From michael.elbaum at weizmann.ac.il Thu Dec 1 10:23:45 2016 From: michael.elbaum at weizmann.ac.il (Michael Elbaum) Date: Thu, 1 Dec 2016 18:23:45 +0000 Subject: [Chimera-users] saving pdb with transformed coordinates Message-ID: <77389ED5A5E5A947A5FEA1B9E8D512CBBE0E60EC@ibwmbx03> Dear Chimera people, I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. thanks for your help, Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Dec 1 11:04:02 2016 From: goddard at sonic.net (Tom Goddard) Date: Thu, 1 Dec 2016 11:04:02 -0800 Subject: [Chimera-users] Unit cell In-Reply-To: References: Message-ID: <7DD6592D-29C9-490F-ABF0-33E3DF32606E@sonic.net> Hi Neha, The space group for 3HR2 is P1 which means the unit cell contains only one copy. This is reported by the Chimera Unit Cell tool (menu Tools / Higher-Order Structure / Unit Cell). To show multiple copies press the Options button on the Unit Cell dialog and change Number of Cells from 1 1 1 to say 2 2 2 and press Make Copies to get molecule copies in a 2 by 2 by 2 grid of unit cells. It sounds like you also want the Unit Cell outline box to have corner at (0,0,0) and that is not what happens. Instead it shows another unit cell outline that contains the center of the molecule. This bizarre structure is 4 times longer than the unit cell so the center likes in a unit cell that does not have corner at (0,0,0). Unfortnately the tool does not let you show other unit cell outlines, just this one centered at the molecule. If you absolutely had to get a different unit cell outline you could try to translate the outline model by multiples of the unit cell axes vectors. But you would need the coordinates of those vectors which would be somewhat tricky to get since the cell is skewed. Tom > On Nov 30, 2016, at 11:04 PM, Neha Gandhi wrote: > > Hi Elaine, > > I have tried to look at the unit cell information of pdb Id :3HR2. It is a fiber diffraction structure of collagen with only CA coordinates. I tried using different programs like VMD to visualise unit cell, the unit cell is at the beginning of N terminus in agreement with experimental paper. Whereas in Chimera it is not the case. How can I visualize the unit cell of 3HR2 structure in Chimera and also number of molecules within one unit cell? > > Many thanks, > Neha > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn <> > Research Gate <> > _______________________________________________ > 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 n.gandhiau at gmail.com Thu Dec 1 11:56:58 2016 From: n.gandhiau at gmail.com (Neha Gandhi) Date: Fri, 2 Dec 2016 05:56:58 +1000 Subject: [Chimera-users] Unit cell In-Reply-To: <7DD6592D-29C9-490F-ABF0-33E3DF32606E@sonic.net> References: <7DD6592D-29C9-490F-ABF0-33E3DF32606E@sonic.net> Message-ID: Thank you Tom for your email. My apologies that my knowledge on microscopy structures is limited. I have a trivial question. Is there a way to extract the coordinates of the unit cell in Chimera rather than working with this 4 times long molecule? If I can do this then it will be easy to make copies or use contacts to get the neighboring molecules. Many thanks, Neha On 2 December 2016 at 05:04, Tom Goddard wrote: > Hi Neha, > > The space group for 3HR2 is P1 which means the unit cell contains only > one copy. This is reported by the Chimera Unit Cell tool (menu Tools / > Higher-Order Structure / Unit Cell). To show multiple copies press the > Options button on the Unit Cell dialog and change Number of Cells from 1 1 > 1 to say 2 2 2 and press Make Copies to get molecule copies in a 2 by 2 by > 2 grid of unit cells. > > It sounds like you also want the Unit Cell outline box to have corner at > (0,0,0) and that is not what happens. Instead it shows another unit cell > outline that contains the center of the molecule. This bizarre structure > is 4 times longer than the unit cell so the center likes in a unit cell > that does not have corner at (0,0,0). Unfortnately the tool does not let > you show other unit cell outlines, just this one centered at the molecule. > If you absolutely had to get a different unit cell outline you could try to > translate the outline model by multiples of the unit cell axes vectors. > But you would need the coordinates of those vectors which would be somewhat > tricky to get since the cell is skewed. > > Tom > > > > On Nov 30, 2016, at 11:04 PM, Neha Gandhi wrote: > > Hi Elaine, > > I have tried to look at the unit cell information of pdb Id :3HR2. It is a > fiber diffraction structure of collagen with only CA coordinates. I tried > using different programs like VMD to visualise unit cell, the unit cell is > at the beginning of N terminus in agreement with experimental paper. > Whereas in Chimera it is not the case. How can I visualize the unit cell of > 3HR2 structure in Chimera and also number of molecules within one unit cell? > > Many thanks, > Neha > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn > Research Gate > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/ > mailman/listinfo/chimera-users > > > -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Dec 1 12:10:56 2016 From: goddard at sonic.net (Tom Goddard) Date: Thu, 1 Dec 2016 12:10:56 -0800 Subject: [Chimera-users] Unit cell In-Reply-To: References: <7DD6592D-29C9-490F-ABF0-33E3DF32606E@sonic.net> Message-ID: <5059249A-2AAD-403F-B336-94D6ECB72947@sonic.net> I don?t understand your question. What do you mean by the ?coordinates of the unit cell?? Do you mean atom coordinates? cell axis vectors? How will you use this? Tom > On Dec 1, 2016, at 11:56 AM, Neha Gandhi wrote: > > Thank you Tom for your email. > > My apologies that my knowledge on microscopy structures is limited. I have a trivial question. Is there a way to extract the coordinates of the unit cell in Chimera rather than working with this 4 times long molecule? If I can do this then it will be easy to make copies or use contacts to get the neighboring molecules. > > Many thanks, > Neha > > On 2 December 2016 at 05:04, Tom Goddard > wrote: > Hi Neha, > > The space group for 3HR2 is P1 which means the unit cell contains only one copy. This is reported by the Chimera Unit Cell tool (menu Tools / Higher-Order Structure / Unit Cell). To show multiple copies press the Options button on the Unit Cell dialog and change Number of Cells from 1 1 1 to say 2 2 2 and press Make Copies to get molecule copies in a 2 by 2 by 2 grid of unit cells. > > It sounds like you also want the Unit Cell outline box to have corner at (0,0,0) and that is not what happens. Instead it shows another unit cell outline that contains the center of the molecule. This bizarre structure is 4 times longer than the unit cell so the center likes in a unit cell that does not have corner at (0,0,0). Unfortnately the tool does not let you show other unit cell outlines, just this one centered at the molecule. If you absolutely had to get a different unit cell outline you could try to translate the outline model by multiples of the unit cell axes vectors. But you would need the coordinates of those vectors which would be somewhat tricky to get since the cell is skewed. > > Tom > > > >> On Nov 30, 2016, at 11:04 PM, Neha Gandhi wrote: >> >> Hi Elaine, >> >> I have tried to look at the unit cell information of pdb Id :3HR2. It is a fiber diffraction structure of collagen with only CA coordinates. I tried using different programs like VMD to visualise unit cell, the unit cell is at the beginning of N terminus in agreement with experimental paper. Whereas in Chimera it is not the case. How can I visualize the unit cell of 3HR2 structure in Chimera and also number of molecules within one unit cell? >> >> Many thanks, >> Neha >> >> -- >> Regards, >> Dr. Neha S. Gandhi, >> Vice Chancellor's Research Fellow, >> Queensland University of Technology, >> 2 George Street, Brisbane, QLD 4000 >> Australia >> LinkedIn <> >> Research Gate <> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn <> > Research Gate <> > _______________________________________________ > 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 sgremesh at lbl.gov Thu Dec 1 12:15:02 2016 From: sgremesh at lbl.gov (Soumya Govinda Remesh) Date: Thu, 1 Dec 2016 12:15:02 -0800 Subject: [Chimera-users] Selected measure angles Message-ID: Hello, I have just modified the loop script available here ( http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html) to measure certain angles and distances. I just want to know if there is a way to export the individual values of angles and distances to a file other than parsing from the reply-log. Thank you. Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh at lbl.gov -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.gandhiau at gmail.com Thu Dec 1 12:19:42 2016 From: n.gandhiau at gmail.com (Neha Gandhi) Date: Fri, 2 Dec 2016 06:19:42 +1000 Subject: [Chimera-users] Unit cell In-Reply-To: <5059249A-2AAD-403F-B336-94D6ECB72947@sonic.net> References: <7DD6592D-29C9-490F-ABF0-33E3DF32606E@sonic.net> <5059249A-2AAD-403F-B336-94D6ECB72947@sonic.net> Message-ID: Yes the atomic coordinates within one unit cell. On 2 December 2016 at 06:10, Tom Goddard wrote: > I don?t understand your question. What do you mean by the ?coordinates of > the unit cell?? Do you mean atom coordinates? cell axis vectors? How > will you use this? > > Tom > > On Dec 1, 2016, at 11:56 AM, Neha Gandhi wrote: > > Thank you Tom for your email. > > My apologies that my knowledge on microscopy structures is limited. I have > a trivial question. Is there a way to extract the coordinates of the unit > cell in Chimera rather than working with this 4 times long molecule? If I > can do this then it will be easy to make copies or use contacts to get the > neighboring molecules. > > Many thanks, > Neha > > On 2 December 2016 at 05:04, Tom Goddard wrote: > >> Hi Neha, >> >> The space group for 3HR2 is P1 which means the unit cell contains only >> one copy. This is reported by the Chimera Unit Cell tool (menu Tools / >> Higher-Order Structure / Unit Cell). To show multiple copies press the >> Options button on the Unit Cell dialog and change Number of Cells from 1 1 >> 1 to say 2 2 2 and press Make Copies to get molecule copies in a 2 by 2 by >> 2 grid of unit cells. >> >> It sounds like you also want the Unit Cell outline box to have corner >> at (0,0,0) and that is not what happens. Instead it shows another unit >> cell outline that contains the center of the molecule. This bizarre >> structure is 4 times longer than the unit cell so the center likes in a >> unit cell that does not have corner at (0,0,0). Unfortnately the tool does >> not let you show other unit cell outlines, just this one centered at the >> molecule. If you absolutely had to get a different unit cell outline you >> could try to translate the outline model by multiples of the unit cell axes >> vectors. But you would need the coordinates of those vectors which would >> be somewhat tricky to get since the cell is skewed. >> >> Tom >> >> >> >> On Nov 30, 2016, at 11:04 PM, Neha Gandhi wrote: >> >> Hi Elaine, >> >> I have tried to look at the unit cell information of pdb Id :3HR2. It is >> a fiber diffraction structure of collagen with only CA coordinates. I tried >> using different programs like VMD to visualise unit cell, the unit cell is >> at the beginning of N terminus in agreement with experimental paper. >> Whereas in Chimera it is not the case. How can I visualize the unit cell of >> 3HR2 structure in Chimera and also number of molecules within one unit cell? >> >> Many thanks, >> Neha >> >> -- >> Regards, >> Dr. Neha S. Gandhi, >> Vice Chancellor's Research Fellow, >> Queensland University of Technology, >> 2 George Street, Brisbane, QLD 4000 >> Australia >> LinkedIn >> Research Gate >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mail >> man/listinfo/chimera-users >> >> >> > > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn > Research Gate > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/ > mailman/listinfo/chimera-users > > > -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Dec 1 12:35:18 2016 From: goddard at sonic.net (Tom Goddard) Date: Thu, 1 Dec 2016 12:35:18 -0800 Subject: [Chimera-users] Unit cell In-Reply-To: References: <7DD6592D-29C9-490F-ABF0-33E3DF32606E@sonic.net> <5059249A-2AAD-403F-B336-94D6ECB72947@sonic.net> Message-ID: <55CE0AE5-549B-452D-B825-5A9BA2DF2B27@sonic.net> I still don?t understand. The atomic coordinates of one copy of the molecule is exactly what is in the PDB file. The molecule extends beyond the unit cell box, but the whole molecule is the asymmetric unit so it would not make sense to truncate it to the atoms that lie within the box. The unit cell box just shows visually the repeat pattern, the whole molecule has to be repeated with this brick spacing to see the crystal packing. Tom > On Dec 1, 2016, at 12:19 PM, Neha Gandhi wrote: > > Yes the atomic coordinates within one unit cell. > > On 2 December 2016 at 06:10, Tom Goddard > wrote: > I don?t understand your question. What do you mean by the ?coordinates of the unit cell?? Do you mean atom coordinates? cell axis vectors? How will you use this? > > Tom > >> On Dec 1, 2016, at 11:56 AM, Neha Gandhi > wrote: >> >> Thank you Tom for your email. >> >> My apologies that my knowledge on microscopy structures is limited. I have a trivial question. Is there a way to extract the coordinates of the unit cell in Chimera rather than working with this 4 times long molecule? If I can do this then it will be easy to make copies or use contacts to get the neighboring molecules. >> >> Many thanks, >> Neha >> >> On 2 December 2016 at 05:04, Tom Goddard > wrote: >> Hi Neha, >> >> The space group for 3HR2 is P1 which means the unit cell contains only one copy. This is reported by the Chimera Unit Cell tool (menu Tools / Higher-Order Structure / Unit Cell). To show multiple copies press the Options button on the Unit Cell dialog and change Number of Cells from 1 1 1 to say 2 2 2 and press Make Copies to get molecule copies in a 2 by 2 by 2 grid of unit cells. >> >> It sounds like you also want the Unit Cell outline box to have corner at (0,0,0) and that is not what happens. Instead it shows another unit cell outline that contains the center of the molecule. This bizarre structure is 4 times longer than the unit cell so the center likes in a unit cell that does not have corner at (0,0,0). Unfortnately the tool does not let you show other unit cell outlines, just this one centered at the molecule. If you absolutely had to get a different unit cell outline you could try to translate the outline model by multiples of the unit cell axes vectors. But you would need the coordinates of those vectors which would be somewhat tricky to get since the cell is skewed. >> >> Tom >> >> >> >>> On Nov 30, 2016, at 11:04 PM, Neha Gandhi wrote: >>> >>> Hi Elaine, >>> >>> I have tried to look at the unit cell information of pdb Id :3HR2. It is a fiber diffraction structure of collagen with only CA coordinates. I tried using different programs like VMD to visualise unit cell, the unit cell is at the beginning of N terminus in agreement with experimental paper. Whereas in Chimera it is not the case. How can I visualize the unit cell of 3HR2 structure in Chimera and also number of molecules within one unit cell? >>> >>> Many thanks, >>> Neha >>> >>> -- >>> Regards, >>> Dr. Neha S. Gandhi, >>> Vice Chancellor's Research Fellow, >>> Queensland University of Technology, >>> 2 George Street, Brisbane, QLD 4000 >>> Australia >>> LinkedIn <> >>> Research Gate <> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> >> >> -- >> Regards, >> Dr. Neha S. Gandhi, >> Vice Chancellor's Research Fellow, >> Queensland University of Technology, >> 2 George Street, Brisbane, QLD 4000 >> Australia >> LinkedIn <> >> Research Gate <> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > Regards, > Dr. Neha S. Gandhi, > Vice Chancellor's Research Fellow, > Queensland University of Technology, > 2 George Street, Brisbane, QLD 4000 > Australia > LinkedIn <> > Research Gate <> -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Dec 1 13:04:25 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 1 Dec 2016 13:04:25 -0800 Subject: [Chimera-users] saving pdb with transformed coordinates In-Reply-To: <77389ED5A5E5A947A5FEA1B9E8D512CBBE0E60EC@ibwmbx03> References: <77389ED5A5E5A947A5FEA1B9E8D512CBBE0E60EC@ibwmbx03> Message-ID: Hi Michael, I was unable to reproduce this problem? I tried ?turn y 90? and then "write #0 ~/Desktop/test.pdb? and it did write the transformed coordinates, and should behave the same way if run via python with rc. I guess you can doublecheck by actually typing commands (let us know if still problematic) and then make sure the same commands are used in your script. A separate issue: I see your script uses ?rock? whereas you probably wanted ?roll? or ?turn? ? note that ?rock y 10 1? will not rotate 10 degrees, but perform 1 frame of a rocking oscillation that would have covered a 10 X 20 = 200-degree angle had it been allowed to perform a full cycle of 136 frames. Instead use ?turn y 10? or ?roll y 10 1? if you want to rotate 10 degrees around Y. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 1, 2016, at 10:23 AM, Michael Elbaum wrote: > Dear Chimera people, > > I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. > > I've tried the following: > for i in xrange(0,90,10): > rc("rock " + "y " + str(i) + " 1") > fn = basefn + str(i) + '.pdb' > rc("write format pdb 0 " + fn) > and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. > > thanks for your help, > Michael From pett at cgl.ucsf.edu Thu Dec 1 13:12:48 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 1 Dec 2016 13:12:48 -0800 Subject: [Chimera-users] saving pdb with transformed coordinates In-Reply-To: References: <77389ED5A5E5A947A5FEA1B9E8D512CBBE0E60EC@ibwmbx03> Message-ID: <0253FF55-A7DF-4017-BC7B-70E9CAEF3E01@cgl.ucsf.edu> Elaine?s response caused me to realize the other problem with your script ? you are going to need to add ?; wait? to the end of any rock/roll/turn command you use. Otherwise the script will keep going without any frames being drawn, which also means that no motion from the rock/roll/turn will have occurred, and therefore the coordinates will be unchanged when the script reaches your ?write? command. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 1, 2016, at 1:04 PM, Elaine Meng wrote: > > Hi Michael, > I was unable to reproduce this problem? I tried ?turn y 90? and then "write #0 ~/Desktop/test.pdb? and it did write the transformed coordinates, and should behave the same way if run via python with rc. I guess you can doublecheck by actually typing commands (let us know if still problematic) and then make sure the same commands are used in your script. > > A separate issue: I see your script uses ?rock? whereas you probably wanted ?roll? or ?turn? ? note that ?rock y 10 1? will not rotate 10 degrees, but perform 1 frame of a rocking oscillation that would have covered a 10 X 20 = 200-degree angle had it been allowed to perform a full cycle of 136 frames. Instead use ?turn y 10? or ?roll y 10 1? if you want to rotate 10 degrees around Y. > > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 1, 2016, at 10:23 AM, Michael Elbaum wrote: > >> Dear Chimera people, >> >> I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. >> >> I've tried the following: >> for i in xrange(0,90,10): >> rc("rock " + "y " + str(i) + " 1") >> fn = basefn + str(i) + '.pdb' >> rc("write format pdb 0 " + fn) >> and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. >> >> thanks for your help, >> Michael > > > _______________________________________________ > 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 Thu Dec 1 13:40:35 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 1 Dec 2016 13:40:35 -0800 Subject: [Chimera-users] Selected measure angles In-Reply-To: References: Message-ID: <5FB382EE-9425-4C1B-BCCD-ABE98C9D83B5@cgl.ucsf.edu> Hi Soumya, Depends on your familiarity with Python really. If you don?t know Python well then it might be easier to parse the reply log. If you have some familiarity with Python then you would use the Python equivalents of the angle/distance commands to get the values and write them to a file (runCommand never returns a value itself). In Python, you could use runCommand to select the atoms you want to measure and then: Outside the loop from Midas import distance, angle Inside the loop, either d = distance() ? write the distance to a file... or a = angle() ? write the angle to a file... ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 1, 2016, at 12:15 PM, Soumya Govinda Remesh wrote: > > Hello, > > I have just modified the loop script available here (http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html ) > to measure certain angles and distances. I just want to know if there is a way to export the individual values of angles and distances to a file other than parsing from the reply-log. Thank you. > > Best, > Soumya Govinda Remesh, Ph.D. > Postdoctoral Fellow at Advanced Light Source > Lawrence Berkeley National Laboratory > > 1 Cyclotron Road MS 6R2100 > Berkeley, CA 94720 > (phone) 510-495-8179 > (cell) 804-402-8730 > > sgremesh at lbl.gov > > _______________________________________________ > 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 michael.elbaum at weizmann.ac.il Thu Dec 1 13:42:04 2016 From: michael.elbaum at weizmann.ac.il (Michael Elbaum) Date: Thu, 1 Dec 2016 21:42:04 +0000 Subject: [Chimera-users] saving pdb with transformed coordinates In-Reply-To: <0253FF55-A7DF-4017-BC7B-70E9CAEF3E01@cgl.ucsf.edu> References: <77389ED5A5E5A947A5FEA1B9E8D512CBBE0E60EC@ibwmbx03> , <0253FF55-A7DF-4017-BC7B-70E9CAEF3E01@cgl.ucsf.edu> Message-ID: <77389ED5A5E5A947A5FEA1B9E8D512CBBE0E6A27@ibwmbx03> Thanks Elaine and Erik! I changed to turn but the wait step was the key. It seems the writing got out of sync with the transform otherwise. working now :-) regards, Michael ________________________________ From: Eric Pettersen [pett at cgl.ucsf.edu] Sent: Thursday, December 01, 2016 23:12 To: chimera-users at cgl.ucsf.edu BB Cc: Michael Elbaum Subject: Re: [Chimera-users] saving pdb with transformed coordinates Elaine?s response caused me to realize the other problem with your script ? you are going to need to add ?; wait? to the end of any rock/roll/turn command you use. Otherwise the script will keep going without any frames being drawn, which also means that no motion from the rock/roll/turn will have occurred, and therefore the coordinates will be unchanged when the script reaches your ?write? command. ?Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 1, 2016, at 1:04 PM, Elaine Meng > wrote: Hi Michael, I was unable to reproduce this problem? I tried ?turn y 90? and then "write #0 ~/Desktop/test.pdb? and it did write the transformed coordinates, and should behave the same way if run via python with rc. I guess you can doublecheck by actually typing commands (let us know if still problematic) and then make sure the same commands are used in your script. A separate issue: I see your script uses ?rock? whereas you probably wanted ?roll? or ?turn? ? note that ?rock y 10 1? will not rotate 10 degrees, but perform 1 frame of a rocking oscillation that would have covered a 10 X 20 = 200-degree angle had it been allowed to perform a full cycle of 136 frames. Instead use ?turn y 10? or ?roll y 10 1? if you want to rotate 10 degrees around Y. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 1, 2016, at 10:23 AM, Michael Elbaum > wrote: Dear Chimera people, I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. thanks for your help, Michael _______________________________________________ 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 sgremesh at lbl.gov Thu Dec 1 16:48:13 2016 From: sgremesh at lbl.gov (Soumya Govinda Remesh) Date: Thu, 1 Dec 2016 16:48:13 -0800 Subject: [Chimera-users] Selected measure angles In-Reply-To: <5FB382EE-9425-4C1B-BCCD-ABE98C9D83B5@cgl.ucsf.edu> References: <5FB382EE-9425-4C1B-BCCD-ABE98C9D83B5@cgl.ucsf.edu> Message-ID: Thank you Eric. On Thu, Dec 1, 2016 at 1:40 PM, Eric Pettersen wrote: > Hi Soumya, > Depends on your familiarity with Python really. If you don?t know Python > well then it might be easier to parse the reply log. If you have some > familiarity with Python then you would use the Python equivalents of the > angle/distance commands to get the values and write them to a file > (runCommand never returns a value itself). > In Python, you could use runCommand to select the atoms you want to > measure and then: > > *Outside the loop* > from Midas import distance, angle > > *Inside the loop, either* > d = distance() > ? write the distance to a file... > > *or* > a = angle() > ? write the angle to a file... > > ?Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > > > > > On Dec 1, 2016, at 12:15 PM, Soumya Govinda Remesh > wrote: > > Hello, > > I have just modified the loop script available here ( > http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html) > to measure certain angles and distances. I just want to know if there is a > way to export the individual values of angles and distances to a file other > than parsing from the reply-log. Thank you. > > Best, > Soumya Govinda Remesh, Ph.D. > Postdoctoral Fellow at Advanced Light Source > Lawrence Berkeley National Laboratory > > 1 Cyclotron Road MS 6R2100 > Berkeley, CA 94720 > (phone) 510-495-8179 > (cell) 804-402-8730 <(804)%20402-8730> > > sgremesh at lbl.gov > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/ > mailman/listinfo/chimera-users > > > -- Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh at lbl.gov -------------- next part -------------- An HTML attachment was scrubbed... URL: From agszabo at bell.net Fri Dec 2 09:33:56 2016 From: agszabo at bell.net (A G Szabo) Date: Fri, 2 Dec 2016 12:33:56 -0500 Subject: [Chimera-users] question Message-ID: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> You have been very helpful in explaining different items that use the command line. I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc. So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number. I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model. Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly. Thank you Arthur G. Szabo -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Dec 2 09:46:39 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 2 Dec 2016 09:46:39 -0800 Subject: [Chimera-users] question In-Reply-To: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> Message-ID: Hi Arthur, Unfortunately ?ribbackbone? only applies to the whole model. However, it is merely an ?enabler? allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don?t want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don?t want to see. So you would have to use ?ribbackbone #0.1? or something like that on the whole model, but then hide all the atoms you don?t want, say ?~disp #0.1? to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like ?disp #0.1:33.A,37.A,38.A? (for example, if they are in chain A of model #0.1). Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 2, 2016, at 9:33 AM, A G Szabo wrote: > You have been very helpful in explaining different items that use the command line. > > I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc. > > So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number. > > I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model. > > Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. > > The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec > > > I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don?t think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. > > So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly. > > Thank you > > Arthur G. Szabo From shrutikhare at mbu.iisc.ernet.in Fri Dec 2 02:45:22 2016 From: shrutikhare at mbu.iisc.ernet.in (Shruti Khare) Date: Fri, 2 Dec 2016 16:15:22 +0530 (IST) Subject: [Chimera-users] difficulty in using chimera for large PDB files Message-ID: <38334.10.16.40.112.1480675522.squirrel@mbu.iisc.ac.in> Dear Sir/Madam, When we use chimera to visualize PDB files with ~18,000 atoms (PDB ID 5FUU) even rotating the molecule is slow in chimera. The computer has 6GB RAM. Would upgrading RAM help or we need to get a graphics card installed? Graphics card capacity should be 2GB or higher? Could you please tell me the minimum computer configuration required by chimera to handle large PDB files? Also what is chimera's maximum limit for handling PDB files given a computer with very good configuration? Thank you. -- Shruti Khare Graduate Student Prof. Raghavan Varadarajan Lab Molecular Biophysics Unit Indian Institute of Science Bangalore +91-80-2293-2612 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From agszabo at bell.net Fri Dec 2 10:33:15 2016 From: agszabo at bell.net (A G Szabo) Date: Fri, 2 Dec 2016 13:33:15 -0500 Subject: [Chimera-users] question In-Reply-To: References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> Message-ID: <013f01d24cca$8b7dade0$a27909a0$@bell.net> Elaine I am including the structure I am working with in Chimera. Don't know if you can see it in the message. So I attached a copy You can see that I have shown a selection of residues. If I were to use the command "~disp #0.1" then the other residues would disappear. I tried to use the command you suggested "disp #0.1:33.K,37.K,38.K" since the Gly residues are on Chain K #0.1. and I wanted to retain the atoms of the displayed side chains on Chain C #0.1 and Chain E #0.1. I had turned ribbackbone off since I thought according to your suggestion I could display all the atoms of the three Gly residues on Chain K #0.1. Unfortunately it didn't work. But thanks for your suggestions. arthur -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: December-02-16 12:47 PM To: A G Szabo Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] question Hi Arthur, Unfortunately "ribbackbone" only applies to the whole model. However, it is merely an "enabler" allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don't want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to see. So you would have to use "ribbackbone #0.1" or something like that on the whole model, but then hide all the atoms you don't want, say "~disp #0.1" to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain A of model #0.1). Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 2, 2016, at 9:33 AM, A G Szabo wrote: > You have been very helpful in explaining different items that use the command line. > > I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc. > > So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number. > > I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model. > > Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. > > The information on the ribbackbone in the Chimera users guide, > indicates that I should be able to do this by using parameters termed > atom-spec. i.e. ribbackbone atom-spec > > > I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. > > So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly. > > Thank you > > Arthur G. Szabo -------------- next part -------------- A non-text attachment was scrubbed... Name: figure for Elaine.pptx Type: application/vnd.openxmlformats-officedocument.presentationml.presentation Size: 127658 bytes Desc: not available URL: From agszabo at bell.net Fri Dec 2 11:21:41 2016 From: agszabo at bell.net (A G Szabo) Date: Fri, 2 Dec 2016 14:21:41 -0500 Subject: [Chimera-users] question In-Reply-To: References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> Message-ID: <014c01d24cd1$4fe96f60$efbc4e20$@bell.net> Elaine The essential issue is that all of the Atoms of Gly are part of the backbone. So in order to visualize those atoms one has to turn them on with ribbackbone. But visualizing the backbone atoms of other residues with longer side chains clutters up the image, and I would rather have the backbone atoms of such amino acids turned off. I sent you a power point attachment with the structure I am working with. This is the partial structure of a beta sheet amyloid made up of the same peptide all in a stack. So in order to show the key intramolecular interactions in one of the peptides in the stack one can show the selected residues. Only issue is that one cannot visualize Gly in any meaningful way unless ribbackbone is turned on. Thanks for your assistance Much appreciated arthur -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: December-02-16 12:47 PM To: A G Szabo Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] question Hi Arthur, Unfortunately "ribbackbone" only applies to the whole model. However, it is merely an "enabler" allowing backbone atoms and ribbon to be shown at the same time, if the atoms and ribbon both happen to be displayed for the same residue. You can still hide (~display) any atoms you don't want to see and hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to see. So you would have to use "ribbackbone #0.1" or something like that on the whole model, but then hide all the atoms you don't want, say "~disp #0.1" to hide all atoms, and then to show all atoms of glycines 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain A of model #0.1). Again, you can use Selection Inspector instead of commands for many things, although commands are better for doing things with specific residue numbers. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 2, 2016, at 9:33 AM, A G Szabo wrote: > You have been very helpful in explaining different items that use the command line. > > I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc. > > So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number. > > I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model. > > Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. > > The information on the ribbackbone in the Chimera users guide, > indicates that I should be able to do this by using parameters termed > atom-spec. i.e. ribbackbone atom-spec > > > I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. > > So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly. > > Thank you > > Arthur G. Szabo From meng at cgl.ucsf.edu Fri Dec 2 12:38:13 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 2 Dec 2016 12:38:13 -0800 Subject: [Chimera-users] showing backbone for some residues and not others In-Reply-To: <014c01d24cd1$4fe96f60$efbc4e20$@bell.net> References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> <014c01d24cd1$4fe96f60$efbc4e20$@bell.net> Message-ID: <35C42BF3-F172-4450-9179-6EDC1FFA2524@cgl.ucsf.edu> Hi Arthur, I believe I understand completely, but I can only repeat my suggestions from before. You would use ?ribbackbone? to allow both ribbon and backbone atoms, and then use ?disp? to show the atoms you want to see and ?~disp? to hide the atoms you don?t want to see. Don?t know what you mean by ?didn?t work?. The exact disp and ~disp commands depend on the models, chains, residues,?. in your structure. Here is an example with PDB entry 2gbp, pretending I want to see all atoms of residues 40-50 but sidechain only of residues 20-30; everything in that structure is chain A: open 2gbp ribbackbone ~disp disp #0:40-50.A disp #0:20-30.A & with CA/C1? The last part of the last line means sidechains only. However, another way to the same result is to display all atoms of those residues but then hide their backbone atoms like we talked about before: disp #0:20-30.A ~disp #0:20-30.A at n,c,o,h Still one more step if you don?t want fake CA-CA bonds between adjacent residues for which you are showing sidechain only: setattr m autochain false Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 2, 2016, at 11:21 AM, A G Szabo wrote: > Elaine > > The essential issue is that all of the Atoms of Gly are part of the > backbone. So in order to visualize those atoms one has to turn them on with > ribbackbone. But visualizing the backbone atoms of other residues with > longer side chains clutters up the image, and I would rather have the > backbone atoms of such amino acids turned off. > > I sent you a power point attachment with the structure I am working with. > This is the partial structure of a beta sheet amyloid made up of the same > peptide all in a stack. So in order to show the key intramolecular > interactions in one of the peptides in the stack one can show the selected > residues. Only issue is that one cannot visualize Gly in any meaningful way > unless ribbackbone is turned on. > > Thanks for your assistance > > Much appreciated > > arthur > > -----Original Message----- > From: Elaine Meng [mailto:meng at cgl.ucsf.edu] > Sent: December-02-16 12:47 PM > To: A G Szabo > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] question > > Hi Arthur, > Unfortunately "ribbackbone" only applies to the whole model. However, it is > merely an "enabler" allowing backbone atoms and ribbon to be shown at the > same time, if the atoms and ribbon both happen to be displayed for the same > residue. You can still hide (~display) any atoms you don't want to see and > hide ribbon (~ribbon) of any residue whose ribbon segment you don't want to > see. > > So you would have to use "ribbackbone #0.1" or something like that on the > whole model, but then hide all the atoms you don't want, say "~disp #0.1" to > hide all atoms, and then to show all atoms of glycines 33,37,38 it could be > something like "disp #0.1:33.A,37.A,38.A" (for example, if they are in chain > A of model #0.1). > > Again, you can use Selection Inspector instead of commands for many things, > although commands are better for doing things with specific residue numbers. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of > Pharmaceutical Chemistry University of California, San Francisco > > > On Dec 2, 2016, at 9:33 AM, A G Szabo wrote: > >> You have been very helpful in explaining different items that use the > command line. >> >> I have a PDB file that was determined by NMR. Thus there are a large > number of chains number as pdb (#0.1) Chain A etc. >> >> So I know that I can select a single chain, and build up an image with > Chains A, B, etc using the #0.1 chain number. >> >> I want to visualize three Gly residues in one chain. So I learned that I > can use the command ribbackbone to visualize the backbone atoms of the > amino acids that I want to show. So when I use that command all the > backbone atoms of the residues selected are visualized including the side > chains. I also know that if I use the command ~ribbackbone all the backbone > atoms are suppressed leaving only the atoms of the side chains. I know that > without any residues or atoms specified the command applies to the whole > model. >> >> Now as I said that I want to visualize three Gly residues in one of the > chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. >> >> The information on the ribbackbone in the Chimera users guide, >> indicates that I should be able to do this by using parameters termed >> atom-spec. i.e. ribbackbone atom-spec >> >> >> I looked elsewhere for how to designate the parameters for atom-spec and > tried a few things, but I was not able to achieve the specificity of showing > the backbone atoms of only the Gly residues. I don't think that I have to > indicate that I want only the Gly residues in Chain K #0.1 because I can > select the Gly residues from the sequence of Chain K #0.1. >> >> So after this long description of what I want to do, would you kindly > inform me of how I can visualize the backbone atoms of only Gly. >> >> Thank you >> >> Arthur G. Szabo > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From kylelmorris at berkeley.edu Fri Dec 2 15:40:20 2016 From: kylelmorris at berkeley.edu (Kyle Morris) Date: Fri, 2 Dec 2016 15:40:20 -0800 Subject: [Chimera-users] pipes and planks Message-ID: <352FE9E0-0385-413C-82E1-F512AF1807E8@berkeley.edu> Dear Chimera dev, I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn?t update the color, only on the original model. Thanks for your help! Best wishes, Kyle From meng at cgl.ucsf.edu Fri Dec 2 16:07:24 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 2 Dec 2016 16:07:24 -0800 Subject: [Chimera-users] pipes and planks In-Reply-To: <352FE9E0-0385-413C-82E1-F512AF1807E8@berkeley.edu> References: <352FE9E0-0385-413C-82E1-F512AF1807E8@berkeley.edu> Message-ID: <9B1D6AAA-5AD2-4532-A4AB-ADE906DBFB73@cgl.ucsf.edu> Hi Kyle, Unfortunately once it?s made, it?s made. Instead you have to get the coloring you want on the original model, and then recreate the pipes (& planks). Each whole pipe would be the same color, though, taken from the ribbon color of the first residue in that helix; it is not divided into independently colorable per-residue segments. The new pipes model should overwrite the existing pipes model, but f you seem to be getting duplicate models, extras can be closed using the Model Panel (under Favorites in the menu). You could try to ?highlight? a position by also displaying the atomic structure CA atom of that residue as a ball or sphere, but I don?t know how well that would meet your needs, sorry. In our next-gen program ChimeraX, not yet publicly available but will be soon (as early development, not a finished product), ...there are helix ?tubes? (like cylinders but curved) that are better integrated with the atomic model and cartoon ribbons, and can be recolored even in per-residue segments after they are shown. Example image with leucine segments in red attached below. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 2, 2016, at 3:40 PM, Kyle Morris wrote: > Dear Chimera dev, > I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn?t update the color, only on the original model. > Thanks for your help! > Best wishes, > Kyle > scription: 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: tube.png Type: image/png Size: 32160 bytes Desc: not available URL: From kylelmorris at berkeley.edu Fri Dec 2 16:34:53 2016 From: kylelmorris at berkeley.edu (Kyle Morris) Date: Fri, 2 Dec 2016 16:34:53 -0800 Subject: [Chimera-users] pipes and planks In-Reply-To: <9B1D6AAA-5AD2-4532-A4AB-ADE906DBFB73@cgl.ucsf.edu> References: <352FE9E0-0385-413C-82E1-F512AF1807E8@berkeley.edu> <9B1D6AAA-5AD2-4532-A4AB-ADE906DBFB73@cgl.ucsf.edu> Message-ID: <94325686-B58F-4B34-966A-0732D69B2F53@berkeley.edu> Hi Elaine, Thanks for this, very helpful! I hadn?t realised that pipes picks up the color from the original model and had been forcing it with helixColor. Can work around using this knowledge. ChimeraX looks like it?s going to be awesome. Thanks, Kyle > On 2 Dec 2016, at 16:07, Elaine Meng wrote: > > Hi Kyle, > Unfortunately once it?s made, it?s made. Instead you have to get the coloring you want on the original model, and then recreate the pipes (& planks). Each whole pipe would be the same color, though, taken from the ribbon color of the first residue in that helix; it is not divided into independently colorable per-residue segments. The new pipes model should overwrite the existing pipes model, but f you seem to be getting duplicate models, extras can be closed using the Model Panel (under Favorites in the menu). > > You could try to ?highlight? a position by also displaying the atomic structure CA atom of that residue as a ball or sphere, but I don?t know how well that would meet your needs, sorry. > > In our next-gen program ChimeraX, not yet publicly available but will be soon (as early development, not a finished product), > > > ...there are helix ?tubes? (like cylinders but curved) that are better integrated with the atomic model and cartoon ribbons, and can be recolored even in per-residue segments after they are shown. Example image with leucine segments in red attached below. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Dec 2, 2016, at 3:40 PM, Kyle Morris > wrote: > >> Dear Chimera dev, >> I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn?t update the color, only on the original model. >> Thanks for your help! >> Best wishes, >> Kyle >> scription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Dec 2 16:41:23 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 2 Dec 2016 16:41:23 -0800 Subject: [Chimera-users] pipes and planks In-Reply-To: <94325686-B58F-4B34-966A-0732D69B2F53@berkeley.edu> References: <352FE9E0-0385-413C-82E1-F512AF1807E8@berkeley.edu> <9B1D6AAA-5AD2-4532-A4AB-ADE906DBFB73@cgl.ucsf.edu> <94325686-B58F-4B34-966A-0732D69B2F53@berkeley.edu> Message-ID: Hi Kyle, Just to clarify, to automatically pick up the ribbon color of the first residue, the color well(s) for Helix color etc. in the PipesAnd Planks dialog have to be set to ?No color?, which is one of the options available in the Color Editor dialog that appears when you click a color well in Chimera. Best, Elaine On Dec 2, 2016, at 4:34 PM, Kyle Morris wrote: > Hi Elaine, > > Thanks for this, very helpful! I hadn?t realised that pipes picks up the color from the original model and had been forcing it with helixColor. Can work around using this knowledge. > > ChimeraX looks like it?s going to be awesome. > > Thanks, > Kyle > >> On 2 Dec 2016, at 16:07, Elaine Meng wrote: >> >> Hi Kyle, >> Unfortunately once it?s made, it?s made. Instead you have to get the coloring you want on the original model, and then recreate the pipes (& planks). Each whole pipe would be the same color, though, taken from the ribbon color of the first residue in that helix; it is not divided into independently colorable per-residue segments. The new pipes model should overwrite the existing pipes model, but f you seem to be getting duplicate models, extras can be closed using the Model Panel (under Favorites in the menu). >> >> You could try to ?highlight? a position by also displaying the atomic structure CA atom of that residue as a ball or sphere, but I don?t know how well that would meet your needs, sorry. >> >> In our next-gen program ChimeraX, not yet publicly available but will be soon (as early development, not a finished product), >> >> ...there are helix ?tubes? (like cylinders but curved) that are better integrated with the atomic model and cartoon ribbons, and can be recolored even in per-residue segments after they are shown. Example image with leucine segments in red attached below. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> On Dec 2, 2016, at 3:40 PM, Kyle Morris wrote: >> >>> Dear Chimera dev, >>> I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn?t update the color, only on the original model. >>> Thanks for your help! >>> Best wishes, >>> Kyle >>> scription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > From goddard at sonic.net Mon Dec 5 11:30:58 2016 From: goddard at sonic.net (Tom Goddard) Date: Mon, 5 Dec 2016 11:30:58 -0800 Subject: [Chimera-users] difficulty in using chimera for large PDB files In-Reply-To: <38334.10.16.40.112.1480675522.squirrel@mbu.iisc.ac.in> References: <38334.10.16.40.112.1480675522.squirrel@mbu.iisc.ac.in> Message-ID: <747C1891-EF5F-42B4-B9D9-7EE1E25FBA55@sonic.net> Hi Shruti, This is certainly a graphics limitation so upgrading the graphics is the way to go. Moving molecules is all done by the graphics not the CPU (unless you have no graphics processor and so the CPU does the graphics). Any current generation graphics will work. To get an idea what people use with Chimera look at the Chimera graphics benchmarks http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks You don?t need a high-end card, the most basic graphics designed for video games will be much faster than no graphics. Most computers from recent years with an Intel processor have an Intel graphics processor (GPU) integrated with the CPU. You didn?t say what you have now so many you already have that. In terms of rotating molecules at say 5-10 frames/sec minimum Chimera can handle 1 million atoms with a good graphics card. But in terms of everything, else, like changing colors, hiding some atoms or chains, stuff done by the CPU, things get slow around a few hundred thousand atom. Chimera is not know for its speed. You should try PyMol or VMD for handling larger molecules. Tom > On Dec 2, 2016, at 2:45 AM, Shruti Khare wrote: > > Dear Sir/Madam, > > When we use chimera to visualize PDB files with ~18,000 atoms (PDB ID 5FUU) even > rotating the molecule is slow in chimera. > The computer has 6GB RAM. Would upgrading RAM help or we need to get a graphics > card installed? > Graphics card capacity should be 2GB or higher? > > Could you please tell me the minimum computer configuration required by chimera > to handle large PDB files? > Also what is chimera's maximum limit for handling PDB files given a computer > with very good configuration? > > > Thank you. > > -- > Shruti Khare > Graduate Student > Prof. Raghavan Varadarajan Lab > Molecular Biophysics Unit > Indian Institute of Science > Bangalore > +91-80-2293-2612 > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From agszabo at bell.net Mon Dec 5 13:54:02 2016 From: agszabo at bell.net (A G Szabo) Date: Mon, 5 Dec 2016 16:54:02 -0500 Subject: [Chimera-users] showing backbone for some residues and not others In-Reply-To: <35C42BF3-F172-4450-9179-6EDC1FFA2524@cgl.ucsf.edu> References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> <014c01d24cd1$4fe96f60$efbc4e20$@bell.net> <35C42BF3-F172-4450-9179-6EDC1FFA2524@cgl.ucsf.edu> Message-ID: <000901d24f42$17b269d0$47173d70$@bell.net> Elaine Your message was helpful as it taught me how to specify residues within one chain out of a large number of chains, i.e. Chain #0.1: Res#.K That is Chain #0.1.K and res#. However, after trying a number of command ideas, I do not think it is possible to do what I would like to do. I know how to hide all the chains in the data base, and visualize the individual the ribbons of the chains that I want. I visualize the ribbons for Chain #0.1 E, and #0.1 K. PDB 2LMN I then go to "Tools" ; "Sequence" and select two chain sequences. I select a residue, Met 35 on #0.1 E, and then, "Actions" ; "Atoms/bonds" ; "Show". The side chain Met 35 pops up on Chain #0.1 E. then "ball and stick" (no problem so far have done this many times) the side chain of Met 35 shows as balls and sticks. If I color the atoms of Met35 a color different from the ribbon, the CA atom is nicely embedded in the ribbon. I also know that when I use the command line and enter "disp #0.1:35.E" I can achieve the same result without having to highlight the residue in the sequence of that chain. I can visualize several residues using the same command style. If I use the command line and enter "ribbackbone", the backbone atoms of Met 35 are displayed. When one visualizes four or five side chains on a chain, the presence of the backbone atoms starts to clutter up the image. The backbone atoms do not add to the information regarding the inter or intramolecular interactions that one would like to display between the different side chains. I then use your suggestion and enter the command "~disp #0.1:35.E @N,C,O,H" The backbone atoms of Met 35 disappear, BUT the rest of the side chain remains sitting above the ribbon. There is a gap between the side chain and the ribbon. Further to this imaging, I would like select and visualize some Gly residues on part of Chain #0.1K. Met35 of Chain #0.1E interacts with these Gly residues. With "ribbackbone" in effect the Gly residues show up as the five backbone atoms, C, N, O, and 2 H atoms. That would be fine but the esthetically it doesn't look good with the Met35 side chain and others just hanging there not attached to ribbon, and if I turn "ribbackbone" off in order to get CA of Met35 in the ribbon, then the Gly residues no longer have any atoms visualized and disappear into the ribbon.. I have tried various permutations, such as "disp #0.1:33.K,37.K,38.K @N,C,O,H" hoping that I might be able to visualize the Gly residues, it doesn't work. So that leads me back to my original statement that I don't think I can achieve the image that I would like to present. A suggestion would be if one could apply "ribbackbone" only to a specific chain in the model instead of to the entire model. Thanks your assistance, I am learning more and more about nuances of Chimera, which I recommend as a very user friendly package especially if you use the menu section. One thing I have had trouble understanding is the "Inspect Selection" menu that is available under "Actions". You have suggested that I use that on a couple of occasions, but it is a bit unfathomable. Tried to check it out in the Help sections but was unable to make any progress in understanding it. Best regards arthur -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: December-02-16 3:38 PM To: A G Szabo Cc: chimera-users at cgl.ucsf.edu Subject: showing backbone for some residues and not others Hi Arthur, I believe I understand completely, but I can only repeat my suggestions from before. You would use "ribbackbone" to allow both ribbon and backbone atoms, and then use "disp" to show the atoms you want to see and "~disp" to hide the atoms you don't want to see. Don't know what you mean by "didn't work". The exact disp and ~disp commands depend on the models, chains, residues,.. in your structure. Here is an example with PDB entry 2gbp, pretending I want to see all atoms of residues 40-50 but sidechain only of residues 20-30; everything in that structure is chain A: open 2gbp ribbackbone ~disp disp #0:40-50.A disp #0:20-30.A & with CA/C1' The last part of the last line means sidechains only. However, another way to the same result is to display all atoms of those residues but then hide their backbone atoms like we talked about before: disp #0:20-30.A ~disp #0:20-30.A at n,c,o,h Still one more step if you don't want fake CA-CA bonds between adjacent residues for which you are showing sidechain only: setattr m autochain false Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 2, 2016, at 11:21 AM, A G Szabo wrote: > Elaine > > The essential issue is that all of the Atoms of Gly are part of the > backbone. So in order to visualize those atoms one has to turn them on > with ribbackbone. But visualizing the backbone atoms of other residues > with longer side chains clutters up the image, and I would rather have > the backbone atoms of such amino acids turned off. > > I sent you a power point attachment with the structure I am working with. > This is the partial structure of a beta sheet amyloid made up of the > same peptide all in a stack. So in order to show the key > intramolecular interactions in one of the peptides in the stack one > can show the selected residues. Only issue is that one cannot > visualize Gly in any meaningful way unless ribbackbone is turned on. > > Thanks for your assistance > > Much appreciated > > arthur > > -----Original Message----- > From: Elaine Meng [mailto:meng at cgl.ucsf.edu] > Sent: December-02-16 12:47 PM > To: A G Szabo > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] question > > Hi Arthur, > Unfortunately "ribbackbone" only applies to the whole model. However, > it is merely an "enabler" allowing backbone atoms and ribbon to be > shown at the same time, if the atoms and ribbon both happen to be > displayed for the same residue. You can still hide (~display) any > atoms you don't want to see and hide ribbon (~ribbon) of any residue > whose ribbon segment you don't want to see. > > So you would have to use "ribbackbone #0.1" or something like that on > the whole model, but then hide all the atoms you don't want, say > "~disp #0.1" to hide all atoms, and then to show all atoms of glycines > 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for > example, if they are in chain A of model #0.1). > > Again, you can use Selection Inspector instead of commands for many > things, although commands are better for doing things with specific residue numbers. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department > of Pharmaceutical Chemistry University of California, San Francisco > > > On Dec 2, 2016, at 9:33 AM, A G Szabo wrote: > >> You have been very helpful in explaining different items that use >> the > command line. >> >> I have a PDB file that was determined by NMR. Thus there are a large > number of chains number as pdb (#0.1) Chain A etc. >> >> So I know that I can select a single chain, and build up an image >> with > Chains A, B, etc using the #0.1 chain number. >> >> I want to visualize three Gly residues in one chain. So I learned >> that I > can use the command ribbackbone to visualize the backbone atoms of > the amino acids that I want to show. So when I use that command all > the backbone atoms of the residues selected are visualized including > the side chains. I also know that if I use the command ~ribbackbone > all the backbone atoms are suppressed leaving only the atoms of the > side chains. I know that without any residues or atoms specified the > command applies to the whole model. >> >> Now as I said that I want to visualize three Gly residues in one of >> the > chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. >> >> The information on the ribbackbone in the Chimera users guide, >> indicates that I should be able to do this by using parameters >> termed atom-spec. i.e. ribbackbone atom-spec >> >> >> I looked elsewhere for how to designate the parameters for atom-spec >> and > tried a few things, but I was not able to achieve the specificity of > showing the backbone atoms of only the Gly residues. I don't think > that I have to indicate that I want only the Gly residues in Chain K > #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. >> >> So after this long description of what I want to do, would you kindly > inform me of how I can visualize the backbone atoms of only Gly. >> >> Thank you >> >> Arthur G. Szabo > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage > subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Mon Dec 5 14:26:25 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 5 Dec 2016 14:26:25 -0800 Subject: [Chimera-users] showing backbone for some residues and not others In-Reply-To: <000901d24f42$17b269d0$47173d70$@bell.net> References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> <014c01d24cd1$4fe96f60$efbc4e20$@bell.net> <35C42BF3-F172-4450-9179-6EDC1FFA2524@cgl.ucsf.edu> <000901d24f42$17b269d0$47173d70$@bell.net> Message-ID: Hi Arthur, You are right, you have hit one of the limitations of Chimera: it is not possible to have ribbackbone on only part of a model, and when it is turned on you can only show the ?real? positions of the backbone atoms which may appear as detached from the ribbon. Two possibilities are to show the CA as a bigger ball so that the detachment is not so obvious, or to use the cardinal spline for the ribbon which goes through the real CA atom positions, as mentioned earlier. This issue of CA floating away from the ribbon and the ways to (try to) solve it are discussed in the manual here: Selection Inspector is simply a dialog that shows the settings of the things you have selected currently, and allows you to change their settings by choosing or entering different values. If using this dialog, you don?t have to remember the commands. For example, instead of using ?ribbackbone? command you can just select any atom in the model and use the Selection Inspector: in that dialog ?Inspect: Molecule model? and then change its setting ?ribbon hides backbone atoms? between true and false. Similarly, then I don?t have to explain the commands to change the ribbon from B-spline to cardinal spline? Instead, using the Selection Inspector and inspecting ?Molecule model? you can change the settings for ?ribbon spline? and ?ribbon (cardinal) smoothing?. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 5, 2016, at 1:54 PM, A G Szabo wrote: > > Elaine > > Your message was helpful as it taught me how to specify residues within one > chain out of a large number of chains, i.e. Chain #0.1: Res#.K That is > Chain #0.1.K and res#. > > However, after trying a number of command ideas, I do not think it is > possible to do what I would like to do. > > > I know how to hide all the chains in the data base, and visualize the > individual the ribbons of the chains that I want. I visualize the ribbons > for Chain #0.1 E, and #0.1 K. PDB 2LMN > > I then go to "Tools" ; "Sequence" and select two chain sequences. I select > a residue, Met 35 on #0.1 E, and then, "Actions" ; "Atoms/bonds" ; "Show". > The side chain Met 35 pops up on Chain #0.1 E. then "ball and stick" (no > problem so far have done this many times) the side chain of Met 35 shows as > balls and sticks. If I color the atoms of Met35 a color different from the > ribbon, the CA atom is nicely embedded in the ribbon. > > I also know that when I use the command line and enter "disp #0.1:35.E" I > can achieve the same result without having to highlight the residue in the > sequence of that chain. I can visualize several residues using the same > command style. > > If I use the command line and enter "ribbackbone", the backbone atoms of Met > 35 are displayed. > > When one visualizes four or five side chains on a chain, the presence of the > backbone atoms starts to clutter up the image. The backbone atoms do not add > to the information regarding the inter or intramolecular interactions that > one would like to display between the different side chains. > > I then use your suggestion and enter the command "~disp #0.1:35.E @N,C,O,H" > > The backbone atoms of Met 35 disappear, BUT the rest of the side chain > remains sitting above the ribbon. There is a gap between the side chain and > the ribbon. > > Further to this imaging, I would like select and visualize some Gly residues > on part of Chain #0.1K. Met35 of Chain #0.1E interacts with these Gly > residues. With "ribbackbone" in effect the Gly residues show up as the five > backbone atoms, C, N, O, and 2 H atoms. > > That would be fine but the esthetically it doesn't look good with the Met35 > side chain and others just hanging there not attached to ribbon, and if I > turn "ribbackbone" off in order to get CA of Met35 in the ribbon, then the > Gly residues no longer have any atoms visualized and disappear into the > ribbon.. > > I have tried various permutations, such as "disp #0.1:33.K,37.K,38.K > @N,C,O,H" hoping that I might be able to visualize the Gly residues, it > doesn't work. > > So that leads me back to my original statement that I don't think I can > achieve the image that I would like to present. > > A suggestion would be if one could apply "ribbackbone" only to a specific > chain in the model instead of to the entire model. > > Thanks your assistance, I am learning more and more about nuances of > Chimera, which I recommend as a very user friendly package especially if you > use the menu section. One thing I have had trouble understanding is the > "Inspect Selection" menu that is available under "Actions". You have > suggested that I use that on a couple of occasions, but it is a bit > unfathomable. Tried to check it out in the Help sections but was unable to > make any progress in understanding it. > > Best regards > > arthur > > > -----Original Message----- > From: Elaine Meng [mailto:meng at cgl.ucsf.edu] > Sent: December-02-16 3:38 PM > To: A G Szabo > Cc: chimera-users at cgl.ucsf.edu > Subject: showing backbone for some residues and not others > > Hi Arthur, > I believe I understand completely, but I can only repeat my suggestions from > before. You would use "ribbackbone" to allow both ribbon and backbone > atoms, and then use "disp" to show the atoms you want to see and "~disp" to > hide the atoms you don't want to see. Don't know what you mean by "didn't > work". > > The exact disp and ~disp commands depend on the models, chains, residues,.. > in your structure. > > Here is an example with PDB entry 2gbp, pretending I want to see all atoms > of residues 40-50 but sidechain only of residues 20-30; everything in that > structure is chain A: > > open 2gbp > ribbackbone > ~disp > disp #0:40-50.A > disp #0:20-30.A & with CA/C1' > > The last part of the last line means sidechains only. However, another way > to the same result is to display all atoms of those residues but then hide > their backbone atoms like we talked about before: > > disp #0:20-30.A > ~disp #0:20-30.A at n,c,o,h > > Still one more step if you don't want fake CA-CA bonds between adjacent > residues for which you are showing sidechain only: > > setattr m autochain false > > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of > Pharmaceutical Chemistry University of California, San Francisco > > > > On Dec 2, 2016, at 11:21 AM, A G Szabo wrote: > >> Elaine >> >> The essential issue is that all of the Atoms of Gly are part of the >> backbone. So in order to visualize those atoms one has to turn them on >> with ribbackbone. But visualizing the backbone atoms of other residues >> with longer side chains clutters up the image, and I would rather have >> the backbone atoms of such amino acids turned off. >> >> I sent you a power point attachment with the structure I am working with. >> This is the partial structure of a beta sheet amyloid made up of the >> same peptide all in a stack. So in order to show the key >> intramolecular interactions in one of the peptides in the stack one >> can show the selected residues. Only issue is that one cannot >> visualize Gly in any meaningful way unless ribbackbone is turned on. >> >> Thanks for your assistance >> >> Much appreciated >> >> arthur >> >> -----Original Message----- >> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] >> Sent: December-02-16 12:47 PM >> To: A G Szabo >> Cc: chimera-users at cgl.ucsf.edu >> Subject: Re: [Chimera-users] question >> >> Hi Arthur, >> Unfortunately "ribbackbone" only applies to the whole model. However, >> it is merely an "enabler" allowing backbone atoms and ribbon to be >> shown at the same time, if the atoms and ribbon both happen to be >> displayed for the same residue. You can still hide (~display) any >> atoms you don't want to see and hide ribbon (~ribbon) of any residue >> whose ribbon segment you don't want to see. >> >> So you would have to use "ribbackbone #0.1" or something like that on >> the whole model, but then hide all the atoms you don't want, say >> "~disp #0.1" to hide all atoms, and then to show all atoms of glycines >> 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for >> example, if they are in chain A of model #0.1). >> >> Again, you can use Selection Inspector instead of commands for many >> things, although commands are better for doing things with specific > residue numbers. >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department >> of Pharmaceutical Chemistry University of California, San Francisco >> >> >> On Dec 2, 2016, at 9:33 AM, A G Szabo wrote: >> >>> You have been very helpful in explaining different items that use >>> the >> command line. >>> >>> I have a PDB file that was determined by NMR. Thus there are a large >> number of chains number as pdb (#0.1) Chain A etc. >>> >>> So I know that I can select a single chain, and build up an image >>> with >> Chains A, B, etc using the #0.1 chain number. >>> >>> I want to visualize three Gly residues in one chain. So I learned >>> that I >> can use the command ribbackbone to visualize the backbone atoms of >> the amino acids that I want to show. So when I use that command all >> the backbone atoms of the residues selected are visualized including >> the side chains. I also know that if I use the command ~ribbackbone >> all the backbone atoms are suppressed leaving only the atoms of the >> side chains. I know that without any residues or atoms specified the >> command applies to the whole model. >>> >>> Now as I said that I want to visualize three Gly residues in one of >>> the >> chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. >>> >>> The information on the ribbackbone in the Chimera users guide, >>> indicates that I should be able to do this by using parameters >>> termed atom-spec. i.e. ribbackbone atom-spec >>> >>> >>> I looked elsewhere for how to designate the parameters for atom-spec >>> and >> tried a few things, but I was not able to achieve the specificity of >> showing the backbone atoms of only the Gly residues. I don't think >> that I have to indicate that I want only the Gly residues in Chain K >> #0.1 because I can select the Gly residues from the sequence of Chain K > #0.1. >>> >>> So after this long description of what I want to do, would you kindly >> inform me of how I can visualize the backbone atoms of only Gly. >>> >>> Thank you >>> >>> Arthur G. Szabo >> >> >> _______________________________________________ >> 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 From agszabo at bell.net Mon Dec 5 15:12:15 2016 From: agszabo at bell.net (A G Szabo) Date: Mon, 5 Dec 2016 18:12:15 -0500 Subject: [Chimera-users] showing backbone for some residues and not others In-Reply-To: References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> <014c01d24cd1$4fe96f60$efbc4e20$@bell.net> <35C42BF3-F172-4450-9179-6EDC1FFA2524@cgl.ucsf.edu> <000901d24f42$17b269d0$47173d70$@bell.net> Message-ID: <000e01d24f4d$051453a0$0f3cfae0$@bell.net> Elaine Thank you for your assistance once again. If you ever have need of some supportive comments in order to ensure grant support I would be very willing to provide it. arthur -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: December-05-16 5:26 PM To: A G Szabo Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] showing backbone for some residues and not others Hi Arthur, You are right, you have hit one of the limitations of Chimera: it is not possible to have ribbackbone on only part of a model, and when it is turned on you can only show the ?real? positions of the backbone atoms which may appear as detached from the ribbon. Two possibilities are to show the CA as a bigger ball so that the detachment is not so obvious, or to use the cardinal spline for the ribbon which goes through the real CA atom positions, as mentioned earlier. This issue of CA floating away from the ribbon and the ways to (try to) solve it are discussed in the manual here: Selection Inspector is simply a dialog that shows the settings of the things you have selected currently, and allows you to change their settings by choosing or entering different values. If using this dialog, you don?t have to remember the commands. For example, instead of using ?ribbackbone? command you can just select any atom in the model and use the Selection Inspector: in that dialog ?Inspect: Molecule model? and then change its setting ?ribbon hides backbone atoms? between true and false. Similarly, then I don?t have to explain the commands to change the ribbon from B-spline to cardinal spline? Instead, using the Selection Inspector and inspecting ?Molecule model? you can change the settings for ?ribbon spline? and ?ribbon (cardinal) smoothing?. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 5, 2016, at 1:54 PM, A G Szabo wrote: > > Elaine > > Your message was helpful as it taught me how to specify residues > within one chain out of a large number of chains, i.e. Chain #0.1: > Res#.K That is Chain #0.1.K and res#. > > However, after trying a number of command ideas, I do not think it is > possible to do what I would like to do. > > > I know how to hide all the chains in the data base, and visualize the > individual the ribbons of the chains that I want. I visualize the > ribbons for Chain #0.1 E, and #0.1 K. PDB 2LMN > > I then go to "Tools" ; "Sequence" and select two chain sequences. I > select a residue, Met 35 on #0.1 E, and then, "Actions" ; "Atoms/bonds" ; "Show". > The side chain Met 35 pops up on Chain #0.1 E. then "ball and stick" (no > problem so far have done this many times) the side chain of Met 35 > shows as balls and sticks. If I color the atoms of Met35 a color > different from the ribbon, the CA atom is nicely embedded in the ribbon. > > I also know that when I use the command line and enter "disp > #0.1:35.E" I can achieve the same result without having to highlight > the residue in the sequence of that chain. I can visualize several > residues using the same command style. > > If I use the command line and enter "ribbackbone", the backbone atoms > of Met > 35 are displayed. > > When one visualizes four or five side chains on a chain, the presence > of the backbone atoms starts to clutter up the image. The backbone > atoms do not add to the information regarding the inter or > intramolecular interactions that one would like to display between the different side chains. > > I then use your suggestion and enter the command "~disp #0.1:35.E @N,C,O,H" > > The backbone atoms of Met 35 disappear, BUT the rest of the side chain > remains sitting above the ribbon. There is a gap between the side > chain and the ribbon. > > Further to this imaging, I would like select and visualize some Gly > residues on part of Chain #0.1K. Met35 of Chain #0.1E interacts with > these Gly residues. With "ribbackbone" in effect the Gly residues show > up as the five backbone atoms, C, N, O, and 2 H atoms. > > That would be fine but the esthetically it doesn't look good with the > Met35 side chain and others just hanging there not attached to ribbon, > and if I turn "ribbackbone" off in order to get CA of Met35 in the > ribbon, then the Gly residues no longer have any atoms visualized and > disappear into the ribbon.. > > I have tried various permutations, such as "disp #0.1:33.K,37.K,38.K > @N,C,O,H" hoping that I might be able to visualize the Gly residues, > it doesn't work. > > So that leads me back to my original statement that I don't think I > can achieve the image that I would like to present. > > A suggestion would be if one could apply "ribbackbone" only to a > specific chain in the model instead of to the entire model. > > Thanks your assistance, I am learning more and more about nuances of > Chimera, which I recommend as a very user friendly package especially > if you use the menu section. One thing I have had trouble > understanding is the "Inspect Selection" menu that is available under > "Actions". You have suggested that I use that on a couple of > occasions, but it is a bit unfathomable. Tried to check it out in the > Help sections but was unable to make any progress in understanding it. > > Best regards > > arthur > > > -----Original Message----- > From: Elaine Meng [mailto:meng at cgl.ucsf.edu] > Sent: December-02-16 3:38 PM > To: A G Szabo > Cc: chimera-users at cgl.ucsf.edu > Subject: showing backbone for some residues and not others > > Hi Arthur, > I believe I understand completely, but I can only repeat my > suggestions from before. You would use "ribbackbone" to allow both > ribbon and backbone atoms, and then use "disp" to show the atoms you > want to see and "~disp" to hide the atoms you don't want to see. > Don't know what you mean by "didn't work". > > The exact disp and ~disp commands depend on the models, chains, residues,.. > in your structure. > > Here is an example with PDB entry 2gbp, pretending I want to see all > atoms of residues 40-50 but sidechain only of residues 20-30; > everything in that structure is chain A: > > open 2gbp > ribbackbone > ~disp > disp #0:40-50.A > disp #0:20-30.A & with CA/C1' > > The last part of the last line means sidechains only. However, > another way to the same result is to display all atoms of those > residues but then hide their backbone atoms like we talked about before: > > disp #0:20-30.A > ~disp #0:20-30.A at n,c,o,h > > Still one more step if you don't want fake CA-CA bonds between > adjacent residues for which you are showing sidechain only: > > setattr m autochain false > > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department > of Pharmaceutical Chemistry University of California, San Francisco > > > > On Dec 2, 2016, at 11:21 AM, A G Szabo wrote: > >> Elaine >> >> The essential issue is that all of the Atoms of Gly are part of the >> backbone. So in order to visualize those atoms one has to turn them >> on with ribbackbone. But visualizing the backbone atoms of other >> residues with longer side chains clutters up the image, and I would >> rather have the backbone atoms of such amino acids turned off. >> >> I sent you a power point attachment with the structure I am working with. >> This is the partial structure of a beta sheet amyloid made up of the >> same peptide all in a stack. So in order to show the key >> intramolecular interactions in one of the peptides in the stack one >> can show the selected residues. Only issue is that one cannot >> visualize Gly in any meaningful way unless ribbackbone is turned on. >> >> Thanks for your assistance >> >> Much appreciated >> >> arthur >> >> -----Original Message----- >> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] >> Sent: December-02-16 12:47 PM >> To: A G Szabo >> Cc: chimera-users at cgl.ucsf.edu >> Subject: Re: [Chimera-users] question >> >> Hi Arthur, >> Unfortunately "ribbackbone" only applies to the whole model. >> However, it is merely an "enabler" allowing backbone atoms and ribbon >> to be shown at the same time, if the atoms and ribbon both happen to >> be displayed for the same residue. You can still hide (~display) any >> atoms you don't want to see and hide ribbon (~ribbon) of any residue >> whose ribbon segment you don't want to see. >> >> So you would have to use "ribbackbone #0.1" or something like that on >> the whole model, but then hide all the atoms you don't want, say >> "~disp #0.1" to hide all atoms, and then to show all atoms of >> glycines >> 33,37,38 it could be something like "disp #0.1:33.A,37.A,38.A" (for >> example, if they are in chain A of model #0.1). >> >> Again, you can use Selection Inspector instead of commands for many >> things, although