From: Sanishvili, R. <rsa...@an...> - 2010-12-22 17:18:29
|
Dear Colleagues, Building on the success of the past 3 years, we are pleased to announce the fourth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2011/index.php Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 7 to 15. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 8. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2011/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... |
From: Sanishvili, R. <rsa...@an...> - 2011-01-18 18:59:53
|
Dear Colleagues, This is a reminder that the on-line applications are being accepted for the 4th annual CCP4 summer school "From data collection to structure refinement and beyond", which will take place early June, 2011 at the APS near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2011/ The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... |
From: Sanishvili, R. <rsa...@an...> - 2011-03-24 21:48:56
|
Dear Colleagues, This is a reminder that the deadline for applications for the 4th annual CCP4 summer school "From data collection to structure refinement and beyond" is April 8. The school will take place June 7-15, 2011 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (the program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2011/ The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... |
From: Sanishvili, R. <rsa...@an...> - 2011-12-19 17:44:24
|
Dear Colleagues, We are pleased to announce the fifth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 19 to 26. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 17. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... |
From: Sanishvili, R. <rsa...@an...> - 2012-03-02 20:24:37
|
Dear Colleagues, This is a reminder that the deadline for applications for the 5th annual CCP4 Summer School "From data collection to structure refinement and beyond" is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... ________________________________ From: Sanishvili, Ruslan [mailto:rsa...@an...] Sent: Monday, December 19, 2011 11:44 AM To: 'pym...@li...' Subject: [PyMOL] Annual CCP4 summer school in USA, at APS, June 19-26 Dear Colleagues, We are pleased to announce the fifth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 19 to 26. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 17. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... |
From: Sanishvili, R. <rsa...@an...> - 2012-04-03 22:16:58
|
Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School "From data collection to structure refinement and beyond" is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will cover all aspects of macromolecular structure determination and validation. Some of the world's leading experts will be providing instruction and hand-on help. We are looking forward to another productive school this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 |
From: Sanishvili, R. <rsa...@an...> - 2012-04-12 15:09:46
|
Dear Colleagues, This is friendly but final reminder that Tuesday, April 17 is the application deadline for the fifth annual CCP4 Summer School "From data collection to structure refinement and beyond". On-line application and all details about the school can be found on its web site: http://www.ccp4.ac.uk/schools/APS-2012/index.php We are looking forward to seeing you at the school. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsa...@an... ________________________________ From: Sanishvili, Ruslan Sent: Tuesday, April 03, 2012 5:17 PM To: 'pym...@li...' Cc: Sanishvili, Ruslan Subject: Application deadline approaching: CCP4 summer school at APS, in USA Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School "From data collection to structure refinement and beyond" is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will cover all aspects of macromolecular structure determination and validation. Some of the world's leading experts will be providing instruction and hand-on help. We are looking forward to another productive school this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 |
From: Martin H. <ma...@bl...> - 2012-04-25 15:35:00
|
Dear List In a crystal structure, there are usually a number of relevant crystal waters, as well as water molecules on the surface. In our approach, we model the protein structure within a dielectric continuum, so surface water molecules are not required (to save computer time). However, waters in the interior should remain in our model. How could we discard the surface waters while keeping the internal waters? Thanks for any feedback. Martin |
From: Thomas H. <sp...@us...> - 2012-04-26 12:47:04
|
Hi Martin & James, is it just a coincident that you both ask almost the same question? You could remove all water atoms with few protein contacts or with a small surface area. For example: remove solvent beyond 3.5 of polymer set dot_solvent get_area solvent, load_b=1 remove solvent and b > 20 Hope that helps. Cheers, Thomas On 04/26/2012 10:55 AM, James Starlight wrote: > Another question- I have my protein.pdb with some inserted crystall > waters within protein interiour as well as water surrounded of my > protein. I want to remove only sorrounding water but prevent internal > water ( wich could be functional relevant ). > > How I could to select such surrounded water ( e.g via some cutoff > radius relative my protein etc) wich I'd like to remove further ? On 04/25/2012 05:34 PM, Martin Hediger wrote: > In a crystal structure, there are usually a number of relevant crystal > waters, as well as water molecules on the surface. In our approach, we > model the protein structure within a dielectric continuum, so surface > water molecules are not required (to save computer time). However, > waters in the interior should remain in our model. How could we discard > the surface waters while keeping the internal waters? -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2012-06-28 07:01:06
|
