I can get what I want using the Actions menu, I can't find a way to create custom rlabels via the command line. Is there a way to do this? > > If possible, I would also like to position each label near the spot on the ribbon closest to the alpha carbon (the "primary atom"). I can see how to do this with the molecule attributes panel, but I'm having difficulty setting the placement through the command line. > > And while I'm at it...is there a way to color a spot on the ribbon closest to the alpha carbon a different color than the rest of the ribbon? > Thanks for the help! > Dan > From meng at cgl.ucsf.edu Mon May 16 10:02:21 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 May 2011 10:02:21 -0700 Subject: [Chimera-users] labeling residues In-Reply-To: References: Message-ID: Also, you can control the offset with the labeling command, for example: rlabel offset .5,.5,.5 Default offsets are given here: On May 16, 2011, at 9:55 AM, Elaine Meng wrote: > Even though you might expect "centroid" residue label positioning to be the same as "primary atom" when only the CA is displayed, it is different because the latter includes an offset. From danielgurnon at depauw.edu Mon May 16 10:49:12 2011 From: danielgurnon at depauw.edu (Daniel Gurnon) Date: Mon, 16 May 2011 13:49:12 -0400 Subject: [Chimera-users] labeling residues In-Reply-To: References: Message-ID: Elaine, this is very close to what I'm looking for (I hadn't heard of "shape tube", but its perfect for what I want to do). As I understand it, if the script is to work with any pdb structure, I will need two segments of python code: 1) custom residue labeling to display only 1-letter code and number, and 2) something that creates a separate tube for each chain in a model, without connecting one tube to the next. I would love to wrap this into a button (e.g., http://www.cgl.ucsf.edu/chimera/1.4/docs/ProgrammersGuide/Examples/Main_ToolbarButton.html) that a student could push once he or she has loaded a structure. If its easy to do and someone else could give me the python snippet for 1) and 2) above, that would be great. Thanks as always for the help. Dan On Mon, May 16, 2011 at 12:55 PM, Elaine Meng wrote: > Hi Dan, > You'd probably also want to undisplay atoms/bonds, so something like > > ~disp; ribbon; ribsc licorice > > (A) label positioning. You could either use residue labels with "primary > atom" positioning or atom labels at CA showing residue info, i.e. : > > rlabel; setattr m residueLabelPos 2 > - OR - > disp @ca; labelopt info residue; la @ca > > (the balloon help on the attributes panel gives the attribute name and its > allowed values for use with "setattr," and "m" indicates it is an attribute > of molecule models). Even though you might expect "centroid" residue label > positioning to be the same as "primary atom" when only the CA is displayed, > it is different because the latter includes an offset. > > (B) custom label content. I don't think it can be done with Chimera > commands, but the Chimera command file could open a python snippet. > Somebody else would need to give the exact code for what you describe, but > this previous message gives something similar for custom residue labeling: > < > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005622.html > > > > (C) color ribbon near CA. I believe you can only color the segment > representing the whole residue. I don't think there is any way to color a > shorter segment of ribbon than that. An alternative, however, is to abandon > ribbons entirely and make a tubular surface that follows the path of the > backbone instead. This allows coloring a narrow band of tube and has the > added advantage of following the true locations of the atoms instead of > making a smooth interpolation like the ribbon. More details here: > < > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset > > > > ... but briefly, something like: > > ~ribbon; rainbow > shape tube :.a at ca radius 0.35 bandLength 2 modelId 1 > > ... where I just used rainbow to color the invisible alpha-carbons so you > can see the colored bands on the resulting tube. The above only makes a > tube for chain a (:.a). If there are multiple chains, you'd want to do them > separately, or else the tube would connect the end of one to the beginning > of the next. modelId is the model number for the resulting output surface. > > To label alpha-carbons, you would need to display them along with the tube > but turn off auto-chaining so that Chimera won't draw straight lines between > them: > > disp @ca; setattr m autochain 0 > > So, if you went with the tube approach your overall script could be > something like > > open 4hhb > ~ribbon; show @ca; setattr m autochain 0 > rlabel; setattr m residueLabelPos 2 > # open python file for custom labeling, not incl here > # color alpha-carbons as you like: > rainbow > shape tube :.a at ca radius 0.35 bandLength 2 modelId 1 > shape tube :.b at ca radius 0.35 bandLength 2 modelId 2 > shape tube :.c at ca radius 0.35 bandLength 2 modelId 3 > shape tube :.d at ca radius 0.35 bandLength 2 modelId 4 > > Image attached. You may want to take a look at the tube options and try > different values: > > > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > On May 15, 2011, at 10:56 AM, Daniel Gurnon wrote: > > > Hi all, > > A student of mine wants to make a wire sculpture of a protein, and I'm > thinking of ways Chimera could make the task easier. Ideally, I would create > a script that would display any protein in wire-form, with residue positions > clearly and unobtrusively labeled. > > > > I'd like to use the command line to display a backbone as a licorice > ribbon with residue numbers and 1-letter codes at the alpha carbon of each > residue. > > so starting out, I would use: > > ribscale licorice; ribbackbone; rlabel @ca; > > > > But instead of "ALA 24.B", I want "A 24". Though I can get what I want > using the Actions menu, I can't find a way to create custom rlabels via the > command line. Is there a way to do this? > > > > If possible, I would also like to position each label near the spot on > the ribbon closest to the alpha carbon (the "primary atom"). I can see how > to do this with the molecule attributes panel, but I'm having difficulty > setting the placement through the command line. > > > > And while I'm at it...is there a way to color a spot on the ribbon > closest to the alpha carbon a different color than the rest of the ribbon? > > Thanks for the help! > > Dan > > > > > -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon at depauw.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From kdryden at virginia.edu Mon May 16 11:54:13 2011 From: kdryden at virginia.edu (Kelly Dryden) Date: Mon, 16 May 2011 14:54:13 -0400 Subject: [Chimera-users] Can eraser position be defined by coordinates? Message-ID: <4DD172D5.9050505@virginia.edu> Hi, I would like to place the origin of the eraser to correspond with the center of my map but haven't found a way to define its position based on coordinates, only by moving it with the mouse. Is there a line command or other menu option that allows me to set the position more precisely? Thanks, Kelly From goddard at sonic.net Mon May 16 12:18:01 2011 From: goddard at sonic.net (Tom Goddard) Date: Mon, 16 May 2011 12:18:01 -0700 Subject: [Chimera-users] Can eraser position be defined by coordinates? In-Reply-To: <4DD172D5.9050505@virginia.edu> References: <4DD172D5.9050505@virginia.edu> Message-ID: <4DD17869.4080201@sonic.net> Hi Kelly, There is no command to position the volume eraser sphere using typed coordinates. If you want to erase a spherical region centered on the center of a virus map use the shape and mask commands: shape sphere radius 120 center 0,0,0 coord #0 color blue mask #0 #1 invert true The first command makes a spherical surface of radius 120 Angstroms at center 0,0,0 (Angstroms) in the map #0 coordinate frame colored blue. The second command copies the region of map #0 outside the sphere #1, making a new volume data set. The main trouble here is figuring out the coordinates of the center of virus map. The virus map origin is set in the Volume dialog Coordinates panel where you specify the grid index for position (0,0,0). In the above example I've got the map origin set to the center of the virus (EMDB 1058, grid index 87 for a size 175 map, base index is 0). You can use shape sphere radius 120 center #0 color blue which puts the center at the center of the bounding box of the displayed surface for map #0. But that doesn't in general give you the exact center of symmetry. So it is better to find the exact grid point that is the center of symmetry used when the map was calculated. Tom > Hi, > > I would like to place the origin of the eraser to correspond with the > center of my map but haven't found a way to define its position based on > coordinates, only by moving it with the mouse. Is there a line command > or other menu option that allows me to set the position more precisely? > > Thanks, > Kelly > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From meng at cgl.ucsf.edu Mon May 16 14:34:02 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 May 2011 14:34:02 -0700 Subject: [Chimera-users] labeling residues In-Reply-To: References: Message-ID: <9B830F34-3F4F-4195-B2AA-15980E246B28@cgl.ucsf.edu> Hi Dan, Python isn't absolutely necessary for #2 - you only need give a separate "shape tube" command for each chain, as in the example in my previous message for chains A-D of the hemoglobin structure 4hhb. However, python would be required to handle the general case where you don't have prior knowledge of the number of chains and whether they are even proteins, i.e., to loop through all protein chains and make a separate tube for each. Alternatively you could just have one command that makes the tube for chain A only and assumes it is protein. In general you can make a Chimera command alias that will then appear in a top-level Aliases menu. Multiple commands can be combined into a single alias with semicolons. However, aliases are comprised of Chimera commands, not python, and they are stored in preferences, so you'd have to supply the students with a pre-existing preferences file if you were to use this approach. Small example: alias ^doit ~disp;ribbon;ribsc licorice;rainbow;set bg_color tan ...then execute it by choosing menu item: Aliases... doit The programmers on the team may be able to help with the python for custom labeling and looping through all chains of a structure, and once you have a python script that handles a sufficiently broad set of structures, how to buttonize it. Alternatively, you could give the students the script and tell them to open it (FIle... Open) in Chimera, but I agree that's not as friendly. Steps for which you already know the Chimera commands can be translated to Python using runCommand as described here: There is a big deadline today, so please bear with us if there is some lag before additional replies. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 16, 2011, at 10:49 AM, Daniel Gurnon wrote: > Elaine, this is very close to what I'm looking for (I hadn't heard of "shape tube", but its perfect for what I want to do). > > As I understand it, if the script is to work with any pdb structure, I will need two segments of python code: > > 1) custom residue labeling to display only 1-letter code and number, and > 2) something that creates a separate tube for each chain in a model, without connecting one tube to the next. > > I would love to wrap this into a button (e.g., http://www.cgl.ucsf.edu/chimera/1.4/docs/ProgrammersGuide/Examples/Main_ToolbarButton.html) that a student could push once he or she has loaded a structure. If its easy to do and someone else could give me the python snippet for 1) and 2) above, that would be great. > > Thanks as always for the help. > Dan > > On Mon, May 16, 2011 at 12:55 PM, Elaine Meng wrote: > Hi Dan, > You'd probably also want to undisplay atoms/bonds, so something like > > ~disp; ribbon; ribsc licorice > > (A) label positioning. You could either use residue labels with "primary atom" positioning or atom labels at CA showing residue info, i.e. : > > rlabel; setattr m residueLabelPos 2 > - OR - > disp @ca; labelopt info residue; la @ca > > (the balloon help on the attributes panel gives the attribute name and its allowed values for use with "setattr," and "m" indicates it is an attribute of molecule models). Even though you might expect "centroid" residue label positioning to be the same as "primary atom" when only the CA is displayed, it is different because the latter includes an offset. > > (B) custom label content. I don't think it can be done with Chimera commands, but the Chimera command file could open a python snippet. Somebody else would need to give the exact code for what you describe, but this previous message gives something similar for custom residue labeling: > > > (C) color ribbon near CA. I believe you can only color the segment representing the whole residue. I don't think there is any way to color a shorter segment of ribbon than that. An alternative, however, is to abandon ribbons entirely and make a tubular surface that follows the path of the backbone instead. This allows coloring a narrow band of tube and has the added advantage of following the true locations of the atoms instead of making a smooth interpolation like the ribbon. More details here: > > > ... but briefly, something like: > > ~ribbon; rainbow > shape tube :.a at ca radius 0.35 bandLength 2 modelId 1 > > ... where I just used rainbow to color the invisible alpha-carbons so you can see the colored bands on the resulting tube. The above only makes a tube for chain a (:.a). If there are multiple chains, you'd want to do them separately, or else the tube would connect the end of one to the beginning of the next. modelId is the model number for the resulting output surface. > > To label alpha-carbons, you would need to display them along with the tube but turn off auto-chaining so that Chimera won't draw straight lines between them: > > disp @ca; setattr m autochain 0 > > So, if you went with the tube approach your overall script could be something like > > open 4hhb > ~ribbon; show @ca; setattr m autochain 0 > rlabel; setattr m residueLabelPos 2 > # open python file for custom labeling, not incl here > # color alpha-carbons as you like: > rainbow > shape tube :.a at ca radius 0.35 bandLength 2 modelId 1 > shape tube :.b at ca radius 0.35 bandLength 2 modelId 2 > shape tube :.c at ca radius 0.35 bandLength 2 modelId 3 > shape tube :.d at ca radius 0.35 bandLength 2 modelId 4 > > Image attached. You may want to take a look at the tube options and try different values: > > > > > I hope this helps, > Elaine > > On May 15, 2011, at 10:56 AM, Daniel Gurnon wrote: > > > Hi all, > > A student of mine wants to make a wire sculpture of a protein, and I'm thinking of ways Chimera could make the task easier. Ideally, I would create a script that would display any protein in wire-form, with residue positions clearly and unobtrusively labeled. > > > > I'd like to use the command line to display a backbone as a licorice ribbon with residue numbers and 1-letter codes at the alpha carbon of each residue. > > so starting out, I would use: > > ribscale licorice; ribbackbone; rlabel @ca; > > > > But instead of "ALA 24.B", I want "A 24". Though I can get what I want using the Actions menu, I can't find a way to create custom rlabels via the command line. Is there a way to do this? > > > > If possible, I would also like to position each label near the spot on the ribbon closest to the alpha carbon (the "primary atom"). I can see how to do this with the molecule attributes panel, but I'm having difficulty setting the placement through the command line. > > > > And while I'm at it...is there a way to color a spot on the ribbon closest to the alpha carbon a different color than the rest of the ribbon? > > Thanks for the help! > > Dan > From pett at cgl.ucsf.edu Mon May 16 14:38:05 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 16 May 2011 14:38:05 -0700 Subject: [Chimera-users] labeling residues In-Reply-To: References: Message-ID: On May 16, 2011, at 10:49 AM, Daniel Gurnon wrote: > As I understand it, if the script is to work with any pdb structure, > I will need two segments of python code: > > 1) custom residue labeling to display only 1-letter code and number, > and > 2) something that creates a separate tube for each chain in a model, > without connecting one tube to the next. Hi Dan, It's actually easier to combine the two, something like this: from chimera import openModels, Molecule, runCommand from chimera.resCode import res3to1 for m in openModels.list(modelTypes=[Molecule]): for chain in m.sequences(): for r in chain.residues: if not r: # SEQRES sequence may include missing structure continue r.label = "%s %d" % (res3to1(r.type), r.id.position) runCommand("shape tube %s:.%s at ca radius 0.35 bandLength 2" % (m.oslIdent(), chain.chainID)) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon May 16 15:58:51 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 May 2011 15:58:51 -0700 Subject: [Chimera-users] morph movie with "shape tube" In-Reply-To: References: <87B693F5-BD4D-4B88-AFE9-3F01C6A70FFA@cgl.ucsf.edu> <4DCD2DAF.9060208@lmb.uni-muenchen.de> Message-ID: <40E2911F-4239-4E5D-A9E6-22D5F05CE79A@cgl.ucsf.edu> Hi Alan, I decided to try showing the morph with "shape tube" and it does work, but took some dorking around. To display the "missing segment" pseudobond, the CA atoms need to be displayed, but unchained so that straight lines aren't drawn between them. Then, it is necessary to make separate tubes for the backbone before and after the missing segment; if a single tube is made it goes right over the pseudobond. Finally, remaking the tubes at each coordinate frame is somewhat slow. I attached my test command file and the two PDB files (made from real PDB entries by superimposing them and deleting a segment from each so that there would be a "missing segment" pseudobond). You could save the command file as plain text, rename as something[dot]com, put the two PDB files in the same location as the command file, and open the command file with Chimera. If you decide to go with this tube approach, you may want to look at the options: Elaine -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: script.txt URL: -------------- next part -------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: model1.pdb Type: chemical/x-pdb Size: 183307 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: model2.pdb Type: chemical/x-pdb Size: 181095 bytes Desc: not available URL: -------------- next part -------------- On May 13, 2011, at 12:34 PM, Elaine Meng wrote: > Hi Alan, > Sorry, there isn't currently a command to apply residue class, only scaling (ribscale) and style (ribrepr): > > > Some possibilities: > - save session with morph already calculated and residue class applied. Your script would then restore the session, play the trajectory, and record the movie. I agree this is not as nice, since then you are saving two files instead of one, and the session file is large. You wouldn't have to wait for the morph to recalculate, however. > > - use a small python script to apply the residue class. Your Chimera script could open that python file, which automatically executes it. One of the other developers would have to supply the python (beyond my skill set, sorry), and that also requires having two files, albeit much smaller than a session file. > > In general when playing a morph with ribbons that show secondary structure, consider whether you need to recalculate the secondary structure assignments with "ksdssp" at each frame. To execute a set of commands at each frame, one would use the "perframe" command in combination with "alias": > > > > > For example, your script could contain something like: > > alias ^redefine ksdssp #2 > perframe redefine > movie record > coordset #2 1,21; wait 21; ~perframe > > I hadn't used ksdssp/perframe in my examples since (perhaps fortuitously) the secondary structure didn't change that much. If you are just displaying a tube or licorice which doesn't show secondary structure with different widths, it doesn't matter, however. > > You're right that the shape tube surface will not automatically morph along with the structures, but it might work to destroy/recreate it at each coordinate frame using "perframe". Interesting idea... I haven't tried it, though! > > I hope this helps, > Elaine > > On May 13, 2011, at 6:10 AM, Alan Cheung wrote: > >> Thanks Elaine! Yes, the reported thickness was 3.333 (pixels?) and that seems to match the width of the pseudobond i see on the video. The width isn't too bad, and i can live with it. >> >> Thanks for the explanations and tip too. >> >> One last question : can I apply a saved residue class (from the ribbon style editor) via a command? I'm morphing a mixture of ribbon and side chain atoms and (for a leucine residue) the CA-CB bond is unrealistically long, but seems ok if i remove the orientation atom (O) from the residue class. I saw the "shape tube" feature in the documentation that draws a tube through CA atoms, but i guessed it's not morphable (and might also not include my precious pseudobond ;) ) >> >> Many thanks again for the quick replies! >> >> Alan >> >> On 12/05/2011 19:22, Elaine Meng wrote: >>> Hi Alan, >>> Never mind about the PDBs, I made up my own by deleting parts of the structures in my favorite morph test case. >>> >>> I think I answered all of your