commands are better for doing things with specific > residue numbers. >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department >> of Pharmaceutical Chemistry University of California, San Francisco >> >> >> On Dec 2, 2016, at 9:33 AM, A G Szabo wrote: >> >>> You have been very helpful in explaining different items that use >>> the >> command line. >>> >>> I have a PDB file that was determined by NMR. Thus there are a large >> number of chains number as pdb (#0.1) Chain A etc. >>> >>> So I know that I can select a single chain, and build up an image >>> with >> Chains A, B, etc using the #0.1 chain number. >>> >>> I want to visualize three Gly residues in one chain. So I learned >>> that I >> can use the command ribbackbone to visualize the backbone atoms of >> the amino acids that I want to show. So when I use that command all >> the backbone atoms of the residues selected are visualized including >> the side chains. I also know that if I use the command ~ribbackbone >> all the backbone atoms are suppressed leaving only the atoms of the >> side chains. I know that without any residues or atoms specified the >> command applies to the whole model. >>> >>> Now as I said that I want to visualize three Gly residues in one of >>> the >> chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. >>> >>> The information on the ribbackbone in the Chimera users guide, >>> indicates that I should be able to do this by using parameters >>> termed atom-spec. i.e. ribbackbone atom-spec >>> >>> >>> I looked elsewhere for how to designate the parameters for atom-spec >>> and >> tried a few things, but I was not able to achieve the specificity of >> showing the backbone atoms of only the Gly residues. I don't think >> that I have to indicate that I want only the Gly residues in Chain K >> #0.1 because I can select the Gly residues from the sequence of Chain >> K > #0.1. >>> >>> So after this long description of what I want to do, would you >>> kindly >> inform me of how I can visualize the backbone atoms of only Gly. >>> >>> Thank you >>> >>> Arthur G. Szabo >> >> >> _______________________________________________ >> 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 From meng at cgl.ucsf.edu Mon Dec 5 15:12:44 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 5 Dec 2016 15:12:44 -0800 Subject: [Chimera-users] Chimera -> Povray In-Reply-To: References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> <014c01d24cd1$4fe96f60$efbc4e20$@bell.net> <35C42BF3-F172-4450-9179-6EDC1FFA2524@cgl.ucsf.edu> <000901d24f42$17b269d0$47173d70$@bell.net> Message-ID: Hi Lothar, If you use "File? Export Scene? (instead of Save Image) or the ?export? command, there is an option to save a file for POV-Ray without rendering: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 5, 2016, at 3:07 PM, esserlo at helix.nih.gov wrote: > > Hi, > currently, I am using chimera to make a figure for publication and render > the result in povray. However the figure is a bit complex - with a gradient > background just to mention one thing- so that I have to edit the .pov file. > Is there a way to ask chimera to output the .pov file but not render it in > povray right away (that would save time as I need to edit it first!). > > Unfortunately in the "save image" menu, using povray, I did not find a > checkbox that would enable chimera to write out .pov only. > Thanks for any advice. > Lothar > From meng at cgl.ucsf.edu Tue Dec 6 09:36:20 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 6 Dec 2016 09:36:20 -0800 Subject: [Chimera-users] showing backbone for some residues and not others In-Reply-To: <000e01d24f4d$051453a0$0f3cfae0$@bell.net> References: <012e01d24cc2$4295b6c0$c7c12440$@bell.net> <014c01d24cd1$4fe96f60$efbc4e20$@bell.net> <35C42BF3-F172-4450-9179-6EDC1FFA2524@cgl.ucsf.edu> <000901d24f42$17b269d0$47173d70$@bell.net> <000e01d24f4d$051453a0$0f3cfae0$@bell.net> Message-ID: <4A99E63D-0CA7-4D63-8AB3-4B91B5C8F3C3@cgl.ucsf.edu> Hi Arthur, I remembered one more ?trick? ? instead of using ribbackbone on a single structure, you could open the same structure twice: In one copy of the structure, show ribbons, and show the residues for which you want to see only the sidechains attached to the ribbon (no ribbackbone). In the other copy of the structure, do not show any ribbons. Show only the atoms of residues for which you want to show backbone atoms. The atoms from the second copy could still be floating away from the ribbon of the first copy, but at least the sidechain-only residues (also from the first copy) would be attached to the ribbon. Best, Elaine > On Dec 5, 2016, at 3:12 PM, A G Szabo wrote: > > Elaine > > Thank you for your assistance once again. If you ever have need of some supportive comments in order to ensure grant support I would be very willing to provide it. > > arthur > > -----Original Message----- > From: Elaine Meng [mailto:meng at cgl.ucsf.edu] > Sent: December-05-16 5:26 PM > To: A G Szabo > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] showing backbone for some residues and not others > > Hi Arthur, > You are right, you have hit one of the limitations of Chimera: it is not possible to have ribbackbone on only part of a model, and when it is turned on you can only show the ?real? positions of the backbone atoms which may appear as detached from the ribbon. > > Two possibilities are to show the CA as a bigger ball so that the detachment is not so obvious, or to use the cardinal spline for the ribbon which goes through the real CA atom positions, as mentioned earlier. > > This issue of CA floating away from the ribbon and the ways to (try to) solve it are discussed in the manual here: > > > Selection Inspector is simply a dialog that shows the settings of the things you have selected currently, and allows you to change their settings by choosing or entering different values. If using this dialog, you don?t have to remember the commands. For example, instead of using ?ribbackbone? command you can just select any atom in the model and use the Selection Inspector: in that dialog ?Inspect: Molecule model? and then change its setting ?ribbon hides backbone atoms? between true and false. > > > > Similarly, then I don?t have to explain the commands to change the ribbon from B-spline to cardinal spline? Instead, using the Selection Inspector and inspecting ?Molecule model? you can change the settings for ?ribbon spline? and ?ribbon (cardinal) smoothing?. > > Best, > Elaine From olivercgrant at gmail.com Tue Dec 6 06:31:24 2016 From: olivercgrant at gmail.com (Oliver Grant) Date: Tue, 6 Dec 2016 15:31:24 +0100 Subject: [Chimera-users] Selective lighting Message-ID: Hi all, Is it possible to use the lighting command and have it apply only to particular models? I'd like my ligand to "pop" out by having a light that only shines on it, and not the protein. Oliver -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Dec 6 12:01:25 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 6 Dec 2016 12:01:25 -0800 Subject: [Chimera-users] Selective lighting In-Reply-To: References: Message-ID: <4FD914C9-02FA-44E9-96B3-8A56A04B115A@cgl.ucsf.edu> Hi Oliver, Sorry, the lighting and shininess settings are global and always apply to all models. In the Lighting dialog (in menu under Tools? Viewing Controls), you can drag the lights around to interactively adjust their directions, but at least in my experience trying to spotlight some area doesn?t help much because other things in the vicinity will be just as shiny. It depends on what you?re showing, but you might try making everything except the ligand transparent. E.g. something like open 2gbp show ligand rep sphere ligand trans 65 ~ ligand ? or if you wanted white background, then back solid white I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 6, 2016, at 6:31 AM, Oliver Grant wrote: > > Hi all, > Is it possible to use the lighting command and have it apply only to particular models? I'd like my ligand to "pop" out by having a light that only shines on it, and not the protein. > Oliver -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 53013 bytes Desc: not available URL: From jmercer at duke.edu Wed Dec 7 08:09:43 2016 From: jmercer at duke.edu (John Mercer, Ph.D.) Date: Wed, 7 Dec 2016 16:09:43 +0000 Subject: [Chimera-users] cif files In-Reply-To: <069D178B-BF76-49EA-B93F-D7D97F1052D2@cgl.ucsf.edu> References: <069D178B-BF76-49EA-B93F-D7D97F1052D2@cgl.ucsf.edu> Message-ID: <43BDB5A6-D5B2-4EDF-9C5F-E19C7B617A97@duke.edu> Hi All, Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif? -John From meng at cgl.ucsf.edu Wed Dec 7 11:39:25 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 7 Dec 2016 11:39:25 -0800 Subject: [Chimera-users] cif files In-Reply-To: <43BDB5A6-D5B2-4EDF-9C5F-E19C7B617A97@duke.edu> References: <069D178B-BF76-49EA-B93F-D7D97F1052D2@cgl.ucsf.edu> <43BDB5A6-D5B2-4EDF-9C5F-E19C7B617A97@duke.edu> Message-ID: Hi John, That is one of the major issues addressed in our next-generation program, ChimeraX. ChimeraX is not yet publicly available, but we plan to make development daily builds available very soon (this month). However, it is in an early stage and lacks many features. It will take some time to become as functionally rich as Chimera, so how useful it will be for you depends on what types of structural analysis you wished to perform. If primarily viewing, it may already fill the bill. We envision people using both packages for a while, depending on their needs. You can get a feel for what ChimeraX can do now from the website and documentation linked below. ChimeraX homepage Advantages shortlist User Guide Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 7, 2016, at 8:09 AM, John Mercer, Ph.D. wrote: > Hi All, > Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif? > -John From goddard at sonic.net Wed Dec 7 11:47:40 2016 From: goddard at sonic.net (Tom Goddard) Date: Wed, 7 Dec 2016 11:47:40 -0800 Subject: [Chimera-users] cif files In-Reply-To: References: <069D178B-BF76-49EA-B93F-D7D97F1052D2@cgl.ucsf.edu> <43BDB5A6-D5B2-4EDF-9C5F-E19C7B617A97@duke.edu> Message-ID: Hi John, The Chimera mmCIF reader is incredibly slow, taking minutes to read a ribosome structure. This code was developed outside our lab and is all in Python. So practically, you would need to download use the multiple PDB format files for structures over 100,000 atoms. The PDB has made this more difficult for new entries because they get a single ID code and only the mmCIF is easily available if the entry has more than 100,000 atoms. For fewer atoms Chimera simply fetches the PDB format if you use fetch or command "open 1xyz?, but it fetches the mmCIF for new entries where the PDB format is not readily available. For those (e.g. 5LZS) you can go to the RCSB web site and use the web page Download menu to get the *.tar.gz file containing several PDB format files representing the model. As Elaine said our new ChimeraX is much faster and uses mmCIF by default. For instance 200,000 atoms of 5LZS opens in 1.5 seconds in ChimeraX. Tom > On Dec 7, 2016, at 11:39 AM, Elaine Meng wrote: > > Hi John, > That is one of the major issues addressed in our next-generation program, ChimeraX. > > ChimeraX is not yet publicly available, but we plan to make development daily builds available very soon (this month). However, it is in an early stage and lacks many features. It will take some time to become as functionally rich as Chimera, so how useful it will be for you depends on what types of structural analysis you wished to perform. If primarily viewing, it may already fill the bill. We envision people using both packages for a while, depending on their needs. You can get a feel for what ChimeraX can do now from the website and documentation linked below. > > ChimeraX homepage > > > Advantages shortlist > > > User Guide > > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 7, 2016, at 8:09 AM, John Mercer, Ph.D. wrote: > >> Hi All, >> Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif? >> -John > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jmercer at duke.edu Wed Dec 7 11:49:46 2016 From: jmercer at duke.edu (John Mercer, Ph.D.) Date: Wed, 7 Dec 2016 19:49:46 +0000 Subject: [Chimera-users] cif files In-Reply-To: References: <069D178B-BF76-49EA-B93F-D7D97F1052D2@cgl.ucsf.edu> <43BDB5A6-D5B2-4EDF-9C5F-E19C7B617A97@duke.edu> Message-ID: <633D3AA8-F916-4022-ADEE-A5B69022991E@duke.edu> Thank you Elaine. Look forward to trying it. Best, -John > On Dec 7, 2016, at 2:39 PM, Elaine Meng wrote: > > Hi John, > That is one of the major issues addressed in our next-generation program, ChimeraX. > > ChimeraX is not yet publicly available, but we plan to make development daily builds available very soon (this month). However, it is in an early stage and lacks many features. It will take some time to become as functionally rich as Chimera, so how useful it will be for you depends on what types of structural analysis you wished to perform. If primarily viewing, it may already fill the bill. We envision people using both packages for a while, depending on their needs. You can get a feel for what ChimeraX can do now from the website and documentation linked below. > > ChimeraX homepage > > > Advantages shortlist > > > User Guide > > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 7, 2016, at 8:09 AM, John Mercer, Ph.D. wrote: > >> Hi All, >> Is there a way to usefully (and conveniently) view ribosomes recognizing that Chimera does not support large structure formats like mmcif? >> -John > From david.haselbach at mpibpc.mpg.de Thu Dec 8 00:16:57 2016 From: david.haselbach at mpibpc.mpg.de (Haselbach, David) Date: Thu, 8 Dec 2016 08:16:57 +0000 Subject: [Chimera-users] How to find symmetry parameters for icosahedral molecule Message-ID: Hi everyone, sorry to ask such a basic question. I have a cryo EM density map 3.2 A of a icosahedral molecule and I already build the model of the monomer. I would like to place the remaining 59 copies and calculate the BioMT matrix for it. I started playing around with the sym command, but I couldn't get it working nicely. It's probably a problem of the coordinate system, but I couldn't figure it out. Than I thought there must be an automatic way and I tried Multifit but also this failed me miserably as the runs fail continuously with "stderr". So I was wondering is there a protocol to do this? Already thank you for any suggestions, David Dr. David Haselbach Max-Planck-Institute for biophysical Chemistry Department for structural Dynamics Am Fassberg 11 37077 Germany Tel. +495512011302 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jirivitali at gmail.com Thu Dec 8 09:43:38 2016 From: jirivitali at gmail.com (chemocev marker) Date: Thu, 8 Dec 2016 18:43:38 +0100 Subject: [Chimera-users] symmetry axis In-Reply-To: References: Message-ID: Dear Dr. Elaine Thanks for your help. I am able to draw the symmetry axis, and can you let me know how can I change the representation of the drawn vector, its color and diameter. and If I make another copy of the same vector how can I move the second vector to a particular axis a by given rotation angle. Sincerely Jiri On Mon, Nov 21, 2016 at 6:48 PM, Elaine Meng wrote: > Hi Jiri, > As I understand it, you would need to open two separate copies of the > structure, superimpose the two sets of atoms for which you want to see the > axis (like A to B, or domain 1 of A to domain 2 of A), and then use command > ?measure rotation?. > measure.html#rotation> > > There are various different ways to superimpose sets of atoms as discussed > here: > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Nov 20, 2016, at 2:30 PM, chemocev marker > wrote: > > > > Hi All > > I am interested to measure the symmetry axis of individual sub-unit > (chain A & chain B) along with the symmetry axis of the heterodimer (AB). > Each chain has 2 domains and 2 fold rotations axis, and I can measure by > removing 1 chain and measure for the other. Is there way to measure the > inter-domain symmetry axis of the heterodimer molecule. > > best > > Jiri > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Dec 8 10:04:30 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 8 Dec 2016 10:04:30 -0800 Subject: [Chimera-users] symmetry axis In-Reply-To: References: Message-ID: <4366C30D-B5EE-49C4-ADEC-A3F51D18FA01@cgl.ucsf.edu> Hi Jiri, The axis from ?measure rotation? is a marker model or fake molecule model made of two ?atoms" with a ?bond" between them. You can adjust it the same ways as you would change the display of sticks in a model. One way is to select the axis (fake bond) with Ctrl-click, then open Selection Inspector such as by clicking the green magnifying glass in the bottom right corner of the Chimera window. In that dialog, under Inspect: Bond, you can change ?color? by clicking the square color well to show the Color Editor and using it to specify a color, and you can change ?radius? stick thickness by entering a different value, and set ?displayed? to ?true? instead of ?if atoms shown? because you may want to hide the end atoms if they are now a different radius than the axis between them. To hide the atoms, you would need to know the model number of the axis, which you can figure out by looking at the Model Panel (under Favorites menu) and then enter a command with that model number, for example: ~disp #2@* ? which means undisplay all atoms in model 2. To move and rotate that axis model you could use ?move? and ?turn? commands. See the command options with commands ?help move? and ?help turn?. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 8, 2016, at 9:43 AM, chemocev marker wrote: > > Dear Dr. Elaine > Thanks for your help. I am able to draw the symmetry axis, and can you let me know how can I change the representation of the drawn vector, its color and diameter. and If I make another copy of the same vector how can I move the second vector to a particular axis a by given rotation angle. > Sincerely > Jiri > > On Mon, Nov 21, 2016 at 6:48 PM, Elaine Meng wrote: > Hi Jiri, > As I understand it, you would need to open two separate copies of the structure, superimpose the two sets of atoms for which you want to see the axis (like A to B, or domain 1 of A to domain 2 of A), and then use command ?measure rotation?. > > > There are various different ways to superimpose sets of atoms as discussed here: > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Nov 20, 2016, at 2:30 PM, chemocev marker wrote: > > > > Hi All > > I am interested to measure the symmetry axis of individual sub-unit (chain A & chain B) along with the symmetry axis of the heterodimer (AB). Each chain has 2 domains and 2 fold rotations axis, and I can measure by removing 1 chain and measure for the other. Is there way to measure the inter-domain symmetry axis of the heterodimer molecule. > > best > > Jiri From goddard at sonic.net Thu Dec 8 11:00:26 2016 From: goddard at sonic.net (Tom Goddard) Date: Thu, 8 Dec 2016 11:00:26 -0800 Subject: [Chimera-users] How to find symmetry parameters for icosahedral molecule In-Reply-To: References: Message-ID: <9BA16F16-2BFA-4218-B687-91C935EE8406@sonic.net> Hi David, If this is a single-particle reconstruction where icosahedral symmetry was imposed on the map you'll want to apply exactly that symmetry to the molecule. The two things you need to know are the grid point that is the center of symmetry, and the orientation of the icosahedral axes (e.g. 2-folds along x,y,z, or 5-fold along z, ...). It is unfortunate that this information is not stored with single particle maps, so you often have to deduce it. Here's my usual approach. I use the Chimera Icosahedron Surface tool (menu Tools / Higher-Order Structure) which shows an icosahedron superimposed on your map. If it is not centered on the map I adjust the map center using the volume viewer dialog menu Features / Coordinates and adjust Origin Index usually to the midpoint of the box (if grid size is 500, I try 250 for the center index, or it could be 249). I adjust the radius of the icosahedron using the icosahedron tool so it matches the map. Then I try the different Orientation settings in the icosahedron tool to find the one that matches the icosahedral symmetry of the map (5-folds match with 5-folds, 3-folds match with 3-folds...). Once you have that and you have a copy of your molecule #1 docked with the map #0 with the map origin set to center of symmetry you can use the sym command to make copies, for example, sym #1 group i,222r center 0,0,0 coordinateSystem #0 Tom > On Dec 8, 2016, at 12:16 AM, Haselbach, David wrote: > > Hi everyone, > > sorry to ask such a basic question. I have a cryo EM density map 3.2 A of a icosahedral molecule and I already build the model of the monomer. I would like to place the remaining 59 copies and calculate the BioMT matrix for it. I started playing around with the sym command, but I couldn?t get it working nicely. It?s probably a problem of the coordinate system, but I couldn?t figure it out. Than I thought there must be an automatic way and I tried Multifit but also this failed me miserably as the runs fail continuously with ?stderr?. So I was wondering is there a protocol to do this? > > Already thank you for any suggestions, > > David > > > Dr. David Haselbach > Max-Planck-Institute for biophysical Chemistry > Department for structural Dynamics > Am Fassberg 11 > 37077 Germany > Tel. +495512011302 > > _______________________________________________ > 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 mike.sivley at vanderbilt.edu Fri Dec 9 09:17:37 2016 From: mike.sivley at vanderbilt.edu (Mike Sivley) Date: Fri, 9 Dec 2016 11:17:37 -0600 Subject: [Chimera-users] Fit-to-window for procedurally generated images Message-ID: <65add29a-ce0f-6fe7-2f0c-c37432eaf1fb@vanderbilt.edu> I am procedurally generating images of protein structures using a Chimera python script. I can center the protein structure within the viewing window, align the protein to emphasize certain elements, set the output size of the final image, and manually apply a scale factor to the view, but I have not found a way to ensure that the protein structure is maximized (but fully contained) within the final image. Is there a "fit-to-window" command that will automatically scale the view in this way? Thanks! Mike Sivley From meng at cgl.ucsf.edu Fri Dec 9 13:45:57 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 9 Dec 2016 13:45:57 -0800 Subject: [Chimera-users] Fit-to-window for procedurally generated images In-Reply-To: <65add29a-ce0f-6fe7-2f0c-c37432eaf1fb@vanderbilt.edu> References: <65add29a-ce0f-6fe7-2f0c-c37432eaf1fb@vanderbilt.edu> Message-ID: <755A751B-9B6B-471F-8C21-C127052BA192@cgl.ucsf.edu> Hi Mike, I have been bothered by this issue myself? There is a ?window? command that is meant to fill that need. However, in my experience, it generally leaves too much space around the structures. Maybe it is a tolerable amount; take a look. One could use ?window? or the similar ?focus? (each without arguments) and then ?scale" up empirically something like 1.2X, but with that approach there is no guarantee some bit won?t fall outside the frame. The extra space is larger in the default perspective mode, as opposed to the orthographic projection (see ?set projection? or the Camera tool if interested). Sorry I don?t have a definitive solution to maximize the use of pixels, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 9, 2016, at 9:17 AM, Mike Sivley wrote: > I am procedurally generating images of protein structures using a Chimera python script. I can center the protein structure within the viewing window, align the protein to emphasize certain elements, set the output size of the final image, and manually apply a scale factor to the view, but I have not found a way to ensure that the protein structure is maximized (but fully contained) within the final image. Is there a "fit-to-window" command that will automatically scale the view in this way? > > Thanks! > Mike Sivley From goddard at sonic.net Fri Dec 9 14:16:29 2016 From: goddard at sonic.net (Tom Goddard) Date: Fri, 9 Dec 2016 14:16:29 -0800 Subject: [Chimera-users] Fit-to-window for procedurally generated images In-Reply-To: <755A751B-9B6B-471F-8C21-C127052BA192@cgl.ucsf.edu> References: <65add29a-ce0f-6fe7-2f0c-c37432eaf1fb@vanderbilt.edu> <755A751B-9B6B-471F-8C21-C127052BA192@cgl.ucsf.edu> Message-ID: Hi Mike, Here's an explanation of why the "window" command doesn't make the molecule exactly fill the window. I don't have any suggestion to remedy this but at least it will help you understand what the window command does. The visible parts of the molecule has a bounding computed in the atomic coordinate system of the molecule. By the coordinate system of the molecule I mean the x,y,z values that came from the PDB file. The window command centers and scales to just fit that bounding box in view. So if you chimera/ a spherical shaped molecule the bounding box has lots of empty space near the corners. If you open it and don't rotate it will fit pretty nicely in the window without extra padding after the "window" command. But if you rotate it 45 degrees so the box corners are now touching the edges of the window then the "window" command appears to leave lots of extra padding at the edge. The ratio of the width of the long diagonal of a cube to its edge length is 1.7 (sqrt(3)) so in this worst case orientation the spherical molecule may actually be scaled 1.7 times smaller than what is necessary for the molecule to touch the edges of the window. All bounds calculation are based on bounding boxes in the molecule coordinate frame, so there is no capability in Chimera to avoid this inaccuracy in the knowing the right scale to fit in a window. Tom > On Dec 9, 2016, at 1:45 PM, Elaine Meng wrote: > > Hi Mike, > I have been bothered by this issue myself? > > There is a ?window? command that is meant to fill that need. However, in my experience, it generally leaves too much space around the structures. Maybe it is a tolerable amount; take a look. One could use ?window? or the similar ?focus? (each without arguments) and then ?scale" up empirically something like 1.2X, but with that approach there is no guarantee some bit won?t fall outside the frame. > > > > > > The extra space is larger in the default perspective mode, as opposed to the orthographic projection (see ?set projection? or the Camera tool if interested). > > > Sorry I don?t have a definitive solution to maximize the use of pixels, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 9, 2016, at 9:17 AM, Mike Sivley wrote: > >> I am procedurally generating images of protein structures using a Chimera python script. I can center the protein structure within the viewing window, align the protein to emphasize certain elements, set the output size of the final image, and manually apply a scale factor to the view, but I have not found a way to ensure that the protein structure is maximized (but fully contained) within the final image. Is there a "fit-to-window" command that will automatically scale the view in this way? >> >> Thanks! >> Mike Sivley > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From dasarnow at gmail.com Mon Dec 12 12:02:11 2016 From: dasarnow at gmail.com (Daniel Asarnow) Date: Mon, 12 Dec 2016 12:02:11 -0800 Subject: [Chimera-users] Multiple transparent objects Message-ID: Hi, I'm having some trouble with a movie of a morph between structures of the same protein bound to two different ligands. The basic idea is a closeup of the binding pocket, and as the morph progresses the initial ligand becomes transparent while the second one becomes opaque. The result is a similar effect to crossfade, only the morph animation is playing simultaneously. I've tried both the screen capture and ray tracing methods, with the following results: Screen capture - When a ligand is almost entirely transparent, a white silhouette is shown at the highest z-order, blocking what's behind. - There is a "pop up" effect when the ligands suddenly switch z-order at the beginning and end of my animation. - Single-layer and flat transparency options don't help. Ray tracing - Multiple transparency is fine. - Reflections and shadows are not made transparent. - E.g. when one ligand is 100% transparent, the reflections and shadows are still visible as white lines and dark spots. Maybe someone here has some insights on my transparency problems? A way to use crossfade instead would be even better. I can record movies with the two ligands separately and then crossfade them manually with ffmpeg. However, it would be nice to have this working entirely in chimera, especially for some more complicated animations I have in the works. Best, -da -------------- next part -------------- An HTML attachment was scrubbed... URL: From olivercgrant at gmail.com Mon Dec 12 00:43:30 2016 From: olivercgrant at gmail.com (Oliver Grant) Date: Mon, 12 Dec 2016 09:43:30 +0100 Subject: [Chimera-users] Selective lighting In-Reply-To: <4FD914C9-02FA-44E9-96B3-8A56A04B115A@cgl.ucsf.edu> References: <4FD914C9-02FA-44E9-96B3-8A56A04B115A@cgl.ucsf.edu> Message-ID: Thanks Elaine, I was able to get the effect by saving a separate image of just the ligand alone and a transparent background. I used different lighting/texture settings for the ligand only image. Then in photoshop I manually superimposed the brighter and shinier ligand on top of my original image. It worked out well, but requires a few steps to see what you get. Oliver On Tue, Dec 6, 2016 at 9:01 PM, Elaine Meng wrote: > Hi Oliver, > Sorry, the lighting and shininess settings are global and always apply to > all models. In the Lighting dialog (in menu under Tools? Viewing > Controls), you can drag the lights around to interactively adjust their > directions, but at least in my experience trying to spotlight some area > doesn?t help much because other things in the vicinity will be just as > shiny. > > It depends on what you?re showing, but you might try making everything > except the ligand transparent. E.g. something like > > open 2gbp > show ligand > rep sphere ligand > trans 65 ~ ligand > > ? or if you wanted white background, then > > back solid white > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Dec 6, 2016, at 6:31 AM, Oliver Grant wrote: > > Hi all, > Is it possible to use the lighting command and have it apply only to > particular models? I'd like my ligand to "pop" out by having a light that > only shines on it, and not the protein. > Oliver > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 53013 bytes Desc: not available URL: From lp212 at cam.ac.uk Mon Dec 12 06:31:37 2016 From: lp212 at cam.ac.uk (Luca Pellegrini) Date: Mon, 12 Dec 2016 14:31:37 +0000 Subject: [Chimera-users] .pyc session file Message-ID: <28A64C74-B748-4B13-96A7-FFF14150A898@cam.ac.uk> Hi, How can I open in Chimera a saved .pyc session file? When I try, Chimera reports the following error message: Error while processing /Users/lp212/Dropbox/: .pyc files are not portable; please use .py file instead Unfortunately I don?t have the .py file, Chimera doesn?t seem to have saved it (not sure why). Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212 at cam.ac.uk Phone: 0044-1223-760469 From xiaoyan.zhu at marquette.edu Mon Dec 12 11:07:15 2016 From: xiaoyan.zhu at marquette.edu (Zhu, Xiaoyan) Date: Mon, 12 Dec 2016 19:07:15 +0000 Subject: [Chimera-users] Hide side chain Message-ID: <1481569636483.53796@marquette.edu> Hello, I am using UCSF Chimera to generate figures of protein crystal structures. Some crystals, if open in Chimera, automatically show the side chains of some amino acids. I want to hide those side chains in my figures. I wonder if there's an easy way to do it. Thank you! Have a good one, Xiaoyan Zhu Ph.D. Candidate Department of Biological Sciences, Marquette University -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Dec 12 13:52:35 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Dec 2016 13:52:35 -0800 Subject: [Chimera-users] Hide side chain In-Reply-To: <1481569636483.53796@marquette.edu> References: <1481569636483.53796@marquette.edu> Message-ID: <1C5D90F9-05DE-4720-B466-8003F7301038@cgl.ucsf.edu> Hello Xiaoyan Zhu, You can hide or show anything, basically. If you want to hide all atoms (keeping the ribbons), some ways are command: ~display - OR - menu: Actions? Atoms/Bonds? hide You can also specify particular atoms, for example, if you want to hide only the protein atoms without hiding other things that are already shown (solvent, ligands, metal ions): command: ~display protein - OR - menu: Select? Structure? protein menu: Actions? Atoms/Bonds? hide menu: Select? Clear Selection You may want to try one or more of the ?Getting Started? tutorials to become familiar with Chimera. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 12, 2016, at 11:07 AM, Zhu, Xiaoyan wrote: > > Hello, > I am using UCSF Chimera to generate figures of protein crystal structures. Some crystals, if open in Chimera, automatically show the side chains of some amino acids. I want to hide those side chains in my figures. I wonder if there's an easy way to do it. Thank you! > > Have a good one, > Xiaoyan Zhu > Ph.D. Candidate > Department of Biological Sciences, Marquette University > From meng at cgl.ucsf.edu Mon Dec 12 13:57:51 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Dec 2016 13:57:51 -0800 Subject: [Chimera-users] .pyc session file In-Reply-To: <28A64C74-B748-4B13-96A7-FFF14150A898@cam.ac.uk> References: <28A64C74-B748-4B13-96A7-FFF14150A898@cam.ac.uk> Message-ID: <1230F681-C544-4C8C-9201-683C709BFDCB@cgl.ucsf.edu> Hi Luca, Unfortunately (as the message suggests) a .pyc file from one computer may not be usable on a different computer. As I understand it, the .py file must have existed at some point, because the .pyc file is created from the .py file. I think you could recreate the .py file by opening the .pyc file on the original computer and saving session again, but I realize that might not be possible or convenient. Sorry, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 12, 2016, at 6:31 AM, Luca Pellegrini wrote: > > Hi, > How can I open in Chimera a saved .pyc session file? When I try, Chimera reports the following error message: > > Error while processing /Users/lp212/Dropbox/: > .pyc files are not portable; please use .py file instead > > Unfortunately I don?t have the .py file, Chimera doesn?t seem to have saved it (not sure why). > > Thanks, > Luca From pett at cgl.ucsf.edu Mon Dec 12 13:58:42 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 12 Dec 2016 13:58:42 -0800 Subject: [Chimera-users] .pyc session file In-Reply-To: <28A64C74-B748-4B13-96A7-FFF14150A898@cam.ac.uk> References: <28A64C74-B748-4B13-96A7-FFF14150A898@cam.ac.uk> Message-ID: Hi Luca, Chimera doesn?t save .pyc files, it saves .py files. When Chimera opens a .py file, a ?compiled? version ? the .pyc file ? is created. .pyc files can be opened in Chimera, but are only guaranteed to open on the same machine that they were originally compiled on. The error message you got indicates that the .pyc file is not compatible with the machine you are trying to open it on. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 12, 2016, at 6:31 AM, Luca Pellegrini wrote: > > Hi, > > How can I open in Chimera a saved .pyc session file? When I try, Chimera reports the following error message: > > Error while processing /Users/lp212/Dropbox/: > .pyc files are not portable; please use .py file instead > > Unfortunately I don?t have the .py file, Chimera doesn?t seem to have saved it (not sure why). > > Thanks, > Luca > > > > Luca Pellegrini, PhD > Department of Biochemistry > University of Cambridge > 80 Tennis Court Road > Cambridge CB2 1GA > UK > > Email: lp212 at cam.ac.uk > Phone: 0044-1223-760469 > > > > > > > > > > > > > _______________________________________________ > 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 goddard at sonic.net Mon Dec 12 14:14:51 2016 From: goddard at sonic.net (Tom Goddard) Date: Mon, 12 Dec 2016 14:14:51 -0800 Subject: [Chimera-users] Multiple transparent objects In-Reply-To: References: Message-ID: Hi Daniel, Chimera does not correctly display two transparent models ? one will appear on top of the other one. The simplest and most practical solution is to fade out one ligand by making it transparent, and immediately after fade in the other ligand, instead of having both ligands intermingled as one fades out and one fades in. If you don?t like that you can try putting both ligands in a single model. Still won?t look great with the one transparent layer setting because you won?t be able to see through one ligand to the other, and if you turn off one transparent layer, then multiple layers don?t even look right within a single molecule model. The way to get exactly what you want is as you suggest, record two times, each with only one ligand and blend the result with ffmpeg. Multiple transparent layers is difficult to do right. Tom > On Dec 12, 2016, at 12:02 PM, Daniel Asarnow wrote: > > Hi, > I'm having some trouble with a movie of a morph between structures of the same protein bound to two different ligands. The basic idea is a closeup of the binding pocket, and as the morph progresses the initial ligand becomes transparent while the second one becomes opaque. The result is a similar effect to crossfade, only the morph animation is playing simultaneously. > > I've tried both the screen capture and ray tracing methods, with the following results: > > Screen capture > When a ligand is almost entirely transparent, a white silhouette is shown at the highest z-order, blocking what's behind. > There is a "pop up" effect when the ligands suddenly switch z-order at the beginning and end of my animation. > Single-layer and flat transparency options don't help. > Ray tracing > Multiple transparency is fine. > Reflections and shadows are not made transparent. > E.g. when one ligand is 100% transparent, the reflections and shadows are still visible as white lines and dark spots. > Maybe someone here has some insights on my transparency problems? > > A way to use crossfade instead would be even better. > > I can record movies with the two ligands separately and then crossfade them manually with ffmpeg. However, it would be nice to have this working entirely in chimera, especially for some more complicated animations I have in the works. > > Best, > -da > _______________________________________________ > 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 xiaoyan.zhu at marquette.edu Mon Dec 12 15:17:29 2016 From: xiaoyan.zhu at marquette.edu (Zhu, Xiaoyan) Date: Mon, 12 Dec 2016 23:17:29 +0000 Subject: [Chimera-users] Hide side chain In-Reply-To: <1C5D90F9-05DE-4720-B466-8003F7301038@cgl.ucsf.edu> References: <1481569636483.53796@marquette.edu> <1C5D90F9-05DE-4720-B466-8003F7301038@cgl.ucsf.edu> Message-ID: Thank you for quick reply! "The command: ~display protein" works perfect for me > On Dec 12, 2016, at 3:52 PM, Elaine Meng wrote: > > Hello Xiaoyan Zhu, > You can hide or show anything, basically. If you want to hide all atoms (keeping the ribbons), some ways are > > command: ~display > - OR - > menu: Actions? Atoms/Bonds? hide > > You can also specify particular atoms, for example, if you want to hide only the protein atoms without hiding other things that are already shown (solvent, ligands, metal ions): > > command: ~display protein > - OR - > menu: Select? Structure? protein > menu: Actions? Atoms/Bonds? hide > menu: Select? Clear Selection > > You may want to try one or more of the ?Getting Started? tutorials to become familiar with Chimera. > > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Dec 12, 2016, at 11:07 AM, Zhu, Xiaoyan wrote: >> >> Hello, >> I am using UCSF Chimera to generate figures of protein crystal structures. Some crystals, if open in Chimera, automatically show the side chains of some amino acids. I want to hide those side chains in my figures. I wonder if there's an easy way to do it. Thank you! >> >> Have a good one, >> Xiaoyan Zhu >> Ph.D. Candidate >> Department of Biological Sciences, Marquette University >> From m.kadlof at cent.uw.edu.pl Fri Dec 16 03:58:31 2016 From: m.kadlof at cent.uw.edu.pl (=?UTF-8?Q?Micha=C5=82_Kadlof?