Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol
Hi Wei *Dead easy* in ccp4mg - display your object as ball and stick, clone it, then display the clone with reduced opacity (or increased transparency). On 20 Jan 2014, at 04:40, Wei Shi wrote: Hi all, Please see attached Fig where they show the ligand both as sticks and spheres at the same time. Does anyone happen to know how to display the ligand like this? Thank you so much! Best, Wei Ligand.ppt Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol
Hi Wei, I think it's easier to do with a surface representation. I'd do something like this: # start script fetch 3b6a, async=0 as cartoon extract ligand, c. c and organic util.chainbow(3b6a) color green, elem c and ligand color oxygen, elem o and ligand show surface, ligand set surface_mode, 1 set surface_color, yellow set transparency=.5 show sticks, ligand set stick_radius, 0.4 show sticks, c. c and i. 130 set cartoon_side_chain_helper, on zoom ligand # end script And then you'd have to mess around with the view/colors of course. Hope this helps Folmer ps: there's actually a PyMOL bulletin board :-) https://lists.sourceforge.net/lists/listinfo/pymol-users 2014/1/20 Wei Shi wei.shi...@gmail.com Hi all, Please see attached Fig where they show the ligand both as sticks and spheres at the same time. Does anyone happen to know how to display the ligand like this? Thank you so much! Best, Wei -- Folmer Fredslund
Re: [ccp4bb] Phasing with Many Monomers/AU
Is the monomer the biggest unit you have to search with? If there is a dimer, tetramer, etc. that is conserved, you could try searching with that. On 01/19/14 14:30, Chris Fage wrote: Thank you all for your responses. I already have a few ideas about how to approach the problem. One of my concerns with so monomers per asymmetric unit at lower resolution was the failure of MR software. Neither PHENIX nor Phaser MR have made progress. I am fairly new to anomalous methods, having solved only two structures by SeMet-based SAD. I've certainly picked up on a number of tricks from the recent messages on heavy atoms, but I thought my case might be a little unusual. I am confident the space group is P1, as it was the only viable option when I indexed four clean albeit low-res datasets. The monomers are ~38 kDa, and the crystals diffracted to 3.4-3.0 at a synchrotron. The conditions for both native and SeMet crystals are: 8-12% PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5. Macromolecular seeding of native crystals into SeMet drops yields the needle-like crystals. Any further input is greatly appreciated! Regards, Chris On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage cdf...@gmail.com mailto:cdf...@gmail.com wrote: Hello Everyone, I am currently trying to phase a structure with an asymmetric unit predicted to contain 20-24 monomers (space group P1). The native crystals, while beautiful in appearance (see attached), only diffract to ~3.4-3.0 angstroms at best, and SeMet-derived crystals grow with poor morphology (small needles). Also, based a fluorescence scan, I know that mercury does not bind appreciably. Other than screening for a new space group, what options might I have for phasing this many monomers at lower resolution? Is there any real chance of solving the structure in this space group? Thank you in advance for any suggestions! Regards, Chris -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Phasing with Many Monomers/AU
I agree. Searching with a larger unit is likely to be successful if you have a good idea of the structure of that larger unit. We had an example of a low homology (29% identity) MR situation with 8 subunits per ASU with twinned data. Not solvable with monomers. Solvable with a dimer search model, then feeding that solution to Parrot and Buccaneer for density modification and automated chain-building using 8-fold NCS. Buccaneer built about 95%+ of the structure correctly. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 1/20/2014 8:41 AM, David Schuller wrote: Is the monomer the biggest unit you have to search with? If there is a dimer, tetramer, etc. that is conserved, you could try searching with that. On 01/19/14 14:30, Chris Fage wrote: Thank you all for your responses. I already have a few ideas about how to approach the problem. One of my concerns with so monomers per asymmetric unit at lower resolution was the failure of MR software. Neither PHENIX nor Phaser MR have made progress. I am fairly new to anomalous methods, having solved only two structures by SeMet-based SAD. I've certainly picked up on a number of tricks from the recent messages on heavy atoms, but I thought my case might be a little unusual. I am confident the space group is P1, as it was the only viable option when I indexed four clean albeit low-res datasets. The monomers are ~38 kDa, and the crystals diffracted to 3.4-3.0 at a synchrotron. The conditions for both native and SeMet crystals are: 8-12% PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5. Macromolecular seeding of native crystals into SeMet drops yields the needle-like crystals. Any further input is greatly appreciated! Regards, Chris On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage cdf...@gmail.com mailto:cdf...@gmail.com wrote: Hello Everyone, I am currently trying to phase a structure with an asymmetric unit predicted to contain 20-24 monomers (space group P1). The native crystals, while beautiful in appearance (see attached), only diffract to ~3.4-3.0 angstroms at best, and SeMet-derived crystals grow with poor morphology (small needles). Also, based a fluorescence scan, I know that mercury does not bind appreciably. Other than screening for a new space group, what options might I have for phasing this many monomers at lower resolution? Is there any real chance of solving the structure in this space group? Thank you in advance for any suggestions! Regards, Chris -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Phasing with Many Monomers/AU