issues except for the pseudobonds completely disappearing with "morph movie nogui true" -- I did reproduce that problem, and it seems like a bug, albeit mysterious. I'll file a report about that one, but in the meanwhile I hope you will be able to manage without using that option. >>> >>> One minor thing is that I generally recommend adding a few more wait frames to the recording after the morph plays, to avoid any "motion blur" effect at the end you might get as a result of encoding. I didn't see much of that effect in my test case proteins using your script, however. It may be because the morph is spread out over 50 frames so there is less differences between adjacent frames, but I was also using different PDBs than you. >>> Best, >>> Elaine >>> >>> On May 12, 2011, at 9:25 AM, Elaine Meng wrote: >>> >>>> Hi Alan, >>>> I haven't tried the whole script yet (can you send me the PDB files? I'll keep them private, i.e. only for the development group here if you send them just to me) but will try to address the low-hanging fruit in your set of questions: >>>> >>>> (A) lines thinner in saved movie. In general, lines such as silhouette edges and pseudobonds may turn out thinner in saved images and movies when you are doing "supersampling," which initially saves a larger image and samples it down to the final requested size. You can check if this is the issue by using File... Save Image to save a single image -- the dialog should report the maximum achievable linewidth given the requested size and amount of supersampling. The reason is that there is an upper limit to how fat your computer can draw the lines (at least via the method used by Chimera). If you have 2x2 supersampling, for example, Chimera will try to make the lines twice as fat in the initial larger image, but may run into this upper limit. Then when the image is sampled down to the final size, the lines may not be as thick as they appear in the interactive display. You could try using lower supersampling. Also make sure you are using a recent version (1.5.3 candida >> te ! >>>> or 1.6) because there was a lines-too-thin-in-images bug a couple of months ago. >>>> >>>> (B) setattr "p" vs. "g" -- this is because some attributes are for individual pseudobonds (p) and some attributes are defined for whole pseudobond groups (g). Individual pseudobonds don't have a linewidth attribute, it is set at the group level. All the pseudobonds in that group (for example, hydrogen bonds) would get the same linewidth and it is not possible to make different ones in the same group have different widths. If you are looking at the Selection Inspector or some other attributes inspector, it will show you which attributes are for individual pseudobonds and which are for groups. The balloon help will give the attribute name and allowed values. >>>> >>>> >>>> I will try to look at your other issues and get back to you, >>>> Elaine >>>> ---------- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>> On May 12, 2011, at 8:54 AM, Alan Cheung wrote: >>>> >>>>> Hi there - i'm scripting a complex movie and am having problems with >>>>> pseudobonds during morphing. Script is pasted at the end. >>>>> >>>>> Part of the movie contains a morph between two structures, both of >>>>> which are missing the same amino acid segment. Loading the two >>>>> structures show the pseudobond for the missing residues and the >>>>> resulting morph also contains the same pseudobond. >>>>> >>>>> I've been changing the thickness of the pseudobond with : >>>>> >>>>> setattr g lineWidth 8 >>>>> >>>>> and while the two static structures and the morph in the chimera >>>>> window have a thicker pseudobond, the resulting movie (encoded to >>>>> .mov) does not. Am i doing something wrong? >>>>> >>>>> Alan >>>>> >>>>> p.s. incidentally, when morphing by script, if one includes "nogui >>>>> true" with the "morph movie" command, pseudobonds aren't kept in the >>>>> morph at all. A bug? >>>>> p.p.s. can someone explain to me the difference between "setattr g" >>>>> and "setattr p"? I've read the manual but i don't understand why only >>>>> the former seems to work for me. >>>>> >>>>> ## movie script >>>>> >>>>> open model1.pdb >>>>> open model2.pdb >>>>> morph start #0 frames 50 name morph1 method linear >>>>> morph interpolate #1 name morph1 >>>>> morph movie name morph1 >>>>> coordset #2 1,1 >>>>> setattr g lineWidth 8 >>>>> ~modeldisplay # >>>>> >>>>> movie record supersample 3 directory ~/TEMP/ >>>>> modeldisplay #2 >>>>> coordset #2 1,51 ; wait 51 >>>>> movie stop >>>>> movie encode output morph1.mov >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users at cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >> >> -- >> Alan Cheung >> Gene Center >> Ludwig-Maximilians-University >> Feodor-Lynen-Str. 25 >> 81377 Munich >> Germany >> Phone: +49-89-2180-76845 >> Fax: +49-89-2180-76999 >> E-mail: cheung at lmb.uni-muenchen.de > From conrad at cgl.ucsf.edu Tue May 17 09:40:59 2011 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Tue, 17 May 2011 09:40:59 -0700 Subject: [Chimera-users] Pseudobonds disappearing during morphing movie In-Reply-To: References: <87B693F5-BD4D-4B88-AFE9-3F01C6A70FFA@cgl.ucsf.edu> <4DCD2DAF.9060208@lmb.uni-muenchen.de> Message-ID: <4DD2A51B.1070404@cgl.ucsf.edu> I just added code for a "ribclass" command that has the same syntax as "ribscale". For example, ribclass "CNS amino acid" :12 will change residue 12 to use the "CNS amino acid" atom class. The quotes are only needed if the class name has whitespace in it. To reset a residue to the default ribbon class, use "none" for the class name. The new command should be available in tomorrow's daily build. Conrad On 5/13/2011 12:34 PM, Elaine Meng wrote: > Sorry, there isn't currently a command to apply residue class, only scaling (ribscale) and style (ribrepr): > From gtzotzos at me.com Wed May 18 10:37:52 2011 From: gtzotzos at me.com (George Tzotzos) Date: Wed, 18 May 2011 19:37:52 +0200 Subject: [Chimera-users] Visualising PDB files from AMBER Message-ID: Hi everybody, I've generated a average pdb structure from an AMBER trajectory. The structure contains one water molecule (named: WAT). I fail to visualise it in Chimera despite the fact that I can select it. I'm using Chimera 1.5.2 on OSX 10.6.7 Any ideas explaining this behaviour? I'm attaching the relevant file. Thank you in advance for your help Best regards George -------------- next part -------------- A non-text attachment was scrubbed... Name: aver.pdb Type: chemical/x-pdb Size: 151072 bytes Desc: not available URL: From meng at cgl.ucsf.edu Wed May 18 12:25:14 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 May 2011 12:25:14 -0700 Subject: [Chimera-users] Visualising PDB files from AMBER In-Reply-To: References: Message-ID: <4BF58F8D-57D5-4414-A257-EE581558BD9D@cgl.ucsf.edu> Hi George, I can see it, but it has supershort bonds: 0.035 and 0.045 angstroms! Perhaps an example of the perils of averaging? Anyway, I can display it without problem, but it just looks like a slightly misshapen little ball because the three atoms are so close together. Open the file and try these commands: show :wat focus :wat ... see the "ball" which is actually compressed sticks. To measure bond lengths, show as wire, zoom in, pause cursor over each bond: rep wire scale 50 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 18, 2011, at 10:37 AM, George Tzotzos wrote: > Hi everybody, > I've generated a average pdb structure from an AMBER trajectory. The structure contains one water molecule (named: WAT). > > I fail to visualise it in Chimera despite the fact that I can select it. I'm using Chimera 1.5.2 on OSX 10.6.7 > > Any ideas explaining this behaviour? I'm attaching the relevant file. > > Thank you in advance for your help > Best regards > George > > From chiendarret at gmail.com Thu May 19 08:04:58 2011 From: chiendarret at gmail.com (Francesco Pietra) Date: Thu, 19 May 2011 17:04:58 +0200 Subject: [Chimera-users] solid-cylinder representation of helices Message-ID: HI: Is any plan about a solid-cylinder representation of protein helices? It would be very useful to represent pathways of ligands inside a protein (in combination with centroid). Helices allow a less defined 3D perspective, especially when all is projected into a screen or paper. Thanks francesco pietra From meng at cgl.ucsf.edu Thu May 19 09:12:58 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 19 May 2011 09:12:58 -0700 Subject: [Chimera-users] solid-cylinder representation of helices In-Reply-To: References: Message-ID: <09FA7DF4-D54C-4818-87DB-D311AD9B1281@cgl.ucsf.edu> Hi Francesco, There are at least two ways to show helices as cylinders in Chimera: (A) PipesAndPlanks (under Tools... Depiction), which also shows beta-strands as rectangular boxes or "planks" (B) Axes/Planes/Centroids (under Tools... Structure Analysis), in which axes are shown as cylinders. You can use any set of atoms to define an axis, but one of the options is to make one for each helix. Method (B) allows you to change cylinder colors individually after they have been created (using the square color wells) and to make measurements involving the axes. Both methods allow you to specify the cylinder radius or have it figured out automatically. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 19, 2011, at 8:04 AM, Francesco Pietra wrote: > HI: > Is any plan about a solid-cylinder representation of protein helices? > It would be very useful to represent pathways of ligands inside a > protein (in combination with centroid). Helices allow a less defined > 3D perspective, especially when all is projected into a screen or > paper. > Thanks > francesco pietra From daniel.hitchcock at mail.chem.tamu.edu Fri May 20 09:00:47 2011 From: daniel.hitchcock at mail.chem.tamu.edu (Daniel Hitchcock) Date: Fri, 20 May 2011 11:00:47 -0500 Subject: [Chimera-users] Completely reinstall chimera Message-ID: Hi, I want to completely uninstall chimera and remove all the settings from the program. I notice though if I uninstall and reinstall though, it still has all the settings and history from before. How can I completely remove Chimera from the computer so I can return to default settings? Thank you -daniel From meng at cgl.ucsf.edu Fri May 20 09:31:02 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 20 May 2011 09:31:02 -0700 Subject: [Chimera-users] Completely reinstall chimera In-Reply-To: References: Message-ID: Dear Daniel, I believe that all non-default Chimera settings are saved in your preferences file, and to return to Chimera defaults only, you would only need to remove that file. To see where your preferences file is, start Chimera, open Preferences (from Favorites menu), go to Preferences category of Preferences. There is a "Reset to factory defaults" button, which will do exactly that, but only for things that are in the Preferences dialog. Additional settings not in the Preferences dialog are also saved in the preferences file, such as sequence alignment display settings from Multalign Viewer and your file history. You could try using the button if you only care about the settings in the Preferences dialog, but if you really want to wipe out all customization: Write down the file location unless you can remember it, quit from Chimera, navigate on your system to that file and delete it (or move it to a different filename if you think you *might* want to go back to using it later). When you restart Chimera, it will have forgotten all your custom settings and file history. More about preferences files: Normally your preferences file is in your own directories and not affected by installing a new version of Chimera, because most don't want to have their settings wiped out by updating the software. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 20, 2011, at 9:00 AM, Daniel Hitchcock wrote: > Hi, > I want to completely uninstall chimera and remove all the settings > from the program. I notice though if I uninstall and reinstall though, > it still has all the settings and history from before. How can I > completely remove Chimera from the computer so I can return to default > settings? > Thank you > -daniel From osmundsj at gmail.com Thu May 19 17:17:37 2011 From: osmundsj at gmail.com (Joe Osmundson) Date: Thu, 19 May 2011 20:17:37 -0400 Subject: [Chimera-users] Pack molecules in Unit Cell Message-ID: Hi everyone, I would like to transform a pdb so that it fits nicely in the unit cell, which seems to be described here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html as "Pack molecules in unit cell". However, this is not an option when I bring up the options in the Unit Cell tool (although literally everything else that should be there IS indeed there). Is there a glitch in the most recent version? Is there an easy way to script this to essentially move the model (and its crystallographic mate) into the center of the unit cell? Thanks, Joe Osmundson Darst Lab Rockefeller University From meng at cgl.ucsf.edu Fri May 20 10:52:12 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 20 May 2011 10:52:12 -0700 Subject: [Chimera-users] Pack molecules in Unit Cell In-Reply-To: References: Message-ID: <98872D8A-EF1D-49C2-8AFD-B13AFE40CAD6@cgl.ucsf.edu> Hi Joe, The packing option is in version 1.6 (daily builds) but not 1.5.x. The daily builds are also available for download, just farther down on the page: The URL you gave is for "development" documentation (latest, synchronized for the most part with the daily build). The documentation included with your download and accessible from the Chimera Help menu should be better synchronized with the features in that same version. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 19, 2011, at 5:17 PM, Joe Osmundson wrote: > Hi everyone, > I would like to transform a pdb so that it fits nicely in the unit > cell, which seems to be described here: > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html > > as "Pack molecules in unit cell". However, this is not an option when > I bring up the options in the Unit Cell tool (although literally > everything else that should be there IS indeed there). > > Is there a glitch in the most recent version? Is there an easy way to > script this to essentially move the model (and its crystallographic > mate) into the center of the unit cell? > Thanks, > Joe Osmundson > Darst Lab > Rockefeller University From osmundsj at gmail.com Fri May 20 10:53:33 2011 From: osmundsj at gmail.com (Joe Osmundson) Date: Fri, 20 May 2011 13:53:33 -0400 Subject: [Chimera-users] Pack molecules in Unit Cell In-Reply-To: <98872D8A-EF1D-49C2-8AFD-B13AFE40CAD6@cgl.ucsf.edu> References: <98872D8A-EF1D-49C2-8AFD-B13AFE40CAD6@cgl.ucsf.edu> Message-ID: Most helpful, I was wondering if there was simply a different (more recent) version. Thanks very much, Joe On Fri, May 20, 2011 at 1:52 PM, Elaine Meng wrote: > Hi Joe, > The packing option is in version 1.6 (daily builds) but not 1.5.x. ?The daily builds are also available for download, just farther down on the page: > > > The URL you gave is for "development" documentation (latest, synchronized for the most part with the daily build). ?The documentation included with your download and accessible from the Chimera Help menu should be better synchronized with the features in that same version. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On May 19, 2011, at 5:17 PM, Joe Osmundson wrote: > >> Hi everyone, >> I would like to transform a pdb so that it fits nicely in the unit >> cell, which seems to be described here: >> >> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html >> >> as "Pack molecules in unit cell". ?However, this is not an option when >> I bring up the options in the Unit Cell tool (although literally >> everything else that should be there IS indeed there). >> >> Is there a glitch in the most recent version? ?Is there an easy way to >> script this to essentially move the model (and its crystallographic >> mate) into the center of the unit cell? >> Thanks, >> Joe Osmundson >> Darst Lab >> Rockefeller University > > From meng at cgl.ucsf.edu Fri May 20 13:45:13 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 20 May 2011 13:45:13 -0700 Subject: [Chimera-users] Pack molecules in Unit Cell In-Reply-To: References: <98872D8A-EF1D-49C2-8AFD-B13AFE40CAD6@cgl.ucsf.edu> Message-ID: <2AFD397A-1272-4D7A-9C04-4397C97F4140@cgl.ucsf.edu> Maybe I don't understand what you are asking. It sounds like you are using version 1.5.3 of Chimera, whereas if you get the 1.6 daily build, it will include the packing feature you mentioned. The daily build includes the very latest changes. Both versions are available from the download page, along with dates. I was just trying to explain why the options shown in the manpage you were viewing might not match the software you were using. If I still haven't answered your question, however, let me know! Elaine On May 20, 2011, at 10:53 AM, Joe Osmundson wrote: > Most helpful, I was wondering if there was simply a different (more > recent) version. > > Thanks very much, > > Joe > > On Fri, May 20, 2011 at 1:52 PM, Elaine Meng wrote: >> Hi Joe, >> The packing option is in version 1.6 (daily builds) but not 1.5.x. The daily builds are also available for download, just farther down on the page: >> >> >> The URL you gave is for "development" documentation (latest, synchronized for the most part with the daily build). The documentation included with your download and accessible from the Chimera Help menu should be better synchronized with the features in that same version. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On May 19, 2011, at 5:17 PM, Joe Osmundson wrote: >> >>> Hi everyone, >>> I would like to transform a pdb so that it fits nicely in the unit >>> cell, which seems to be described here: >>> >>> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html >>> >>> as "Pack molecules in unit cell". However, this is not an option when >>> I bring up the options in the Unit Cell tool (although literally >>> everything else that should be there IS indeed there). >>> >>> Is there a glitch in the most recent version? Is there an easy way to >>> script this to essentially move the model (and its crystallographic >>> mate) into the center of the unit cell? >>> Thanks, >>> Joe Osmundson >>> Darst Lab >>> Rockefeller University >> From gtzotzos at me.com Sun May 22 05:39:54 2011 From: gtzotzos at me.com (George Tzotzos) Date: Sun, 22 May 2011 14:39:54 +0200 Subject: [Chimera-users] PipesAndPlanks Message-ID: <66E68EEB-1818-4179-A71A-A1481C37DCA0@me.com> Hi everybody, I'm dealing with a dimeric hexahelical bundle. I've been trying to name the individual helices (e.g. a1, a2, etc) and colour them differently to no avail. Obviously, I'm missing something. Your guidance will be greatly appreciated. Have a good weekend George PS. Sorry if you receive this message for a second time. It was sent from a different address earlier and I'm not sure if it reached the list. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sun May 22 09:51:33 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 22 May 2011 09:51:33 -0700 Subject: [Chimera-users] PipesAndPlanks In-Reply-To: <66E68EEB-1818-4179-A71A-A1481C37DCA0@me.com> References: <66E68EEB-1818-4179-A71A-A1481C37DCA0@me.com> Message-ID: <2EA73689-F3D3-4877-B699-811E4AC7EC23@cgl.ucsf.edu> Hi George, As mentioned in this recent post, you can do this with the Axes/Planes/Centroids tool (not PipesAndPlanks). If you define axes, one of the choices is to show an axis (cylinder) for each helix. You can specify cylinder radii or have them determined automatically, and after the axes (cylinders) are created, you can use the square color wells in the Axes/Planes/Centroids table to change their colors. Documentation: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 22, 2011, at 5:39 AM, George Tzotzos wrote: > Hi everybody, > I'm dealing with a dimeric hexahelical bundle. I've been trying to name the individual helices (e.g. a1, a2, etc) and colour them differently to no avail. > Obviously, I'm missing something. > Your guidance will be greatly appreciated. > Have a good weekend > George > > PS. Sorry if you receive this message for a second time. It was sent from a different address earlier and I'm not sure if it reached the list. From marek.maly at ujep.cz Mon May 23 07:39:39 2011 From: marek.maly at ujep.cz (Marek Maly) Date: Mon, 23 May 2011 16:39:39 +0200 Subject: [Chimera-users] How to select whole molecule ? In-Reply-To: <2EA73689-F3D3-4877-B699-811E4AC7EC23@cgl.ucsf.edu> References: <66E68EEB-1818-4179-A71A-A1481C37DCA0@me.com> <2EA73689-F3D3-4877-B699-811E4AC7EC23@cgl.ucsf.edu> Message-ID: Hello all, is there any possibility how to select all atoms which belongs to the given molecule ? I mean something which allow me to select whole molecule to which belongs previously selected atom. Unfortunately ZONE selection is not useful here as it allow to select only atoms or residues, not whole molecular structures. Selection by hand/mouse is not possible to use in cases when two or more molecules are very close together. Thanks a lot in advance for advices ! Best wishes, Marek Maly From meng at cgl.ucsf.edu Mon May 23 09:32:53 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 23 May 2011 09:32:53 -0700 Subject: [Chimera-users] How to select whole molecule ? In-Reply-To: References: <66E68EEB-1818-4179-A71A-A1481C37DCA0@me.com> <2EA73689-F3D3-4877-B699-811E4AC7EC23@cgl.ucsf.edu> Message-ID: <5FA395F2-F199-42E5-A646-CCB35306ED3F@cgl.ucsf.edu> Hello Marek Maly, If you already have the one atom selected, you can press the up arrow key (on the keyboard) to expand the selection to whole residue, then again for the whole chain, then whole molecule model. Depending on the structure, there may be fewer layers; for example, the whole chain may be the same as the whole molecule model. To go back down, you could use the down arrow key. Also, the commands "select up" and "select down" do the same thing. If you didn't have any atom selected but you know you want to select all the atoms in a particular model, you can use the select command with the model number (example: select #0), or you could open the Model Panel from the Favorites menu, and in that panel choose the model on the left side and click the "select" button on the right side. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 23, 2011, at 7:39 AM, Marek Maly wrote: > Hello all, > is there any possibility how to select all atoms which belongs to the given > molecule ? > > I mean something which allow me to select whole molecule to which belongs previously > selected atom. Unfortunately ZONE selection is not useful here as it allow to select > only atoms or residues, not whole molecular structures. > > Selection by hand/mouse is not possible to use in cases when > two or more molecules are very close together. > > Thanks a lot in advance for advices ! > Best wishes, > Marek Maly From marek.maly at ujep.cz Mon May 23 09:43:06 2011 From: marek.maly at ujep.cz (Marek Maly) Date: Mon, 23 May 2011 18:43:06 +0200 Subject: [Chimera-users] How to select whole molecule ? In-Reply-To: <5FA395F2-F199-42E5-A646-CCB35306ED3F@cgl.ucsf.edu> References: <66E68EEB-1818-4179-A71A-A1481C37DCA0@me.com> <2EA73689-F3D3-4877-B699-811E4AC7EC23@cgl.ucsf.edu> <5FA395F2-F199-42E5-A646-CCB35306ED3F@cgl.ucsf.edu> Message-ID: Dear Elaine, first of all thank you very much for your prompt response ! Unfortunately your suggestions do not cover cases when one has molecular system composed of two or more molecules loaded as one "Chimera molecular model" without possibility to recognize individual molecules using chain ID (e.g. visualization of frames from MD trajectory). For such cases only solution (in my opinion) is, some general routine which can quickly find all the atoms which could be accessed from the previously selected one through several (1,2 ....N) covalent bonds. Is something like this implemented in actual version of Chimera ? Do you see any solution for above described case ? Thank you very much in advance for this additional info, Best wishes, Marek Dne Mon, 23 May 2011 18:32:53 +0200 Elaine Meng napsal/-a: > Hello Marek Maly, > If you already have the one atom selected, you can press the up arrow > key (on the keyboard) to expand the selection to whole residue, then > again for the whole chain, then whole molecule model. Depending on the > structure, there may be fewer layers; for example, the whole chain may > be the same as the whole molecule model. To go back down, you could use > the down arrow key. Also, the commands "select up" and "select down" do > the same thing. > > > > > If you didn't have any atom selected but you know you want to select all > the atoms in a particular model, you can use the select command with the > model number (example: select #0), or you could open the Model Panel > from the Favorites menu, and in that panel choose the model on the left > side and click the "select" button on the right side. > > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On May 23, 2011, at 7:39 AM, Marek Maly wrote: > >> Hello all, >> is there any possibility how to select all atoms which belongs to the >> given >> molecule ? >> >> I mean something which allow me to select whole molecule to which >> belongs previously >> selected atom. Unfortunately ZONE selection is not useful here as it >> allow to select >> only atoms or residues, not whole molecular structures. >> >> Selection by hand/mouse is not possible to use in cases when >> two or more molecules are very close together. >> >> Thanks a lot in advance for advices ! >> Best wishes, >> Marek Maly > > > __________ Informace od ESET NOD32 Antivirus, verze databaze 6145 > (20110523) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > > > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ From meng at cgl.ucsf.edu Mon May 23 10:04:56 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 23 May 2011 10:04:56 -0700 Subject: [Chimera-users] How to select whole molecule ? In-Reply-To: References: <66E68EEB-1818-4179-A71A-A1481C37DCA0@me.com> <2EA73689-F3D3-4877-B699-811E4AC7EC23@cgl.ucsf.edu> <5FA395F2-F199-42E5-A646-CCB35306ED3F@cgl.ucsf.edu> Message-ID: <81E55394-D23F-495F-9F62-65751AFBCC8C@cgl.ucsf.edu> Hi Marek, There is nothing exactly like that in Chimera, but here are a couple more ideas: - the "select chain(s)" function in the Model Panel has a "by connectivity" option that could allow you to get the whole bonded molecule even if the chain ID or the whole model would include more atoms than that. - you could use the "select" command with specific chain ID, residue numbers, and atom names. However, figuring out what they are is more work for you. I remember someone else on the chimera-users list asking about selection through a specified number of covalent connections, but I don't remember the details -- that person may have written some python code to do it. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 23, 2011, at 9:43 AM, Marek Maly wrote: > Dear Elaine, > > first of all thank you very much for your prompt response ! > > Unfortunately your suggestions do not cover cases when one has molecular > system composed of two or more > molecules loaded as one "Chimera molecular model" without possibility to > recognize > individual molecules using chain ID (e.g. visualization of frames from MD > trajectory). > > For such cases only solution (in my opinion) is, some general routine > which can quickly > find all the atoms which could be accessed from the previously selected > one through several > (1,2 ....N) covalent bonds. Is something like this implemented in actual > version of Chimera ? > > Do you see any solution for above described case ? > > Thank you very much in advance for this additional info, > Best wishes, > Marek > > Dne Mon, 23 May 2011 18:32:53 +0200 Elaine Meng > napsal/-a: > >> Hello Marek Maly, >> If you already have the one atom selected, you can press the up arrow >> key (on the keyboard) to expand the selection to whole residue, then >> again for the whole chain, then whole molecule model. Depending on the >> structure, there may be fewer layers; for example, the whole chain may >> be the same as the whole molecule model. To go back down, you could use >> the down arrow key. Also, the commands "select up" and "select down" do >> the same thing. >> >> >> >> >> If you didn't have any atom selected but you know you want to select all >> the atoms in a particular model, you can use the select command with the >> model number (example: select #0), or you could open the Model Panel >> from the Favorites menu, and in that panel choose the model on the left >> side and click the "select" button on the right side. >> >> >> >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On May 23, 2011, at 7:39 AM, Marek Maly wrote: >> >>> Hello all, >>> is there any possibility how to select all atoms which belongs to the >>> given >>> molecule ? >>> >>> I mean something which allow me to select whole molecule to which >>> belongs previously >>> selected atom. Unfortunately ZONE selection is not useful here as it >>> allow to select >>> only atoms or residues, not whole molecular structures. >>> >>> Selection by hand/mouse is not possible to use in cases when >>> two or more molecules are very close together. >>> >>> Thanks a lot in advance for advices ! >>> Best wishes, >>> Marek Maly >> >> >> __________ Informace od ESET NOD32 Antivirus, verze databaze 6145 >> (20110523) __________ >> >> Tuto zpravu proveril ESET NOD32 Antivirus. >> >> http://www.eset.cz >> >> >> > > > -- > Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: > http://www.opera.com/mail/ > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From marek.maly at ujep.cz Mon May 23 10:03:49 2011 From: marek.maly at ujep.cz (Marek Maly) Date: Mon, 23 May 2011 19:03:49 +0200 Subject: [Chimera-users] How to select whole molecule ? In-Reply-To: <81E55394-D23F-495F-9F62-65751AFBCC8C@cgl.ucsf.edu> References: <66E68EEB-1818-4179-A71A-A1481C37DCA0@me.com> <2EA73689-F3D3-4877-B699-811E4AC7EC23@cgl.ucsf.edu> <5FA395F2-F199-42E5-A646-CCB35306ED3F@cgl.ucsf.edu> <81E55394-D23F-495F-9F62-65751AFBCC8C@cgl.ucsf.edu> Message-ID: Dear Elanie, thanks again very much ! Your suggestion ( the "select chain(s)" function in the Model Panel has a "by connectivity" ) was exactly what I was looking for ! Best wishes, Marek Dne Mon, 23 May 2011 19:04:56 +0200 Elaine Meng napsal/-a: > Hi Marek, > There is nothing exactly like that in Chimera, but here are a couple > more ideas: > > - the "select chain(s)" function in the Model Panel has a "by > connectivity" option that could allow you to get the whole bonded > molecule even if the chain ID or the whole model would include more > atoms than that. > > - you could use the "select" command with specific chain ID, residue > numbers, and atom names. However, figuring out what they are is more > work for you. > > I remember someone else on the chimera-users list asking about selection > through a specified number of covalent connections, but I don't remember > the details -- that person may have written some python code to do it. > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On May 23, 2011, at 9:43 AM, Marek Maly wrote: > >> Dear Elaine, >> >> first of all thank you very much for your prompt response ! >> >> Unfortunately your suggestions do not cover cases when one has molecular >> system composed of two or more >> molecules loaded as one "Chimera molecular model" without possibility to >> recognize >> individual molecules using chain ID (e.g. visualization of frames from >> MD >> trajectory). >> >> For such cases only solution (in my opinion) is, some general routine >> which can quickly >> find all the atoms which could be accessed from the previously selected >> one through several >> (1,2 ....N) covalent bonds. Is something like this implemented in actual >> version of Chimera ? >> >> Do you see any solution for above described case ? >> >> Thank you very much in advance for this additional info, >> Best wishes, >> Marek >> >> Dne Mon, 23 May 2011 18:32:53 +0200 Elaine Meng >> napsal/-a: >> >>> Hello Marek Maly, >>> If you already have the one atom selected, you can press the up arrow >>> key (on the keyboard) to expand the selection to whole residue, then >>> again for the whole chain, then whole molecule model. Depending