=) Date: Fri, 16 Dec 2016 12:58:31 +0100 Subject: [Chimera-users] Surface clip coloring Message-ID: How can color volume by value with binning several values into single color? I achived the effect partialy by opening several times the same map. set different thresholds and colors to each one and playing with Per-Model Clipping tool, but it have some drawbacks. Planes can't be at exact same level because I observe artifacts. So I tried to move slightly inner layers upp, but still I observe "staris" effect. I also tried with Surface color tool, but it uses interpolation and blends colors togather. In other words I need something like this: https://1.bp.blogspot.com/-5B5ueLHCBPY/T4II4IddvwI/AAAAAAAAB_w/rYwqsJNldY0/s1600/contour1.png instead of something like this: https://i.stack.imgur.com/hQmry.png -- pozdrawiam serdecznie Micha? Kadlof -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.kadlof at cent.uw.edu.pl Fri Dec 16 05:21:19 2016 From: m.kadlof at cent.uw.edu.pl (=?UTF-8?Q?Micha=C5=82_Kadlof?=) Date: Fri, 16 Dec 2016 14:21:19 +0100 Subject: [Chimera-users] probably a bug Message-ID: Hello, I visualize density of my data two different way with the same thresholds and observe different sizes of regions. Isn't it a bug? -- pozdrawiam serdecznie Micha? Kadlof -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image2.png Type: image/png Size: 727347 bytes Desc: not available URL: From meng at cgl.ucsf.edu Fri Dec 16 10:03:15 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 16 Dec 2016 10:03:15 -0800 Subject: [Chimera-users] probably a bug In-Reply-To: References: Message-ID: Hi Micha?, This probably relates also to your previous question. My best guess is not a bug, but there are several factors to consider: (1) probably most important, only the left image is isosurfaces at distinct levels, where as the right shows a gradual coloring. Say you have defined orange as level=1. In that case the isosurface will only enclose 1 or higher. However, the gradual color shading will look orange even at lower values as it shades into the next color. I.e. if in the right image you used white for level=.5, then even values less than 1 but more than .5 will be between orange and white. (2) step values (subsampling of data) for the isosurface display and surface smoothing settings may also significantly affect the volume enclosed in a contour (3) the fineness of the triangles (vertex density) of the surface will also affect the spread of coloring in the image on the right So, getting at your previous question, if you wanted orange only for 1 or higher in the gradual coloring view, you would need to define another color/level immediately below it, say white for 0.9999. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 16, 2016, at 5:21 AM, Micha? Kadlof wrote: > Hello, > > I visualize density of my data two different way with the same thresholds and observe different sizes of regions. Isn't it a bug? > > -- > pozdrawiam serdecznie > Micha? Kadlof > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Fri Dec 16 10:17:30 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 16 Dec 2016 10:17:30 -0800 Subject: [Chimera-users] Surface clip coloring In-Reply-To: References: Message-ID: Hi Micha?, Just to clarify the previous answer. Surface color will only do a gradual coloring, not discrete. However, you can approximate the discrete coloring with somewhat more effort, by putting the same color at the top and bottom of each range, for example: white 0 white 0.99 red 1.0 red 1.99 [?] You can also try using a finer triangulation on that surface cap although that will increase the computational load for moving the clipping plane and rendering the colors. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 16, 2016, at 3:58 AM, Micha? Kadlof wrote: > How can color volume by value with binning several values into single color? > > I achived the effect partialy by opening several times the same map. set different thresholds and colors to each one and playing with Per-Model Clipping tool, but it have some drawbacks. Planes can't be at exact same level because I observe artifacts. So I tried to move slightly inner layers upp, but still I observe "staris" effect. > > I also tried with Surface color tool, but it uses interpolation and blends colors togather. > > In other words I need something like this: https://1.bp.blogspot.com/-5B5ueLHCBPY/T4II4IddvwI/AAAAAAAAB_w/rYwqsJNldY0/s1600/contour1.png > > instead of something like this: > https://i.stack.imgur.com/hQmry.png > > -- > pozdrawiam serdecznie > Micha? Kadlof > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From kartheek.p at research.iiit.ac.in Mon Dec 19 07:43:28 2016 From: kartheek.p at research.iiit.ac.in (Kartheek) Date: Mon, 19 Dec 2016 21:13:28 +0530 (IST) Subject: [Chimera-users] (no subject) Message-ID: <923034912.158258.1482162208901.JavaMail.zimbra@research.iiit.ac.in> Hi UCSF CHIMERA users, I am trying to make a movie in chimera using MD movie and pdb option. However I have been stumbled with the following error "Residue 256.C not in first model on line 20792 of /tmp/tmpvr4a2t.pdb". I do not have any end records, how can I rectify the error ?? -- Sincerely, P.Kartheek, Research Scholar, IIIT-H, Hyderabad, INDIA. -------------- next part -------------- A non-text attachment was scrubbed... Name: 15.pdb Type: application/x-palm-database Size: 854457 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon Dec 19 09:27:51 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 19 Dec 2016 09:27:51 -0800 Subject: [Chimera-users] problems with your PDB file In-Reply-To: <923034912.158258.1482162208901.JavaMail.zimbra@research.iiit.ac.in> References: <923034912.158258.1482162208901.JavaMail.zimbra@research.iiit.ac.in> Message-ID: <143E424E-2815-4516-AAC2-B053F96261F4@cgl.ucsf.edu> Hi Karthak, The file you attached only has one structure, so you wouldn?t use MD Movie to view it anyway. MD Movie is for trajectories of multiple structures (conformations) of the same set of atoms. I can open it as a single structure using the main File? Open, but not in MD Movie because it is only one structure. For an example of a single PDB file with multiple structures, see 1G1P in the Protein DataBank: http://www.rcsb.org/pdb/explore/explore.do?structureId=1g1p I do not get the error message you report. However, maybe this is not a Chimera question but a file-editing question. You would have to use a text editor to add END lines (if you need them, I can?t tell) or to add missing atoms or residues to your PDB file. If you want to view a trajectory in MD Movie, however, your file would need to have multiple conformations separated by MODEL and ENDMDL lines as in 1G1P. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 19, 2016, at 7:43 AM, Kartheek wrote: > > Hi UCSF CHIMERA users, > I am trying to make a movie in chimera using MD movie and pdb option. However I have been stumbled with the following error "Residue 256.C not in first model on line 20792 of /tmp/tmpvr4a2t.pdb". I do not have any end records, how can I rectify the error ?? > > -- > Sincerely, > P.Kartheek, > Research Scholar, > IIIT-H, Hyderabad, > INDIA.<15.pdb> From meng at cgl.ucsf.edu Mon Dec 19 09:31:00 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 19 Dec 2016 09:31:00 -0800 Subject: [Chimera-users] problems with your PDB file In-Reply-To: <143E424E-2815-4516-AAC2-B053F96261F4@cgl.ucsf.edu> References: <923034912.158258.1482162208901.JavaMail.zimbra@research.iiit.ac.in> <143E424E-2815-4516-AAC2-B053F96261F4@cgl.ucsf.edu> Message-ID: > On Dec 19, 2016, at 9:27 AM, Elaine Meng wrote: > > Hi Karthak, Should be P.Kartheek ? sorry for getting your name wrong! Guess I need to clean my glasses this morning. Elaine From dasarnow at gmail.com Tue Dec 20 13:52:49 2016 From: dasarnow at gmail.com (Daniel Asarnow) Date: Tue, 20 Dec 2016 13:52:49 -0800 Subject: [Chimera-users] Crossfade and disp Message-ID: Hello Chimera experts, Here is another movie making question. I noticed that disp and ~disp trigger frames to be recorded, without a call to wait. For example: disp #2 movie crossfade 25 ~disp #2 disp #3 This would produce a movie that crossfades from model #2 to blank, with #3 suddenly appearing. To get crossfades between two ligands, I had to use: disp #2 movie crossfade 25 perframe "~disp #2" frames 1 disp #3 movie crossfade 25 Based on the documentation I wasn't sure if this was intended behavior or a bug. Did I miss a more elegant way to crossfade between two models? Thanks, -da -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Tue Dec 20 13:59:09 2016 From: goddard at sonic.net (Tom Goddard) Date: Tue, 20 Dec 2016 13:59:09 -0800 Subject: [Chimera-users] Crossfade and disp In-Reply-To: References: Message-ID: Hi Daniel, Yes there is a frame drawn between each command that is on a separate line in the Chimera command file. So the crossfade you want should use commands disp #2 movie crossfade 25 ~disp #2 ; disp #3 where the display of model #3 is done on the same line, separated by a colon, after the crossfade command. You can put as many commands on a line as you want separated by semicolons. These behaviors are documented although there is so much Chimera documentation it may be hard to find. Tom > On Dec 20, 2016, at 1:52 PM, Daniel Asarnow wrote: > > Hello Chimera experts, > Here is another movie making question. I noticed that disp and ~disp trigger frames to be recorded, without a call to wait. > > For example: > > disp #2 > movie crossfade 25 > ~disp #2 > disp #3 > > This would produce a movie that crossfades from model #2 to blank, with #3 suddenly appearing. > > To get crossfades between two ligands, I had to use: > > disp #2 > movie crossfade 25 > perframe "~disp #2" frames 1 > disp #3 > movie crossfade 25 > > Based on the documentation I wasn't sure if this was intended behavior or a bug. Did I miss a more elegant way to crossfade between two models? > > Thanks, > -da > _______________________________________________ > 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 ihholmes at gmail.com Tue Dec 20 15:39:52 2016 From: ihholmes at gmail.com (Ian Holmes) Date: Tue, 20 Dec 2016 15:39:52 -0800 Subject: [Chimera-users] Multiscale models command Message-ID: Hello Chimera gurus, I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module. Here is the rough order of what I am doing from the graphical user interface: Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight) Here is what I've got so far in terms of equivalent Python code: import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues Your help would be appreciated - thanks! Ian -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Tue Dec 20 15:49:57 2016 From: goddard at sonic.net (Tom Goddard) Date: Tue, 20 Dec 2016 15:49:57 -0800 Subject: [Chimera-users] Multiscale models command In-Reply-To: References: Message-ID: Hi Ian, To show the 2qa0 virus capsid as ribbons open 2qa0 sym #0 Then to zoom to show the full virus window The sym command also has options to make surfaces like the multiscale model if you want those. Tom > On Dec 20, 2016, at 3:39 PM, Ian Holmes wrote: > > Hello Chimera gurus, > > I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module. > > Here is the rough order of what I am doing from the graphical user interface: > > Open model 2QA0 > Tools menu -> Higher-order structure -> Multiscale Models panel > (The following actions are all in the Multiscale Models panel) > Click "Make models" button in "Models from molecules and matrices" section > Click "All" button in "Select chains:" section > Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection > Click "All" button in "Select chains:" section (again) > Select "Ribbon" from "Style" menu in "Act on selected chains" section > (then back to the main view) > Zoom out (with mouse wheel) > Favorites menu -> Command Line > Type "select :10,20,30" (amino acids I want to highlight) > > > Here is what I've got so far in terms of equivalent Python code: > > import os > from chimera import runCommand as rc > rc("open 2QA0") > # make multiscale model here? > rc("select :10,20,30") # select some residues > > > Your help would be appreciated - thanks! > Ian > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Tue Dec 20 15:56:07 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 20 Dec 2016 15:56:07 -0800 Subject: [Chimera-users] Multiscale models command In-Reply-To: References: Message-ID: <661833BB-51E2-4CA0-AC2E-FE1579665D4E@cgl.ucsf.edu> Hi Ian, You would use the ?sym? command. There is an option to create the multiscale-type low-resolution surfaces instead of loading all the atomic copies, but since you want ribbons rather than the surfaces, there is no need. So, I?m thinking commands: open 2qa0 sym #0 focus sel :300,600 (this file doesn?t have residues 10,20,30) I think you can just use the runcommand thing to convert to python: sym: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 20, 2016, at 3:39 PM, Ian Holmes wrote: > > Hello Chimera gurus, > > I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module. > > Here is the rough order of what I am doing from the graphical user interface: > > Open model 2QA0 > Tools menu -> Higher-order structure -> Multiscale Models panel > (The following actions are all in the Multiscale Models panel) > Click "Make models" button in "Models from molecules and matrices" section > Click "All" button in "Select chains:" section > Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection > Click "All" button in "Select chains:" section (again) > Select "Ribbon" from "Style" menu in "Act on selected chains" section > (then back to the main view) > Zoom out (with mouse wheel) > Favorites menu -> Command Line > Type "select :10,20,30" (amino acids I want to highlight) > > > Here is what I've got so far in terms of equivalent Python code: > > import os > from chimera import runCommand as rc > rc("open 2QA0") > # make multiscale model here? > rc("select :10,20,30") # select some residues > > > Your help would be appreciated - thanks! > Ian > > > _______________________________________________ > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From ihholmes at gmail.com Tue Dec 20 16:55:16 2016 From: ihholmes at gmail.com (Ian Holmes) Date: Tue, 20 Dec 2016 16:55:16 -0800 Subject: [Chimera-users] Multiscale models command In-Reply-To: <661833BB-51E2-4CA0-AC2E-FE1579665D4E@cgl.ucsf.edu> References: <661833BB-51E2-4CA0-AC2E-FE1579665D4E@cgl.ucsf.edu> Message-ID: Thank you very much Elaine and Tom! Ian On Tue, Dec 20, 2016 at 3:56 PM, Elaine Meng wrote: > Hi Ian, > You would use the ?sym? command. There is an option to create the > multiscale-type low-resolution surfaces instead of loading all the atomic > copies, but since you want ribbons rather than the surfaces, there is no > need. So, I?m thinking commands: > > open 2qa0 > sym #0 > focus > sel :300,600 > > (this file doesn?t have residues 10,20,30) > > I think you can just use the runcommand thing to convert to python: > > > sym: > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Dec 20, 2016, at 3:39 PM, Ian Holmes wrote: > > > > Hello Chimera gurus, > > > > I am using multiscale models to view a virus capsid (PDB 2QA0) in > Chimera. I would like to create a Python script to render the capsid as a > multiscale model and then highlight (i.e. select) certain residues. > However, I can't figure out the command-line syntax to create a multiscale > model. The docs also suggest the Midas Python module as an alternative way > of scripting Chimera in Python, but I haven't yet found that module. > > > > Here is the rough order of what I am doing from the graphical user > interface: > > > > Open model 2QA0 > > Tools menu -> Higher-order structure -> Multiscale Models panel > > (The following actions are all in the Multiscale Models panel) > > Click "Make models" button in "Models from molecules and matrices" > section > > Click "All" button in "Select chains:" section > > Click "Hide" button in "Act on selected chains" section, "Selected > chains" subsection > > Click "All" button in "Select chains:" section (again) > > Select "Ribbon" from "Style" menu in "Act on selected chains" section > > (then back to the main view) > > Zoom out (with mouse wheel) > > Favorites menu -> Command Line > > Type "select :10,20,30" (amino acids I want to highlight) > > > > > > Here is what I've got so far in terms of equivalent Python code: > > > > import os > > from chimera import runCommand as rc > > rc("open 2QA0") > > # make multiscale model here? > > rc("select :10,20,30") # select some residues > > > > > > Your help would be appreciated - thanks! > > Ian > > > > > > _______________________________________________ > > 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 dasarnow at gmail.com Tue Dec 20 17:22:18 2016 From: dasarnow at gmail.com (Daniel Asarnow) Date: Tue, 20 Dec 2016 17:22:18 -0800 Subject: [Chimera-users] Crossfade and disp In-Reply-To: References: Message-ID: Thanks, Tom! Now, I understand why wait and crossfade work the way they do as well. I'll take a deeper dive into the docs and try and find it. Best, -da On Tue, Dec 20, 2016 at 1:59 PM, Tom Goddard wrote: > Hi Daniel, > > Yes there is a frame drawn between each command that is on a separate > line in the Chimera command file. So the crossfade you want should use > commands > > disp #2 > movie crossfade 25 > ~disp #2 ; disp #3 > > where the display of model #3 is done on the same line, separated by a > colon, after the crossfade command. You can put as many commands on a line > as you want separated by semicolons. These behaviors are documented > although there is so much Chimera documentation it may be hard to find. > > Tom > > On Dec 20, 2016, at 1:52 PM, Daniel Asarnow wrote: > > Hello Chimera experts, > Here is another movie making question. I noticed that disp and ~disp > trigger frames to be recorded, without a call to wait. > > For example: > > disp #2 > movie crossfade 25 > ~disp #2 > disp #3 > > This would produce a movie that crossfades from model #2 to blank, with #3 > suddenly appearing. > > To get crossfades between two ligands, I had to use: > > disp #2 > movie crossfade 25 > perframe "~disp #2" frames 1 > disp #3 > movie crossfade 25 > > Based on the documentation I wasn't sure if this was intended behavior or > a bug. Did I miss a more elegant way to crossfade between two models? > > Thanks, > -da > _______________________________________________ > 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 meng at cgl.ucsf.edu Wed Dec 21 08:40:27 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 21 Dec 2016 08:40:27 -0800 Subject: [Chimera-users] Crossfade and disp In-Reply-To: References: Message-ID: <8CA67F8E-9022-41FA-97DC-7F9E9933BBFF@cgl.ucsf.edu> Hi Daniel, The general command-file description mentions the implicit ?wait" at end-of-line, and combining commands with semicolons: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 20, 2016, at 5:22 PM, Daniel Asarnow wrote: > Thanks, Tom! > > Now, I understand why wait and crossfade work the way they do as well. I'll take a deeper dive into the docs and try and find it. > > Best, > -da > > On Tue, Dec 20, 2016 at 1:59 PM, Tom Goddard wrote: > Hi Daniel, > > Yes there is a frame drawn between each command that is on a separate line in the Chimera command file. So the crossfade you want should use commands > > disp #2 > movie crossfade 25 > ~disp #2 ; disp #3 > > where the display of model #3 is done on the same line, separated by a colon, after the crossfade command. You can put as many commands on a line as you want separated by semicolons. These behaviors are documented although there is so much Chimera documentation it may be hard to find. > > Tom > >> On Dec 20, 2016, at 1:52 PM, Daniel Asarnow wrote: >> >> Hello Chimera experts, >> Here is another movie making question. I noticed that disp and ~disp trigger frames to be recorded, without a call to wait. >> >> For example: >> >> disp #2 >> movie crossfade 25 >> ~disp #2 >> disp #3 >> >> This would produce a movie that crossfades from model #2 to blank, with #3 suddenly appearing. >> >> To get crossfades between two ligands, I had to use: >> >> disp #2 >> movie crossfade 25 >> perframe "~disp #2" frames 1 >> disp #3 >> movie crossfade 25 >> >> Based on the documentation I wasn't sure if this was intended behavior or a bug. Did I miss a more elegant way to crossfade between two models? >> >> Thanks, >> -da From m.kadlof at cent.uw.edu.pl Wed Dec 21 00:12:05 2016 From: m.kadlof at cent.uw.edu.pl (=?UTF-8?Q?Micha=C5=82_Kadlof?