Hi Thomas, I wounder to know what corrections should I add to the below selection in case of multi state object remove solvent beyond 3.5 of polymer e.g I'm working with the MD trajectory saved in PDB format. I've decided to deleate all solvent from all 100 frames simultaneously but the above command works fine only in case of 1 state object . James 2012/4/26 Thomas Holder <sp...@us...> > Hi Martin & James, > > is it just a coincident that you both ask almost the same question? > > You could remove all water atoms with few protein contacts or with a small > surface area. For example: > > remove solvent beyond 3.5 of polymer > set dot_solvent > get_area solvent, load_b=1 > remove solvent and b > 20 > > Hope that helps. > > Cheers, > Thomas > > On 04/26/2012 10:55 AM, James Starlight wrote: > >> Another question- I have my protein.pdb with some inserted crystall >> waters within protein interiour as well as water surrounded of my >> protein. I want to remove only sorrounding water but prevent internal >> water ( wich could be functional relevant ). >> >> How I could to select such surrounded water ( e.g via some cutoff >> radius relative my protein etc) wich I'd like to remove further ? >> > > On 04/25/2012 05:34 PM, Martin Hediger wrote: > >> In a crystal structure, there are usually a number of relevant crystal >> waters, as well as water molecules on the surface. In our approach, we >> model the protein structure within a dielectric continuum, so surface >> water molecules are not required (to save computer time). However, >> waters in the interior should remain in our model. How could we discard >> the surface waters while keeping the internal waters? >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: Thomas H. <sp...@us...> - 2012-07-02 13:40:07
|
Hi James, the "beyond" operator yields true only if the considered atom pair distance is beyond the threshold in ALL states. To remove atoms which are beyond threshold in ANY state, try this: python for i in range(cmd.count_states()): cmd.select('tmp', 'solvent beyond 5 of polymer', state=i+1) cmd.remove('tmp') python end Hope that helps. Cheers, Thomas On 06/28/2012 09:01 AM, James Starlight wrote: > Hi Thomas, > > I wounder to know what corrections should I add to the below selection > in case of multi state object > > remove solvent beyond 3.5 of polymer > > e.g I'm working with the MD trajectory saved in PDB format. I've decided > to deleate all solvent from all 100 frames simultaneously but the above > command works fine only in case of 1 state object . > > James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Martin H. <ma...@bl...> - 2012-10-04 13:13:46
|
Dear PyMOL Users I'm trying to remove water molecules from a crystal structure which are on the crystal surface while preserving the ones within the crystal interior. What I do is: select waters, resn HOH # cmd.select("waters", "(waters extend 1)", enable=1) get_area waters, load_b=1 remove waters and b>20 This only works partially because of some waters, only the oxygen atom is removed, while of others only one of the hydrogens is removed (some waters are completely removed which is good). It does not make a difference if I include the commented command above. Also, what does "load_b=1" mean? Further feedback would be greatly appreciated. Martin On 26.04.12 14:46, Thomas Holder wrote: > Hi Martin & James, > > is it just a coincident that you both ask almost the same question? > > You could remove all water atoms with few protein contacts or with a > small surface area. For example: > > remove solvent beyond 3.5 of polymer > set dot_solvent > get_area solvent, load_b=1 > remove solvent and b > 20 > > Hope that helps. > > Cheers, > Thomas > > On 04/26/2012 10:55 AM, James Starlight wrote: >> Another question- I have my protein.pdb with some inserted crystall >> waters within protein interiour as well as water surrounded of my >> protein. I want to remove only sorrounding water but prevent internal >> water ( wich could be functional relevant ). >> >> How I could to select such surrounded water ( e.g via some cutoff >> radius relative my protein etc) wich I'd like to remove further ? > > On 04/25/2012 05:34 PM, Martin Hediger wrote: >> In a crystal structure, there are usually a number of relevant crystal >> waters, as well as water molecules on the surface. In our approach, we >> model the protein structure within a dielectric continuum, so surface >> water molecules are not required (to save computer time). However, >> waters in the interior should remain in our model. How could we discard >> the surface waters while keeping the internal waters? > |
From: Folmer F. <fo...@gm...> - 2012-10-04 13:42:09
|
Hi Martin, 2012/10/4 Martin Hediger <ma...@bl...> > Dear PyMOL Users > I'm trying to remove water molecules from a crystal structure which are > on the crystal surface while preserving the ones within the crystal > interior. > > What I do is: > > select waters, resn HOH > # cmd.select("waters", "(waters extend 1)", enable=1) > get_area waters, load_b=1 > remove waters and b>20 > > This only works partially because of some waters, only the oxygen atom > is removed, while of others only one of the hydrogens is removed (some > waters are completely removed which is good). It does not make a > difference if I include the commented command above. > You might want to read up on the selection algebra of PyMOL ( http://www.pymolwiki.org/index.php/Selection_Algebra) which is quite powerfull. You can use the "by residue" selection to select the entire residue that fits you description, so in your case remove byres waters and b>20 Will remove every residues within your selection waters, where at least one atom has a b factor of more than 20. (and of course now you have altered the b factor according to the calculated surface area) Also, what does "load_b=1" mean? > > http://www.pymolwiki.org/index.php/Get_Area It is explained in the last example (3) "load_b=1" will put the value of the surface area into the b factor column. Hope that helps! Best regards, Folmer > Further feedback would be greatly appreciated. > Martin > > > > > > On 26.04.12 14:46, Thomas Holder wrote: > > Hi Martin & James, > > > > is it just a coincident that you both ask almost the same question? > > > > You could remove all water atoms with few protein contacts or with a > > small surface area. For example: > > > > remove solvent beyond 3.5 of polymer > > set dot_solvent > > get_area solvent, load_b=1 > > remove solvent and b > 20 > > > > Hope that helps. > > > > Cheers, > > Thomas > > > > On 04/26/2012 10:55 AM, James Starlight wrote: > >> Another question- I have my protein.pdb with some inserted crystall > >> waters within protein interiour as well as water surrounded of my > >> protein. I want to remove only sorrounding water but prevent internal > >> water ( wich could be functional relevant ). > >> > >> How I could to select such surrounded water ( e.g via some cutoff > >> radius relative my protein etc) wich I'd like to remove further ? > > > > On 04/25/2012 05:34 PM, Martin Hediger wrote: > >> In a crystal structure, there are usually a number of relevant crystal > >> waters, as well as water molecules on the surface. In our approach, we > >> model the protein structure within a dielectric continuum, so surface > >> water molecules are not required (to save computer time). However, > >> waters in the interior should remain in our model. How could we discard > >> the surface waters while keeping the internal waters? > > > > > > ------------------------------------------------------------------------------ > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Folmer Fredslund |