From huiya at tamu.edu Tue Sep 3 08:24:22 2019 From: huiya at tamu.edu (Huiya Zhou) Date: Tue, 3 Sep 2019 10:24:22 -0500 Subject: [Chimera-users] How could I know the segment label Message-ID: <7C71CD8D-9E7C-42E2-B13B-C253D305D50B@tamu.edu> Hi, I use the ?Segment Map? for the volume data to divide the density map into parts. How could I know the information of each region? For example, the label, the average value of each region. I also would like to know the regions which are connected with one specific region. How could I obtain information in python script? Thanks, Huiya From jamendozam at unal.edu.co Mon Sep 2 18:46:32 2019 From: jamendozam at unal.edu.co (Jose Alirio Mendoza Mesa) Date: Mon, 2 Sep 2019 20:46:32 -0500 Subject: [Chimera-users] Support chimera Message-ID: Hi there, my name is Jose Alirio Mendoza. Currently, I am carrying out my PHD thesis in which I am using the chimera program to show the tomography results. Nevertheless, I am being presented some problems when trying to measure my particle in Chimera. The file of my product is ?mrc? and I have been investigating about chimera usage where I have realized that the file must be ?pdb? for the program to recognize it. I do not really know how to convert my molecule to the required file, and I guess that is the problem by which I cannot measure the distance of my particle. When I click ?tools ? structure analysis ? distance? it does not appear the code of my molecule as in picture below [image: imagen.png] This is my particle and what I get when using the tool for measuring. I have other three tomography for one publication. [image: imagen.png] There is not any code in the tool square and that is why I guess to no be able to measure the particle. Other tool I tried to use is the scale bar, however the value of it is not according to my calibration. [image: imagen.png] How may I change that calibration? In our research group we want the publish the articles citing chimera as visualization tool so we would really appreciate your help. Here is attached the file we have worked in chimera. pollo 13.mrc -- *Qco. JOSE ALIRIO MENDOZA MESA* Candidato a Doctor en ciencias Universidad Nacional de Colombia. 3165000 Ext. 14475 *LABORATORIO DE CATALISIS HETEREOGENEA* -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: imagen.png Type: image/png Size: 63463 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: imagen.png Type: image/png Size: 82213 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: imagen.png Type: image/png Size: 84951 bytes Desc: not available URL: From meng at cgl.ucsf.edu Tue Sep 3 08:48:08 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 3 Sep 2019 08:48:08 -0700 Subject: [Chimera-users] Support chimera In-Reply-To: References: Message-ID: Hello Jose Alirio Mendoza, Chimera can read ?.mrc? files and many other map formats, as listed here. When you open the mrc file, it will be displayed, as you already show in your images. (You do not need a .pdb file, which is instead for atomic coordinates. Since those two kinds of file formats contain different information, you cannot convert between them.) Then you can measure the surface area and the surface-enclosed volume with other tools in the menu under Tools? Volume Data: Measure and Color Blobs, Measure Volume and Area. See their help pages for details: If you want to measure distance, however, you have to first add ?markers? on the surface to define the endpoints of the distance measurement. See Tools? Volume Data? Volume Tracer for information on adding markers. The markers are essentially fake atoms, and you can select any pair of markers that you previously added and then use the Distances tool (the same one that is used for atomic distances) to measure the distance between them: However, before you measure anything, you may need to define the size of your map correctly (this should also set the calibration for scale bar). In the Volume Viewer tool with the map histogram that is automatically shown when you open the mrc file, use menu: Features.. Coordinates to show more options in the tool, and then adjust ?voxel size? values as needed. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 2, 2019, at 6:46 PM, Jose Alirio Mendoza Mesa wrote: > > Hi there, my name is Jose Alirio Mendoza. Currently, I am carrying out my PHD thesis in which I am using the chimera program to show the tomography results. Nevertheless, I am being presented some problems when trying to measure my particle in Chimera. The file of my product is ?mrc? and I have been investigating about chimera usage where I have realized that the file must be ?pdb? for the program to recognize it. I do not really know how to convert my molecule to the required file, and I guess that is the problem by which I cannot measure the distance of my particle. When I click ?tools ? structure analysis ? distance? it does not appear the code of my molecule as in picture below > > This is my particle and what I get when using the tool for measuring. I have other three tomography for one publication. > > > There is not any code in the tool square and that is why I guess to no be able to measure the particle. > > Other tool I tried to use is the scale bar, however the value of it is not according to my calibration. > > > How may I change that calibration? > > In our research group we want the publish the articles citing chimera as visualization tool so we would really appreciate your help. > > Here is attached the file we have worked in chimera. > > pollo 13.mrc > > -- > Qco. JOSE ALIRIO MENDOZA MESA > Candidato a Doctor en ciencias > Universidad Nacional de Colombia. > 3165000 Ext. 14475 > > LABORATORIO DE CATALISIS HETEREOGENEA From goddard at sonic.net Tue Sep 3 15:37:44 2019 From: goddard at sonic.net (Tom Goddard) Date: Tue, 3 Sep 2019 15:37:44 -0700 Subject: [Chimera-users] How could I know the segment label In-Reply-To: <7C71CD8D-9E7C-42E2-B13B-C253D305D50B@tamu.edu> References: <7C71CD8D-9E7C-42E2-B13B-C253D305D50B@tamu.edu> Message-ID: <50F572C5-23FD-495D-8C05-D9D5A7AA7781@sonic.net> Hi Huiya, The Segment Map tool has an Attributes Table under the Region menu that gives some info about each segmented region, although not the average density value. To extract the per-region values you will need to be comfortable reading other people's complex and messy Python code. The Segment Map code was written outside our lab (by Greg Pintilie) and is many thousands of lines of code. The code is in your Chimera distribution chimera/share/Segger/*.py or on Mac (Chimera.app/Contents/Resources/Share/Segger/*.py). You would want to look at regions.py at the Segmentation and Region classes. Here's an example accessing the region data from Python where I just typed Python into the Chimera Python shell (menu Tools / General Controls / IDLE). >>> chimera.openModels.list() [, <_molecule.Molecule object at 0x7fd58943ed78>, ] >>> s = chimera.openModels.list()[2] >>> s.regions set([, , , , , , , , , , , , , , , , , , , , , , , , , , , ]) >>> v = chimera.openModels.list()[0] >>> for r in s.regions: p = r.map_points() vals = v.interpolated_values(p) print ('region ', r.rid, ' average density ', vals.mean()) ('region ', 572, ' average density ', 1.4155183789779682) ('region ', 573, ' average density ', 1.4989512825784412) ('region ', 574, ' average density ', 1.4972014250578705) ('region ', 575, ' average density ', 1.4125457019340701) ('region ', 576, ' average density ', 1.5008908941625652) ('region ', 577, ' average density ', 1.4134244018033972) ('region ', 578, ' average density ', 1.4970225423711425) ('region ', 579, ' average density ', 1.5016543386711971) ('region ', 580, ' average density ', 1.5008901873280978) ('region ', 581, ' average density ', 1.4134236579258075) ('region ', 582, ' average density ', 1.5004523296628476) ('region ', 583, ' average density ', 1.4154380056984164) ('region ', 584, ' average density ', 1.4950021844161183) ('region ', 585, ' average density ', 1.5016561743149943) ('region ', 586, ' average density ', 1.4153593474743413) ('region ', 587, ' average density ', 1.4154392068823032) ('region ', 588, ' average density ', 1.4101623202035325) ('region ', 589, ' average density ', 1.4101611357735748) ('region ', 590, ' average density ', 1.4110644353261694) ('region ', 591, ' average density ', 1.4967169173433399) ('region ', 592, ' average density ', 1.4972017867476852) ('region ', 593, ' average density ', 1.4930268474402093) ('region ', 594, ' average density ', 1.4155168848492963) ('region ', 595, ' average density ', 1.5004516876702199) ('region ', 596, ' average density ', 1.4125473394626524) ('region ', 597, ' average density ', 1.4153560563629748) ('region ', 598, ' average density ', 1.4989507177649652) ('region ', 571, ' average density ', 1.4110653252676943) >>> Tom > On Sep 3, 2019, at 8:24 AM, Huiya Zhou wrote: > > Hi, > > I use the ?Segment Map? for the volume data to divide the density map into parts. How could I know the information of each region? For example, the label, the average value of each region. I also would like to know the regions which are connected with one specific region. How could I obtain information in python script? > > Thanks, > Huiya > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From pett at cgl.ucsf.edu Tue Sep 3 16:24:28 2019 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 3 Sep 2019 16:24:28 -0700 Subject: [Chimera-users] Way to compute residue wise RMSD using python script in chimera: In-Reply-To: References: Message-ID: Hi Kamalesh, If you are familiar with Python, there is a script attached to this previous mailing-list message: [Chimera-users] Writing alignment and RMSD out that would be easy to modify to do what you want. You would just remove the parts the parts that used Multalign Viewer to write the sequence alignment. The RMSD that the MatchMaker.match() function returns is a carbon-alpha RMSD, so if you needed a full-backbone RMSD that would be more work. Let me know and I can offer guidance on that. Also, match() returns the overall RMSD of the match. To get the per-residue RMSD you would loop over the atom lists returned by the match() function and for corresponding pairs get the distance (== RMSD for two atoms) with: atom1.xformCoord().distance(atom2.xformCoord()). For output purposes you can get a string representation of an atom?s residue with str(atom.residue). Also, unfortunately the attachment to the message has a ?.bin? suffix despite being from a Python file that had a ?.py? suffix, so if that?s a problem let me know and I can send you the .py file directly. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Aug 31, 2019, at 7:20 AM, Kamalesh Damodaran wrote: > > Dear sir/madam, > > I would like to superimpose the two structures and compute the residue wise RMSD values. With Gui support in chimera, I opened the two structures and used Matchmaker to superimpose two structures. In Matchmaker, I checked the box 'Show pairwise alignment(s)' and click Apply, subsequently it displays MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone --> Save --> filenamegiven. This process would give me residue wise RMSD score only for backbone atoms in .hdr format. > > I wants to write python script to do the same, so that I will compare large number of structures, and my script is able to perform till the procedure of superimposition using matchmaker and display MultAlignViewer dialogue box. I don't know the way to store the RMSD : backbone and RMSD : calpha in .hdr format using python script through chimera. > > Can some one please help me in this. The reason why I specifically want to do in this approach is, because among the two structures, some residues of one structure is missing. Since this approach will compute RMSD only for the matching residues, I am interested in this. > > Hope my question is not confusing. Thanks in advance. > > Best regards, > Kamalesh D. > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From artur.biela at uj.edu.pl Thu Sep 5 01:10:47 2019 From: artur.biela at uj.edu.pl (Artur Biela) Date: Thu, 5 Sep 2019 08:10:47 +0000 Subject: [Chimera-users] cage builder Message-ID: <6e89fcfdca87496a835ae09a19ccefe4@MB3.uj.edu.pl> Hi all, I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. My question is: is there any option to use for example octagons, decagons or even more-gons? Thank in advance Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow artur.biela at uj.edu.pl http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory publons =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Sep 5 09:41:11 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 5 Sep 2019 09:41:11 -0700 Subject: [Chimera-users] cage builder In-Reply-To: <6e89fcfdca87496a835ae09a19ccefe4@MB3.uj.edu.pl> References: <6e89fcfdca87496a835ae09a19ccefe4@MB3.uj.edu.pl> Message-ID: <73545D03-25AC-45B7-8FB1-A8FDF31F5C1C@cgl.ucsf.edu> Hi Artur, Sorry, there is no option for polygons with N sides >7 in the Cage Builder tool. You can create arbitrary polygon objects and other shapes in the BILD input format (a simple text file), but in that case you have to specify the vertex coordinates yourself ? it doesn?t automatically form enclosed cages. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 5, 2019, at 1:10 AM, Artur Biela wrote: > > Hi all, > > I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. > My question is: is there any option to use for example octagons, decagons or even more-gons? > > Thank in advance > Artur > From goddard at sonic.net Thu Sep 5 10:55:41 2019 From: goddard at sonic.net (Tom Goddard) Date: Thu, 5 Sep 2019 10:55:41 -0700 Subject: [Chimera-users] cage builder In-Reply-To: <6e89fcfdca87496a835ae09a19ccefe4@MB3.uj.edu.pl> References: <6e89fcfdca87496a835ae09a19ccefe4@MB3.uj.edu.pl> Message-ID: Hi Artur, You can modify one line of the Cage Builder python code in your copy of Chimera to create buttons to make polygons with more sides. The file to modify is chimera/share/CageBuilder/gui.py or on Mac Chimera.app/Contents/Resources/share/CageBuilder/gui.py and the line to modify is apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,8)] which you could change replacing 8 by 16 to get apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,16)] which would create buttons in the Cage Builder panel for polygons with 3 through 15 sides. After you edit the file with a text editor (keep the indentation of the line the same as this is important in Python), then restart Chimera and it will have the new buttons. Tom > On Sep 5, 2019, at 1:10 AM, Artur Biela wrote: > > Hi all, > > I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. > My question is: is there any option to use for example octagons, decagons or even more-gons? > > Thank in advance > Artur > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > Artur BIELA, PhD > Scientific Assistant > Bionanoscience and Biochemistry Laboratory > Malopolska Centre of Biotechnology > Jagiellonian University > 7A, Gronostajowa Street > 30-387 Krakow > Poland > > Department of Cell Biology and Imaging > Institute of Zoology and Biomedical Research > Jagiellonian University > Gronostajowa 9 > 30-387 Krakow > > artur.biela at uj.edu.pl > http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory > publons > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From artur.biela at uj.edu.pl Fri Sep 6 00:01:41 2019 From: artur.biela at uj.edu.pl (Artur Biela) Date: Fri, 6 Sep 2019 07:01:41 +0000 Subject: [Chimera-users] ODP: cage builder In-Reply-To: References: <6e89fcfdca87496a835ae09a19ccefe4@MB3.uj.edu.pl>, Message-ID: <9c899983d2464300b3702313e4da5066@MB3.uj.edu.pl> Thank you Tom, Everything is working now perfectly. Best, Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow artur.biela at uj.edu.pl http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory publons =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Od: Tom Goddard Wys?ano: czwartek, 5 wrze?nia 2019 19:55 Do: Artur Biela DW: chimera-users at cgl.ucsf.edu Temat: Re: [Chimera-users] cage builder Hi Artur, You can modify one line of the Cage Builder python code in your copy of Chimera to create buttons to make polygons with more sides. The file to modify is chimera/share/CageBuilder/gui.py or on Mac Chimera.app/Contents/Resources/share/CageBuilder/gui.py and the line to modify is apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,8)] which you could change replacing 8 by 16 to get apb = [('%d' % n , lambda n=n: self.attach_polygons(n)) for n in range(3,16)] which would create buttons in the Cage Builder panel for polygons with 3 through 15 sides. After you edit the file with a text editor (keep the indentation of the line the same as this is important in Python), then restart Chimera and it will have the new buttons. Tom On Sep 5, 2019, at 1:10 AM, Artur Biela > wrote: Hi all, I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. My question is: is there any option to use for example octagons, decagons or even more-gons? Thank in advance Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow artur.biela at uj.edu.pl http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory publons =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From kamaleshdams at gmail.com Mon Sep 9 06:31:11 2019 From: kamaleshdams at gmail.com (Kamalesh Damodaran) Date: Mon, 9 Sep 2019 19:01:11 +0530 Subject: [Chimera-users] Way to compute residue wise RMSD using python script in chimera: In-Reply-To: References: Message-ID: Hi Eric, Thank you so much for your guidance and the python script. I got everything what I was looking for. Thanks and regards, Kamalesh D. On Wed, 4 Sep 2019 at 04:54, Eric Pettersen wrote: > Hi Kamalesh, > If you are familiar with Python, there is a script attached to this > previous mailing-list message: [Chimera-users] Writing alignment and > RMSD out > that > would be easy to modify to do what you want. You would just remove the > parts the parts that used Multalign Viewer to write the sequence > alignment. The RMSD that the MatchMaker.match() function