=) Date: Wed, 21 Dec 2016 09:12:05 +0100 Subject: [Chimera-users] change default color maps Message-ID: I found Palette Editor Tool, but I don't know how to use it. How can I apply chosen pallete in Surface Color Tool or load colors from palette into rainbow tool? -- pozdrawiam serdecznie Micha? Kadlof -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Dec 21 10:51:42 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 21 Dec 2016 10:51:42 -0800 Subject: [Chimera-users] change default color maps In-Reply-To: References: Message-ID: <5D1ACB2C-46FF-42A0-AEEE-020863DCCC0A@cgl.ucsf.edu> Hi Micha?, Although I believe the original intent was to integrate palettes more widely, unfortunately only gradient-coloring of the background can directly use a palette. The annoying long way to use a built-in or saved palette in Rainbow (if 5 colors) or Surface Color is to show the palette as color wells in the Palette Editor (find the palette you want and then use the Custom tab to show the wells) and then drag and drop from each color into the corresponding color well of the Rainbow or Surface Color dialog. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 21, 2016, at 12:12 AM, Micha? Kadlof wrote: > I found Palette Editor Tool, but I don't know how to use it. How can I apply chosen pallete in Surface Color Tool or load colors from palette into rainbow tool? > -- > pozdrawiam serdecznie > Micha? Kadlof From smuk at coh.org Thu Dec 22 08:11:00 2016 From: smuk at coh.org (Muk, Sanychen) Date: Thu, 22 Dec 2016 16:11:00 +0000 Subject: [Chimera-users] Saving Output From Match Align Message-ID: Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) --------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From kylelmorris at berkeley.edu Thu Dec 22 13:57:47 2016 From: kylelmorris at berkeley.edu (Kyle Morris) Date: Thu, 22 Dec 2016 13:57:47 -0800 Subject: [Chimera-users] color zone on command line Message-ID: Hi Chimera dev, Following on from this post back from 2009: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003514.html How would one also split map in this python script? Thanks! Kyle -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Dec 22 16:19:30 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 22 Dec 2016 16:19:30 -0800 Subject: [Chimera-users] ChimeraX daily builds available! Message-ID: <0083E7F3-C52C-4090-BBEB-5618A2ACD276@cgl.ucsf.edu> Prerelease daily builds of UCSF ChimeraX are now available to the public! UCSF ChimeraX home: http://www.rbvi.ucsf.edu/chimerax/ Download: http://www.rbvi.ucsf.edu/chimerax/download.html Please keep in mind that ChimeraX features are currently quite limited, that ChimeraX may not work on older machines and/or graphics cards, and that due to the upcoming holidays, responses may be slow if you contact us. On behalf of the Chimera/ChimeraX team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From pett at cgl.ucsf.edu Thu Dec 22 16:43:30 2016 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 22 Dec 2016 16:43:30 -0800 Subject: [Chimera-users] Saving Output From Match Align In-Reply-To: References: Message-ID: <56B67D34-39EC-48F6-B883-11B69A25E919@cgl.ucsf.edu> Hi Sanychen, Doing exactly what you request is not possible, because Render By Attribute is basically not scriptable. However, I believe you can get close enough for your purposes. From your description I?m guessing it?s a Python script. I sure hope so because what you want is only possible in Python! Also, from your mail I?m not sure how much of the script you?ve got working so far, but I?m going to guess you?ve gotten the MAV from Match->Align showing and I?ll go from there. First you need to find the Multalign Viewer instance that Match->Align created. This chimera-users message discusses how to do that. Also, as mentioned in that message, you should call mav.Quit() when you are done with that particular Multalign Viewer instance. Then you need to invoke the ?Assess Match? functionality in your MAV instance. So assuming your reference structure is in a variable named 'ref? and that your evaluation structures are in a list called ?evalStructs? and that you want the resulting attribute named ?matchDist?, then you would do this: mav.assessMatch(ref, evalStructs, ?matchDist?) Now is when you would have had Render By Attribute write out the matchDist attribute values, but instead you will have to do it ?by hand?. Namely you will have to iterate through the residues of the evaluation structures (i.e. their ?.residues? attribute) and for the residues with a ?matchDist? attribute (i.e. hasattr(r, ?matchDist?) == True) you write the residue and value to a file (?str(r)? will get you a text description of the residue). ?Eric Eric Pettersen UCSF Computer Graphics Lab > On Dec 22, 2016, at 8:11 AM, Muk, Sanychen wrote: > > Hello, > > I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. > > Best, > Sanychen Muk > > --------------------------------------------------------------------- > *SECURITY/CONFIDENTIALITY WARNING: > This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) > --------------------------------------------------------------------- > _______________________________________________ > 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 J.R.J.Healey at warwick.ac.uk Fri Dec 23 09:14:25 2016 From: J.R.J.Healey at warwick.ac.uk (Healey, Joe) Date: Fri, 23 Dec 2016 17:14:25 +0000 Subject: [Chimera-users] Chimera-users Digest, Vol 164, Issue 26 In-Reply-To: References: Message-ID: I might be able to offer a bit of help here, the Chimera team and Jaime helped me with basically this exact problem. I have a script here https://github.com/jrjhealey/bioinfo-tools/blob/master/strucfit.py that you could take from. You'll probably want to look specifically at lines 216-240. (Note - you'll also need to look at the relevant module imports for match and pychimera etc. The script will need Jaime's implementation of pychimera too (he's super helpful!) https://github.com/insilichem/pychimera The script gives output as below, as the script automatically finds the best matching PDB file (that's what the first 150 lines or so is looking for), there is additional information there. Best Model I'm Hit Comparing RMSD Assorted homology metrics 2k4r PAK_01796_model5.pdb 2.81843275676 37.5 13 0.00035 21.5 2k4r PAK_01796_model4.pdb 12.6869844869 37.5 13 0.00035 21.5 2k4r PAK_01796_model3.pdb 14.4133021316 37.5 13 0.00035 21.5 2k4r PAK_01796_model1.pdb 0.459177533295 37.5 13 0.00035 21.5 2k4r PAK_01796_model2.pdb 15.1861411912 37.5 13 0.00035 21.5 Hope that's useful! Happy to offer more help (though I'm sure the chimera team have it covered!) Joe M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey at warwick.ac.uk Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry) Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738 ________________________________ From: chimera-users-bounces at cgl.ucsf.edu on behalf of chimera-users-request at cgl.ucsf.edu Sent: 22 December 2016 20:00 To: chimera-users at cgl.ucsf.edu Subject: Chimera-users Digest, Vol 164, Issue 26 Send Chimera-users mailing list submissions to chimera-users at cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request at cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner at cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Saving Output From Match Align (Muk, Sanychen) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Dec 2016 16:11:00 +0000 From: "Muk, Sanychen" To: "chimera-users at cgl.ucsf.edu" Subject: [Chimera-users] Saving Output From Match Align Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wi! sh to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) --------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 164, Issue 26 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sat Dec 24 08:38:41 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 24 Dec 2016 08:38:41 -0800 Subject: [Chimera-users] color zone on command line In-Reply-To: References: Message-ID: Hi Kyle, Now there are Chimera commands to color zone and split by zone, so you could use them directly or via the python approach to run Chimera commands. http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html For color zone, see ?scolor zone? http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html Splitting a map by the resulting color zones is a little harder to find because it?s not a regular command but a keyboard shortcut ?sm? ? however, it can be run with the regular command ?ac sm? http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ac.html http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 22, 2016, at 1:57 PM, Kyle Morris wrote: > Hi Chimera dev, > Following on from this post back from 2009: > > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003514.html > > How would one also split map in this python script? > Thanks! > Kyle > From pconesa at cnb.csic.es Fri Dec 30 00:21:09 2016 From: pconesa at cnb.csic.es (Pablo Conesa) Date: Fri, 30 Dec 2016 09:21:09 +0100 Subject: [Chimera-users] Showing color key programatically colouring from a volume... Message-ID: <51572eaf-bf20-7dbb-6a64-32c22a4fb43c@cnb.csic.es> Dear all We have this simple script to open a volume (#0) coloured using values from a second volume (#1): open betaGal.mrc open extra/MG_Chimera_resolution.vol volume #1 voxelSize 3.54 vol #1 hide scolor #0 volume #1 cmap rainbow reverseColors True For scolor command we are using a volume. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume It would be nice to achieve something like this at start up (note the color key is based on the volume): I've did it dragging the mouse over the canvas while "Color key" utility is open. And, is there a posibility to round up the values. Some kind of: Psaudocode: Give the resulting color key for each round values display the color key I guess that if there is a way to get the color key, then rest can be done through commands. Cheers, Pablo. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: jgkcdgelomgoibdp.png Type: image/png Size: 218789 bytes Desc: not available URL: From pconesa at cnb.csic.es Fri Dec 30 01:20:35 2016 From: pconesa at cnb.csic.es (Pablo Conesa) Date: Fri, 30 Dec 2016 10:20:35 +0100 Subject: [Chimera-users] Showing color key programatically colouring from a volume... In-Reply-To: <51572eaf-bf20-7dbb-6a64-32c22a4fb43c@cnb.csic.es> References: <51572eaf-bf20-7dbb-6a64-32c22a4fb43c@cnb.csic.es> Message-ID: <49c02995-5ffe-b518-86a4-07b90462d622@cnb.csic.es> Sorry! I realized that I created the color key through the "Surface color" tool. So, by default there is no color key. I think now this is not doable unless I set the color key in the script. On 30/12/16 09:21, Pablo Conesa wrote: > Dear all > > We have this simple script to open a volume (#0) coloured using values > from a second volume (#1): > > > open betaGal.mrc > open extra/MG_Chimera_resolution.vol > volume #1 voxelSize 3.54 > vol #1 hide > scolor #0 volume #1 cmap rainbow reverseColors True > > > For scolor command we are using a volume. > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume > > It would be nice to achieve something like this at start up (note the > color key is based on the volume): > > > I've did it dragging the mouse over the canvas while "Color key" > utility is open. > > And, is there a posibility to round up the values. Some kind of: > Psaudocode: > Give the resulting color key > for each round values > display the color key > > I guess that if there is a way to get the color key, then rest can be > done through commands. > > Cheers, Pablo. > > > > _______________________________________________ > 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: not available Type: image/png Size: 218789 bytes Desc: not available URL: From meng at cgl.ucsf.edu Fri Dec 30 08:55:10 2016 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 30 Dec 2016 08:55:10 -0800 Subject: [Chimera-users] Showing color key programatically colouring from a volume... In-Reply-To: <49c02995-5ffe-b518-86a4-07b90462d622@cnb.csic.es> References: <51572eaf-bf20-7dbb-6a64-32c22a4fb43c@cnb.csic.es> <49c02995-5ffe-b518-86a4-07b90462d622@cnb.csic.es> Message-ID: <0424190D-F1EF-4E21-8086-20174F71D512@cgl.ucsf.edu> Hi Pablo, Unfortunately ?scolor? lacks a ?key? option. Some other color-by-value commands (coulombic, rangecolor) have this option, which automatically starts the Color Key dialog and fills it in with colors and values. However, it is similar to using the Surface Color dialog?s option to create color key, in that you still have to use the mouse to set color key location and dimensions in the window, and manually edit the value labels in the Color Key dialog if you want to round them or omit some of them from the display. For non-interactive, completely scripted Color Key drawing, you would have to use the ?colorkey? command with explicit values and colors. It does not ?know? about your data, so you?d have to determine the appropriate values programatically. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/colorkey.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 30, 2016, at 1:20 AM, Pablo Conesa wrote: > Sorry! I realized that I created the color key through the "Surface color" tool. > > So, by default there is no color key. I think now this is not doable unless I set the color key in the script. > > On 30/12/16 09:21, Pablo Conesa wrote: >> Dear all >> We have this simple script to open a volume (#0) coloured using values from a second volume (#1): >> >> open betaGal.mrc >> open extra/MG_Chimera_resolution.vol >> volume #1 voxelSize 3.54 >> vol #1 hide >> scolor #0 volume #1 cmap rainbow reverseColors True >> >> For scolor command we are using a volume. >> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume >> >> It would be nice to achieve something like this at start up (note the color key is based on the volume): >> >> >> I've did it dragging the mouse over the canvas while "Color key" utility is open. >> >> And, is there a posibility to round up the values. Some kind of: >> Psaudocode: >> Give the resulting color key >> for each round values >> display the color key >> >> I guess that if there is a way to get the color key, then rest can be done through commands. >> Cheers, Pablo. From pconesa at cnb.csic.es Sat Dec 31 08:06:52 2016 From: pconesa at cnb.csic.es (Pablo Conesa) Date: Sat, 31 Dec 2016 17:06:52 +0100 Subject: [Chimera-users] Showing color key programatically colouring from a volume... In-Reply-To: <0424190D-F1EF-4E21-8086-20174F71D512@cgl.ucsf.edu> References: <51572eaf-bf20-7dbb-6a64-32c22a4fb43c@cnb.csic.es> <49c02995-5ffe-b518-86a4-07b90462d622@cnb.csic.es> <0424190D-F1EF-4E21-8086-20174F71D512@cgl.ucsf.edu> Message-ID: Hi Elaine, Thank you very much for your detailed explanation. We finally got it working specifying a cmap for the scolor and setting same values for color key. Cheers, Pablo. On 30/12/16 17:55, Elaine Meng wrote: > Hi Pablo, > Unfortunately ?scolor? lacks a ?key? option. Some other color-by-value commands (coulombic, rangecolor) have this option, which automatically starts the Color Key dialog and fills it in with colors and values. However, it is similar to using the Surface Color dialog?s option to create color key, in that you still have to use the mouse to set color key location and dimensions in the window, and manually edit the value labels in the Color Key dialog if you want to round them or omit some of them from the display. > > For non-interactive, completely scripted Color Key drawing, you would have to use the ?colorkey? command with explicit values and colors. It does not ?know? about your data, so you?d have to determine the appropriate values programatically. > > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/colorkey.html > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Dec 30, 2016, at 1:20 AM, Pablo Conesa wrote: > >> Sorry! I realized that I created the color key through the "Surface color" tool. >> >> So, by default there is no color key. I think now this is not doable unless I set the color key in the script. >> >> On 30/12/16 09:21, Pablo Conesa wrote: >>> Dear all >>> We have this simple script to open a volume (#0) coloured using values from a second volume (#1): >>> >>> open betaGal.mrc >>> open extra/MG_Chimera_resolution.vol >>> volume #1 voxelSize 3.54 >>> vol #1 hide >>> scolor #0 volume #1 cmap rainbow reverseColors True >>> >>> For scolor command we are using a volume. >>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume >>> >>> It would be nice to achieve something like this at start up (note the color key is based on the volume): >>> >>> >>> I've did it dragging the mouse over the canvas while "Color key" utility is open. >>> >>> And, is there a posibility to round up the values. Some kind of: >>> Psaudocode: >>> Give the resulting color key >>> for each round values >>> display the color key >>> >>> I guess that if there is a way to get the color key, then rest can be done through commands. >>> Cheers, Pablo.