What is the sequence identity of your best search model? Finding that many copies in P1 with 3A data is a challenge but certainly not impossible if there is a reasonably close (20-25% identity) search model available. I would suggest spending some time on preparing a very good search model with tools like Sculptor as well as manually trimming loops and using ensembles of conserved folds from several homologous structures. It is also worth remembering that there are a number of different programs available for molecular replacement and it is worth investing some time in learning how to use Molrep and Amore as well as Phaser as they all have different strengths and weaknesses. Is your data otherwise devoid of any other problems like pseudo-translational symmetry? These can be readily identified with tools like phenix.xtriage. PST can complicate matters quite considerably in molecular replacement. SAD phases, even if obtained at low-resolution, can still be very useful if combined with molecular replacement, so it is well worth pursuing all lines of attack simultaneously. Hope this helps. Eugene On 19 January 2014 19:30, Chris Fage cdf...@gmail.com wrote: Thank you all for your responses. I already have a few ideas about how to approach the problem. One of my concerns with so monomers per asymmetric unit at lower resolution was the failure of MR software. Neither PHENIX nor Phaser MR have made progress. I am fairly new to anomalous methods, having solved only two structures by SeMet-based SAD. I've certainly picked up on a number of tricks from the recent messages on heavy atoms, but I thought my case might be a little unusual. I am confident the space group is P1, as it was the only viable option when I indexed four clean albeit low-res datasets. The monomers are ~38 kDa, and the crystals diffracted to 3.4-3.0 at a synchrotron. The conditions for both native and SeMet crystals are: 8-12% PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5. Macromolecular seeding of native crystals into SeMet drops yields the needle-like crystals. Any further input is greatly appreciated! Regards, Chris On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage cdf...@gmail.com wrote: Hello Everyone, I am currently trying to phase a structure with an asymmetric unit predicted to contain 20-24 monomers (space group P1). The native crystals, while beautiful in appearance (see attached), only diffract to ~3.4-3.0 angstroms at best, and SeMet-derived crystals grow with poor morphology (small needles). Also, based a fluorescence scan, I know that mercury does not bind appreciably. Other than screening for a new space group, what options might I have for phasing this many monomers at lower resolution? Is there any real chance of solving the structure in this space group? Thank you in advance for any suggestions! Regards, Chris -- Dr Eugene Valkov Room 3N049 Division of Structural Studies MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. Email: eval...@mrc-lmb.cam.ac.uk Tel: +44 (0) 1223 267358
Re: [ccp4bb] Phasing with Many Monomers/AU
It will be useful if you share the unit cell dimensions, may be it belongs to a higher symmetry, given the low resolution, you may have missed it out. Sridhar From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eugene Valkov Sent: Monday, January 20, 2014 6:37 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Phasing with Many Monomers/AU What is the sequence identity of your best search model? Finding that many copies in P1 with 3A data is a challenge but certainly not impossible if there is a reasonably close (20-25% identity) search model available. I would suggest spending some time on preparing a very good search model with tools like Sculptor as well as manually trimming loops and using ensembles of conserved folds from several homologous structures. It is also worth remembering that there are a number of different programs available for molecular replacement and it is worth investing some time in learning how to use Molrep and Amore as well as Phaser as they all have different strengths and weaknesses. Is your data otherwise devoid of any other problems like pseudo-translational symmetry? These can be readily identified with tools like phenix.xtriage. PST can complicate matters quite considerably in molecular replacement. SAD phases, even if obtained at low-resolution, can still be very useful if combined with molecular replacement, so it is well worth pursuing all lines of attack simultaneously. Hope this helps. Eugene On 19 January 2014 19:30, Chris Fage cdf...@gmail.com mailto:cdf...@gmail.com wrote: Thank you all for your responses. I already have a few ideas about how to approach the problem. One of my concerns with so monomers per asymmetric unit at lower resolution was the failure of MR software. Neither PHENIX nor Phaser MR have made progress. I am fairly new to anomalous methods, having solved only two structures by SeMet-based SAD. I've certainly picked up on a number of tricks from the recent messages on heavy atoms, but I thought my case might be a little unusual. I am confident the space group is P1, as it was the only viable option when I indexed four clean albeit low-res datasets. The monomers are ~38 kDa, and the crystals diffracted to 3.4-3.0 at a synchrotron. The conditions for both native and SeMet crystals are: 8-12% PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5. Macromolecular seeding of native crystals into SeMet drops yields the needle-like crystals. Any further input is greatly appreciated! Regards, Chris On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage cdf...