on the >>> structure, there may be fewer layers; for example, the whole chain may >>> be the same as the whole molecule model. To go back down, you could >>> use >>> the down arrow key. Also, the commands "select up" and "select down" >>> do >>> the same thing. >>> >>> >>> >>> >>> If you didn't have any atom selected but you know you want to select >>> all >>> the atoms in a particular model, you can use the select command with >>> the >>> model number (example: select #0), or you could open the Model Panel >>> from the Favorites menu, and in that panel choose the model on the >>> left >>> side and click the "select" button on the right side. >>> >>> >>> >>> I hope this helps, >>> Elaine >>> ---------- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> On May 23, 2011, at 7:39 AM, Marek Maly wrote: >>> >>>> Hello all, >>>> is there any possibility how to select all atoms which belongs to the >>>> given >>>> molecule ? >>>> >>>> I mean something which allow me to select whole molecule to which >>>> belongs previously >>>> selected atom. Unfortunately ZONE selection is not useful here as it >>>> allow to select >>>> only atoms or residues, not whole molecular structures. >>>> >>>> Selection by hand/mouse is not possible to use in cases when >>>> two or more molecules are very close together. >>>> >>>> Thanks a lot in advance for advices ! >>>> Best wishes, >>>> Marek Maly >>> >>> >>> __________ Informace od ESET NOD32 Antivirus, verze databaze 6145 >>> (20110523) __________ >>> >>> Tuto zpravu proveril ESET NOD32 Antivirus. >>> >>> http://www.eset.cz >>> >>> >>> >> >> >> -- >> Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: >> http://www.opera.com/mail/ >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > __________ Informace od ESET NOD32 Antivirus, verze databaze 6145 > (20110523) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > > > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ From rfr06 at fsu.edu Mon May 23 10:29:34 2011 From: rfr06 at fsu.edu (Roni Rayes) Date: Mon, 23 May 2011 13:29:34 -0400 Subject: [Chimera-users] centering a volume to an atom's coordinate Message-ID: Hi, I am trying to center volumes (cylinders and spheres that I created using spider) to an atom from a pdb file. When I created the volumes I made sure that their center is in the middle of the box containing the volume. I tried to set the coordinate of the volume to the atom's coordinate (in the coordinate tab under volume viewer) but the position of the volume was not centered to the coordinates provided. Any idea on how to do that? Thank you Roni From goddard at sonic.net Mon May 23 11:17:51 2011 From: goddard at sonic.net (Tom Goddard) Date: Mon, 23 May 2011 11:17:51 -0700 Subject: [Chimera-users] centering a volume to an atom's coordinate In-Reply-To: References: Message-ID: <4DDAA4CF.2010602@sonic.net> Hi Roni, The origin set in the Chimera volume dialog coordinates panel is the volume grid index corresponding to x,y,z position 0,0,0. So it requires a little calculation to figure out what to set that to to make the center of the volume box land on a specific atom (x,y,z) position. Here's an example volume grid size (201,201,201) volume center grid index (100,100,100) (indices start at 0 in Chimera) atom position xyz = (25, 50, 75) volume grid spacing 2.5 Angstroms atom position xyz divided by grid spacing (10, 20, 30) set volume origin in coordinates panel to (90,80,70) will make grid index (100,100,100) align with atom. Tom > Hi, > > I am trying to center volumes (cylinders and spheres that I created using spider) to an atom from a pdb file. > When I created the volumes I made sure that their center is in the middle of the box containing the volume. > I tried to set the coordinate of the volume to the atom's coordinate (in the coordinate tab under volume viewer) but the position of the volume was not centered to the coordinates provided. > > Any idea on how to do that? > > Thank you > > Roni > From coyote_v2002 at yahoo.com Mon May 23 22:53:52 2011 From: coyote_v2002 at yahoo.com (Visvaldas K.) Date: Mon, 23 May 2011 22:53:52 -0700 (PDT) Subject: [Chimera-users] Proline sidechain broken (with backbone as a ribbon)? Message-ID: <560779.37117.qm@web111720.mail.gq1.yahoo.com> Hi, I really like the default view of a loaded PDB file, where the whole protein is shown as a ribbon, but also the sidechains next to the heterogroups are shown. Proline shows up in this representation as a sort of rhomboid (or kite) shape, which is okay. However, I cannot achieve the same effect for proline when I select proline manually. If I do Actions->Atom/bonds->sidechain/base->show, the proline sidechain appears as a broken rhomboid, which looks more like a hook, i.e. a one of the bonds is missing to close the loop. How do I obtain a "closed" proline sidechain look? Thank you, Vis -------------- next part -------------- An HTML attachment was scrubbed... URL: From coyote_v2002 at yahoo.com Mon May 23 23:14:23 2011 From: coyote_v2002 at yahoo.com (Visvaldas K.) Date: Mon, 23 May 2011 23:14:23 -0700 (PDT) Subject: [Chimera-users] Proline sidechain broken (with backbone as a ribbon)? Message-ID: <703471.22364.qm@web111721.mail.gq1.yahoo.com> I'm very sorry, I take my question back. Actions->Atoms/bonds->Show will do the trick. Vis -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue May 24 09:01:11 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 24 May 2011 09:01:11 -0700 Subject: [Chimera-users] Proline sidechain broken (with backbone as a ribbon)? In-Reply-To: <703471.22364.qm@web111721.mail.gq1.yahoo.com> References: <703471.22364.qm@web111721.mail.gq1.yahoo.com> Message-ID: <4E5B7E76-137D-482E-B3E2-3874BC8A133D@cgl.ucsf.edu> Hi Vis, It's OK -- I'm glad you found the solution! Showing only the side chain is "smart" enough to include a bond to the backbone CA atom, but (as you saw) not the bond from the proline sidechain to the backbone N atom until that N atom is also displayed. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 23, 2011, at 11:14 PM, Visvaldas K. wrote: > I'm very sorry, I take my question back. Actions->Atoms/bonds->Show will do the trick. > Vis From bharat.85.monu at gmail.com Tue May 24 06:24:10 2011 From: bharat.85.monu at gmail.com (bharat gupta) Date: Tue, 24 May 2011 22:24:10 +0900 Subject: [Chimera-users] installation of headless chimera Message-ID: Hi, I am new to chimera and I am trying to install it on fedora core 6 . After followng the instructions given in installation manual nothing happens in my system. Can anybody tell me how can I install the headless version of chimera .. Thanks in advance for help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46010 at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Tue May 24 11:51:18 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 24 May 2011 11:51:18 -0700 Subject: [Chimera-users] installation of headless chimera In-Reply-To: References: Message-ID: <4DDBFE26.2070403@cgl.ucsf.edu> So everyone knows, the headless version of chimera does not provide a visible graphics window. It is designed to run chimera and Python scripts and export data or save images, and is usually installed for use by web servers. So if you are new to chimera, it is the wrong version to use. So I'd recommend downloading and installing the chimera 1.5.3 release candidate (the actual release should be out within a day, so if you can wait a day, do so). The Linux installer needs to be make executable (chmod +x installer.bin) and run in a Terminal window. When the installer pauses for input, you will see that it has filled out the answer for you with a default value. If you don't like that value, use your normal terminal line editing to change it (ie., use DEL to delete a character, ^U to delete the line, etc.). HTH, Greg On 05/24/2011 06:24 AM, bharat gupta wrote: > Hi, > > I am new to chimera and I am trying to install it on fedora core 6 . > After followng the instructions given in installation manual nothing > happens in my system. > Can anybody tell me how can I install the headless version of chimera .. > > > Thanks in advance for help > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46010 at yahoo.com > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Tue May 24 12:05:15 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 24 May 2011 12:05:15 -0700 Subject: [Chimera-users] installation of headless chimera In-Reply-To: <4DDBFE26.2070403@cgl.ucsf.edu> References: <4DDBFE26.2070403@cgl.ucsf.edu> Message-ID: <4DDC016B.5010004@cgl.ucsf.edu> One more thing, you would be be much better off running a newer version of Linux, preferably a desktop version. And I would strongly recommend using an AMD/ATI or NVIDIA graphics card and installing the vendor's proprietary driver. The proprietary drivers are typically faster and more robust than the open source drivers. If you stick with Fedora core 6, a proprietary driver is mandatory because the older open source drivers are too buggy for chimera. (Fedora core 6 was released on October 24, 2006, and the current version is Fedora core 15 which was released today.) -- Greg On 05/24/2011 11:51 AM, Greg Couch wrote: > So everyone knows, the headless version of chimera does not provide a > visible graphics window. It is designed to run chimera and Python > scripts and export data or save images, and is usually installed for > use by web servers. So if you are new to chimera, it is the wrong > version to use. > > So I'd recommend downloading and installing the chimera 1.5.3 release > candidate (the actual release should be out within a day, so if you > can wait a day, do so). The Linux installer needs to be make > executable (chmod +x installer.bin) and run in a Terminal window. > When the installer pauses for input, you will see that it has filled > out the answer for you with a default value. If you don't like that > value, > use your normal terminal line editing to change it (ie., use DEL to > delete a character, ^U to delete the line, etc.). > > HTH, > > Greg > > On 05/24/2011 06:24 AM, bharat gupta wrote: >> Hi, >> >> I am new to chimera and I am trying to install it on fedora core 6 . >> After followng the instructions given in installation manual nothing >> happens in my system. >> Can anybody tell me how can I install the headless version of chimera .. >> >> >> Thanks in advance for help >> >> -- >> Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46010 at yahoo.com >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From bobbylaird at tamu.edu Wed May 25 14:09:40 2011 From: bobbylaird at tamu.edu (Bobby Laird) Date: Wed, 25 May 2011 16:09:40 -0500 Subject: [Chimera-users] question about "measure rotation" Message-ID: I am using the measure rotation command in chimera to calculate the degree of rotation between two