returns is a > carbon-alpha RMSD, so if you needed a full-backbone RMSD that would be more > work. Let me know and I can offer guidance on that. Also, match() returns > the overall RMSD of the match. To get the per-residue RMSD you would loop > over the atom lists returned by the match() function and for corresponding > pairs get the distance (== RMSD for two atoms) with: > atom1.xformCoord().distance(atom2.xformCoord()). For output purposes you > can get a string representation of an atom?s residue with str(atom.residue). > Also, unfortunately the attachment to the message has a ?.bin? suffix > despite being from a Python file that had a ?.py? suffix, so if that?s a > problem let me know and I can send you the .py file directly. > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > On Aug 31, 2019, at 7:20 AM, Kamalesh Damodaran > wrote: > > Dear sir/madam, > > I would like to superimpose the two structures and compute the residue > wise RMSD values. With Gui support in chimera, I opened the two structures > and used Matchmaker to superimpose two structures. In Matchmaker, I checked > the box 'Show pairwise alignment(s)' and click Apply, subsequently it > displays MultAlignViewer dialogue box, where --> Headers --> RMSD : > backbone --> Save --> filenamegiven. This process would give me residue > wise RMSD score only for backbone atoms in .hdr format. > > I wants to write python script to do the same, so that I will compare > large number of structures, and my script is able to perform till the > procedure of superimposition using matchmaker and display MultAlignViewer > dialogue box. I don't know the way to store the RMSD : backbone and RMSD : > calpha in .hdr format using python script through chimera. > > Can some one please help me in this. The reason why I specifically want to > do in this approach is, because among the two structures, some residues of > one structure is missing. Since this approach will compute RMSD only for > the matching residues, I am interested in this. > > Hope my question is not confusing. Thanks in advance. > > Best regards, > Kamalesh D. > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Sep 9 07:34:35 2019 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 9 Sep 2019 07:34:35 -0700 Subject: [Chimera-users] Way to compute residue wise RMSD using python script in chimera: In-Reply-To: References: Message-ID: <50E8457A-0CF1-43A0-9C9D-9A78FEEEF4A1@cgl.ucsf.edu> Great! ?Eric > On Sep 9, 2019, at 6:31 AM, Kamalesh Damodaran wrote: > > Hi Eric, > > Thank you so much for your guidance and the python script. I got everything what I was looking for. > > Thanks and regards, > Kamalesh D. > > On Wed, 4 Sep 2019 at 04:54, Eric Pettersen > wrote: > Hi Kamalesh, > If you are familiar with Python, there is a script attached to this previous mailing-list message: [Chimera-users] Writing alignment and RMSD out that would be easy to modify to do what you want. You would just remove the parts the parts that used Multalign Viewer to write the sequence alignment. The RMSD that the MatchMaker.match() function returns is a carbon-alpha RMSD, so if you needed a full-backbone RMSD that would be more work. Let me know and I can offer guidance on that. Also, match() returns the overall RMSD of the match. To get the per-residue RMSD you would loop over the atom lists returned by the match() function and for corresponding pairs get the distance (== RMSD for two atoms) with: atom1.xformCoord().distance(atom2.xformCoord()). For output purposes you can get a string representation of an atom?s residue with str(atom.residue). > Also, unfortunately the attachment to the message has a ?.bin? suffix despite being from a Python file that had a ?.py? suffix, so if that?s a problem let me know and I can send you the .py file directly. > > ?Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > >> On Aug 31, 2019, at 7:20 AM, Kamalesh Damodaran > wrote: >> >> Dear sir/madam, >> >> I would like to superimpose the two structures and compute the residue wise RMSD values. With Gui support in chimera, I opened the two structures and used Matchmaker to superimpose two structures. In Matchmaker, I checked the box 'Show pairwise alignment(s)' and click Apply, subsequently it displays MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone --> Save --> filenamegiven. This process would give me residue wise RMSD score only for backbone atoms in .hdr format. >> >> I wants to write python script to do the same, so that I will compare large number of structures, and my script is able to perform till the procedure of superimposition using matchmaker and display MultAlignViewer dialogue box. I don't know the way to store the RMSD : backbone and RMSD : calpha in .hdr format using python script through chimera. >> >> Can some one please help me in this. The reason why I specifically want to do in this approach is, because among the two structures, some residues of one structure is missing. Since this approach will compute RMSD only for the matching residues, I am interested in this. >> >> Hope my question is not confusing. Thanks in advance. >> >> Best regards, >> Kamalesh D. >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From woolim at gist.ac.kr Mon Sep 9 09:55:30 2019 From: woolim at gist.ac.kr (Woorim Choi) Date: Tue, 10 Sep 2019 01:55:30 +0900 Subject: [Chimera-users] DNA drawing inquiry In-Reply-To: References: <632ad178-a5b4-9750-9eea-233b37803b91@fourmentinguilbert.org> Message-ID: An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Sep 9 14:42:02 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 9 Sep 2019 14:42:02 -0700 Subject: [Chimera-users] DNA drawing inquiry In-Reply-To: References: <632ad178-a5b4-9750-9eea-233b37803b91@fourmentinguilbert.org> Message-ID: <5D486B69-B632-4E04-B7AC-C2702315334B@cgl.ucsf.edu> HI Woorim Choi, Sorry no, Chimera does not have molecule creation by hand-drawing. It does not have random structure generation either. Sincerely, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 9, 2019, at 9:55 AM, Woorim Choi wrote: > >> Dear Chimera >> My name is Woorim. > In Chimera, I want to draw the random position of DNA. It is possible? > > And is it possible to input random x,y,z coordinate for the drawing? > > And I want to know whether the coding command or command function is supported or not. > > > > Thank you > > Sincerely, > > Woorim Choi > > > --------- ?? ?? --------- > ???? : "Damien Larivi?re" > ???? : Woorim Choi , > ???? : 2019? Sep 9?(Mon) 16:18:40 > ?? : Re: Molecule drawing problem > Dear Woorim, > > Thanks for using the GraphiteLifeExplorer software. > > This is a common issue, I guess, you are facing. > > Once the software is launched, you have this blue screen which is empty. What you have done so far is to create your DNA molecule directly from this empty space. > Before creating any DNA molecule, you first must open a PDB file, the one you want, or a previous DNA model. Once the molecule corresponding to the PDB file is displayed, then you can start drawing your DNA trace and display it as an atomic model. Once your DNA molecule is rendered as an atomic model you can delete the molecule corresponding to the PDB file you opened in first instance. > The reason for doing this way is that the default width of the blue screen at the start is less than the length of 1 base pair (and the software must display 1 bp at least). Opening a PDB file adjusts automatically the width of the screen. We should have corrected this issue by fixing a default width at the start. > > This is explained here (jump to the section "Starting DNA modeling from scratch: What you must be aware of"): http://www.lifeexplorer.info/tutorials/getting-started/ > > Let us know if it is OK now. I am also interested in what you plan to do with the tool. > Best, > > Damien > > Le 08/09/2019 ? 17:11, Woorim Choi a ?crit : >> Dear Life explorer, >> >> My name is Woorim. >> I follow the tutorial for drawing DNA molecule. >> https://www.youtube.com/watch?v=9db1hXZARoo >> However, I cant see the molecules.( I have attached my setting) >> Furthermore, can I get an old version of the SW like the link? >> >> Thank you >> >> >> Sincerely, >> >> >> Woorim Choi From samo.lesnik at gmail.com Tue Sep 10 09:36:26 2019 From: samo.lesnik at gmail.com (=?UTF-8?B?U2FtbyBMZcWhbmlr?=) Date: Tue, 10 Sep 2019 18:36:26 +0200 Subject: [Chimera-users] Modeller from a Python script Message-ID: Dear Madam/Sir, I would like to run the Modeller missing loop function implemented in Chimera by using a Python script, as I want to go through a number of protein structures. Is this possible? I do not find the appropriate commands in the comand list. I would use a local instalation of Modeller. Thank you for your help. Best regards, Samo -------------- next part -------------- An HTML attachment was scrubbed... URL: From underoath006 at gmail.com Tue Sep 10 11:15:19 2019 From: underoath006 at gmail.com (Ahmad Khalifa) Date: Tue, 10 Sep 2019 14:15:19 -0400 Subject: [Chimera-users] APBS electrostatic potential map not visible Message-ID: Hello, After PDB2PQR and APBS calculation, I get an .dx that I can't view (doesn't appear when I click show), let alone color. I tried to launch volume viewer, it does display a surface. What am I doing wrong? Regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Sep 10 12:53:06 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 10 Sep 2019 12:53:06 -0700 Subject: [Chimera-users] Modeller from a Python script In-Reply-To: References: Message-ID: Hi Samo, I believe it would make more sense to script Modeller directly since you have a local installation. Chimera doesn?t have commands for running Modeller. If you just script Modeller, you have access to all its options, not just the few that happen to show up in the Chimera interface. See the Modeller website and documentation there: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 10, 2019, at 9:36 AM, Samo Le?nik wrote: > > Dear Madam/Sir, > I would like to run the Modeller missing loop function implemented in Chimera by using a Python script, as I want to go through a number of protein structures. > > Is this possible? I do not find the appropriate commands in the comand list. I would use a local instalation of Modeller. > > Thank you for your help. > Best regards, > Samo From meng at cgl.ucsf.edu Tue Sep 10 13:01:38 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 10 Sep 2019 13:01:38 -0700 Subject: [Chimera-users] APBS electrostatic potential map not visible In-Reply-To: References: Message-ID: <3696B2C6-1CD4-499E-89D2-0F5E69D27EFE@cgl.ucsf.edu> Hi Ahmad, I do not understand your description, because you said that volume view does display a surface? so it IS shown. Maybe you mean that when it is first opened, nothing displays. By default it might not be displayed because usually these electrostatic potential (ESP) maps are used to color some other surface, the surface of the protein. So you would need to show the surface of the protein in the usual way (e.g. command ?surface?) and then use the Surface Color (Electrostatic Surface Coloring) tool or ?scolor? command to color that molecular surface by the values in the ESP map. This tool may appear automatically when you open the ESP file (.dx or .phi). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 10, 2019, at 11:15 AM, Ahmad Khalifa wrote: > > Hello, > After PDB2PQR and APBS calculation, I get an .dx that I can't view (doesn't appear when I click show), let alone color. > I tried to launch volume viewer, it does display a surface. > What am I doing wrong? > Regards. From sunyeping at aliyun.com Wed Sep 11 04:08:46 2019 From: sunyeping at aliyun.com (sunyeping) Date: Wed, 11 Sep 2019 19:08:46 +0800 Subject: [Chimera-users] =?utf-8?q?How_to_analyze_cryo-EM_reconstruction_m?= =?utf-8?q?ap_of_virus_and_prepare_publishable_figures=3F?= Message-ID: Dear all, I am new to cryo-EM structural biology. Now I have a cryo-EM reconstruction map for a virus particle. I wish to analyze the characteristics of the virus, such as the h, k and t number, the component of an cryo-EM asymmetric unit of the capid and prepare some publishable figures. I have no idea how to do these things. Could all these be done with Chimera? Is there any tutorials or manual for these calculation, visualization and drawing? If you could recommend some ways by which I can learn to do these, I would be greatly grateful. Best regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Sep 11 10:09:21 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Sep 2019 10:09:21 -0700 Subject: [Chimera-users] How to analyze cryo-EM reconstruction map of virus and prepare publishable figures? In-Reply-To: References: Message-ID: <84025DF8-88ED-44C3-8D97-3E58ABEF6053@cgl.ucsf.edu> Hello, It is beyond the scope of this mailing list to explain all steps of cryo-EM map analysis and processing (even if I had that knowledge, which I don?t). There are probably entire textbooks on the subject. Some ideas are to work with experienced cryoEM laboratories, and to read the experimental methods sections of papers. Some journals even have protocols with more details about the steps of the analysis. As for Chimera specifically, it can help with some (but perhaps not all, depending on the project) tasks related to segmentation and fitting atomic structures, and you can certainly use it to make figures for publications. See the Guide to Volume Data Display in Chimera: See the online tutorials, several of which include cryoEM data: The User Guide also fully describes each of the tools in menu: Tools? Volume Data? [several tools]. You can press the Help button on each dialog to see its help page. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 11, 2019, at 4:08 AM, sunyeping wrote: > > Dear all, > I am new to cryo-EM structural biology. Now I have a cryo-EM reconstruction map for a virus particle. I wish to analyze the characteristics of the virus, such as the h, k and t number, the component of an cryo-EM asymmetric unit of the capid and prepare some publishable figures. I have no idea how to do these things. Could all these be done with Chimera? Is there any tutorials or manual for these calculation, visualization and drawing? If you could recommend some ways by which I can learn to do these, I would be greatly grateful. > Best regards From meng at cgl.ucsf.edu Wed Sep 11 15:23:37 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Sep 2019 15:23:37 -0700 Subject: [Chimera-users] Electrostatic potential molecular surfaces In-Reply-To: References: Message-ID: <3725992C-B638-4531-9385-CB5148BCACA2@cgl.ucsf.edu> Hi Fernando, Our resources don?t allow spending much time on consulting with individual research projects, sorry, and I can only answer mostly as it pertains to Chimera as I don?t know the details of parameters developed by other people or other programs. Also Chimera questions should be sent to this mailing list instead of to me directly so that other people can also benefit, unless private data are discussed or attached. You found an old script that is really special-purpose, finding the surface area that is more red than blue after coloring by electrostatic potential. Note that this would include surface that looks white but has a tiny, tiny tint of pinkishness. Also, the surface area that is more blue than red is just the complement of the surface that is more red than blue. In other words, if the surface is 75% red>blue then it is 25% blue>red because very little if any will be pure white. They always add up to the total surface. So no, you cannot use these scripts to figure out how much of the surface is polar or nonpolar. It may not matter given the above, but which method, set of charges, and what parameter values to use for electrostatic potential (ESP) calculations are research decisions that I cannot make for you. There are always tradeoffs, and different people have different opinions, etc. I don?t know python, but your generalization to coloring by hydrophobicity by identifying cornflower blue vs.goldenrod might be wrong. Red vs. blue is simpler since they are RGB color components. However, even if the color comparison is done correctly, the logical problem is the same, they always add up to the whole surface, and nearly white areas will always be combined with one side or the other. However, you can get the total surface area given some range of hydrophobicity values independent of any coloring. Hydrophobicity in this case is just a constant lookup value for each type of amino acid, according to this table (kdHydrophobicity column): You would have to decide yourself which range of values is polar or nonpolar, but then you could just select all the residues that are less than or more than a certain value, e.g. command: select :/kdHydrophobicity>0.0 Alternatively you could just use command: select polar select ~polar ?but you might not agree with what amino acids are considered polar, as shown in a table in this page: Then if surface is shown you could add up the area for the selected residues, e.g. menu: Tools? Structure Analysis? Attribute Calculator, and in that tool calculate attribute named whatever you want for ?molecules? with Formula: sum(areaSAS.residue) (? or SES instead of SAS, to be compared with the corresponding total area given in the Reply Log when you show the surface) with option to ?Restrict formula domain to current selection? and ?Show calculation results in Reply Log" turned on, other options turned off, click Apply. Totally separate and not related to Chimera, but I happen to know of this web server you might be interested in, for comparing ESP of related proteins: Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 11, 2019, at 2:16 PM, Fernando Villa wrote: > > > Dear Elaine C. Meng, Ph.D > > I have some questions about electrostatic potential molecular surfaces and protein comparison. > > 1. The following scripts are added, edited from the redarea.py script of link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts, considering that the script