Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
Er considering this forum, why not try CCP4MG ? Tony. On 30 May 2013, at 22:24, Petr Leiman petr.lei...@epfl.chmailto:petr.lei...@epfl.ch wrote: On May 30, 2013, at 5:31 PM, Phoebe A. Rice pr...@uchicago.edumailto:pr...@uchicago.edu wrote: In the olden days, when dinosaurs did roam, Ribbons had a nice fix-up feature that would gently move the alpha carbon end of the stick so that it met the ribbon. Looked MUCH better than the current wavy ribbon one gets with side chain helper, and I haven't been able to find a trick like that in pymol. So pymol developers, please consider yourselves wheedled ... Well, there is another program, which is probably (no flames please!) more powerful, feature-rich than pymol and at the same time much easier to use called… drumroll… UCSF Chimera. One can display wavy and smooth secondary structure cartoons with it. The Chimera engine takes care of connecting side chains to the secondary structure cartoons in both representations. The command to control the cartoon representation is in the Ribbon Style Editor menu: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html The name of the command (can be run from the command line prompt in Chimera or chosen from the above menu) is ribspline: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html Best wishes, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] on behalf of Jason Vertrees [jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com] Sent: Thursday, May 30, 2013 10:17 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol Hi Jacob, Sure, but I believe Donghui wanted to only show sidechains, not any backbone atoms, as sticks. Doing this will leave fragments floating in space as the original email noted. Cheers, -- Jason On Thu, May 30, 2013 at 10:13 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.commailto:wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120tel:%2B1%20%28603%29%20374-7120 -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org *** -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Sebastiano, that's good to know. Thanks for the comment! Tim On 05/30/2013 06:58 PM, Sebastiano Pasqualato wrote: Tim, if I'm not wrong, if you judo type dss on the pymol command line you will apply dssp to your pdb and have your model checked for secondary structure elements. Ciao, S -- Sebastiano On 30/mag/2013, at 18:35, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Donghui, did you actually check this stretch IS a beta-strand, given how distorted it looks? I am asking because in my experience people tend to believe what programs like pymol or molscript tell them to believe without checking the model e.g. for a hydrogen bonding network supporting the secondary structure definition. I may also remember incorrectly, but as far as I know pymol does not use the DSSP algorithm as e.g. molscript and often comes up with different boundaries for the secondary structure elements. I believe the dssp algorithm is more accurate, although this may be because I like molscript (typing) better than pymol (clicking). Regards, Tim On 05/30/2013 05:29 AM, wu donghui wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRqEykUxlJ7aRr7hoRAhcZAJ9u1OhVI1OqiRECB1wQREg9lDeLowCfXx+F tQ11l9/W+DkNNYYQWUbrWDk= =uQms -END PGP SIGNATURE-
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
Hi Jacob, Sure, but I believe Donghui wanted to only show sidechains, not any backbone atoms, as sticks. Doing this will leave fragments floating in space as the original email noted. Cheers, -- Jason On Thu, May 30, 2013 at 10:13 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
In the olden days, when dinosaurs did roam, Ribbons had a nice fix-up feature that would gently move the alpha carbon end of the stick so that it met the ribbon. Looked MUCH better than the current wavy ribbon one gets with side chain helper, and I haven't been able to find a trick like that in pymol. So pymol developers, please consider yourselves wheedled ... ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jason Vertrees [jason.vertr...@schrodinger.com] Sent: Thursday, May 30, 2013 10:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol Hi Jacob, Sure, but I believe Donghui wanted to only show sidechains, not any backbone atoms, as sticks. Doing this will leave fragments floating in space as the original email noted. Cheers, -- Jason On Thu, May 30, 2013 at 10:13 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.commailto:wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120tel:%2B1%20%28603%29%20374-7120 -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org *** -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
To me, that's not a problem. The wavy representation is more accurate (as far as cartoon accuracy can go), as the strand actually follows the alpha carbons. This is why Pauling called it a pleated sheet --- it's got pleats. Beta sheets/strands *should* be wavy. On May 29, 2013, at 11:29 PM, wu donghui wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui Distorsion and connectivity in pymol for strand.pdf
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you actually check this stretch IS a beta-strand, given how distorted it looks? I am asking because in my experience people tend to believe what programs like pymol or molscript tell them to believe without checking the model e.g. for a hydrogen bonding network supporting the secondary structure definition. I may also remember incorrectly, but as far as I know pymol does not use the DSSP algorithm as e.g. molscript and often comes up with different boundaries for the secondary structure elements. I believe the dssp algorithm is more accurate, although this may be because I like molscript (typing) better than pymol (clicking). Regards, Tim On 05/30/2013 05:29 AM, wu donghui wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRp3/cUxlJ7aRr7hoRAkV+AJ9QkNSlAhSC4VAKe2UHt+YpqSY3SwCfQ+Zw ry5vjpLD1hRVZGU7qHnajj4= =yxdy -END PGP SIGNATURE-
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
Tim, if I'm not wrong, if you judo type dss on the pymol command line you will apply dssp to your pdb and have your model checked for secondary structure elements. Ciao, S -- Sebastiano On 30/mag/2013, at 18:35, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you actually check this stretch IS a beta-strand, given how distorted it looks? I am asking because in my experience people tend to believe what programs like pymol or molscript tell them to believe without checking the model e.g. for a hydrogen bonding network supporting the secondary structure definition. I may also remember incorrectly, but as far as I know pymol does not use the DSSP algorithm as e.g. molscript and often comes up with different boundaries for the secondary structure elements. I believe the dssp algorithm is more accurate, although this may be because I like molscript (typing) better than pymol (clicking). Regards, Tim On 05/30/2013 05:29 AM, wu donghui wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRp3/cUxlJ7aRr7hoRAkV+AJ9QkNSlAhSC4VAKe2UHt+YpqSY3SwCfQ+Zw ry5vjpLD1hRVZGU7qHnajj4= =yxdy -END PGP SIGNATURE-
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
On May 30, 2013, at 5:31 PM, Phoebe A. Rice pr...@uchicago.edumailto:pr...@uchicago.edu wrote: In the olden days, when dinosaurs did roam, Ribbons had a nice fix-up feature that would gently move the alpha carbon end of the stick so that it met the ribbon. Looked MUCH better than the current wavy ribbon one gets with side chain helper, and I haven't been able to find a trick like that in pymol. So pymol developers, please consider yourselves wheedled ... Well, there is another program, which is probably (no flames please!) more powerful, feature-rich than pymol and at the same time much easier to use called… drumroll… UCSF Chimera. One can display wavy and smooth secondary structure cartoons with it. The Chimera engine takes care of connecting side chains to the secondary structure cartoons in both representations. The command to control the cartoon representation is in the Ribbon Style Editor menu: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html The name of the command (can be run from the command line prompt in Chimera or chosen from the above menu) is ribspline: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html Best wishes, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] on behalf of Jason Vertrees [jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com] Sent: Thursday, May 30, 2013 10:17 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol Hi Jacob, Sure, but I believe Donghui wanted to only show sidechains, not any backbone atoms, as sticks. Doing this will leave fragments floating in space as the original email noted. Cheers, -- Jason On Thu, May 30, 2013 at 10:13 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.commailto:wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120tel:%2B1%20%28603%29%20374-7120 -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org *** -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