dimers, which make up a tetramer. I am using the following commands to accomplish this: mmaker #1:.A,.B #0:.A,.B pair ss write relative #0 #1 /tmp/ab-aligned.pdb close #1 open #1 /tmp/ab-aligned.pdb mmaker #1:.C,.D #0:.C,.D pair ss measure rotation #0 #1 I have noticed that when I use the "measure rotation" command that can get two different answers. I realize that the two answers are the result of an arbitrary decision made by the measure tool that result in a +/- of the same angle (i.e. 6 versus 174 degrees). Since I am looking at more several crystal structures, is there a way to force "measure rotation" to always make the same decision so that I know what relative direction the rotations are in to each other? Thanks _______________________________ Bobby W. Laird From goddard at sonic.net Wed May 25 15:27:12 2011 From: goddard at sonic.net (Tom Goddard) Date: Wed, 25 May 2011 15:27:12 -0700 Subject: [Chimera-users] question about "measure rotation" In-Reply-To: References: Message-ID: <4DDD8240.8050207@sonic.net> Hi Bobby, The "measure rotation #0 #1" command determines the axis of rotation as a vector and then reports the angle of rotation in a right-hand sense around that vector that carries #0 into #1. You are right it there could be an ambiguity. The sign of the axis vector can be flipped. Then the rotation angle reported would be (360 - angle). Notice the possibilities are (angle) and (360-angle). It always reports the one that has the angle <= 180 degrees. So "measure rotation" always gives a consistent result -- the angle <= 180 degrees. This doesn't solve your problem. If you compare the rotation of models B and C to A you may have B rotated by 10 degrees and C rotated by 15 degrees. But it would be nice to know if those rotations are in opposite directions about the same axis (25 degrees apart), or in the same directions (5 degrees apart), or if they are around different rotation axes. In general B and C will be rotated into A about axes that are not parallel. If the two rotation axes point more or less in the same direction then it still might make sense to say that the rotations are approximately in opposite or approximately in the same direction. In order to assess this you should look at the coordinates of the rotation axis vector that are reported by the "measure rotation" command in the Reply Log. From this you can observe if the axis vectors are roughly opposite one another. To quantify this further you may want to consider the angle between the rotation vectors. Tom > I am using the measure rotation command in chimera to calculate the degree of rotation between two dimers, which make up a tetramer. I am using the following commands to accomplish this: > > mmaker #1:.A,.B #0:.A,.B pair ss > write relative #0 #1 /tmp/ab-aligned.pdb > close #1 > open #1 /tmp/ab-aligned.pdb > mmaker #1:.C,.D #0:.C,.D pair ss > measure rotation #0 #1 > > I have noticed that when I use the "measure rotation" command that can get two different answers. I realize that the two answers are the result of an arbitrary decision made by the measure tool that result in a +/- of the same angle (i.e. 6 versus 174 degrees). Since I am looking at more several crystal structures, is there a way to force "measure rotation" to always make the same decision so that I know what relative direction the rotations are in to each other? > > Thanks > _______________________________ > Bobby W. Laird From heuser at brandeis.edu Fri May 27 11:44:12 2011 From: heuser at brandeis.edu (Thomas Heuser) Date: Fri, 27 May 2011 14:44:12 -0400 Subject: [Chimera-users] Import IMOD models into Chimera Message-ID: Hi all, Is it possible to open IMOD model files in Chimera? I have used IMOD (with imodmesh) to generate a model of my structure and would now like to load this IMOD model file (.mod) as a volume into Chimera. Is that doable? Thanks a lot in advance and big cheers, Tom -- XXXXXXXXXXXXXXXXXXXXXXX Thomas Heuser Nicastro Lab Rosenstiel Center, MS029 Brandeis University 415 South Street Waltham, MA 02454-9110 Phone: (+ 1) 781 736 2608 From goddard at sonic.net Fri May 27 11:59:03 2011 From: goddard at sonic.net (Tom Goddard) Date: Fri, 27 May 2011 11:59:03 -0700 Subject: [Chimera-users] Import IMOD models into Chimera In-Reply-To: References: Message-ID: <4DDFF477.6020901@sonic.net> Hi Tom, Yes, you should be able to use Chimera File/Open... to open your IMOD surfaces (*.mod). Chimera only reads the binary ".mod" files not the ASCII ones. The IMOD files contain surfaces, not volume data. I think IMOD often uses the file suffix ".rec" for the volume data itself. I think "rec" stands for reconstruction and the actual format is MRC format. Tom > Hi all, > > Is it possible to open IMOD model files in Chimera? I have used IMOD > (with imodmesh) to generate a model of my structure and would now like > to load this IMOD model file (.mod) as a volume into Chimera. Is that > doable? > Thanks a lot in advance and big cheers, > Tom From chimera.maillist at dejung.net Fri May 27 20:57:18 2011 From: chimera.maillist at dejung.net (Mario Dejung) Date: Sat, 28 May 2011 05:57:18 +0200 Subject: [Chimera-users] system freeze completly with ubuntu 10.10 Message-ID: Hello, I have some trouble with chimera on my old laptop. My complete system is freezing after a few seconds. I can not restart X server or switching to a console or anything, even the mouse pointer is not moving. I tried 32 bit chimera 1.5.2 and 1.5.3, both have the same problem. I have 64 MB graphical memory available, but the maps I am loading are very small, like less then 4MB and the system crashs also, even if I open just one map. Does anyone has a good suggestion? Since the whole system is freezing, I am not able to switch back to a terminal to look for error messages or similar. Kind regards Mario From gregc at cgl.ucsf.edu Fri May 27 22:59:34 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Fri, 27 May 2011 22:59:34 -0700 Subject: [Chimera-users] system freeze completly with ubuntu 10.10 In-Reply-To: References: Message-ID: <4DE08F46.6040106@cgl.ucsf.edu> Sounds like a graphics driver bug or a possible graphics card hardware failure or other hardware failure. If you have ATI or NVIDIA graphics, then you should install the proprietary driver. The proprietary drivers are currently faster and more robust than the open-source ones. If you have Intel graphics, my condolences, you'll have to upgrade to Ubuntu 11.04 to get a better graphics driver. To check if it is a hardware problem, if you can boot into Windows, try running the Windows version of Chimera too. If that fails, then it's probably a hardware bug, if it works, then it's probably a software bug. For a better answer, start up chimera, use the Report a Bug dialog, and then exit chimera so your system doesn't freeze. The bug report will tell me what graphics card you have versus what graphics driver you have installed and a few other clues that could help figure this out. -- Greg On 5/27/2011 8:57 PM, Mario Dejung wrote: > Hello, > I have some trouble with chimera on my old laptop. My complete system is > freezing after a few seconds. I can not restart X server or switching to a > console or anything, even the mouse pointer is not moving. > I tried 32 bit chimera 1.5.2 and 1.5.3, both have the same problem. > I have 64 MB graphical memory available, but the maps I am loading are > very small, like less then 4MB and the system crashs also, even if I open > just one map. > > Does anyone has a good suggestion? Since the whole system is freezing, I > am not able to switch back to a terminal to look for error messages or > similar. > > Kind regards > Mario > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Mon May 30 10:10:21 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 30 May 2011 10:10:21 -0700 Subject: [Chimera-users] An ellipsoid around a protein In-Reply-To: <3637.10.128.10.28.1306730718.squirrel@mbu.iisc.ernet.in> References: <3637.10.128.10.28.1306730718.squirrel@mbu.iisc.ernet.in> Message-ID: <257A2D0C-DE98-4C0C-B76F-19CAA56EE699@cgl.ucsf.edu> Dear M, Chimera questions should be sent to chimera-users at cgl.ucsf.edu (CC'd here). In Chimera you can calculate and display the inertia ellispoid for any set of atoms with the command "measure inertia." For example, you could open the protein structure in Chimera, show the command line (from Favorites menu) and then enter the command: measure inertia protein The principal axis information is given in the Reply Log. There are other keywords, such as to control the color of the ellipsoid. See: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 29, 2011, at 9:45 PM, mselvaraj at mbu.iisc.ernet.in wrote: > Dear sir, > I would like to calcualte an ellipsoid with its principle axis for a > protein molecule,given its PDB. I came across your discussion on > chimera-users discussion.. Do you have a program that can calculate the > ellipsoid and its principle axes. It would be very help ful for my > analysis. Thanks in advance. > > yours sincerely, > M. Selvaraj, > Graduate student, > Molecular Biophysis Unit, > Indian Institute of Science, > Bangalore 560 012 > From gtzotzos at me.com Mon May 30 11:25:39 2011 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 30 May 2011 20:25:39 +0200 Subject: [Chimera-users] Molecular representation & FindHbond Message-ID: <4B6DBF1A-767F-4D92-B368-53BFF925112F@me.com> Hi everybody, I've successfully loaded my protein. It is represented in ribbon. I want to select three specific residues (e.g. HIS22, TYR53 and VAL124), show them in ball & stick and find Hbonds between them. I follow the procedure below: 1. select #0:22,53,124. Chimera returns: 55 atoms, 54 bonds 2. show sel 3. repr bs sel 4. FindHbond (see snapshot). Nothing is displayed. Instead, I see under the command window: 109 hydrogen bonds found. These are ALL the Hbonds found in the protein. I'd appreciate your guidance how to deal with this. Another related issue is the carboxy terminal residue. In this case VAL124. It is deprotonated. Is it possible to protonate it and then look for Hbons? Thanks in advance for your advice Regards George From gtzotzos at me.com Mon May 30 11:41:34 2011 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 30 May 2011 20:41:34 +0200 Subject: [Chimera-users] Molecular representation & FindHbond In-Reply-To: <4B6DBF1A-767F-4D92-B368-53BFF925112F@me.com> References: <4B6DBF1A-767F-4D92-B368-53BFF925112F@me.com> Message-ID: <41C4BFF6-2330-41D1-89CA-B4E277FA29E7@me.com> Apologies. I did not attach the snapshot. I do so now Many thanks George -------------- next part -------------- A non-text attachment was scrubbed... Name: snapshot.tiff Type: image/tiff Size: 91636 bytes Desc: not available URL: -------------- next part -------------- On May 30, 2011, at 8:25 PM, George Tzotzos wrote: > Hi everybody, > > I've successfully loaded my protein. It is represented in ribbon. > > I want to select three specific residues (e.g. HIS22, TYR53 and VAL124), show them in ball & stick and find Hbonds between them. > > I follow the procedure below: > > 1. select #0:22,53,124. Chimera returns: 55 atoms, 54 bonds > > 2. show sel > > 3. repr bs sel > > 4. FindHbond (see snapshot). Nothing is displayed. Instead, I see under the command window: 109 hydrogen bonds found. These are ALL the Hbonds found in the protein. > > I'd appreciate your guidance how to deal with this. > > Another related issue is the carboxy terminal residue. In this case VAL124. It is deprotonated. Is it possible to protonate it and then look for Hbons? > > Thanks in advance for your advice > > Regards > > George > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Tue May 31 09:09:22 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 31 May 2011 09:09:22 -0700 Subject: [Chimera-users] Molecular representation & FindHbond In-Reply-To: <41C4BFF6-2330-41D1-89CA-B4E277FA29E7@me.com> References: <4B6DBF1A-767F-4D92-B368-53BFF925112F@me.com> <41C4BFF6-2330-41D1-89CA-B4E277FA29E7@me.com> Message-ID: <01159EC2-D29D-4258-9A83-398D68A9E144@cgl.ucsf.edu> Hi George, Your dialog shows you chose to find H-bonds between the selection and atom spec, but you did not enter any atom spec (command-line-style atom specification). Since the atom spec is blank, the calculation just uses the whole structure. I'm guessing you meant one of the other choices instead, only find H-bonds with at least one end selected, or exactly one end selected, or both ends selected. See: By default the C-term carboxyl is treated as an acceptor only. However, if you really wanted to protonate it you could manually change the atom type of one of the oxygens, for example with a command something like (would change the type of the atom named OXT): setattr a idatmType O3 @oxt Then run AddH, then run FindHBond. However, normally you would not need to add hydrogens before running FIndHBond. Information on atom types: Or, rather than changing the type and adding hydrogens you could just see what atoms are near the C-term carboxyl to "manually" infer whether it could be protonated and H-bonding. The pKa of that group is fairly low, so I would guess that it is very rarely protonated. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 30, 2011, at 11:41 AM, George Tzotzos wrote: > Apologies. I did not attach the snapshot. I do so now > > Many thanks > > George > > > > > > > On May 30, 2011, at 8:25 PM, George Tzotzos wrote: > >> Hi everybody, >> >> I've successfully loaded my protein. It is represented in ribbon. >> >> I want to select three specific residues (e.g. HIS22, TYR53 and VAL124), show them in ball & stick and find Hbonds between them. >> >> I follow the procedure below: >> >> 1. select #0:22,53,124. Chimera returns: 55 atoms, 54 bonds >> >> 2. show sel >> >> 3. repr bs sel >> >> 4. FindHbond (see snapshot). Nothing is displayed. Instead, I see under the command window: 109 hydrogen bonds found. These are ALL the Hbonds found in the protein. >> >> I'd appreciate your guidance how to deal with this. >> >> Another related issue is the carboxy terminal residue. In this case VAL124. It is deprotonated. Is it possible to protonate it and then look for Hbons? >> >> Thanks in advance for your advice >> >> Regards >> >> George >> >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From brianfochtman at gmail.com Fri May 27 08:48:26 2011 From: brianfochtman at gmail.com (Brian Fochtman) Date: Fri, 27 May 2011 11:48:26 -0400 Subject: [Chimera-users] Asymmetric partial charges on symmetric atoms Message-ID: Hi, When adding partial charges (AM1-BCC) to small molecules in chimera, we observed that atoms in symmetrical groups are not assigned the same partial charge. Specifically, the two oxygens in a carboxyl group are not assigned the same partial charge. See excerpt from mol2 file below: carboxyl: 20 C20 23.4850 19.6920 64.8870 C.2 1 BCZ 0.9226 21 O21 22.2660 19.7760 65.0340 O.co2 1 BCZ -0.9253 22 O22 24.2040 20.8120 64.7970 O.co2 1 BCZ -0.7643 There is a significant difference in partial charge between the two carboxyl oxygens (0.161). This problem was observed in both older (with mopac) and newer (with sqm) versions of chimera. The molecule is peramivir from the pdb1L7F crystal structure. Similar problems were observed for other molecules that inhibit Neuraminidase for example those 1L__ pdb structures. This problem is also observed when assigning am1bcc charges to the mol2 file using antechamber/sqm directly. Best Regards, Brian Fochtman, Trent Balius, Sudipto Mukherjee -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1l7f.lig.mol2 Type: application/octet-stream Size: 5236 bytes Desc: not available URL: From mselvaraj at mbu.iisc.ernet.in Tue May 31 01:54:10 2011 From: mselvaraj at mbu.iisc.ernet.in (mselvaraj at mbu.iisc.ernet.in) Date: Tue, 31 May 2011 14:24:10 +0530 (IST) Subject: [Chimera-users] Chimera with 50000 pdb files Message-ID: <36559.10.128.10.28.1306832050.squirrel@mbu.iisc.ernet.in> Dear all, I have some 50000 pdbs obtained from a md simulation of my protein. I would like to calculate ellipsoid (with 'measure inertia' command) around the protein molecule in each pdb and get their axes. Is there a provision/script in chimera to run multiple pdbs and get the axes in a file separately? Any suggestions on this will be helpful. Thanks in advance. yours truly, M. Selvaraj, Graduate student, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From meng at cgl.ucsf.edu Tue May 31 11:20:29 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 31 May 2011 11:20:29 -0700 Subject: [Chimera-users] Chimera with 50000 pdb files In-Reply-To: <36559.10.128.10.28.1306832050.squirrel@mbu.iisc.ernet.in> References: <36559.10.128.10.28.1306832050.squirrel@mbu.iisc.ernet.in> Message-ID: Dear M, There are a few possibilities: (A) open the PDBs as a trajectory in our trajectory viewer, MD Movie, then in that tool, define a per-frame script that includes the measure inertia command. Opening all those PDBs may take a lot of memory... it might not be possible to open them all at once. (B) instead of PDBs, open the trajectory in its original format in MD Movie, then use per-frame script as above. MD Movie understands several formats (see below), and most are more memory-efficient in Chimera than multiple PDBs. (C) use python script to loop through all your PDB files, opening a file, running the command(s), closing, opening the next one, etc. This would use less memory than (A) or (B). In all cases, the information would go to the Reply Log (under Favorites in the menu), and you can save its contents to a text file. More details: (A) or (B). Start MD Movie from menu, under Tools... MD/Ensemble Analysis. Choose input format and then browse to your files. See the MD Movie man page: The "Startup and Input" section lists the known formats. The "Per-Frame Scripts" section talks about how to run Chimera command(s) for each frame of the trajectory. Your per-frame Chimera script could be something like: measure inertia protein showEllipsoid false (C). Here is info on how to loop through multiple structures in Chimera using Python: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 31, 2011, at 1:54 AM, mselvaraj at mbu.iisc.ernet.in wrote: > Dear all, > I have some 50000 pdbs obtained from a md simulation of my protein. I > would like to calculate ellipsoid (with 'measure inertia' command) around > the protein molecule in each pdb and get their axes. Is there a > provision/script in chimera to run multiple pdbs and get the axes in a > file separately? Any suggestions on this will be helpful. Thanks in > advance. > > yours truly, > M. Selvaraj, > Graduate student, > Molecular Biophysics Unit, > Indian Institute of Science, > Bangalore 560 012. > From pett at cgl.ucsf.edu Tue May 31 11:56:42 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 31 May 2011 11:56:42 -0700 Subject: [Chimera-users] Asymmetric partial charges on symmetric atoms In-Reply-To: References: Message-ID: Hi Brian, Both sqm and mopac are doing a QM charge calculation, which considers the overall electronic environment. The more negatively charged carboxylate oxygen is on the "side" of the molecule that has the positively-charged guanidinium group which seems to cause some of the negative charge to be shifted to that oxygen. Chopping out the guanidinium group results in the carboxylate oxygens being given charges that differ by 0.011. If I eliminate all other ring substituents, which leaves a much truer symmetric environment for the carboxylate oxygens, then sqm computes equal charges for the oxygens (mol2 file attached): 5 C6 23.4850 19.6920 64.8870 C.2 1 BCZ 0.9126 6 O8 22.2660 19.7760 65.0340 O.co2 1 BCZ -0.8493 7 O7 24.2040 20.8120 64.7970 O.co2 1 BCZ -0.8493 I guess the take home is that the asymmetric charges on the carboxylate oxygens is actually the expected behavior. Now, if you feel that the charge transfer is unrealistically high you would have to take that issue up with the folks on the Amber mailing list -- I certainly don't have the expertise to make those kinds of changes! Or if you felt that Chimera should be invoking sqm with something other than sqm's default settings, that is something I could offer control over at least. Let me know if that is the case. --Eric -------------- next part -------------- A non-text attachment was scrubbed... Name: ring.mol2 Type: chemical/x-mol2 Size: 1728 bytes Desc: not available URL: -------------- next part -------------- On May 27, 2011, at 8:48 AM, Brian Fochtman wrote: > Hi, > > When adding partial charges (AM1-BCC) to small molecules in chimera, > we observed that atoms in symmetrical groups are not assigned the > same partial charge. Specifically, the two oxygens in a carboxyl > group are not assigned the same partial charge. See excerpt from > mol2 file below: > > carboxyl: > 20 C20 23.4850 19.6920 64.8870 C.2 1 BCZ > 0.9226 > 21 O21 22.2660 19.7760 65.0340 O.co2 1 BCZ > -0.9253 > 22 O22 24.2040 20.8120 64.7970 O.co2 1 BCZ > -0.7643 > > There is a significant difference in partial charge between the two > carboxyl oxygens (0.161). > > This problem was observed in both older (with mopac) and newer (with > sqm) versions of chimera. > > The molecule is peramivir from the pdb1L7F crystal structure. > Similar problems were observed for other molecules that inhibit > Neuraminidase for example those 1L__ pdb structures. > > This problem is also observed when assigning am1bcc charges to the > mol2 file using antechamber/sqm directly. > > Best Regards, > > Brian Fochtman, > Trent Balius, > Sudipto Mukherjee > > > <1l7f.lig.mol2>_______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users