allows reading the surface in ?2 colored more red than blue area. > > 1. Add scripts: > > Command: > > > open > > -blue_area_03.py > > -cornflowerblue_area_03.py > > -goldenrod_area_02.py > > -red_area_02.py > > (the scripts are attached) > > > 2. I used the following commands: > > > open 4MZ2 > > > delete solvent > > > addh > > > addcharge > > > Surface > > coulombic -10 red 0 white 10 blue > > > The electrostatic potential surface is presented by Coulombing coloring Surface: > > > > > I execute the commands: > > > redarea #0 > > red area 3562, total area 5730, ratio 0.6217 > > > bluearea #0 > > blue area 2168, total area 5730, ratio 0.3783 > > > The dominant areas of both colors are obtained. > > The following command is input: > > > rangecolor kdHydrophobicity min cornflowerblue 0 white max goldenrod > > > > > Next: > > > cornflowerbluearea # 0 > > cornflowerblue area 4109, total area 5730, ratio 0.7171 > > > > goldenrodarea # 0 > > Goldenrod area 1621, total area 5730, ratio 0.2829 > > > So, I believe (I'm not sure): > > Blue area + Red area = PSA ? Is correct? > > White area = NPSA ? Is correct? > > > So, the real blue and red areas would be (not sure): > > > (Redarea * PSA) / Total surf = Real Red area > > (Bluearea * PSA) / Total surf = Real Blue area > > So: > > Bluearea = 1554.6792 > > Redarea = 2554.3208 > > > Is this calculation correct? > > > Could I apply these calculations to compare them with other proteins of the same family? > > For example: > > Protein members of the immunoglobulin family. > > > > In the Chimera version 1.14, I Download the following programs pdb2pqr-windows-bin64-2.1.1 > > apbs1.5_win64 > > Downloaded from the website: http://www.poissonboltzmann.org > > Next, I assign charges and radii with the following parameters of PDB2PQR > > > > And I saved the file. Pqr > > > > Later I opened the file 001_B4.pqr with Chimera 1.14 > > > > I use the following command: > > > surface > > And run the APBS interface with the following default parameters: > > > > As a result, the color gradient of the molecular surface appeared as shown: > > > > > > > However, my question is: > > Are these parameters correct using the force field PARSE of PDB2PQR? Or, is it necessary to use a different force field? > > > Could I apply the scripts: > > -blue_area_03.py > > -cornflowerblue_area_03.py > > -goldenrod_area_02.py > > -red_area_02.py > > > to calculate the redarea and bluearea and compare it with other proteins? > > > Is there a script that gives me the correct areas of both red and blue colors? > > > Sorry for my long email, as I am new to this area. And I really need help. > > I apologize for so many questions. > > I would greatly appreciate your help. > > > Best regards, > > Fer. > > > > > From meng at cgl.ucsf.edu Wed Sep 11 15:52:47 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Sep 2019 15:52:47 -0700 Subject: [Chimera-users] Electrostatic potential molecular surfaces In-Reply-To: <3725992C-B638-4531-9385-CB5148BCACA2@cgl.ucsf.edu> References: <3725992C-B638-4531-9385-CB5148BCACA2@cgl.ucsf.edu> Message-ID: <4D6A7189-731E-49A9-A3AE-250448C6CF8D@cgl.ucsf.edu> Yet another issue I should mention is that in the methods I described, the whole amino acid residue is assigned a given kdHydrophobicity value or polar/nonpolar classification, not distinguishing between which atoms in the residue are more polar than other atoms in the same residue. To distinguish polar vs. nonpolar at the atom level instead of whole residues, you?d have to use some other program or approach. I just remembered another web server not related to Chimera. At least when I tried it many years ago, the results included a column for the apolar area: Elaine > On Sep 11, 2019, at 3:23 PM, Elaine Meng wrote: > > Hi Fernando, > Our resources don?t allow spending much time on consulting with individual research projects, sorry, and I can only answer mostly as it pertains to Chimera as I don?t know the details of parameters developed by other people or other programs. Also Chimera questions should be sent to this mailing list instead of to me directly so that other people can also benefit, unless private data are discussed or attached. > > You found an old script that is really special-purpose, finding the surface area that is more red than blue after coloring by electrostatic potential. Note that this would include surface that looks white but has a tiny, tiny tint of pinkishness. Also, the surface area that is more blue than red is just the complement of the surface that is more red than blue. In other words, if the surface is 75% red>blue then it is 25% blue>red because very little if any will be pure white. They always add up to the total surface. So no, you cannot use these scripts to figure out how much of the surface is polar or nonpolar. > > It may not matter given the above, but which method, set of charges, and what parameter values to use for electrostatic potential (ESP) calculations are research decisions that I cannot make for you. There are always tradeoffs, and different people have different opinions, etc. > > I don?t know python, but your generalization to coloring by hydrophobicity by identifying cornflower blue vs.goldenrod might be wrong. Red vs. blue is simpler since they are RGB color components. However, even if the color comparison is done correctly, the logical problem is the same, they always add up to the whole surface, and nearly white areas will always be combined with one side or the other. > > However, you can get the total surface area given some range of hydrophobicity values independent of any coloring. Hydrophobicity in this case is just a constant lookup value for each type of amino acid, according to this table (kdHydrophobicity column): > > > You would have to decide yourself which range of values is polar or nonpolar, but then you could just select all the residues that are less than or more than a certain value, e.g. command: > > select :/kdHydrophobicity>0.0 > > Alternatively you could just use command: > > select polar > select ~polar > ?but you might not agree with what amino acids are considered polar, as shown in a table in this page: > > > Then if surface is shown you could add up the area for the selected residues, e.g. menu: Tools? Structure Analysis? Attribute Calculator, and in that tool calculate attribute named whatever you want for ?molecules? with Formula: > > sum(areaSAS.residue) > > (? or SES instead of SAS, to be compared with the corresponding total area given in the Reply Log when you show the surface) with option to ?Restrict formula domain to current selection? and ?Show calculation results in Reply Log" turned on, other options turned off, click Apply. > > > Totally separate and not related to Chimera, but I happen to know of this web server you might be interested in, for comparing ESP of related proteins: > > > Best regards, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Sep 11, 2019, at 2:16 PM, Fernando Villa wrote: >> >> >> Dear Elaine C. Meng, Ph.D >> >> I have some questions about electrostatic potential molecular surfaces and protein comparison. >> >> 1. The following scripts are added, edited from the redarea.py script of link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts, considering that the script allows reading the surface in ?2 colored more red than blue area. >> >> 1. Add scripts: >> >> Command: >> >>> open >> >> -blue_area_03.py >> >> -cornflowerblue_area_03.py >> >> -goldenrod_area_02.py >> >> -red_area_02.py >> >> (the scripts are attached) >> >> >> 2. I used the following commands: >> >>> open 4MZ2 >> >>> delete solvent >> >>> addh >> >>> addcharge >> >>> Surface >> >> coulombic -10 red 0 white 10 blue >> >> >> The electrostatic potential surface is presented by Coulombing coloring Surface: >> >> >> >> >> I execute the commands: >> >>> redarea #0 >> >> red area 3562, total area 5730, ratio 0.6217 >> >>> bluearea #0 >> >> blue area 2168, total area 5730, ratio 0.3783 >> >> >> The dominant areas of both colors are obtained. >> >> The following command is input: >> >>> rangecolor kdHydrophobicity min cornflowerblue 0 white max goldenrod >> >> >> >> >> Next: >> >>> cornflowerbluearea # 0 >> >> cornflowerblue area 4109, total area 5730, ratio 0.7171 >> >> >>> goldenrodarea # 0 >> >> Goldenrod area 1621, total area 5730, ratio 0.2829 >> >> >> So, I believe (I'm not sure): >> >> Blue area + Red area = PSA ? Is correct? >> >> White area = NPSA ? Is correct? >> >> >> So, the real blue and red areas would be (not sure): >> >> >> (Redarea * PSA) / Total surf = Real Red area >> >> (Bluearea * PSA) / Total surf = Real Blue area >> >> So: >> >> Bluearea = 1554.6792 >> >> Redarea = 2554.3208 >> >> >> Is this calculation correct? >> >> >> Could I apply these calculations to compare them with other proteins of the same family? >> >> For example: >> >> Protein members of the immunoglobulin family. >> >> >> >> In the Chimera version 1.14, I Download the following programs pdb2pqr-windows-bin64-2.1.1 >> >> apbs1.5_win64 >> >> Downloaded from the website: http://www.poissonboltzmann.org >> >> Next, I assign charges and radii with the following parameters of PDB2PQR >> >> >> >> And I saved the file. Pqr >> >> >> >> Later I opened the file 001_B4.pqr with Chimera 1.14 >> >> >> >> I use the following command: >> >>> surface >> >> And run the APBS interface with the following default parameters: >> >> >> >> As a result, the color gradient of the molecular surface appeared as shown: >> >> >> >> >> >> >> However, my question is: >> >> Are these parameters correct using the force field PARSE of PDB2PQR? Or, is it necessary to use a different force field? >> >> >> Could I apply the scripts: >> >> -blue_area_03.py >> >> -cornflowerblue_area_03.py >> >> -goldenrod_area_02.py >> >> -red_area_02.py >> >> >> to calculate the redarea and bluearea and compare it with other proteins? >> >> >> Is there a script that gives me the correct areas of both red and blue colors? >> >> >> Sorry for my long email, as I am new to this area. And I really need help. >> >> I apologize for so many questions. >> >> I would greatly appreciate your help. >> >> >> Best regards, >> >> Fer. >> >> >> >> >> > From fer.vdl1928 at gmail.com Wed Sep 11 18:05:06 2019 From: fer.vdl1928 at gmail.com (Fernando Villa) Date: Wed, 11 Sep 2019 20:05:06 -0500 Subject: [Chimera-users] Electrostatic potential molecular surfaces In-Reply-To: <4D6A7189-731E-49A9-A3AE-250448C6CF8D@cgl.ucsf.edu> References: <3725992C-B638-4531-9385-CB5148BCACA2@cgl.ucsf.edu> <4D6A7189-731E-49A9-A3AE-250448C6CF8D@cgl.ucsf.edu> Message-ID: Querida Elaine Gracias por responder algunas de mis dudas y contestarme el correo con varios par?metros que yo no conoc?a. Estoy muy agradecido por su tiempo. Las preguntas que tenga a futuro las mandare al grupo. Soy un gran fan de Quimera y aprecio mucho su ayuda. saludos cordiales, Fernando ATTE Fernando Villa D?az El mi?., 11 de sep. de 2019 a la(s) 17:52, Elaine Meng (meng at cgl.ucsf.edu) escribi?: > Yet another issue I should mention is that in the methods I described, the > whole amino acid residue is assigned a given kdHydrophobicity value or > polar/nonpolar classification, not distinguishing between which atoms in > the residue are more polar than other atoms in the same residue. To > distinguish polar vs. nonpolar at the atom level instead of whole residues, > you?d have to use some other program or approach. > > I just remembered another web server not related to Chimera. At least > when I tried it many years ago, the results included a column for the > apolar area: > > > Elaine > > > On Sep 11, 2019, at 3:23 PM, Elaine Meng wrote: > > > > Hi Fernando, > > Our resources don?t allow spending much time on consulting with > individual research projects, sorry, and I can only answer mostly as it > pertains to Chimera as I don?t know the details of parameters developed by > other people or other programs. Also Chimera questions should be sent to > this mailing list instead of to me directly so that other people can also > benefit, unless private data are discussed or attached. > > > > You found an old script that is really special-purpose, finding the > surface area that is more red than blue after coloring by electrostatic > potential. Note that this would include surface that looks white but has a > tiny, tiny tint of pinkishness. Also, the surface area that is more blue > than red is just the complement of the surface that is more red than blue. > In other words, if the surface is 75% red>blue then it is 25% blue>red > because very little if any will be pure white. They always add up to the > total surface. So no, you cannot use these scripts to figure out how much > of the surface is polar or nonpolar. > > > > It may not matter given the above, but which method, set of charges, > and what parameter values to use for electrostatic potential (ESP) > calculations are research decisions that I cannot make for you. There are > always tradeoffs, and different people have different opinions, etc. > > > > I don?t know python, but your generalization to coloring by > hydrophobicity by identifying cornflower blue vs.goldenrod might be wrong. > Red vs. blue is simpler since they are RGB color components. However, even > if the color comparison is done correctly, the logical problem is the same, > they always add up to the whole surface, and nearly white areas will always > be combined with one side or the other. > > > > However, you can get the total surface area given some range of > hydrophobicity values independent of any coloring. Hydrophobicity in this > case is just a constant lookup value for each type of amino acid, according > to this table (kdHydrophobicity column): > > > > > > You would have to decide yourself which range of values is polar or > nonpolar, but then you could just select all the residues that are less > than or more than a certain value, e.g. command: > > > > select :/kdHydrophobicity>0.0 > > > > Alternatively you could just use command: > > > > select polar > > select ~polar > > ?but you might not agree with what amino acids are considered polar, as > shown in a table in this page: > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.html#aacat > > > > > > Then if surface is shown you could add up the area for the selected > residues, e.g. menu: Tools? Structure Analysis? Attribute Calculator, and > in that tool calculate attribute named whatever you want for ?molecules? > with Formula: > > > > sum(areaSAS.residue) > > > > (? or SES instead of SAS, to be compared with the corresponding total > area given in the Reply Log when you show the surface) with option to > ?Restrict formula domain to current selection? and ?Show calculation > results in Reply Log" turned on, other options turned off, click Apply. > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html > > > > > > Totally separate and not related to Chimera, but I happen to know of > this web server you might be interested in, for comparing ESP of related > proteins: > > > > > > Best regards, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > >> On Sep 11, 2019, at 2:16 PM, Fernando Villa > wrote: > >> > >> > >> Dear Elaine C. Meng, Ph.D > >> > >> I have some questions about electrostatic potential molecular surfaces > and protein comparison. > >> > >> 1. The following scripts are added, edited from the redarea.py script > of link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts, considering > that the script allows reading the surface in ?2 colored more red than blue > area. > >> > >> 1. Add scripts: > >> > >> Command: > >> > >>> open > >> > >> -blue_area_03.py > >> > >> -cornflowerblue_area_03.py > >> > >> -goldenrod_area_02.py > >> > >> -red_area_02.py > >> > >> (the scripts are attached) > >> > >> > >> 2. I used the following commands: > >> > >>> open 4MZ2 > >> > >>> delete solvent > >> > >>> addh > >> > >>> addcharge > >> > >>> Surface > >> > >> coulombic -10 red 0 white 10 blue > >> > >> > >> The electrostatic potential surface is presented by Coulombing coloring > Surface: > >> > >> > >> > >> > >> I execute the commands: > >> > >>> redarea #0 > >> > >> red area 3562, total area 5730, ratio 0.6217 > >> > >>> bluearea #0 > >> > >> blue area 2168, total area 5730, ratio 0.3783 > >> > >> > >> The dominant areas of both colors are obtained. > >> > >> The following command is input: > >> > >>> rangecolor kdHydrophobicity min cornflowerblue 0 white max goldenrod > >> > >> > >> > >> > >> Next: > >> > >>> cornflowerbluearea # 0 > >> > >> cornflowerblue area 4109, total area 5730, ratio 0.7171 > >> > >> > >>> goldenrodarea # 0 > >> > >> Goldenrod area 1621, total area 5730, ratio 0.2829 > >> > >> > >> So, I believe (I'm not sure): > >> > >> Blue area + Red area = PSA ? Is correct? > >> > >> White area = NPSA ? Is correct? > >> > >> > >> So, the real blue and red areas would be (not sure): > >> > >> > >> (Redarea * PSA) / Total surf = Real Red area > >> > >> (Bluearea * PSA) / Total surf = Real Blue area > >> > >> So: > >> > >> Bluearea = 1554.6792 > >> > >> Redarea = 2554.3208 > >> > >> > >> Is this calculation correct? > >> > >> > >> Could I apply these calculations to compare them with other proteins of > the same family? > >> > >> For example: > >> > >> Protein members of the immunoglobulin family. > >> > >> > >> > >> In the Chimera version 1.14, I Download the following programs > pdb2pqr-windows-bin64-2.1.1 > >> > >> apbs1.5_win64 > >> > >> Downloaded from the website: http://www.poissonboltzmann.org > >> > >> Next, I assign charges and radii with the following parameters of > PDB2PQR > >> > >> > >> > >> And I saved the file. Pqr > >> > >> > >> > >> Later I opened the file 001_B4.pqr with Chimera 1.14 > >> > >> > >> > >> I use the following command: > >> > >>> surface > >> > >> And run the APBS interface with the following default parameters: > >> > >> > >> > >> As a result, the color gradient of the molecular surface appeared as > shown: > >> > >> > >> > >> > >> > >> > >> However, my question is: > >> > >> Are these parameters correct