@gmail.com mailto:cdf...@gmail.com wrote: Hello Everyone, I am currently trying to phase a structure with an asymmetric unit predicted to contain 20-24 monomers (space group P1). The native crystals, while beautiful in appearance (see attached), only diffract to ~3.4-3.0 angstroms at best, and SeMet-derived crystals grow with poor morphology (small needles). Also, based a fluorescence scan, I know that mercury does not bind appreciably. Other than screening for a new space group, what options might I have for phasing this many monomers at lower resolution? Is there any real chance of solving the structure in this space group? Thank you in advance for any suggestions! Regards, Chris -- Dr Eugene Valkov Room 3N049 Division of Structural Studies MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. Email: eval...@mrc-lmb.cam.ac.uk mailto:eval...@mrc-lmb.cam.ac.uk Tel: +44 (0) 1223 267358
Re: [ccp4bb] Phasing with Many Monomers/AU
Hi, In the past I had two cases where seemingly unsuccessful MR became successful simply by collecting the missing cusp, which is due to exist in your P1 case if you collected your data by rotation of the crystal around a single orientation. However, I don't know if modern MR programs use techniques that overcome that problem. Carlos G. Sridhar Prasad wrote: It will be useful if you share the unit cell dimensions, may be it belongs to a higher symmetry, given the low resolution, you may have missed it out. Sridhar From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eugene Valkov Sent: Monday, January 20, 2014 6:37 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Phasing with Many Monomers/AU What is the sequence identity of your best search model? Finding that many copies in P1 with 3A data is a challenge but certainly not impossible if there is a reasonably close (20-25% identity) search model available. I would suggest spending some time on preparing a very good search model with tools like Sculptor as well as manually trimming loops and using ensembles of conserved folds from several homologous structures. It is also worth remembering that there are a number of different programs available for molecular replacement and it is worth investing some time in learning how to use Molrep and Amore as well as Phaser as they all have different strengths and weaknesses. Is your data otherwise devoid of any other problems like pseudo-translational symmetry? These can be readily identified with tools like phenix.xtriage. PST can complicate matters quite considerably in molecular replacement. SAD phases, even if obtained at low-resolution, can still be very useful if combined with molecular replacement, so it is well worth pursuing all lines of attack simultaneously. Hope this helps. Eugene On 19 January 2014 19:30, Chris Fage cdf...@gmail.com mailto:cdf...@gmail.com wrote: Thank you all for your responses. I already have a few ideas about how to approach the problem. One of my concerns with so monomers per asymmetric unit at lower resolution was the failure of MR software. Neither PHENIX nor Phaser MR have made progress. I am fairly new to anomalous methods, having solved only two structures by SeMet-based SAD. I've certainly picked up on a number of tricks from the recent messages on heavy atoms, but I thought my case might be a little unusual. I am confident the space group is P1, as it was the only viable option when I indexed four clean albeit low-res datasets. The monomers are ~38 kDa, and the crystals diffracted to 3.4-3.0 at a synchrotron. The conditions for both native and SeMet crystals are: 8-12% PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5. Macromolecular seeding of native crystals into SeMet drops yields the needle-like crystals. Any further input is greatly appreciated! Regards, Chris On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage cdf...@gmail.com mailto:cdf...@gmail.com wrote: Hello Everyone, I am currently trying to phase a structure with an asymmetric unit predicted to contain 20-24 monomers (space group P1). The native crystals, while beautiful in appearance (see attached), only diffract to ~3.4-3.0 angstroms at best, and SeMet-derived crystals grow with poor morphology (small needles). Also, based a fluorescence scan, I know that mercury does not bind appreciably. Other than screening for a new space group, what options might I have for phasing this many monomers at lower resolution? Is there any real chance of solving the structure in this space group? Thank you in advance for any suggestions! Regards, Chris -- Dr Eugene Valkov Room 3N049 Division of Structural Studies MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. Email: eval...@mrc-lmb.cam.ac.uk mailto:eval...@mrc-lmb.cam.ac.uk Tel: +44 (0) 1223 267358 -- ** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666 FAX:(351)-214433644 e-mail: fra...@itqb.unl.pt www.itqb.unl.pt
Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol
Hi guys, Thank you so much for the suggestions! The suggestion to make two objects of your ligand, display one as sphere and the other as stick. Then change the transparency setting for the spheres works!! This way, the sphere and the stick can colored differently. And, I also found that show the ligand as sphere and change transparency could also show the sphere and stick as the same time, but just in the same color. Thank you so much! Best, Wei On Mon, Jan 20, 2014 at 6:54 AM, Folmer Fredslund folm...@gmail.com wrote: Hi Wei, I think it's easier to do with a surface representation. I'd do something like this: # start script fetch 3b6a, async=0 as cartoon extract ligand, c. c and organic util.chainbow(3b6a) color green, elem c and ligand color oxygen, elem o and ligand show surface, ligand set surface_mode, 1 set surface_color, yellow set transparency=.5 show sticks, ligand set stick_radius, 0.4 show sticks, c. c and i. 130 set cartoon_side_chain_helper, on zoom ligand # end script And then you'd have to mess around with the view/colors of course. Hope this helps Folmer ps: there's actually a PyMOL bulletin board :-) https://lists.sourceforge.net/lists/listinfo/pymol-users 2014/1/20 Wei Shi wei.shi...@gmail.com Hi all, Please see attached Fig where they show the ligand both as sticks and spheres at the same time. Does anyone happen to know how to display the ligand like this? Thank you so much! Best, Wei -- Folmer Fredslund
Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol
Not a pymol approach but I've noticed this dual mode display with transparency is the default in Molsoft ICM browser if you toggle on ball and sticks together with spacefill for the same atoms. Molsoft ball-and-stick also shows the bond order or aromaticity of ligand atoms - which I guess is a motivation for combining sticks with spacefill. Can export higher res png of the graphics too. all the best Martyn From: Wei Shi wei.shi...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 20 January 2014, 4:40 Subject: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol Hi all, Please see attached Fig where they show the ligand both as sticks and spheres at the same time. Does anyone happen to know how to display the ligand like this? Thank you so much! Best, Wei
[ccp4bb] Permanent Biophysics position at the Research Complex at Harwell (UK).
Hello All, I would like to draw your attention to this position: http://www.topcareer.jobs/Vacancy/irc126313_4020.aspx which is for a biophysics instrumentation technician located in the Research Complex at Harwell (www.rc-harwell.ac.ukhttp://www.rc-harwell.ac.uk/). This is a post that is available to anyone with relevant BSc, MSc or PhD experience, and is an open-ended i.e. permanent position. The person would be expected to run instrumentation such as an analytical ultracentrifuge, ITC, Biacore and SEC-MALLS. The RCaH is located adjacent to the Diamond Light Source, and within the Rutherford Appleton Laboratory (Oxfordshire, UK)- where the ISIS neutron source is also located; MX, SAXS, SANS and solid state NMR techniques are all available on site. The position is open now for applications. Please feel free to circulate to potential candidates. I am happy to answer informal enquiries about the post and it's duties, but formal applications must be made through the link above. Best wishes Dave Scott Dr. David J. Scott Group Leader in Biophysical Methods Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA United Kingdom +44 1235 567846 and Associate Professor and Reader in Physical Biochemistry National Centre for Macromolecular Hydrodynamics School of Biosciences University of Nottingham Sutton Bonington Campus Leicestershire LE12 5RD United Kingdom +44 115 9516221
[ccp4bb] Two PhD positions at the New Zealand Institute for Plant and Food Research, Auckland
We are looking for two PhD students to work in the field of plant hormone signalling. Details on the projects can be found here: https://www.careers.sciencenewzealand.org/jobdetails/ajid/FtNj7/4971-PhD-Studentship-Plant-Hormone-Signalling,4971.html and https://www.careers.sciencenewzealand.org/jobdetails/ajid/WINj7/4972-PhD-Studentship-Plant-Hormone-Receptors,4972.html Project 4972 has a strong component in structural biology, while project 4971 is more oriented towards biochemistry/molecular biology. Applicants are expected to apply via the above website. For informal information on any of these projects please contact: Dr Kim Snowden (kimberley.snow...@plantandfood.co.nzmailto:kimberley.snow...@plantandfood.co.nz), Dr Cyril Hamiaux (cyril.hami...@plantandfood.co.nzmailto:cyril.hami...@plantandfood.co.nz) or Professor Richard Newcomb (richard.newc...@plantandfood.co.nzmailto:richard.newc...@plantandfood.co.nz). Regards, Cyril The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.
Re: [ccp4bb] Phasing with Many Monomers/AU
I am grateful for all of the suggestions. I think I have enough tricks to try at this point, but I may check back with this group if things don't work out. Many thanks once again, Chris On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage cdf...@gmail.com wrote: Hello Everyone, I am currently trying to phase a structure with an asymmetric unit predicted to contain 20-24 monomers (space group P1). The native crystals, while beautiful in appearance (see attached), only diffract to ~3.4-3.0 angstroms at best, and SeMet-derived crystals grow with poor morphology (small needles). Also, based a fluorescence scan, I know that mercury does not bind appreciably. Other than screening for a new space group, what options might I have for phasing this many monomers at lower resolution? Is there any real chance of solving the structure in this space group? Thank you in advance for any suggestions! Regards, Chris