using the force field PARSE of PDB2PQR? > Or, is it necessary to use a different force field? > >> > >> > >> Could I apply the scripts: > >> > >> -blue_area_03.py > >> > >> -cornflowerblue_area_03.py > >> > >> -goldenrod_area_02.py > >> > >> -red_area_02.py > >> > >> > >> to calculate the redarea and bluearea and compare it with other > proteins? > >> > >> > >> Is there a script that gives me the correct areas of both red and blue > colors? > >> > >> > >> Sorry for my long email, as I am new to this area. And I really need > help. > >> > >> I apologize for so many questions. > >> > >> I would greatly appreciate your help. > >> > >> > >> Best regards, > >> > >> Fer. > >> > >> > >> > >> > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fer.vdl1928 at gmail.com Wed Sep 11 18:05:43 2019 From: fer.vdl1928 at gmail.com (Fernando Villa) Date: Wed, 11 Sep 2019 20:05:43 -0500 Subject: [Chimera-users] Electrostatic potential molecular surfaces In-Reply-To: <4D6A7189-731E-49A9-A3AE-250448C6CF8D@cgl.ucsf.edu> References: <3725992C-B638-4531-9385-CB5148BCACA2@cgl.ucsf.edu> <4D6A7189-731E-49A9-A3AE-250448C6CF8D@cgl.ucsf.edu> Message-ID: Dear Elaine Thank you for answering some of my questions and answering the email with several parameters that I did not know. I am very grateful for your time. The questions I have in the future I will send to the group. I am a big fan of Chimera and I really appreciate your help. best regards, Fernando ATTE Fernando Villa D?az El mi?., 11 de sep. de 2019 a la(s) 17:52, Elaine Meng (meng at cgl.ucsf.edu) escribi?: > Yet another issue I should mention is that in the methods I described, the > whole amino acid residue is assigned a given kdHydrophobicity value or > polar/nonpolar classification, not distinguishing between which atoms in > the residue are more polar than other atoms in the same residue. To > distinguish polar vs. nonpolar at the atom level instead of whole residues, > you?d have to use some other program or approach. > > I just remembered another web server not related to Chimera. At least > when I tried it many years ago, the results included a column for the > apolar area: > > > Elaine > > > On Sep 11, 2019, at 3:23 PM, Elaine Meng wrote: > > > > Hi Fernando, > > Our resources don?t allow spending much time on consulting with > individual research projects, sorry, and I can only answer mostly as it > pertains to Chimera as I don?t know the details of parameters developed by > other people or other programs. Also Chimera questions should be sent to > this mailing list instead of to me directly so that other people can also > benefit, unless private data are discussed or attached. > > > > You found an old script that is really special-purpose, finding the > surface area that is more red than blue after coloring by electrostatic > potential. Note that this would include surface that looks white but has a > tiny, tiny tint of pinkishness. Also, the surface area that is more blue > than red is just the complement of the surface that is more red than blue. > In other words, if the surface is 75% red>blue then it is 25% blue>red > because very little if any will be pure white. They always add up to the > total surface. So no, you cannot use these scripts to figure out how much > of the surface is polar or nonpolar. > > > > It may not matter given the above, but which method, set of charges, > and what parameter values to use for electrostatic potential (ESP) > calculations are research decisions that I cannot make for you. There are > always tradeoffs, and different people have different opinions, etc. > > > > I don?t know python, but your generalization to coloring by > hydrophobicity by identifying cornflower blue vs.goldenrod might be wrong. > Red vs. blue is simpler since they are RGB color components. However, even > if the color comparison is done correctly, the logical problem is the same, > they always add up to the whole surface, and nearly white areas will always > be combined with one side or the other. > > > > However, you can get the total surface area given some range of > hydrophobicity values independent of any coloring. Hydrophobicity in this > case is just a constant lookup value for each type of amino acid, according > to this table (kdHydrophobicity column): > > > > > > You would have to decide yourself which range of values is polar or > nonpolar, but then you could just select all the residues that are less > than or more than a certain value, e.g. command: > > > > select :/kdHydrophobicity>0.0 > > > > Alternatively you could just use command: > > > > select polar > > select ~polar > > ?but you might not agree with what amino acids are considered polar, as > shown in a table in this page: > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.html#aacat > > > > > > Then if surface is shown you could add up the area for the selected > residues, e.g. menu: Tools? Structure Analysis? Attribute Calculator, and > in that tool calculate attribute named whatever you want for ?molecules? > with Formula: > > > > sum(areaSAS.residue) > > > > (? or SES instead of SAS, to be compared with the corresponding total > area given in the Reply Log when you show the surface) with option to > ?Restrict formula domain to current selection? and ?Show calculation > results in Reply Log" turned on, other options turned off, click Apply. > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html > > > > > > Totally separate and not related to Chimera, but I happen to know of > this web server you might be interested in, for comparing ESP of related > proteins: > > > > > > Best regards, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > >> On Sep 11, 2019, at 2:16 PM, Fernando Villa > wrote: > >> > >> > >> Dear Elaine C. Meng, Ph.D > >> > >> I have some questions about electrostatic potential molecular surfaces > and protein comparison. > >> > >> 1. The following scripts are added, edited from the redarea.py script > of link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts, considering > that the script allows reading the surface in ?2 colored more red than blue > area. > >> > >> 1. Add scripts: > >> > >> Command: > >> > >>> open > >> > >> -blue_area_03.py > >> > >> -cornflowerblue_area_03.py > >> > >> -goldenrod_area_02.py > >> > >> -red_area_02.py > >> > >> (the scripts are attached) > >> > >> > >> 2. I used the following commands: > >> > >>> open 4MZ2 > >> > >>> delete solvent > >> > >>> addh > >> > >>> addcharge > >> > >>> Surface > >> > >> coulombic -10 red 0 white 10 blue > >> > >> > >> The electrostatic potential surface is presented by Coulombing coloring > Surface: > >> > >> > >> > >> > >> I execute the commands: > >> > >>> redarea #0 > >> > >> red area 3562, total area 5730, ratio 0.6217 > >> > >>> bluearea #0 > >> > >> blue area 2168, total area 5730, ratio 0.3783 > >> > >> > >> The dominant areas of both colors are obtained. > >> > >> The following command is input: > >> > >>> rangecolor kdHydrophobicity min cornflowerblue 0 white max goldenrod > >> > >> > >> > >> > >> Next: > >> > >>> cornflowerbluearea # 0 > >> > >> cornflowerblue area 4109, total area 5730, ratio 0.7171 > >> > >> > >>> goldenrodarea # 0 > >> > >> Goldenrod area 1621, total area 5730, ratio 0.2829 > >> > >> > >> So, I believe (I'm not sure): > >> > >> Blue area + Red area = PSA ? Is correct? > >> > >> White area = NPSA ? Is correct? > >> > >> > >> So, the real blue and red areas would be (not sure): > >> > >> > >> (Redarea * PSA) / Total surf = Real Red area > >> > >> (Bluearea * PSA) / Total surf = Real Blue area > >> > >> So: > >> > >> Bluearea = 1554.6792 > >> > >> Redarea = 2554.3208 > >> > >> > >> Is this calculation correct? > >> > >> > >> Could I apply these calculations to compare them with other proteins of > the same family? > >> > >> For example: > >> > >> Protein members of the immunoglobulin family. > >> > >> > >> > >> In the Chimera version 1.14, I Download the following programs > pdb2pqr-windows-bin64-2.1.1 > >> > >> apbs1.5_win64 > >> > >> Downloaded from the website: http://www.poissonboltzmann.org > >> > >> Next, I assign charges and radii with the following parameters of > PDB2PQR > >> > >> > >> > >> And I saved the file. Pqr > >> > >> > >> > >> Later I opened the file 001_B4.pqr with Chimera 1.14 > >> > >> > >> > >> I use the following command: > >> > >>> surface > >> > >> And run the APBS interface with the following default parameters: > >> > >> > >> > >> As a result, the color gradient of the molecular surface appeared as > shown: > >> > >> > >> > >> > >> > >> > >> However, my question is: > >> > >> Are these parameters correct using the force field PARSE of PDB2PQR? > Or, is it necessary to use a different force field? > >> > >> > >> Could I apply the scripts: > >> > >> -blue_area_03.py > >> > >> -cornflowerblue_area_03.py > >> > >> -goldenrod_area_02.py > >> > >> -red_area_02.py > >> > >> > >> to calculate the redarea and bluearea and compare it with other > proteins? > >> > >> > >> Is there a script that gives me the correct areas of both red and blue > colors? > >> > >> > >> Sorry for my long email, as I am new to this area. And I really need > help. > >> > >> I apologize for so many questions. > >> > >> I would greatly appreciate your help. > >> > >> > >> Best regards, > >> > >> Fer. > >> > >> > >> > >> > >> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fer.vdl1928 at gmail.com Wed Sep 11 19:27:24 2019 From: fer.vdl1928 at gmail.com (Fernando Villa) Date: Wed, 11 Sep 2019 21:27:24 -0500 Subject: [Chimera-users] Electrostatic Potential Message-ID: Dear all Chimera users In UCSF ChimeraX version 0.91 (2019-08-30) I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file (generated with APBS in Chimera 1.14) Then I input the commands: >surface >color electrostatic #1 map #2 palette -10,red:0,white:10,blue [image: image.png] Is it possible to calculate the red and blue area in ?2 of the molecule? Best regards, Fernando ATTE Fernando Villa D?az -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 522940 bytes Desc: not available URL: From meng at cgl.ucsf.edu Thu Sep 12 08:02:04 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 12 Sep 2019 08:02:04 -0700 Subject: [Chimera-users] Electrostatic Potential In-Reply-To: References: Message-ID: Hi Fernando, An important thing to understand is that the color is changed gradually from red to white, and gradually from white to blue. So there is a lot of surface coloring that is ?between? red and white, and between white and blue. Only the surface points with values -10 or lower are actually red, and those with 10 or higher are actually blue. It is unclear exactly what quantity you want to measure. There is no simple feature like a command to do it. You would have to use python scripting, but somebody else would have to advise on any details of that. Also, first think carefully about what you really want to measure. This electrostatic surface coloring is really meant for visualization, comparison ?by eye.? For quantitative analyses, maybe the two websites I mentioned earlier would be better tools. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 11, 2019, at 7:27 PM, Fernando Villa wrote: > > Dear all Chimera users > > In UCSF ChimeraX version 0.91 (2019-08-30) > I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file (generated with APBS in Chimera 1.14) > > Then I input the commands: > > >surface > >color electrostatic #1 map #2 palette -10,red:0,white:10,blue > > > Is it possible to calculate the red and blue area in ?2 of the molecule? > > Best regards, > > Fernando From jurgen.sygusch at umontreal.ca Thu Sep 12 13:09:43 2019 From: jurgen.sygusch at umontreal.ca (Sygusch Jurgen) Date: Thu, 12 Sep 2019 20:09:43 +0000 Subject: [Chimera-users] Command line equivalence for Render by Attribute radii Message-ID: Hello, I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI. In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius). What is the command line equivalence for doing this? I cannot seem to find it. Thank you for looking into this. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: jurgen_sygusch.vcf Type: text/x-vcard Size: 411 bytes Desc: jurgen_sygusch.vcf URL: From meng at cgl.ucsf.edu Fri Sep 13 08:25:50 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 13 Sep 2019 08:25:50 -0700 Subject: [Chimera-users] Command line equivalence for Render by Attribute radii In-Reply-To: References: Message-ID: Hello Jurgen, Sorry, there is no command-line equivalent for the ?Radii? section of Render by Attribute, nor is there one for ?Worms? ? there?s only one for coloring, the ?rangecolor? command. Surely it could be done with python scripting, but somebody else would have to advise on that. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 12, 2019, at 1:09 PM, Sygusch Jurgen wrote: > > Hello, > I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI. > > In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius). > > What is the command line equivalence for doing this? I cannot seem to find it. > Thank you for looking into this. From fer.vdl1928 at gmail.com Fri Sep 13 18:13:36 2019 From: fer.vdl1928 at gmail.com (Fernando Villa) Date: Fri, 13 Sep 2019 20:13:36 -0500 Subject: [Chimera-users] Electrostatic Potential In-Reply-To: References: Message-ID: Thank you very much Dr. Elaine and the Chimera work group, now I have a better picture of what I have to do. Thank you for guiding me in this part, I appreciate it Best regards, Fer ATTE Fernando Villa D?az El jue., 12 de sep. de 2019 a la(s) 10:02, Elaine Meng (meng at cgl.ucsf.edu) escribi?: > Hi Fernando, > An important thing to understand is that the color is changed gradually > from red to white, and gradually from white to blue. So there is a lot of > surface coloring that is ?between? red and white, and between white and > blue. Only the surface points with values -10 or lower are actually red, > and those with 10 or higher are actually blue. It is unclear exactly what > quantity you want to measure. > > There is no simple feature like a command to do it. You would have to use > python scripting, but somebody else would have to advise on any details of > that. Also, first think carefully about what you really want to measure. > > This electrostatic surface coloring is really meant for visualization, > comparison ?by eye.? For quantitative analyses, maybe the two websites I > mentioned earlier would be better tools. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 11, 2019, at 7:27 PM, Fernando Villa > wrote: > > > > Dear all Chimera users > > > > In UCSF ChimeraX version 0.91 (2019-08-30) > > I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then > I opened a .dx file (generated with APBS in Chimera 1.14) > > > > Then I input the commands: > > > > >surface > > >color electrostatic #1 map #2 palette -10,red:0,white:10,blue > > > > > > Is it possible to calculate the red and blue area in ?2 of the molecule? > > > > Best regards, > > > > Fernando > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunyeping at aliyun.com Sun Sep 15 22:03:31 2019 From: sunyeping at aliyun.com (sunyeping) Date: Mon, 16 Sep 2019 13:03:31 +0800 Subject: [Chimera-users] =?utf-8?q?Where_is_the_radius=2Enc_map_file_in_th?= =?utf-8?q?e_Semliki_Forest_virus=3F?= Message-ID: Dear everyone, The Semliki Forest virus tutorial (https://www.cgl.ucsf.edu/chimera/data/tutorials/semliki/semliki.html) mentioned a radius.nc which is used for visualization of the layer. However, the tutorial doesn't describe where the reader can download it. Do you know where to get thid file? Thank you in advance. Yeping Sun -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgoliver at protonmail.com Fri Sep 13 11:52:02 2019 From: cgoliver at protonmail.com (Carlos G. Oliver) Date: Fri, 13 Sep 2019 18:52:02 +0000 Subject: [Chimera-users] Selecting residues with zones when reference is absent Message-ID: Hello, I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins. The selection command I have so far is: `select nucleic acid z<10 & protein z>10 & ligand` This works for PDBs that contain both nucleic acids and protein. However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand. I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases. Thanks! Carlos G. Oliver -------------- next part -------------- An HTML attachment was scrubbed... URL: From a01406823 at unet.univie.ac.at Mon Sep 16 05:09:16 2019 From: a01406823 at unet.univie.ac.at (=?UTF-8?Q?Danilo_Bo=C5=A1kovic?=) Date: Mon, 16 Sep 2019 14:09:16 +0200 Subject: [Chimera-users] Max 100 residues for local bug? Message-ID: <885fdaed4b932ef3779c72f37eb4fe34@unet.univie.ac.at> Dear caretakers, I tried to do autodock vina but as soon as i did i got an error that i can only do max 100 residues. I use a local installation of AVina. Is this a bug or is there somewhere something im missing? 41965 build number 1.13.1 version Sincerely, D. B. From a01406823 at unet.univie.ac.at Mon Sep 16 05:11:18 2019 From: a01406823 at unet.univie.ac.at (=?UTF-8?Q?Danilo_Bo=C5=A1kovic?=) Date: Mon, 16 Sep 2019 14:11:18 +0200 Subject: [Chimera-users] Dockprep OT2 C terminal question Message-ID: <54f0454fa1e4dfee755633df9a4f308f@unet.univie.ac.at> Dear caretakers, I have a non-standard residue OT2 (C terminus last O atom) that does not get recognized in the amber force field (everything else is fine). How do i rename this residue so it is properly accounted when adding charge? Sincerely, D. Boskovic From meng at cgl.ucsf.edu Mon Sep 16 09:30:14 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Sep 2019 09:30:14 -0700 Subject: [Chimera-users] Where is the radius.nc map file in the Semliki Forest virus? In-Reply-To: References: Message-ID: Dear Yepin Sun, That is a very old tutorial (2005) ? now radial coloring does not require another map. Instead you just use the by ?radius? option in the Surface Color dialog, as described here: The Semliki Forest virus tutorial uses EMDB 1015, and in that case the ?origin? to use in Surface Color dialog for coloring by radius is 0 0 0. In other data it might be in a different location. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 15, 2019, at 10:03 PM, sunyeping wrote: > > Dear everyone, > The Semliki Forest virus tutorial (https://www.cgl.ucsf.edu/chimera/data/tutorials/semliki/semliki.html) mentioned a radius.nc which is used for visualization of the layer. However, the tutorial doesn't describe where the reader can download it. > Do you know where to get thid file? > Thank you in advance. > Yeping Sun From meng at cgl.ucsf.edu Mon Sep 16 09:34:49 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Sep 2019 09:34:49 -0700 Subject: [Chimera-users] Max 100 residues for local bug? In-Reply-To: <885fdaed4b932ef3779c72f37eb4fe34@unet.univie.ac.at> References: <885fdaed4b932ef3779c72f37eb4fe34@unet.univie.ac.at> Message-ID: <2FD20A03-4A4A-43FB-AA02-8F2127605653@cgl.ucsf.edu> Hi DB, I believe that is an error message that you may have chosen the wrong model for the ligand. Since the ligand is generally a small molecule, not another protein, we put this block in because many people were choosing the same model as both the ligand and receptor by mistake and wasting the computational resources. Whether you were using Autodock Vina locally or not makes no difference to the Chimera tool, it still has the same error checking. If you want to avoid these checks in the Chimera tool, you should just use your local Autodock Vina program directly (not through the Chimera tool). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 16, 2019, at 5:09 AM, Danilo Bo?kovic wrote: > > Dear caretakers, > I tried to do autodock vina but as soon as i did i got an error that i can only do max 100 residues. I use a local installation of AVina. Is this a bug or is there somewhere something im missing? > 41965 build number 1.13.1 version > Sincerely, > D. B. From meng at cgl.ucsf.edu Mon Sep 16 09:58:52 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Sep 2019 09:58:52 -0700 Subject: [Chimera-users] Dockprep OT2 C terminal question In-Reply-To: <54f0454fa1e4dfee755633df9a4f308f@unet.univie.ac.at> References: <54f0454fa1e4dfee755633df9a4f308f@unet.univie.ac.at> Message-ID: <871D22B9-6881-43B4-945C-E6C417D424DE@cgl.ucsf.edu> Dear D. It is impossible to answer since I don?t know what OT2 is? it?s not a residue name in the RCSB PDB database. You would have to attach an example file. Maybe you mean it is just one atom added to make a C-terminal carboxylate. In that case you could try editing the file to make it have the same residue name and residue number as rest of the end residue, with atom name OXT (the other carboxylate oxygen is just named O). If it?s some other nonstandard residue with multiple atoms, then it should automatically go through Antechamber charge calculations when you use Add Charge. If the default method of charge calculation fails you could try the simpler Gasteiger method instead. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 16, 2019, at 5:11 AM, Danilo Bo?kovic wrote: > > Dear caretakers, > > I have a non-standard residue OT2 (C terminus last O atom) that does not get recognized in the amber force field (everything else is fine). How do i rename this residue so it is properly accounted when adding charge? > > Sincerely, > > D. Boskovic From meng at cgl.ucsf.edu Mon Sep 16 10:44:42 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Sep 2019 10:44:42 -0700 Subject: [Chimera-users] Selecting residues with zones when reference is absent In-Reply-To: References: Message-ID: <3CE4783D-56BA-4881-981E-CCAF1CF71F07@cgl.ucsf.edu> Hello Carlos, Try these commands: select ligand & nucleic acid z<10 ~select protein z<10 I tried it on examples of nucleic acid structures with ligand and with and without protein: 6raw and 6gld, respectively. If you want just one line of commands, you can put them together with a semicolon between. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 13, 2019, at 11:52 AM, Carlos G. Oliver wrote: > > Hello, > > I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins. > > The selection command I have so far is: > > `select nucleic acid z<10 & protein z>10 & ligand` > > This works for PDBs that contain both nucleic acids and protein. > > However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand. > > I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases. > > Thanks! > > Carlos G. Oliver From goddard at sonic.net Mon Sep 16 11:03:08 2019 From: goddard at sonic.net (Tom Goddard) Date: Mon, 16 Sep 2019 11:03:08 -0700 Subject: [Chimera-users] Electrostatic Potential In-Reply-To: References: Message-ID: <04AC3357-276E-4B5A-B5E2-F321099934CD@sonic.net> Hi Fernando, Instead of thinking about the coloring, it would be clearer to ask how much surface area has electrostatic potential value >= 5. Chimera does not have any code to compute that, although it is something we could add to ChimeraX. Tom > On Sep 11, 2019, at 7:27 PM, Fernando Villa wrote: > > Dear all Chimera users > > In UCSF ChimeraX version 0.91 (2019-08-30) > I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file (generated with APBS in Chimera 1.14) > > Then I input the commands: > > >surface > >color electrostatic #1 map #2 palette -10,red:0,white:10,blue > > > Is it possible to calculate the red and blue area in ?2 of the molecule? > > Best regards, > > Fernando > > > ATTE > Fernando Villa D?az > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgoliver at protonmail.com Mon Sep 16 11:29:36 2019 From: cgoliver at protonmail.com (Carlos G. Oliver) Date: Mon, 16 Sep 2019 18:29:36 +0000 Subject: [Chimera-users] Selecting residues with zones when reference is absent In-Reply-To: <3CE4783D-56BA-4881-981E-CCAF1CF71F07@cgl.ucsf.edu> References: <3CE4783D-56BA-4881-981E-CCAF1CF71F07@cgl.ucsf.edu> Message-ID: <1NBcvIRj2wXZ1yfAtyq7aCkt794A9-7ZdYhlQDtGRHuX2ayrqMgJBwBJPMys0Wije5iUlnS5ALoc-ZYeSu4IAtDqhK5Hv89iBnTrxppxvO0=@protonmail.com> Hello Elaine, That is perfect. Thank you very much! Carlos Sent with ProtonMail Secure Email. ??????? Original Message ??????? On Monday, September 16, 2019 1:44 PM, Elaine Meng wrote: > Hello Carlos, > Try these commands: > > select ligand & nucleic acid z<10 > ~select protein z<10 > > I tried it on examples of nucleic acid structures with ligand and with and without protein: 6raw and 6gld, respectively. > > If you want just one line of commands, you can put them together with a semicolon between. > I hope this helps, > Elaine > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 13, 2019, at 11:52 AM, Carlos G. Oliver cgoliver at protonmail.com wrote: > > Hello, > > I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins. > > The selection command I have so far is: > > `select nucleic acid z<10 & protein z>10 & ligand` > > This works for PDBs that contain both nucleic acids and protein. > > However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand. > > I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases. > > Thanks! > > Carlos G. Oliver From onken031 at umn.edu Mon Sep 16 12:23:38 2019 From: onken031 at umn.edu (Bailey Onken) Date: Mon, 16 Sep 2019 14:23:38 -0500 Subject: [Chimera-users] Unable to Find Function Message-ID: Hello, I am currently a student in Biochemistry. I have a protein and I am trying to separate polar and nonpolar residues located on the surface of these molecules and then finding the values for the surface area associated with polar and nonpolar areas. If you can help me get to this function I would be very grateful. Thank you very much, Bailey -- *Bailey Onken *| Student, University of Minnesota Rochester 507.329.7409 | onken031 at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Sep 16 12:57:53 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Sep 2019 12:57:53 -0700 Subject: [Chimera-users] nonpolar and polar surface area In-Reply-To: References: Message-ID: <18A2393B-0DCE-45EB-A8A4-599B00C54587@cgl.ucsf.edu> Hi Bailey, You will have to decide for yourself which residues you want to consider as polar and nonpolar. Then after you show the surface of the protein, you can select any subset of the residues (or atoms) and then sum the surface area from that subset using the Attribute Calculator tool. This is described in more detail in this recent post. Skip down to the fourth paragraph, starting "However, you can get the total surface area given some range of hydrophobicity values?? Alternatively, you could take a look at the GetArea web server mentioned in this follow-up: (I changed the subject line of the message to something more descriptive to help others find it later.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 16, 2019, at 12:23 PM, Bailey Onken wrote: > > Hello, > I am currently a student in Biochemistry. I have a protein and I am trying to separate polar and nonpolar residues located on the surface of these molecules and then finding the values for the surface area associated with polar and nonpolar areas. If you can help me get to this function I would be very grateful. > Thank you very much, > Bailey From fer.vdl1928 at gmail.com Mon Sep 16 13:20:24 2019 From: fer.vdl1928 at gmail.com (Fernando Villa) Date: Mon, 16 Sep 2019 15:20:24 -0500 Subject: [Chimera-users] Electrostatic Potential In-Reply-To: <04AC3357-276E-4B5A-B5E2-F321099934CD@sonic.net> References: <04AC3357-276E-4B5A-B5E2-F321099934CD@sonic.net> Message-ID: Dear Tom and Chimera users, In ChimeraX or Chimera, is it possible to calculate the number of vertices and their respective total charges? I calculated the electrostatic potential surface (Coulombic) with another program, it gave me the following results (attached in this email) and I calculated the area in red and blue, above and below a threshold = 0. Unfortunately, these results do not help me, because I need to obtain an electrostatics calculations from Adaptive Poisson-Boltzmann Solver (Calculations that I have already made for study proteins with PDB2PQR and APBS, in interface with Chimera: .pqr and .dx files and emulated in Chimera X) e.g. [image: image.png] Now my question is: Can I obtain these results of vertices and charges in a file from Chimera or Chimera X (possibly .cvs, .txt, etc.), so that I can make the corresponding calculations? I would greatly appreciate your help best regards, Fer El lun., 16 de sep. de 2019 a la(s) 13:03, Tom Goddard (goddard at sonic.net) escribi?: > Hi Fernando, > > Instead of thinking about the coloring, it would be clearer to ask how > much surface area has electrostatic potential value >= 5. Chimera does not > have any code to compute that, although it is something we could add to > ChimeraX. > > Tom > > > On Sep 11, 2019, at 7:27 PM, Fernando Villa wrote: > > Dear all Chimera users > > In UCSF ChimeraX version 0.91 (2019-08-30) > I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I > opened a .dx file (generated with APBS in Chimera 1.14) > > Then I input the commands: > > >surface > >color electrostatic #1 map #2 palette -10,red:0,white:10,blue > > > Is it possible to calculate the red and blue area in ?2 of the molecule? > > Best regards, > > Fernando > > > ATTE > Fernando Villa D?az > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: > 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: image.png Type: image/png Size: 306082 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Test_MEP_Protein.xlsx Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Size: 6605 bytes Desc: not available URL: From fer.vdl1928 at gmail.com Mon Sep 16 13:25:17 2019 From: fer.vdl1928 at gmail.com (Fernando Villa) Date: Mon, 16 Sep 2019 15:25:17 -0500 Subject: [Chimera-users] Electrostatic Potential In-Reply-To: References: <04AC3357-276E-4B5A-B5E2-F321099934CD@sonic.net> Message-ID: an apology, don't attach the file correctly, here it goes, regards ATTE Fernando Villa D?az El lun., 16 de sep. de 2019 a la(s) 15:20, Fernando Villa ( fer.vdl1928 at gmail.com) escribi?: > Dear Tom and Chimera users, > > In ChimeraX or Chimera, is it possible to calculate the number of vertices > and their respective total charges? > > I calculated the electrostatic potential surface (Coulombic) with another > program, it gave me the following results (attached in this email) and I > calculated the area in red and blue, above and below a threshold = 0. > > Unfortunately, these results do not help me, because I need to obtain an > electrostatics calculations from Adaptive Poisson-Boltzmann Solver > (Calculations that I have already made for study proteins with PDB2PQR and > APBS, in interface with Chimera: .pqr and .dx files and emulated in Chimera > X) > > e.g. > [image: image.png] > > Now my question is: > Can I obtain these results of vertices and charges in a file from Chimera > or Chimera X (possibly .cvs, .txt, etc.), so that I can make the > corresponding calculations? > > I would greatly appreciate your help > > best regards, > > Fer > > > > El lun., 16 de sep. de 2019 a la(s) 13:03, Tom Goddard (goddard at sonic.net) > escribi?: > >> Hi Fernando, >> >> Instead of thinking about the coloring, it would be clearer to ask how >> much surface area has electrostatic potential value >= 5. Chimera does not >> have any code to compute that, although it is something we could add to >> ChimeraX. >> >> Tom >> >> >> On Sep 11, 2019, at 7:27 PM, Fernando Villa >> wrote: >> >> Dear all Chimera users >> >> In UCSF ChimeraX version 0.91 (2019-08-30) >> I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I >> opened a .dx file (generated with APBS in Chimera 1.14) >> >> Then I input the commands: >> >> >surface >> >color electrostatic #1 map #2 palette -10,red:0,white:10,blue >> >> >> Is it possible to calculate the red and blue area in ?2 of the molecule? >> >> Best regards, >> >> Fernando >> >> >> ATTE >> Fernando Villa D?az >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: >> 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: image.png Type: image/png Size: 306082 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Test_MEP_Protein.xlsx Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Size: 1561781 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon Sep 16 14:28:52 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Sep 2019 14:28:52 -0700 Subject: [Chimera-users] Electrostatic Potential In-Reply-To: References: <04AC3357-276E-4B5A-B5E2-F321099934CD@sonic.net> Message-ID: <80C455C4-01D8-45AA-B8E0-1BF30FFA9FF8@cgl.ucsf.edu> Hi Fernando, This is not answering your specific request, but some points that may be important to consider: (1) Electrostatic potential (the values in dx files) is not the same as charge. Maybe you already know that, but I?m just making sure it is clear. The charge on each atom is already in the pqr file, so if you just wanted the total charge of the molecule, you would add those up. You could even select the surface atoms only, and then add their charges. (2) maybe it is not meaningful to count points that have electrostatic potential values very close to zero. (3) similarly, maybe it is not meaningful to consider points with very small values as having equal importance as points with very large values (that is what you are doing if you only care about the sign) (4) the spatial distribution of the values is important for molecular recognition, not just the number of points with some value. It is very different to have positive and negative intermixed all over the molecule, as compared to positive concentrated on one end of the molecule and negative concentrated on the other end, but those two situations might give identical % areas in your calculation. I understand what you want, but I?m concerned it may not be biologically/physically meaningful. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco From goddard at sonic.net Mon Sep 16 15:39:04 2019 From: goddard at sonic.net (Tom Goddard) Date: Mon, 16 Sep 2019 15:39:04 -0700 Subject: [Chimera-users] Electrostatic Potential In-Reply-To: References: <04AC3357-276E-4B5A-B5E2-F321099934CD@sonic.net> Message-ID: <25CD92E6-D3C5-47AC-A6FA-69C779BF68A4@sonic.net> Hi Fernando, I don't understand what you need vertex coordinates for. But you could put a print statement into the Chimera Python code that does surface coloring to output vertex coordinates and potential values. This would be in file chimera/share/SurfaceColor/__init__.py or on Mac in Chimera.app/Contents/Resources/share/SurfaceColor/__init__.py in the volume_values() routine change def volume_values(self, surface_piece): p = surface_piece xf = p.model.openState.xform v = p.geometry[0] n = p.normals return self.offset_values(v, n, xf) to def volume_values(self, surface_piece): p = surface_piece xf = p.model.openState.xform v = p.geometry[0] n = p.normals values, outside = self.offset_values(v, n, xf) print '\n'.join('%.5g %.5g %.5g %.5g' % (x, y, z, val) for (x,y,z), val in zip(v, values)) return values, outside Use the Surface Color tool and the vertices and values will be printed to the reply log. Tom > On Sep 16, 2019, at 1:20 PM, Fernando Villa wrote: > > Dear Tom and Chimera users, > > In ChimeraX or Chimera, is it possible to calculate the number of vertices and their respective total charges? > > I calculated the electrostatic potential surface (Coulombic) with another program, it gave me the following results (attached in this email) and I calculated the area in red and blue, above and below a threshold = 0. > > Unfortunately, these results do not help me, because I need to obtain an electrostatics calculations from Adaptive Poisson-Boltzmann Solver (Calculations that I have already made for study proteins with PDB2PQR and APBS, in interface with Chimera: .pqr and .dx files and emulated in Chimera X) > > e.g. > > > Now my question is: > Can I obtain these results of vertices and charges in a file from Chimera or Chimera X (possibly .cvs, .txt, etc.), so that I can make the corresponding calculations? > > I would greatly appreciate your help > > best regards, > > Fer > > > > El lun., 16 de sep. de 2019 a la(s) 13:03, Tom Goddard (goddard at sonic.net ) escribi?: > Hi Fernando, > > Instead of thinking about the coloring, it would be clearer to ask how much surface area has electrostatic potential value >= 5. Chimera does not have any code to compute that, although it is something we could add to ChimeraX. > > Tom > > >> On Sep 11, 2019, at 7:27 PM, Fernando Villa > wrote: >> >> Dear all Chimera users >> >> In UCSF ChimeraX version 0.91 (2019-08-30) >> I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file (generated with APBS in Chimera 1.14) >> >> Then I input the commands: >> >> >surface >> >color electrostatic #1 map #2 palette -10,red:0,white:10,blue >> >> >> Is it possible to calculate the red and blue area in ?2 of the molecule? >> >> Best regards, >> >> Fernando >> >> >> ATTE >> Fernando Villa D?az >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Sep 16 15:43:09 2019 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 16 Sep 2019 15:43:09 -0700 Subject: [Chimera-users] Command line equivalence for Render by Attribute radii In-Reply-To: References: Message-ID: <555D01E5-629C-41F5-AB28-9DB746AD08E3@cgl.ucsf.edu> This is really simple to do in Python though. The code is: from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): for a in m.atoms: a.radius = a.bfactor If you put the above into a file with a ?.py? suffix, you can execute it simply by opening it with the ?open? command. Keep in mind that indentation is relevant in Python, so preserve the indentation. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 13, 2019, at 8:25 AM, Elaine Meng wrote: > > Hello Jurgen, > Sorry, there is no command-line equivalent for the ?Radii? section of Render by Attribute, nor is there one for ?Worms? ? there?s only one for coloring, the ?rangecolor? command. > > > > > Surely it could be done with python scripting, but somebody else would have to advise on that. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Sep 12, 2019, at 1:09 PM, Sygusch Jurgen wrote: >> >> Hello, >> I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI. >> >> In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius). >> >> What is the command line equivalence for doing this? I cannot seem to find it. >> Thank you for looking into this. > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunyeping at aliyun.com Tue Sep 17 07:24:39 2019 From: sunyeping at aliyun.com (sunyeping) Date: Tue, 17 Sep 2019 22:24:39 +0800 Subject: [Chimera-users] =?utf-8?q?How_to_draw_3-fold_axis_of_a_Icosahedro?= =?utf-8?q?n?= Message-ID: <1e2e206d-6297-4396-8757-0b4e13447d7b.sunyeping@aliyun.com> Dear everyone, I created an icoshedron with "Tool>high-order structre>Icoshedron surface" menu. Do you know how to draw 3-fold axis of a Icosahedron so that I can see the 3-fold symmetry center on the icoshedron surface? Thank you in advacne. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jurgen.sygusch at umontreal.ca Mon Sep 16 15:50:06 2019 From: jurgen.sygusch at umontreal.ca (Sygusch Jurgen) Date: Mon, 16 Sep 2019 22:50:06 +0000 Subject: [Chimera-users] Command line equivalence for Render by Attribute radii In-Reply-To: <555D01E5-629C-41F5-AB28-9DB746AD08E3@cgl.ucsf.edu> References: <555D01E5-629C-41F5-AB28-9DB746AD08E3@cgl.ucsf.edu> Message-ID: <60e76a1c-2d82-9ede-c56f-5fc493bb1715@umontreal.ca> Wow, thank you very much. On 2019-09-16 6:43 p.m., Eric Pettersen wrote: This is really simple to do in Python though. The code is: from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): for a in m.atoms: a.radius = a.bfactor If you put the above into a file with a ?.py? suffix, you can execute it simply by opening it with the ?open? command. Keep in mind that indentation is relevant in Python, so preserve the indentation. ?Eric Eric Pettersen UCSF Computer Graphics Lab On Sep 13, 2019, at 8:25 AM, Elaine Meng > wrote: Hello Jurgen, Sorry, there is no command-line equivalent for the ?Radii? section of Render by Attribute, nor is there one for ?Worms? ? there?s only one for coloring, the ?rangecolor? command. Surely it could be done with python scripting, but somebody else would have to advise on that. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 12, 2019, at 1:09 PM, Sygusch Jurgen > wrote: Hello, I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI. In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius). What is the command line equivalence for doing this? I cannot seem to find it. Thank you for looking into this. _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: 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: jurgen_sygusch.vcf Type: text/x-vcard Size: 411 bytes Desc: jurgen_sygusch.vcf URL: From meng at cgl.ucsf.edu Tue Sep 17 08:31:28 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 17 Sep 2019 08:31:28 -0700 Subject: [Chimera-users] How to draw 3-fold axis of a Icosahedron In-Reply-To: <1e2e206d-6297-4396-8757-0b4e13447d7b.sunyeping@aliyun.com> References: <1e2e206d-6297-4396-8757-0b4e13447d7b.sunyeping@aliyun.com> Message-ID: Hi, There isn?t an option to draw the symmetry axes in this tool. However, the orientation options in the Icosahedron Surface tool describe which direction it is, for example "x 2-fold, z 3-fold (2n3) - with a two-fold symmetry axis of the icosahedron along the x axis and a three-fold symmetry axis along the z axis? So if you pick the orientation named ?2n3", the 3-fold axis is pointing straight at you going in and out of the screen. You could try creating the axis as a 3D object by making a BILD format file. For example, if you made a 2n3 icosahedron with radius 100, you could create a text file named something.bild containing something like the following lines and open it in Chimera: .color yellow .cylinder 0 0 -100 0 0 +100 5 See BILD format description: I also attached this as a file named test.bild (just open with ?open? command or menu: File?Open). You can change the color, coordinates (length and direction), and the radius, and also there are other BILD shapes available, such as arrow instead of cylinder. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco -------------- next part -------------- A non-text attachment was scrubbed... Name: test.bild Type: application/octet-stream Size: 44 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 9510 bytes Desc: not available URL: -------------- next part -------------- > On Sep 17, 2019, at 7:24 AM, sunyeping wrote: > > Dear everyone, > > I created an icoshedron with "Tool>high-order structre>Icoshedron surface" menu. Do you know how to draw 3-fold axis of a Icosahedron so that I can see the 3-fold symmetry center on the icoshedron surface? > Thank you in advacne. > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From onken031 at umn.edu Tue Sep 17 08:31:28 2019 From: onken031 at umn.edu (Bailey Onken) Date: Tue, 17 Sep 2019 10:31:28 -0500 Subject: [Chimera-users] nonpolar and polar surface area In-Reply-To: <18A2393B-0DCE-45EB-A8A4-599B00C54587@cgl.ucsf.edu> References: <18A2393B-0DCE-45EB-A8A4-599B00C54587@cgl.ucsf.edu> Message-ID: Thank you for the feedback. Could you go into more description as to how to decide and choose which residues are polar and nonpolar. Thank you, Bailey On Mon, Sep 16, 2019, 3:52 PM Elaine Meng wrote: > Hi Bailey, > You will have to decide for yourself which residues you want to consider > as polar and nonpolar. Then after you show the surface of the protein, you > can select any subset of the residues (or atoms) and then sum the surface > area from that subset using the Attribute Calculator tool. > > This is described in more detail in this recent post. Skip down to the > fourth paragraph, starting "However, you can get the total surface area > given some range of hydrophobicity values?? > < > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html > > > > Alternatively, you could take a look at the GetArea web server mentioned > in this follow-up: > < > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html > > > > (I changed the subject line of the message to something more descriptive > to help others find it later.) > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 16, 2019, at 12:23 PM, Bailey Onken wrote: > > > > Hello, > > I am currently a student in Biochemistry. I have a protein and I am > trying to separate polar and nonpolar residues located on the surface of > these molecules and then finding the values for the surface area associated > with polar and nonpolar areas. If you can help me get to this function I > would be very grateful. > > Thank you very much, > > Bailey > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Sep 17 13:07:33 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 17 Sep 2019 13:07:33 -0700 Subject: [Chimera-users] nonpolar and polar surface area In-Reply-To: References: <18A2393B-0DCE-45EB-A8A4-599B00C54587@cgl.ucsf.edu> Message-ID: <6DF7FFBF-E76F-4B04-B0D7-CAF3B117CF38@cgl.ucsf.edu> Hi Bailey, As I said before, this is a research judgment call that you should decide for yourself, as different scientists have different opinions, and there is no single universally agreed-upon answer. You also have to consider what you you want to use these values for. In the previous replies I mentioned you could already use the words ?polar? and ?nonpolar? but they are based on one publication and not everybody agrees with which amino acids it puts in those groups, and there was a link to a table listing what they are, as well as the citation of that publication. Another possibility in Chimera (also described in the previous replies with link to table and literature references) is to use a cutoff in kdHydrophobicity value. It is beyond the scope of this helpdesk to provide general research consulting. I have semi-informed opinions, but I?m not the oracle. If you just want to put in your protein and get results for its polar and apolar solvent-accessible surface areas without having to decide what you want to put in each category, take a look at the GetArea web server mentioned in the second link. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 17, 2019, at 8:31 AM, Bailey Onken wrote: > > Thank you for the feedback. > > Could you go into more description as to how to decide and choose which residues are polar and nonpolar. > > Thank you, > Bailey > > On Mon, Sep 16, 2019, 3:52 PM Elaine Meng wrote: > Hi Bailey, > You will have to decide for yourself which residues you want to consider as polar and nonpolar. Then after you show the surface of the protein, you can select any subset of the residues (or atoms) and then sum the surface area from that subset using the Attribute Calculator tool. > > This is described in more detail in this recent post. Skip down to the fourth paragraph, starting "However, you can get the total surface area given some range of hydrophobicity values?? > > > Alternatively, you could take a look at the GetArea web server mentioned in this follow-up: > > > (I changed the subject line of the message to something more descriptive to help others find it later.) > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 16, 2019, at 12:23 PM, Bailey Onken wrote: > > > > Hello, > > I am currently a student in Biochemistry. I have a protein and I am trying to separate polar and nonpolar residues located on the surface of these molecules and then finding the values for the surface area associated with polar and nonpolar areas. If you can help me get to this function I would be very grateful. > > Thank you very much, > > Bailey > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From turin005 at umn.edu Wed Sep 18 07:41:20 2019 From: turin005 at umn.edu (Danny Turin) Date: Wed, 18 Sep 2019 09:41:20 -0500 Subject: [Chimera-users] Chimera inquiry Message-ID: Dear Sirs and Madames, I first want to start by sharing my appreciation with you for creating this program. It has been very helpful in my biochemistry course. I have been using the program to compute the total area and volume. Is there a way to only select either the polar or non-polar residue in the surface structure to determine volume and area. Thank you for your time. Sincerely, *--Daniel Turin * University of Minnesota Class of 2021, B.S. Health Sciences l turin005 at umn.edu l (651)-600-0805 l -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Sep 18 09:36:42 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Sep 2019 09:36:42 -0700 Subject: [Chimera-users] Chimera polar and nonpolar surface area In-Reply-To: References: Message-ID: <4F40D7D5-BBBB-404A-94FF-396841C65AA5@cgl.ucsf.edu> Hi Daniel, We?re glad Chimera has been useful to you. I?m guessing this is some kind of class assignment because others have been asking the same question lately. Please see this recent response, and links therein: ?including the following, which has with more details starting at the fifth paragraph, ?However, you can get the total surface area given some range of hydrophobicity values?? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 18, 2019, at 7:41 AM, Danny Turin wrote: > > Dear Sirs and Madames, > I first want to start by sharing my appreciation with you for creating this program. It has been very helpful in my biochemistry course. I have been using the program to compute the total area and volume. Is there a way to only select either the polar or non-polar residue in the surface structure to determine volume and area. > Thank you for your time. > Sincerely, > --Daniel Turin > University of Minnesota > Class of 2021, B.S. Health Sciences > l turin005 at umn.edu l (651)-600-0805 l From meng at cgl.ucsf.edu Wed Sep 18 12:14:53 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Sep 2019 12:14:53 -0700 Subject: [Chimera-users] Fwd: chimera install problem References: <1c7730b9.bbbd.16d3f347ada.Coremail.519198561@163.com> Message-ID: <784570B6-B021-4E66-8507-2C58603580D5@cgl.ucsf.edu> Oh sorry, I was waiting for someone else to answer because I didn?t realize until now that you sent this message to only me. I don?t know anything about this subject, so I?m forwarding your message to the chimera-users mailing list for somebody else to reply. We recommend sending Chimera questions to this list instead of to individual developers. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: ??? <519198561 at 163.com> > Subject: chimera install problem > Date: September 17, 2019 at 5:31:06 AM PDT > To: meng at cgl.ucsf.edu > > Hi! > I have a problem when install chimera-1.13.1-linux_x86_64.bin in my computer, its opensuse system. > can you tell me how to solve this problem? as i am not familiar with linux system. > sincerely! > Liuqing Chen > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: erro.jpeg Type: image/jpeg Size: 79580 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: erro.jpeg Type: image/jpeg Size: 79580 bytes Desc: not available URL: From gregc at cgl.ucsf.edu Wed Sep 18 12:22:10 2019 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 18 Sep 2019 12:22:10 -0700 Subject: [Chimera-users] Fwd: chimera install problem In-Reply-To: <784570B6-B021-4E66-8507-2C58603580D5@cgl.ucsf.edu> References: <1c7730b9.bbbd.16d3f347ada.Coremail.519198561@163.com> <784570B6-B021-4E66-8507-2C58603580D5@cgl.ucsf.edu> Message-ID: <132a4666-830c-77eb-d5fd-85fc01c1410f@cgl.ucsf.edu> This bug with libfontconfig.so.1 is fixed in the Chimera daily build.? So please remove version 1.13 from your system and install the daily build instead. ??? -- Greg On 9/18/19 12:14 PM, Elaine Meng wrote: > Oh sorry, I was waiting for someone else to answer because I didn?t > realize until now that you sent this message to only me. ?I don?t know > anything about this subject, so I?m forwarding your message to the > chimera-users mailing list for somebody else to reply. > > We recommend sending Chimera questions to this list instead of to > individual developers. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical?Chemistry > University of California, San Francisco > >> Begin forwarded message: >> >> *From: *??? <519198561 at 163.com > >> *Subject: **chimera install problem* >> *Date: *September 17, 2019 at 5:31:06 AM PDT >> *To: *meng at cgl.ucsf.edu >> >> Hi! >> I have a problem when install chimera-1.13.1-linux_x86_64.bin >> >> in my computer,? its opensuse? system. >> can you tell me how to solve this problem?? as i am not familiar with >> linux system. >> sincerely! >> Liuqing Chen >> >> >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: 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: erro.jpeg Type: image/jpeg Size: 79580 bytes Desc: not available URL: From asingletary at boxx.com Thu Sep 19 12:46:55 2019 From: asingletary at boxx.com (Aron Singletary) Date: Thu, 19 Sep 2019 19:46:55 +0000 Subject: [Chimera-users] Chimera laptop features required Message-ID: I was looking for system specs and ran across this comment: "I don't think you can buy one anymore, but the best laptops were those with NVIDIA Quadro (not NVS) graphics and a 3D stereo display (120Mhz, 3D glasses). Chimera needs workstation graphics (NVIDIA Quadro or AMD FirePro/FireGL), to support 3D stereo viewing." Just wanted to let you know there are still many great systems available with Quadro and FirePro graphics, they will usually be a good bit more expensive than traditional consumer laptops though. Our older GoBOXX SLM available in 15" with the Quadro P3200. https://www.boxx.com/systems/mobile-workstations/goboxx-slm/goboxx-slm-vr Our newer GoBOXX SLM available in 15" or 17" with Quadro RTX300-, RTX4000 or RTX5000. https://www.boxx.com/systems/mobile-workstations/goboxx-slm/goboxx-slm-15 Or if you are looking for a true desktop replacement we have our GoBOXX MXL. https://www.boxx.com/systems/mobile-workstations/goboxx-mxl Thank you, Aron Singletary Enterprise Representative BOXX Technologies 10435 Burnet Road, Austin, TX 78758 Work: (512) 852-3347 Toll Free: (877)877-2699 x347 Fax: (512) 835-0434 Email: asingletary at boxx.com www.boxx.com [BOXX_Logo_email] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4369 bytes Desc: image001.png URL: From Robert.Gampe at pfizer.com Fri Sep 20 15:29:49 2019 From: Robert.Gampe at pfizer.com (Gampe, Robert) Date: Fri, 20 Sep 2019 22:29:49 +0000 Subject: [Chimera-users] calculating virus surface in prep for radial color display Message-ID: Hi Chimera Users I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. However the: 1. Action, Surface, Show command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn't see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. Any solutions greatly appreciated and thanks. Rob [cid:image003.jpg at 01D56FE1.62351B70] [cid:image004.jpg at 01D56FE1.62351B70] _________________________ Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. 7030 Kit Creek Rd, Morrisville, NC 27560 Office: 919-666-5969| Robert.Gampe at pfizer.com [cid:image006.jpg at 01D4D043.EB786830] _________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 23861 bytes Desc: image003.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image004.jpg Type: image/jpeg Size: 2402 bytes Desc: image004.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image005.jpg Type: image/jpeg Size: 4389 bytes Desc: image005.jpg URL: From Robert.Gampe at pfizer.com Fri Sep 20 17:01:02 2019 From: Robert.Gampe at pfizer.com (Gampe, Robert) Date: Sat, 21 Sep 2019 00:01:02 +0000 Subject: [Chimera-users] calculating virus surface in prep for radial color display Message-ID: Hi Chimera Users This is 2nd send to you after I enrolled as a CHIMERA user :), thanks. I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. However the: 1. Action, Surface, Show command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn't see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. Any solutions greatly appreciated and thanks. Rob [cid:image001.jpg at 01D56FEE.1FF9C5A0][cid:image002.jpg at 01D56FEE.1FF9C5A0] _________________________ Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. 7030 Kit Creek Rd, Morrisville, NC 27560 Office: 919-666-5969| Robert.Gampe at pfizer.com [cid:image006.jpg at 01D4D043.EB786830] _________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 22786 bytes Desc: image001.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 2387 bytes Desc: image002.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.jpg Type: image/jpeg Size: 4389 bytes Desc: image003.jpg URL: From susannalopez18 at gmail.com Sat Sep 21 15:12:40 2019 From: susannalopez18 at gmail.com (=?UTF-8?Q?Susy_L=C3=B3pez?=) Date: Sat, 21 Sep 2019 17:12:40 -0500 Subject: [Chimera-users] (no subject) Message-ID: Dear all I am starting to use Chimera as a master's student and I have some difficulties. I know how to select the amino acids that are part of the surface of my protein. However, I don't know how to select the atoms of the surface. Specifically, the atoms accessible to the solvent. My second question is: I would like to know how polar amino acids (arginine, asparagine, aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine, isoleucine, leucine, etc.) can appear. Is there any configuration that allows me to identify polar and non-polar amino acids for edit them? Is it possible to customize those amino acids when I select them? I would be grateful if someone could help me, thank you. Best regards, Susanna -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Sep 23 09:45:23 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 23 Sep 2019 09:45:23 -0700 Subject: [Chimera-users] calculating virus surface in prep for radial color display In-Reply-To: References: Message-ID: <55689F19-EF4F-4560-949D-AFFE6FC9E19F@cgl.ucsf.edu> Hi Rob, It wasn?t necessary to send the question again ? questions from people not yet signed up to the list will still appear on the list after the moderator approves them (if they?re clearly not spam). Normally this type of radial coloring is done on a density map isosurface, not on a molecular surface calculated from the atomic positions, the kind of surface you were trying to show. You can look for AAV electron microscopy maps at EMDB (I find 11 maps there for organism ?adeno-associated virus") and choose one of them to show, adjust the isosurface in Volume Viewer if needed, and then use Surface Color for radial coloring. In Chimera, you can fetch directly from EMDB using menu: File? Fetch by ID, choosing EMDB in the dialog and entering the ID, e.g. 0535 If you really want to use a specific atomic structure, you could instead try showing low-resolution ?multiscale? surfaces for that atomic structure instead of the standard molecular surfaces that are prone to calculation failures. Menu: Tools? Higher-Order Structure? Multiscale Models, and in that dialog click the ?Make models? button near the bottom, then use Surface Color for radial coloring. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 20, 2019, at 5:01 PM, Gampe, Robert wrote: > > > Hi Chimera Users > This is 2nd send to you after I enrolled as a CHIMERA user J, thanks. > > I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. > > However the: > ? Action, Surface, Show > command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). > > Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn?t see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. > > Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. > > Any solutions greatly appreciated and thanks. > Rob > > From meng at cgl.ucsf.edu Mon Sep 23 09:54:41 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 23 Sep 2019 09:54:41 -0700 Subject: [Chimera-users] polar and nonpolar surface area In-Reply-To: References: Message-ID: Dear Susanna, This sounds like the same question others have been asking recently? maybe a class assignment. If so, you can tell the others in the class so that they don?t have to ask here again! :-) Please see this recent response, and links therein: ?including the following, which has with more details starting at the fifth paragraph, ?However, you can get the total surface area given some range of hydrophobicity values?? ?or a web server you could try instead of Chimera: These answers suggest selecting polar and nonpolar residues, giving a few different options for deciding which ones are polar and nonpolar, and then just adding up the surface area from the selection. Maybe by ?customize? you meant deciding for yourself which is polar and nonpolar? You can just select a list of whatever residue types you want, e.g. command: select :asp,glu,his,lys,arg You don?t have to worry about selecting only the atoms on the surface, because if they are not on the surface they will just add zero area to the total and the result will be the same. Selecting a residue selects all the atoms in that residue. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 21, 2019, at 3:12 PM, Susy L?pez wrote: > > Dear all > I am starting to use Chimera as a master's student and I have some difficulties. > > I know how to select the amino acids that are part of the surface of my protein. However, I don't know how to select the atoms of the surface. Specifically, the atoms accessible to the solvent. > > My second question is: > > I would like to know how polar amino acids (arginine, asparagine, aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine, isoleucine, leucine, etc.) can appear. Is there any configuration that allows me to identify polar and non-polar amino acids for edit them? Is it possible to customize those amino acids when I select them? > > I would be grateful if someone could help me, thank you. > > Best regards, > > > Susanna From goddard at sonic.net Mon Sep 23 10:59:41 2019 From: goddard at sonic.net (Tom Goddard) Date: Mon, 23 Sep 2019 10:59:41 -0700 Subject: [Chimera-users] calculating virus surface in prep for radial color display In-Reply-To: <55689F19-EF4F-4560-949D-AFFE6FC9E19F@cgl.ucsf.edu> References: <55689F19-EF4F-4560-949D-AFFE6FC9E19F@cgl.ucsf.edu> Message-ID: Or you can try using the molmap command to make a density map from the atomic model. If the atomic model is #0 then molmap #0 4 will simulate a density map at resolution 4 Angstroms. Then you can color the contour surface of that density map. Tom > On Sep 23, 2019, at 9:45 AM, Elaine Meng wrote: > > Hi Rob, > It wasn?t necessary to send the question again ? questions from people not yet signed up to the list will still appear on the list after the moderator approves them (if they?re clearly not spam). > > Normally this type of radial coloring is done on a density map isosurface, not on a molecular surface calculated from the atomic positions, the kind of surface you were trying to show. > > You can look for AAV electron microscopy maps at EMDB (I find 11 maps there for organism ?adeno-associated virus") and choose one of them to show, adjust the isosurface in Volume Viewer if needed, and then use Surface Color for radial coloring. > > > > > > In Chimera, you can fetch directly from EMDB using menu: File? Fetch by ID, choosing EMDB in the dialog and entering the ID, e.g. 0535 > > If you really want to use a specific atomic structure, you could instead try showing low-resolution ?multiscale? surfaces for that atomic structure instead of the standard molecular surfaces that are prone to calculation failures. Menu: Tools? Higher-Order Structure? Multiscale Models, and in that dialog click the ?Make models? button near the bottom, then use Surface Color for radial coloring. > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Sep 20, 2019, at 5:01 PM, Gampe, Robert wrote: >> >> >> Hi Chimera Users >> This is 2nd send to you after I enrolled as a CHIMERA user J, thanks. >> >> I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. >> >> However the: >> ? Action, Surface, Show >> command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). >> >> Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn?t see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. >> >> Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. >> >> Any solutions greatly appreciated and thanks. >> Rob >> >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From David.Bhella at glasgow.ac.uk Tue Sep 24 00:42:14 2019 From: David.Bhella at glasgow.ac.uk (David Bhella) Date: Tue, 24 Sep 2019 07:42:14 +0000 Subject: [Chimera-users] calculating virus surface in prep for radial color display In-Reply-To: References: Message-ID: <69078D18-1954-4FA4-84BE-75CFF00B0321@glasgow.ac.uk> The figure you shared looks more like the cryoEM map than a surface generated from a pdb file. Why not download a map from EMDB? There are several AAV maps, I made the attached image using EMD6470. Looks even better in ChimeraX! D David Bhella Professor of Structural Virology Associate Director - MRC-University of Glasgow Centre for Virus Research Director - Scottish Centre for Macromolecular Imaging Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella On 20 Sep 2019, at 23:29, Gampe, Robert > wrote: Hi Chimera Users I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. However the: 1. Action, Surface, Show command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn?t see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. Any solutions greatly appreciated and thanks. Rob _________________________ Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. 7030 Kit Creek Rd, Morrisville, NC 27560 Office: 919-666-5969| Robert.Gampe at pfizer.com _________________________ _______________________________________________ Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users [cid:161A7792-8107-4E96-A859-1BC82D7ED578 at campus.gla.ac.uk][cid:E305E84F-4D52-49DE-B575-24F6C576B920 at campus.gla.ac.uk] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AAV_EMD6470_chimeraX.jpg Type: image/jpeg Size: 483580 bytes Desc: AAV_EMD6470_chimeraX.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AAV_EMD6470_chimera.jpg Type: image/jpeg Size: 735387 bytes Desc: AAV_EMD6470_chimera.jpg URL: From susannalopez18 at gmail.com Tue Sep 24 07:24:40 2019 From: susannalopez18 at gmail.com (=?UTF-8?Q?Susy_L=C3=B3pez?=) Date: Tue, 24 Sep 2019 09:24:40 -0500 Subject: [Chimera-users] (no subject) Message-ID: Dear Tom Goddard I would just like to know if there is any command in Chimera, which allows me to identify the atoms that are part of the total solvent accessible surface area (SAS). I will try to explain my question with an example. First, Commands: open 121p select :62 show sel Select>residue>all nonstandard Actions>Atoms/Bonds>delete select :62 at OE1 surface sel [image: image.png] As shown in the image, I have identified an atom that forms the surface accessible to the solvent. However, to identify the total atoms of that protein I have to select atom by atom, which implies a lot of time and more if I have several proteins. So, I would like to know, if it?s possible to obtain a command that allows me to select all the atoms at the same time, specifying the atoms that are part of the total solvent accessible surface area(SAS). Thank you (: kind regards, Susanna -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 80740 bytes Desc: not available URL: From omar.debei.unipr at gmail.com Tue Sep 24 07:38:11 2019 From: omar.debei.unipr at gmail.com (Omar De Bei) Date: Tue, 24 Sep 2019 15:38:11 +0100 Subject: [Chimera-users] (no subject) In-Reply-To: References: Message-ID: Dear Susanna, I recommend you to follow this short tutorial. http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html Best, Omar Il 9/24/2019 3:24 PM, Susy L?pez ha scritto: > > Dear Tom Goddard > > > I would just like to know if there is any command in Chimera, which > allows me to identify the atoms that are part of the total solvent > accessible surface area (SAS). > > I will try to explain my question with an example. > > First, > > Commands: > > open 121p > > select :62 > > show sel > > Select>residue>all nonstandard > > Actions>Atoms/Bonds>delete > > select :62 at OE1 > > surface sel > > image.png > > > As shown in the image, I have identified an atom that forms the > surface accessible to the solvent. However, to identify the total > atoms of that protein I have to select atom by atom, which implies a > lot of time and more if I have several proteins. > > So, I would like to know, if it?s possible to obtain a command that > allows me to select all the atoms at the same time, specifying the > atoms that are part of the total solvent accessible surface area(SAS). > > Thank you (: > > kind regards, > > Susanna > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: 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: image.png Type: image/png Size: 80740 bytes Desc: not available URL: From susannalopez18 at gmail.com Mon Sep 23 15:35:36 2019 From: susannalopez18 at gmail.com (=?UTF-8?Q?Susy_L=C3=B3pez?=) Date: Mon, 23 Sep 2019 17:35:36 -0500 Subject: [Chimera-users] polar and nonpolar surface area In-Reply-To: References: Message-ID: Dear all This does not answer my question. Maybe, I don't explain it properly. I would just like to know if there is any command in Chimera, which allows me to identify the atoms that are part of the total solvent accessible surface area (SAS). I will try to explain my question with an example. First, Commands: open 121p select :62 show sel Select>residue>all nonstandard Actions>Atoms/Bonds>delete select :62 at OE1 surface sel [image: image.png] As shown in the image, I have identified an atom that forms the surface accessible to the solvent. However, to identify the total atoms of that protein I have to select atom by atom, which implies a lot of time and more if I have several proteins. So, I would like to know, if it?s possible to obtain a command that allows me to select all the atoms at the same time, specifying the atoms that are part of the total solvent accessible surface area(SAS). Thank you (: kind regards, Susanna El lun., 23 sept. 2019 a las 17:33, Susy L?pez () escribi?: > Dear all > > > > This does not answer my question. Maybe, I don't explain it properly. > > I would just like to know if there is any command in Chimera, which allows > me to identify the atoms that are part of the total solvent accessible > surface area (SAS). > > > > I will try to explain my question with an example. > > First, > > Commands: > > open 121p > > select :62 > > show sel > > Select>residue>all nonstandard > > Actions>Atoms/Bonds>delete > > select :62 at OE1 > > surface sel > > > > As shown in the image, I have identified an atom that forms the surface > accessible to the solvent. However, to identify the total atoms of that > protein I have to select atom by atom, which implies a lot of time and more > if I have several proteins. > > So, I would like to know, if it?s possible to obtain a command that allows > me to select all the atoms at the same time, specifying the atoms that are > part of the total solvent accessible surface area(SAS). > > > > Thank you (: > > > > kind regards, > > Susanna > > > > > > > > > > El lun., 23 sept. 2019 a las 11:54, Elaine Meng () > escribi?: > >> Dear Susanna, >> This sounds like the same question others have been asking recently? >> maybe a class assignment. If so, you can tell the others in the class so >> that they don?t have to ask here again! :-) >> >> Please see this recent response, and links therein: >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016160.html >> > >> >> ?including the following, which has with more details starting at the >> fifth paragraph, ?However, you can get the total surface area given some >> range of hydrophobicity values?? >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html >> > >> >> ?or a web server you could try instead of Chimera: >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html >> > >> >> These answers suggest selecting polar and nonpolar residues, giving a few >> different options for deciding which ones are polar and nonpolar, and then >> just adding up the surface area from the selection. Maybe by ?customize? >> you meant deciding for yourself which is polar and nonpolar? You can just >> select a list of whatever residue types you want, e.g. command: select >> :asp,glu,his,lys,arg >> >> You don?t have to worry about selecting only the atoms on the surface, >> because if they are not on the surface they will just add zero area to the >> total and the result will be the same. Selecting a residue selects all the >> atoms in that residue. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Sep 21, 2019, at 3:12 PM, Susy L?pez >> wrote: >> > >> > Dear all >> > I am starting to use Chimera as a master's student and I have some >> difficulties. >> > >> > I know how to select the amino acids that are part of the surface of my >> protein. However, I don't know how to select the atoms of the surface. >> Specifically, the atoms accessible to the solvent. >> > >> > My second question is: >> > >> > I would like to know how polar amino acids (arginine, asparagine, >> aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine, >> isoleucine, leucine, etc.) can appear. Is there any configuration that >> allows me to identify polar and non-polar amino acids for edit them? Is it >> possible to customize those amino acids when I select them? >> > >> > I would be grateful if someone could help me, thank you. >> > >> > Best regards, >> > >> > >> > Susanna >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 80740 bytes Desc: not available URL: From meng at cgl.ucsf.edu Tue Sep 24 09:16:31 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 24 Sep 2019 09:16:31 -0700 Subject: [Chimera-users] specifying surface atoms In-Reply-To: References: Message-ID: <4FA16E7F-79B6-4ADB-AF4D-AF09432867DD@cgl.ucsf.edu> Hi Susy, Besides the video that Omar suggested, > I recommend you to follow this short tutorial. > http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html > Best, > Omar ... see also this previous post ?identifying surface residues?: It describes the same process as shown in the video, as well as possible commands. First you always have to show the molecular surface. You can just show it for the whole molecule. Then, the process is very similar to identify surface atoms instead of whole residues. In the Select by Attribute dialog, you would just select by attribute of ?atoms? instead of ?residues?. You can write a list of selected atoms or residues with menu: Actions? Write List, or you can use the selection in some other command, for example: color red sel Or if you wanted to use commands to select by area instead of the dialog, that previous post showed an example for residues: select :/areaSES>30 To use it instead for atoms, could be something like select @/areaSES>4.0 or select @/areaSAS>3.0 ? where you would have to decide the minimum value of surface area that you want to use, and whether it should be SAS (solvent-accessible surface) or SES (solvent-excluded surface). You can even limit the selection by element or by residue type, for example: select @/areaSAS>3 & ~C (select atoms by area and not-carbon) select @/areaSAS>3 & :asp,glu,his,lys,arg (select atoms by area and that are also in the named residue types) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 23, 2019, at 3:35 PM, Susy L?pez wrote: > > Dear all > This does not answer my question. Maybe, I don't explain it properly. > > I would just like to know if there is any command in Chimera, which allows me to identify the atoms that are part of the total solvent accessible surface area (SAS). > > I will try to explain my question with an example. > > First, > > Commands: > open 121p > select :62 > show sel > Select>residue>all nonstandard > Actions>Atoms/Bonds>delete > select :62 at OE1 > surface sel > > > > As shown in the image, I have identified an atom that forms the surface accessible to the solvent. However, to identify the total atoms of that protein I have to select atom by atom, which implies a lot of time and more if I have several proteins. > > So, I would like to know, if it?s possible to obtain a command that allows me to select all the atoms at the same time, specifying the atoms that are part of the total solvent accessible surface area(SAS). > Thank you (: > kind regards, > Susanna > From susannalopez18 at gmail.com Tue Sep 24 10:39:45 2019 From: susannalopez18 at gmail.com (=?UTF-8?Q?Susy_L=C3=B3pez?=) Date: Tue, 24 Sep 2019 12:39:45 -0500 Subject: [Chimera-users] specifying surface atoms In-Reply-To: <4FA16E7F-79B6-4ADB-AF4D-AF09432867DD@cgl.ucsf.edu> References: <4FA16E7F-79B6-4ADB-AF4D-AF09432867DD@cgl.ucsf.edu> Message-ID: Dear Dr. Elaine Meng Thank you, thank you very much!!!. I'm very grateful. Finally I could, it helped me a lot. Dear Omar Really, thank you (: King regards, Susy El mar., 24 sept. 2019 a las 11:16, Elaine Meng () escribi?: > Hi Susy, > Besides the video that Omar suggested, > > > I recommend you to follow this short tutorial. > > http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html > > Best, > > Omar > > ... see also this previous post ?identifying surface residues?: > > > > It describes the same process as shown in the video, as well as possible > commands. First you always have to show the molecular surface. You can > just show it for the whole molecule. > > Then, the process is very similar to identify surface atoms instead of > whole residues. In the Select by Attribute dialog, you would just select > by attribute of ?atoms? instead of ?residues?. You can write a list of > selected atoms or residues with menu: Actions? Write List, or you can use > the selection in some other command, for example: color red sel > > Or if you wanted to use commands to select by area instead of the dialog, > that previous post showed an example for residues: > > select :/areaSES>30 > > To use it instead for atoms, could be something like > > select @/areaSES>4.0 > or > select @/areaSAS>3.0 > > ? where you would have to decide the minimum value of surface area that > you want to use, and whether it should be SAS (solvent-accessible surface) > or SES (solvent-excluded surface). > > You can even limit the selection by element or by residue type, for > example: > > select @/areaSAS>3 & ~C > (select atoms by area and not-carbon) > > select @/areaSAS>3 & :asp,glu,his,lys,arg > (select atoms by area and that are also in the named residue types) > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 23, 2019, at 3:35 PM, Susy L?pez > wrote: > > > > Dear all > > This does not answer my question. Maybe, I don't explain it properly. > > > > I would just like to know if there is any command in Chimera, which > allows me to identify the atoms that are part of the total solvent > accessible surface area (SAS). > > > > I will try to explain my question with an example. > > > > First, > > > > Commands: > > open 121p > > select :62 > > show sel > > Select>residue>all nonstandard > > Actions>Atoms/Bonds>delete > > select :62 at OE1 > > surface sel > > > > > > > > As shown in the image, I have identified an atom that forms the surface > accessible to the solvent. However, to identify the total atoms of that > protein I have to select atom by atom, which implies a lot of time and more > if I have several proteins. > > > > So, I would like to know, if it?s possible to obtain a command that > allows me to select all the atoms at the same time, specifying the atoms > that are part of the total solvent accessible surface area(SAS). > > Thank you (: > > kind regards, > > Susanna > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sudatt.lam at gmail.com Wed Sep 25 00:26:10 2019 From: sudatt.lam at gmail.com (Su Datt Lam) Date: Wed, 25 Sep 2019 15:26:10 +0800 Subject: [Chimera-users] Docking with UCSF Chimera Message-ID: Dear Chimera, Dear Chimera, I am trying to use your software to run molecular docking of sucrose onto a structure. I've provided the ligand and also the receptor structure in the email. I've added the charge for the ligand (using Tools->Structure editing-> Add charge) and selected Gasteiger ad the charge method. After that, I prep the ligand (using Tools -> Structure editing-> Dock Prep). Then, I performed the docking thru Tools ->Surface/Binding Analysis ->AutoDock Vina. Vina program managed to run, but with some errors. The ligand bound to the structure is not the right structure of sucrose, but a hairball. I suspect there's something wrong with the Ligand prepping method in chimera that causes the structure to go crazy. Can you help me with this problem? Many thanks, Su -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fructose.sdf Type: application/octet-stream Size: 1214 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: full_model_8117_1.pdb Type: chemical/x-pdb Size: 416340 bytes Desc: not available URL: From meng at cgl.ucsf.edu Wed Sep 25 08:32:06 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 25 Sep 2019 08:32:06 -0700 Subject: [Chimera-users] Docking with UCSF Chimera In-Reply-To: References: Message-ID: <834B82C3-DA82-4315-BF10-CD6F25010FB0@cgl.ucsf.edu> Dear Su, Your ligand file is a 2D SDF, not a 3D structure of a molecule. You have to use a 3D structure, not this flat drawing, which also has bonds much too short for a real molecule. The chemical recognition in Dock Prep requires reasonable bond lengths and a 3D structure (which might be flat if it were benzene, but sucrose should not be flat). Furthermore, sucrose is a disaccharide and this SDF is clearly a monosaccharide (only one sugar ring). One way to get a 3D structure is to fetch into Chimera using a Pubchem CID. E.g. go to the PubChem Compound database and search for what you want, then use Chimera menu: File? Fetch by ID, choose PubChem, and enter the CID for that compound. If sucrose is what you actually want, it is Pubchem CID 5988: Below I attached a picture from opening your SDF and also using Chimera command: open pubchem:5988 Your SDF is on the left, the Pubchem structure on the right. Also to note is that Autodock Vina docking is not ?inside? Chimera. This tool in Chimera connects to an outside web service that is running Autodock Vina, which is developed by another group. You should be aware that the web service does not allow very much sampling, so if you want to a very in-depth search you would need to use a different approach. This is explained in the help page: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 25, 2019, at 12:26 AM, Su Datt Lam wrote: > > Dear Chimera, > I am trying to use your software to run molecular docking of sucrose onto a structure. I've provided the ligand and also the receptor structure in the email. > > I've added the charge for the ligand (using Tools->Structure editing-> Add charge) and selected Gasteiger ad the charge method. After that, I prep the ligand (using Tools -> Structure editing-> Dock Prep). Then, I performed the docking thru Tools ->Surface/Binding Analysis ->AutoDock Vina. > > Vina program managed to run, but with some errors. The ligand bound to the structure is not the right structure of sucrose, but a hairball. I suspect there's something wrong with the Ligand prepping method in chimera that causes the structure to go crazy. Can you help me with this problem? > > Many thanks, > Su > _ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 29755 bytes Desc: not available URL: From bixia.zhang at wsu.edu Fri Sep 27 10:14:07 2019 From: bixia.zhang at wsu.edu (Zhang, Bixia) Date: Fri, 27 Sep 2019 17:14:07 +0000 Subject: [Chimera-users] Question about selecting residues In-Reply-To: References: , Message-ID: Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia ________________________________ From: Zhang, Bixia Sent: Friday, September 27, 2019 10:11 To: chimera-users at cgl.ucsf.edu Subject: Re: Question about selecting residues Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia ________________________________ From: Zhang, Bixia Sent: Friday, September 27, 2019 10:06 To: chimera-users at cgl.ucsf.edu Subject: Question about selecting residues Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Sep 27 12:16:31 2019 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Sep 2019 12:16:31 -0700 Subject: [Chimera-users] Question about selecting residues In-Reply-To: References: Message-ID: <70A88A63-FBD6-453E-8C65-7918F93B6CF5@cgl.ucsf.edu> Dear Bixia, The ?smart initial display? (what is shown automatically when you open the structure) uses the same rules as the ribbons preset described here: "most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 ? of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.? This is just to show the parts of the structure that might be interesting to many people. However, we are not claiming that they are the only interactions or all interactions. Depending on how you define ?interaction,? you can use several different methods described below to select residues around the ligand, and then write a list of those residues with menu: Actions? Write List. Three ways to select residues that might be interacting with the ligand: (1) select residues near your ligand based on distance cutoff, which could be whatever you want (not necessarily 3.6 angstroms). E.g. select your ligand molecule (many ways: with Ctrl-click on atom and then press keyboard up arrow to select whole residue, or menu: Select? Residue?[ligand residue name]) and then use menu: Select? Zone, ... or use command-line zone specifications, e.g. command: select ligand zr<4.2 (2) select residues with H-bonds to your ligand. See tool ?FindHBond? or command ?findhbond? ? they have an option to select (3) select residues with contacts to your ligand. See tool ?Find Clashes/Contacts? or command ?findclash? ? they have an option to select You can also take a look at the tutorial ?Structure Analysis and Comparison? for examples of using those tools. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 27, 2019, at 10:14 AM, Zhang, Bixia wrote: > > Dear Chimera Developers, > I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! > Best, > Bixia > From bixia.zhang at wsu.edu Fri Sep 27 12:42:01 2019 From: bixia.zhang at wsu.edu (Zhang, Bixia) Date: Fri, 27 Sep 2019 19:42:01 +0000 Subject: [Chimera-users] Question about selecting residues In-Reply-To: <70A88A63-FBD6-453E-8C65-7918F93B6CF5@cgl.ucsf.edu> References: , <70A88A63-FBD6-453E-8C65-7918F93B6CF5@cgl.ucsf.edu> Message-ID: Thank you Elaine! That's really helpful. I appreciate your help. Have a good weekend! Best, Bixia ________________________________ From: Elaine Meng Sent: Friday, September 27, 2019 12:16 To: Zhang, Bixia Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Question about selecting residues Dear Bixia, The ?smart initial display? (what is shown automatically when you open the structure) uses the same rules as the ribbons preset described here: "most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 ? of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.? This is just to show the parts of the structure that might be interesting to many people. However, we are not claiming that they are the only interactions or all interactions. Depending on how you define ?interaction,? you can use several different methods described below to select residues around the ligand, and then write a list of those residues with menu: Actions? Write List. Three ways to select residues that might be interacting with the ligand: (1) select residues near your ligand based on distance cutoff, which could be whatever you want (not necessarily 3.6 angstroms). E.g. select your ligand molecule (many ways: with Ctrl-click on atom and then press keyboard up arrow to select whole residue, or menu: Select? Residue?[ligand residue name]) and then use menu: Select? Zone, ... or use command-line zone specifications, e.g. command: select ligand zr<4.2 (2) select residues with H-bonds to your ligand. See tool ?FindHBond? or command ?findhbond? ? they have an option to select (3) select residues with contacts to your ligand. See tool ?Find Clashes/Contacts? or command ?findclash? ? they have an option to select You can also take a look at the tutorial ?Structure Analysis and Comparison? for examples of using those tools. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 27, 2019, at 10:14 AM, Zhang, Bixia wrote: > > Dear Chimera Developers, > I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! > Best, > Bixia > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yepingsun80 at gmail.com Sat Sep 28 22:48:58 2019 From: yepingsun80 at gmail.com (Sun Yeping) Date: Sun, 29 Sep 2019 13:48:58 +0800 Subject: [Chimera-users] How to launch chimera in a remote server Message-ID: Dear everyone, Chimera is installed in a remote CentOS 7 server, and it works properly if working directly on the server. However, when I login to that server from my local machine (also centos 7 system) wish ssh and try to launch chimera, an error information window appears which reads: "Display misconfiguration. Please Increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera Installation Instructions" I googled this error and find that someone solve it by installing virtualGL, so I also installed virtualGL and try to launch chimera with: $vglrun chimera But get the following errorL # vglrun chimera [VGL] WARNING: The OpenGL rendering context obtained on X display [VGL] :0 is indirect, which may cause performance to suffer. [VGL] If :0 is a local X display, then the framebuffer device [VGL] permissions may be set incorrectly. [VGL] WARNING: The OpenGL rendering context obtained on X display [VGL] :0 is indirect, which may cause performance to suffer. [VGL] If :0 is a local X display, then the framebuffer device [VGL] permissions may be set incorrectly. X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 36 Current serial number in output stream: 36 Do you know what the error is about and how to solve it? Thanks in advacnce Yeping Sun -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertel2421 at gmail.com Mon Sep 30 19:02:40 2019 From: bertel2421 at gmail.com (sergio Bertel Perez) Date: Mon, 30 Sep 2019 21:02:40 -0500 Subject: [Chimera-users] Download chimney Message-ID: It does not allow me to download the program, I accept the terms and it sends me a message (Thank you for considering UCSF Chimera. Please let us know what part of the UCSF Chimera license agreement you found unacceptable). Libre de virus. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -------------- next part -------------- An HTML attachment was scrubbed... URL: