Re: [COOT] duplication of the model during refinement
Hi Ela, It may be some other software interfering with Coot. Have you looked at: https://bernhardcl.github.io/coot/wincoot-faq.html#mozTocId358284 On Windows mysterious things can happen... B *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > On Behalf Of Elzbieta Dorota Wator > Sent: Tuesday, June 11, 2024 3:53 PM > To: COOT@JISCMAIL.AC.UK > Subject: duplication of the model during refinement > > You don't often get email from elzbietadorotawa...@gmail.com. > Learn why this is important > <https://aka.ms/LearnAboutSenderIdentification> > > Dear Coot fellow, > I recently several encounter the same problem during structure refinement > in Coot (Wincoot to be more specific, different versions). During adding > waters/going along the protein chain, sometimes the opened pdb file get > "duplicates" and I end up with e.g. 3 the same model opened in one session. > I didn't find any explanation of the problem online. Maybe one of you > experienced something similar and has solution or at least cause of that? > > Best regards, > Ela > > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w.jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7C9c6eed07b081492b885608dc8a1f7f16%7Cbff7eef1cf4b4f32 > be3da1dda043c05d%7C0%7C0%7C638537115175449470%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C0%7C%7C%7C&sdata=1uy5sG%2F03gPnch01%2BMXotKRk > ckk8WZog7rcHTA7GFZc%3D&reserved=0> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/om-ki/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://staff.ki.se/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Disable NCS calculations
... well, it can be quite slow using SSM if you have a large number of chains (and a slow computer). Hence you can change the way Coot calculates the NCS matrices by: set_ncs_matrix_type(int flag) Int flag is an integer. 0 - default SSM 1 - LSQ (on CA) 2- LSQ with only every 2nd CA So, the fastest you can be is (pythonic): set_ncs_matrix_type(2) HTH, B *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > On Behalf Of Paul Emsley > Sent: Tuesday, June 18, 2024 12:04 AM > To: COOT@JISCMAIL.AC.UK > Subject: Re: Disable NCS calculations > > On 17/06/2024 17:39, Auffinger Pascal wrote: > > > > -- > > > > Hi, > > > > I would like to disable automatic NCS calculations in coot. > > Is there a script command for that ? > > > > I don't think that there is a way. What harm do they do? > > Paul. > > > > > To unsubscribe from the COOT list, click the following link: > https://www/. > jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7C8ba960bc75a94f25351d08dc8f197986%7Cbff7eef1cf4b4f32 > be3da1dda043c05d%7C0%7C0%7C638542586924204460%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C0%7C%7C%7C&sdata=crEmRFx4vAkdLTtim6lOpwXRHXV% > 2BTPzFfxhZKlAIINk%3D&reserved=0 > > This message was issued to members of > http://www.ji/ > scmail.ac.uk%2FCOOT&data=05%7C02%7CBernhard.Lohkamp%40KI.SE%7C8 > ba960bc75a94f25351d08dc8f197986%7Cbff7eef1cf4b4f32be3da1dda043c05 > d%7C0%7C0%7C638542586924211466%7CUnknown%7CTWFpbGZsb3d8eyJ > WIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D% > 7C0%7C%7C%7C&sdata=G%2FIO5Pmmpn8MAcd8qdgY85SOcH5X1zsqjhb24M > 7A9Nw%3D&reserved=0, a mailing list hosted by > http://www.ji/ > scmail.ac.uk%2F&data=05%7C02%7CBernhard.Lohkamp%40KI.SE%7C8ba960 > bc75a94f25351d08dc8f197986%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0 > %7C0%7C638542586924216139%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC > 4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C% > 7C%7C&sdata=C4985gfa%2FCeYEab3DBw7%2ByiAFBWnHI9pH7IZLsrVY6M%3 > D&reserved=0, terms & conditions are available at > https://www/. > jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7CBernhard.Lohka > mp%40KI.SE%7C8ba960bc75a94f25351d08dc8f197986%7Cbff7eef1cf4b4f32b > e3da1dda043c05d%7C0%7C0%7C638542586924219612%7CUnknown%7CTW > FpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJX > VCI6Mn0%3D%7C0%7C%7C%7C&sdata=wNfiy9mjhYPdreT%2F1wXd2vyfuXW > cR8NIEIu%2FXMOWPZQ%3D&reserved=0 När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/om-ki/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://staff.ki.se/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Release 1.1.04
I have put together a WinCoot 1.1.07 beta release: https://github.com/bernhardcl/coot/releases/tag/Release-1.1.07 There is no installer as yet but easy enough to run: just unzip and double click wincoot.bat. Please let me know if you encounter any issues (beyond the ones already known). Cheers, Bernhard *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > On Behalf Of Paul Emsley > Sent: Monday, January 15, 2024 2:57 AM > To: COOT@JISCMAIL.AC.UK > Subject: Release 1.1.04 > > Source: > > https://www/ > 2.mrc- > lmb.cam.ac.uk%2Fpersonal%2Fpemsley%2Fcoot%2Fsource%2Freleases%2Fc > oot- > 1.1.04.tar.gz&data=05%7C02%7CBernhard.Lohkamp%40KI.SE%7C207c0b8d0 > 80840dd2f7708dc156d7105%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7 > C0%7C638408807135644638%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4w > LjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C > %7C%7C&sdata=Ff4aONIPJzgeG6oMw30W9DNUhUu9RUhH%2BRQdCr5RhLo > %3D&reserved=0 > > >Release 1.1.04 > >o FEATURE: Particle effects for done difference map peaks > >o CHANGE: Refinement cannot now proceed if there are no bond restraints > for any > of the refining residues > >o BUG-FIX: Add coot namespace to state save file > >o BUG-FIX: Fix symmetry of difference map peaks > > > > > To unsubscribe from the COOT list, click the following link: > https://www/. > jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7C207c0b8d080840dd2f7708dc156d7105%7Cbff7eef1cf4b4f3 > 2be3da1dda043c05d%7C0%7C0%7C638408807135644638%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=e1HAqipjjJbAqvLv3aVPNAG5x4p > TDK1zMwZQg4qLr%2B8%3D&reserved=0 > > This message was issued to members of > http://www.ji/ > scmail.ac.uk%2FCOOT&data=05%7C02%7CBernhard.Lohkamp%40KI.SE%7C2 > 07c0b8d080840dd2f7708dc156d7105%7Cbff7eef1cf4b4f32be3da1dda043c05 > d%7C0%7C0%7C638408807135644638%7CUnknown%7CTWFpbGZsb3d8eyJ > WIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D% > 7C3000%7C%7C%7C&sdata=TfTDI0pJ511k7UAUvBDMAEZFaUkpXoiqmJ%2Fhv > gUx9EI%3D&reserved=0, a mailing list hosted by > http://www.ji/ > scmail.ac.uk%2F&data=05%7C02%7CBernhard.Lohkamp%40KI.SE%7C207c0b > 8d080840dd2f7708dc156d7105%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C > 0%7C0%7C638408807135644638%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiM > C4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000 > %7C%7C%7C&sdata=awFllYGKj3o%2BSrY2zSeKBl9EltOW0rjMHQ8ceLBg8RQ% > 3D&reserved=0, terms & conditions are available at > https://www/. > jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7CBernhard.Lohka > mp%40KI.SE%7C207c0b8d080840dd2f7708dc156d7105%7Cbff7eef1cf4b4f32 > be3da1dda043c05d%7C0%7C0%7C638408807135644638%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5jwF4ZBKtiwV6dzhyRypnuuXbn > LAK2OxTVd2DhNCLoc%3D&reserved=0 När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] How does COOT determine protonation states
Dear Kate, Just to clear up some potential confusion and contradiction between Lucrezia's and my answer. Coot has various ways in generating hydrogens, internally using the dictionaries as Lucrezia nicely mentioned and explained, and externally using e.g. refmac or reduce (as I mentioned earlier). In the 0.9 series of Coot which you are using, the Validation function Probe clashes will use reduce. You can see this in the command line output which will state something about reduce (followed by probe). HTH, B *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > On Behalf Of Lucrezia Catapano > Sent: Friday, February 2, 2024 3:21 PM > To: COOT@JISCMAIL.AC.UK > Subject: Re: How does COOT determine protonation states > > You don't often get email from ade43f7741e4-dmarc- > requ...@jiscmail.ac.uk. Learn why this is important > <https://aka.ms/LearnAboutSenderIdentification> > > > Dear Kate, > > > > Coot adds hydrogen atoms according to the dictionary. If you want to change > the protonation of a ligand, you'd do that by modifying the actual monomer > dictionary. We typically use Acedrg to generate dictionaries. > > For example, in the case of a ASP residue, the modification which describes > the addition of the proton, encapsulates all the local changes (bond order, > angles etc.) of the monomer, providing the (probably) expected geometry. > > > > Look in your coot-molprobity output directory. These files are used by > Reduce to protonate ligands - Coot converts the (Acedrg, or whatever else) > dictionary you have given it, to these files of connection records. > > > > Regards, > > Lucrezia > > > > > > From: Mailing list for users of COOT Crystallographic Software > on behalf of Kim, Sun Kyung <bc51fd01f63f- > dmarc-requ...@jiscmail.ac.uk> > Date: Tuesday, 30 January 2024 at 00:36 > To: COOT@JISCMAIL.AC.UK > Subject: How does COOT determine protonation states > > Some people who received this message don't often get email from > bc51fd01f63f-dmarc-requ...@jiscmail.ac.uk. Learn why this is > important <https://aka.ms/LearnAboutSenderIdentification> > > > > Hello, > > > > I’m using the Coot 0.9.8.91 EL. I am working jointly with a computational > team who are doing simulations on our PDB model. I’ve added hydrogens to > my model using Coot’s Validate -> Probe clashes function. The computational > team asks, when COOT adds protons using the probe clashes function, how > does it assign protonation states to residues? Is it using something > sophisticated that we can trust for our computational simulations or should > the computational scientists use their own methods for determining > protonation states? > > > > Thank you for your time answering this question, much appreciated! > > > > Best, > > ‘Kate’ Sun Kyung Kim > > > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w.jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7C32075b8c26224728999e08dc23fa3dcd%7Cbff7eef1cf4b4f32 > be3da1dda043c05d%7C0%7C0%7C638424805036984658%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EFvE4QxPtUrW7li1GnGIi4jm%2B8n > AWfn6f7s%2BMy7y0Lc%3D&reserved=0> > > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w.jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7C32075b8c26224728999e08dc23fa3dcd%7Cbff7eef1cf4b4f32 > be3da1dda043c05d%7C0%7C0%7C638424805036993462%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C0%7C%7C%7C&sdata=N4tugnCcn0Tp5iXaW5mKHRAgvshc > 24zko5pwww5u9sc%3D&reserved=0> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<
Re: [COOT] How does COOT determine protonation states
> Hello, > > > > I’m using the Coot 0.9.8.91 EL. I am working jointly with a computational > team who are doing simulations on our PDB model. I’ve added hydrogens to > my model using Coot’s Validate -> Probe clashes function. The computational > team asks, when COOT adds protons using the probe clashes function, how > does it assign protonation states to residues? Is it using something > sophisticated that we can trust for our computational simulations or should > the computational scientists use their own methods for determining > protonation states? Coot uses (in this case) the programme/method reduce from the Richardson lab to add hydrogens. You will find more information on reduce here: http://kinemage.biochem.duke.edu/software/reduce/ HTH, B > > Thank you for your time answering this question, much appreciated! > > > > Best, > > ‘Kate’ Sun Kyung Kim > > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w.jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7C72deacec99e34d17ea2d08dc212b7cbb%7Cbff7eef1cf4b4f3 > 2be3da1dda043c05d%7C0%7C0%7C638421718169055485%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C0%7C%7C%7C&sdata=uonT4Uc19QH6B7M2PiSaPmmOwa > dhK3ITmwZu7mzwcXs%3D&reserved=0> *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Error in Wincoot0.9.8.7
> -Original Message- > From: Mailing list for users of COOT Crystallographic Software > On Behalf Of Goode Shelter > Sent: Thursday, October 12, 2023 6:47 AM > To: COOT@JISCMAIL.AC.UK > Subject: Error in Wincoot0.9.8.7 > > You don't often get email from sht7...@gmail.com. Learn why this is > important <https://aka.ms/LearnAboutSenderIdentification> > > Dear Sir/Madam, > I am a user of Wincoot0.9.8.7 in win10 system. When I click "undo" button, > there is an error in coot that I cannot fix it. However, same files (PDB and > MTZ) in other's computer, the "undo" button can work. The details is below: > restoring from backup 3 3 > WARNING:: Error reading E:\Lab119\structure refinement\wincoot\WinCoot- > 0.9.8.92\WinCoot\\coot- > backup/E__Lab119_structure_refinement_Phenix_files_DYRK2_Phenix_4-98- > 2_Refine_29_DYRK_refine_29-coot- > 0.pdb_Thu_Oct_12_12_39_24_2023_modification_1.pdb.gz > DEBUG:: apply_undo: (end) history_index: 1 max_history_index: 3 > apply_undo () > > > > please help me to solve this problem, it is very important for me to analyze > this structure. Thank you very much. > Looking forward to hearing from you. Just to double check, which WinCoot version do you use? 0.9.8.7 as in the subject line or the latest 0.9.8.92 as in the path mentioned? Anyway, I don’t think this should make a difference in that respect. I can think of several reasons why this may happen 1. you (i.e. WinCoot) do not have permission to write to that particular directory and the backup file wasn’t written 2. there is an issue with spaces in the path 3. there is an issue with the path/filename length. For 1., please check that the directory and file is actually there (as Paul pointed out it can be read in directly - even drag and drop should work). Note: You can set COOT_BACKUP_DIR in wincoot.bat to point to a writable directory. I would have though 2 is in the past and fixed for good but I may have to double check. You could try to replace the space in "structure refinement" with and e.g. an underscore. Similarly I wouldn’t really expect 3 to be an issue but maybe there is one. Please let me know how you get on and I can dig into one or the other more if necessary. Cheers, B > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w.jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C01%7CBernhard.Lohk > amp%40KI.SE%7C2c36fb86217844cffe8f08dbcadfdc15%7Cbff7eef1cf4b4f32b > e3da1dda043c05d%7C0%7C0%7C638326835187289309%7CUnknown%7CTW > FpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJX > VCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bc52CsgCTHfEYBCyhQv8xEIuvnC > 9xs3CKJNi6ObTuSY%3D&reserved=0> *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Can't download pdb files nor density maps in WinCoot 0.9.8.1 EL
Hi Dale,
The file link Paul sent should be the same WinCoot has. I believe the issue is
with a relocation of the EDS files. I believe these are the ones you are after
(fetch from EBI as such should work). No idea where/if EDS files are still
available at the EBI. Maybe Sameer knows...
B
***
Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent
Teaching Unit/Biomedicum D9
Dept. of Medical Biochemistry and Biophysics (MBB) |
Karolinska Institutet
SE-171 77 Stockholm
Sweden
+46 8 52487055
bernhard.lohk...@ki.se | ki.se
> -Original Message-
> From: Mailing list for users of COOT Crystallographic Software
> On Behalf Of Paul Emsley
> Sent: Thursday, June 8, 2023 12:55 PM
> To: COOT@JISCMAIL.AC.UK
> Subject: Re: Can't download pdb files nor density maps in WinCoot 0.9.8.1 EL
>
>
>
>
> Hi Dale,
>
> Without testing, I guess that you can replace get_ebi.py with this one
>
> https://github.com/pemsley/coot/blob/refinement/python/get_ebi.py
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithu
> b.com%2Fpemsley%2Fcoot%2Fblob%2Frefinement%2Fpython%2Fget_ebi.py
> &data=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C7781e97a5001413dac9e
> 08db680edfe3%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C63821
> 8185468716853%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLC
> JQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sda
> ta=UWnV1KWvMH62eMRSVIyte8BVugqgRX3AS%2FHW4yDsDHI%3D&reserve
> d=0>
>
> (use Raw of course)
>
> Paul.
>
>
>
>
> On 08/06/2023 08:35, Sameer Velankar wrote:
>
>
>
> CAUTION: This email originated from outside of the LMB.
> Do not click links or open attachments unless you recognize the
> sender and know the content is safe.
> .-owner-c...@jiscmail.ac.uk-.
>
>
>
> Hi Dale
>
> The correct url for accessing files are as follows -
> 1. PDB file - https://www.ebi.ac.uk/pdbe/entry-files/pdb1cbs.ent
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww
> w.ebi.ac.uk%2Fpdbe%2Fentry-
> files%2Fpdb1cbs.ent&data=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C77
> 81e97a5001413dac9e08db680edfe3%7Cbff7eef1cf4b4f32be3da1dda043c05d
> %7C0%7C0%7C638218185468873076%7CUnknown%7CTWFpbGZsb3d8eyJWI
> joiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3
> 000%7C%7C%7C&sdata=fOmGfhmQSp0fXKr%2BmCLzO7ZGEx3fE1gSZVHKax6
> 5f%2FA%3D&reserved=0>
> 2. mmCIF file - https://www.ebi.ac.uk/pdbe/entry-files/1cbs.cif
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww
> w.ebi.ac.uk%2Fpdbe%2Fentry-
> files%2F1cbs.cif&data=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C7781e97
> a5001413dac9e08db680edfe3%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0
> %7C0%7C638218185468873076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC
> 4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%
> 7C%7C%7C&sdata=6IA6JacL3iZw04wWFlKZv6xXa0bEbzpN5mjRjEf02tg%3D&r
> eserved=0>
>
> Kind regards
> Sameer
>
>
>
> On 8 Jun 2023, at 07:25, Dale Tronrud
> <mailto:de...@daletronrud.com>
> wrote:
>
> Hi,
>
> When I click on "Fetch PDB entry using Accession Code..." or
> "Fetch PDB & Map using EDS..." I get
>
> PDB Accession Code: 3eoj
> DEBUG:: extracted accession code handle mode n 1
> BL WARNING:: retrieve of url https://www.ebi.ac.uk/pdbe-
> srv/view/files/3eoj.ent
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww
> w.ebi.ac.uk%2Fpdbe-
> srv%2Fview%2Ffiles%2F3eoj.ent&data=05%7C01%7CBernhard.Lohkamp%40
> KI.SE%7C7781e97a5001413dac9e08db680edfe3%7Cbff7eef1cf4b4f32be3da1
> dda043c05d%7C0%7C0%7C638218185468873076%7CUnknown%7CTWFpbGZ
> sb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6M
> n0%3D%7C3000%7C%7C%7C&sdata=%2FJJGmg36m7HvIVLfW%2FT5L3qiYrm
> PWUgcnNt7OMgxp5s%3D&reserved=0> failed
> handle_read_draw_molecule_with_recentre ("coot-
> download/3eoj.pdb.ent".1)
> WARNING:: Error reading coot-download/3eoj.pdb.ent
>
> That web site, indeed, does not exist and I presume the
> PDBe has moved the data.
>
> To the best of my knowledge this is the most recent version
> of WinCoot. I've downloaded the "unstable" version 1.0.01 and it fails in the
> same way (but does show a very pretty display when downloading from PDB
> Redo).
>
> I've done my best to search the "coot" and "ccp4bb"
> archives and don't see mention of this problem, but my search
Re: [COOT] WinCoot preferences
Hi David,
In the output you sent you have a scheme command in your .coot.py file:
"set-show-symmetry-master (1)"
Replace the "-" with "_" and you will be fine.
B
*******
Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent
Teaching Unit/Biomedicum D9
Dept. of Medical Biochemistry and Biophysics (MBB) |
Karolinska Institutet
SE-171 77 Stockholm
Sweden
+46 8 52487055
bernhard.lohk...@ki.se | ki.se
> -Original Message-
> From: Mailing list for users of COOT Crystallographic Software
> On Behalf Of David Dranow
> Sent: Thursday, May 18, 2023 8:11 PM
> To: COOT@JISCMAIL.AC.UK
> Subject: WinCoot preferences
>
> [You don't often get email from a1df4b9c22b9-dmarc-
> requ...@jiscmail.ac.uk. Learn why this is important at
> https://aka.ms/LearnAboutSenderIdentification ]
>
> Hi Friends,
>
> I have sucessfully used preference files for WinCoot for that last 8 years
> across 3 laptops, but with this new laptop it's not working. It looks like the
> files are read, but I don't see the output in the terminal to indicate that
> it has
> any effect. And the preferences are not updated. I've always put coot.py and
> coot_preferences.py into C:\WinCoot\.coot-preferences. I've attached my
> preferences files and the terminal output. Any ideas what changed? I'm
> using Wincoot 0.9.8.1.
>
> These are the commands I'm most interested in having run on each startup:
> set_show_symmetry_master (1)
> set_show_environment_distances (1)
> set_environment_distances_label_atom (1)
> set_refine_ramachandran_angles (1)
> set_default_initial_contour_level_for_map (1)
> set_nomenclature_errors_on_read ("ignore")
>
>
> Thanks!
> -David
>
>
>
>
> To unsubscribe from the COOT list, click the following link:
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Re: [COOT] wincoot latest?
Hi Frank, The page is correct but the latest in the 0.9 is 0.9.8.1 and there is a 1.0 as well (without installer though). Not sure why it says latest 0.9.4.1, this is ancient. Maybe some java script issue!? Anyway, you can go directly to the release page (where all latest releases are found): http://bernhardcl.github.io/coot/wincoot-releases.html Or check manually on github: https://github.com/bernhardcl/coot/releases Note to self: I should automate the "last update" since this is manually not update since then... (but releases should update automatically). HTH, B *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > On Behalf Of Frank von Delft > Sent: 10 January 2023 00:04 > To: COOT@JISCMAIL.AC.UK > Subject: wincoot latest? > > [You don't often get email from 68d7a4fdd833-dmarc- > requ...@jiscmail.ac.uk. Learn why this is important at > https://aka.ms/LearnAboutSenderIdentification ] > > Hello > > I'm looking for wincoot, and my Google takes me to this page: > > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbernhard > cl.github.io%2Fcoot%2Fwincoot- > download.html&data=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C107ddad9 > 0a7741d1e09808daf2985f6b%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0% > 7C0%7C638089033954601642%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4 > wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C > %7C%7C&sdata=AQ5clnvJClvgtmLlfqbC7pn98Mrybf4GUvln7r0ZV0g%3D&reser > ved=0 > > with the latest version being 0.9.4.1 > > Is that indeed (a) the official wincoot page and (b) the latest version of > coot > available for windows? > > (The page says "last modified 2017".) > > > If none of this is accurate - how can I find the Real Coot? > > Thanks! > Frank > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you > are not the intended addressee or an authorised recipient of the addressee > please notify us of receipt by returning the e-mail and do not use, copy, > retain, > distribute or disclose the information in or attached to the e-mail. > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > ### > # > > To unsubscribe from the COOT list, click the following link: > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jis > cmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C01%7CBernhard.Lohka > mp%40KI.SE%7C107ddad90a7741d1e09808daf2985f6b%7Cbff7eef1cf4b4f32b > e3da1dda043c05d%7C0%7C0%7C638089033954601642%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ABC62fCwXWDrqf8bE%2BruBXjw > uNQuowf%2BxGvTIhZXIrY%3D&reserved=0 > > This message was issued to members of > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2FCOOT&data=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C107d > dad90a7741d1e09808daf2985f6b%7Cbff7eef1cf4b4f32be3da1dda043c05d%7 > C0%7C0%7C638089033954601642%7CUnknown%7CTWFpbGZsb3d8eyJWIjoi > MC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C300 > 0%7C%7C%7C&sdata=i5CLgZjY%2FknM2zKH5%2B7KZw5d%2FOz2Im79HVacO > p1gtAw%3D&reserved=0, a mailing list hosted by > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2F&data=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C107ddad9 > 0a7741d1e09808daf2985f6b%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0% > 7C0%7C638089033954601642%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4 > wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C > %7C%7C&sdata=GySZI9jINDy9n5GnDSHyus2GnZb3oCFX%2FNH%2FSxlndO4% > 3D&reserved=0, terms & conditions are available at > https://eur01.safelinks.prot
Re: [COOT] Real-space refine - show old conformation
> Dear all, > Is there a way to show the previous/old conformation of the active zone during > real-space refinement in coot? Another option.. you can undo (Ctrl-Y) and redo (Ctrl-Z). This doesn’t clutter your display and you do not need to activate/deactivate molecules and get confused. And if you don’t like it you continue with the "undo" model. B > I am using 0.9.6 at the moment, and in previous versions this was default - I > do > not know when it changed. The old zone/chain/residue was shown in a different > color during refinement. Can I switch this feature on somewhere? > > Cheers, > christian > > > > > > > # > ### > > To unsubscribe from the COOT list, click the following link: > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jis > cmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C01%7CBernhard. > Lohkamp%40KI.SE%7Cd8c7c25fe6e44a226b7d08da50a0c545%7Cbff7eef1cf4 > b4f32be3da1dda043c05d%7C0%7C0%7C637910948836501644%7CUnknown > %7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haW > wiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=27evHs99C77jtccRXjN > Q7tCqW8J8It2EqfrsDhrBYpQ%3D&reserved=0 > > This message was issued to members of > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2FCOOT&data=05%7C01%7CBernhard.Lohkamp%40KI.SE%7 > Cd8c7c25fe6e44a226b7d08da50a0c545%7Cbff7eef1cf4b4f32be3da1dda043c > 05d%7C0%7C0%7C637910948836501644%7CUnknown%7CTWFpbGZsb3d8e > yJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D% > 7C3000%7C%7C%7C&sdata=%2FujMAxL3UkPgq0wcwIo%2FFbT%2BUnQ > Tu%2FwjsZxMo6EPWTI%3D&reserved=0, a mailing list hosted by > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2F&data=05%7C01%7CBernhard.Lohkamp%40KI.SE%7Cd8c7 > c25fe6e44a226b7d08da50a0c545%7Cbff7eef1cf4b4f32be3da1dda043c05d% > 7C0%7C0%7C637910948836501644%7CUnknown%7CTWFpbGZsb3d8eyJWIj > oiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C30 > 00%7C%7C%7C&sdata=f6QYHTGRA%2FcOreJ53t8DNdX%2FcKxQ7oKrBelI > u9Hsmt0%3D&reserved=0, terms & conditions are available at > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jis > cmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C01%7CBernhard.Lohk > amp%40KI.SE%7Cd8c7c25fe6e44a226b7d08da50a0c545%7Cbff7eef1cf4b4f3 > 2be3da1dda043c05d%7C0%7C0%7C637910948836501644%7CUnknown%7C > TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JM%2BvjOvoL0nx5oRrMiVI > UvZU2GcCQV3oqHQ9s1LxzwQ%3D&reserved=0 *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] WinCoot 1
For Coot users under Windows I have put together a simple zip archive to test and try WinCoot 1 (actually 1.0.01). https://github.com/bernhardcl/coot/releases/tag/Release-1.0.01 Or https://bernhardcl.github.io/coot/wincoot-releases.html At this point there is no installer and the zip archive misses the ligand dictionary (*) and potentially some other auxiliary files. But it's simple enough to run: - unzip - double click "wincoot.bat" (in the directory WinCoot-1.0.01) There are known missing features (see Paul's announcement on Coot-1; https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2204&L=COOT&O=D&P=47) and known bugs (see e.g. https://github.com/pemsley/coot/issues ). Any other issues (esp. Windows related) please let me know (by email, here or https://github.com/bernhardcl/coot/issues). Bernhard P.S. I will make an installer eventually (when I tested more myself and fixed some more issues). (*) It should pick it up from the ccp4 installation anyway. ******* Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Release 0.9.7
Sorry for the past post. This was of course meant for Paul only... I blame the email client I am forced to use nowadays. Anyway, now it is clear that it will take a moment to fix the Windows release 😉 Not too long I hope though. B *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > On Behalf Of Bernhard Lohkamp > Sent: 25 January 2022 15:53 > To: COOT@JISCMAIL.AC.UK > Subject: Re: Release 0.9.7 > > > Finally 😉 Well, still some merge conflicts. Not sure what they are yet. Only > had > a brief look and that confused me more than anything. Maybe too ill. I had > some > reaction on the booster but was fine then. Only for two days later to be > completely out and not fully recovered. I just went for a test. How are you? > Anyway, from a diff to your branch it doesn’t look too bad though 😉 with the > exception of extensions.py. From what I see this is messed as it wont fill the > menuitems but rather be an extensions menu. Most important for python only > (i.e. Windows) so probably not too much of an issue overall. I will certainly > keep > this for my branch and windows build 😉 > > B > > *** > > Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent > > Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry > and Biophysics (MBB) | Karolinska Institutet > SE-171 77 Stockholm > Sweden > +46 8 52487055 > bernhard.lohk...@ki.se | ki.se > > > -Original Message- > > From: Mailing list for users of COOT Crystallographic Software > > On Behalf Of Paul Emsley > > Sent: 25 January 2022 02:42 > > To: COOT@JISCMAIL.AC.UK > > Subject: Release 0.9.7 > > > > We are pleased to (at last) announce the release of 0.9.7 > > > > source > > > > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww2. > > mrc- > > > lmb.cam.ac.uk%2Fpersonal%2Fpemsley%2Fcoot%2Fsource%2Freleases%2Fco > > ot- > > > 0.9.7.tar.gz&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cccd2fd2 > > > 795df40f8ef5908d9dfa3f3e9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0% > > > 7C0%7C637786717935815442%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4 > > > wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&a > > > mp;sdata=EDg9UEkpFqMHAdEc9zmUQp65%2FvutBVQULPTk2CipXS8%3D&am > > p;reserved=0 > > > > binaries > > > > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww2. > > mrc- > > > lmb.cam.ac.uk%2Fpersonal%2Fpemsley%2Fcoot%2Fbinaries%2Frelease%2Fco > > ot-0.9.7-binary-Linux-x86_64-scientific-linux-7.6-python- > > > gtk2.tar.gz&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cccd2fd2 > > > 795df40f8ef5908d9dfa3f3e9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0% > > > 7C0%7C637786717935815442%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4 > > > wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&a > > > mp;sdata=%2Bnn5whEDByejLG7%2BmL6jvrnMJ1Z2GOPts3dpbb2Gk4g%3D&a > > mp;reserved=0 > > > > > > Release 0.9.7 > > > > > >o FEATURE: Add angles in coot-ligand-validation > > > >o FEATURE: "Updating Maps" added to the API and GUI > > > >o FEATURE: Stereo style can now be switched back to how it used to > > be in > > 2010 [Dirk Kostrewa] > > > >o CHANGE: Better B-factors for added waters > > > >o CHANGE: Windows build script updates > > > >o CHANGE: RSR GM restraints now filtered by distance difference > > > >o BUG-FIX: Python GUI and updates to match scheme version - now > > pyrogen work on Windows > > > >o BUG-FIX: Fix gui simple mutation crash [John Bollinger]. > > > >o BUG-FIX: add a null function (no-coot-tips) for those that have > > this in their startup scripts > > > >o BUG-FIX: Fix crash when coot tries to exit while the refinement > > is still refining [James Holton] > > > > > # > > ### > > > > To unsubscribe from the COOT list, click the following link: > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww. > > > jis%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C
Re: [COOT] Release 0.9.7
Finally 😉 Well, still some merge conflicts. Not sure what they are yet. Only had a brief look and that confused me more than anything. Maybe too ill. I had some reaction on the booster but was fine then. Only for two days later to be completely out and not fully recovered. I just went for a test. How are you? Anyway, from a diff to your branch it doesn’t look too bad though 😉 with the exception of extensions.py. From what I see this is messed as it wont fill the menuitems but rather be an extensions menu. Most important for python only (i.e. Windows) so probably not too much of an issue overall. I will certainly keep this for my branch and windows build 😉 B *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se > -Original Message- > From: Mailing list for users of COOT Crystallographic Software > On Behalf Of Paul Emsley > Sent: 25 January 2022 02:42 > To: COOT@JISCMAIL.AC.UK > Subject: Release 0.9.7 > > We are pleased to (at last) announce the release of 0.9.7 > > source > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww2. > mrc- > lmb.cam.ac.uk%2Fpersonal%2Fpemsley%2Fcoot%2Fsource%2Freleases%2Fco > ot- > 0.9.7.tar.gz&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cccd2fd2 > 795df40f8ef5908d9dfa3f3e9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0% > 7C0%7C637786717935815442%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4 > wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&a > mp;sdata=EDg9UEkpFqMHAdEc9zmUQp65%2FvutBVQULPTk2CipXS8%3D&am > p;reserved=0 > > binaries > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww2. > mrc- > lmb.cam.ac.uk%2Fpersonal%2Fpemsley%2Fcoot%2Fbinaries%2Frelease%2Fco > ot-0.9.7-binary-Linux-x86_64-scientific-linux-7.6-python- > gtk2.tar.gz&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cccd2fd2 > 795df40f8ef5908d9dfa3f3e9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0% > 7C0%7C637786717935815442%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4 > wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&a > mp;sdata=%2Bnn5whEDByejLG7%2BmL6jvrnMJ1Z2GOPts3dpbb2Gk4g%3D&a > mp;reserved=0 > > > Release 0.9.7 > > >o FEATURE: Add angles in coot-ligand-validation > >o FEATURE: "Updating Maps" added to the API and GUI > >o FEATURE: Stereo style can now be switched back to how it used to be in > 2010 [Dirk Kostrewa] > >o CHANGE: Better B-factors for added waters > >o CHANGE: Windows build script updates > >o CHANGE: RSR GM restraints now filtered by distance difference > >o BUG-FIX: Python GUI and updates to match scheme version - now pyrogen > work on Windows > >o BUG-FIX: Fix gui simple mutation crash [John Bollinger]. > >o BUG-FIX: add a null function (no-coot-tips) for those that have this in > their > startup scripts > >o BUG-FIX: Fix crash when coot tries to exit while the refinement is still > refining > [James Holton] > > # > ### > > To unsubscribe from the COOT list, click the following link: > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jis > cmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard. > Lohkamp%40KI.SE%7Cccd2fd2795df40f8ef5908d9dfa3f3e9%7Cbff7eef1cf4b4 > f32be3da1dda043c05d%7C0%7C0%7C637786717935815442%7CUnknown% > 7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwi > LCJXVCI6Mn0%3D%7C3000&sdata=yj3e5vupqgDZt2NgcP8tTPGyrmygMK > %2BcGTinn8w54Hk%3D&reserved=0 > > This message was issued to members of > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2FCOOT&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7 > Cccd2fd2795df40f8ef5908d9dfa3f3e9%7Cbff7eef1cf4b4f32be3da1dda043c0 > 5d%7C0%7C0%7C637786717935815442%7CUnknown%7CTWFpbGZsb3d8eyJ > WIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7 > C3000&sdata=o3r9irbYRIqcn84srigigLGg3VIZlGUoqju2V1eyiGA%3D& > ;reserved=0, a mailing list hosted by > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cccd2f > d2795df40f8ef5908d9dfa3f3e9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C > 0%7C0%7C637786717935815442%7CUnknown%7CTWFpbGZsb3d8eyJWIjoi > MC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C300 > 0&sdata=%2FcDo7jQ1ACg%2FSEqlT%2FKpvgn291v9B5%
Re: [COOT] add alternate residue range ?
Hi Vincent, > is it possible to add alternate conformation to a residue range, not just one > residue? > I have a loop that has 2 main conformations and I would like to model both as > alt res for a 20 residues stretch. What would be the best way to do this? I had a similar scenario and thought it would be good to have a function for this. You should find in python scripting the following. HTH B # Duplication of a given residue range (in alt conf of course) # def duplicate_residue_range(imol, chain_id, res_no_start, res_no_end, occ_split=0.5): """ This function duplicates the given residue range and makes two alternative conformations of it. The occupancies are split 50:50 by default. Args: imol: molecule number chain_id: chain res_no_start: start of residue range res_no_end: end of residue range Keyword Args: occ_split: alt conformation occupancy for alt conf A (default 0.5) """ > Thank you > Vincent > > -- > > > Vincent Chaptal, PhD > > Director of GdR APPICOM > > Drug Resistance and Membrane Proteins Lab > > > > > MMSB -UMR5086 > > 7 passage du Vercors > > 69007 LYON > > FRANCE > > +33 4 37 65 29 01 > > http://www.appicom.cnrs.fr > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.a > ppicom.cnrs.fr%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C50e1 > 1bf793cf445e352908d9d44e2dae%7Cbff7eef1cf4b4f32be3da1dda043c05d% > 7C0%7C0%7C637774255098064559%7CUnknown%7CTWFpbGZsb3d8eyJWIj > oiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C20 > 00&sdata=osxJcgFPQus%2FofAOWjKpW1JgJDhDDjHBnf%2FWh%2FxY%2FQU > %3D&reserved=0> > > http://mmsb.cnrs.fr/en/ > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmmsb.c > nrs.fr%2Fen%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C50e11bf > 793cf445e352908d9d44e2dae%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0 > %7C0%7C637774255098064559%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiM > C4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000 > &sdata=1k%2B4s24nCorfRJvT29OdYKGNnv4jEprpx3l1ezAbwQo%3D&reserved > =0> > > > > > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.j > iscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohk > amp%40KI.SE%7C50e11bf793cf445e352908d9d44e2dae%7Cbff7eef1cf4b4f3 > 2be3da1dda043c05d%7C0%7C0%7C637774255098064559%7CUnknown%7C > TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C2000&sdata=hD5nuwkxPTaZBwGjYXOm2GhTc4MwDJ87u > GsQqx5PKd8%3D&reserved=0> *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] How to turn off prompt for nomenclature errors?
Happy New Year...
> Eddie Snell quickly helped:
>
>
>
> cootrc file found in X:\YourWinCootDirectory\share\coot
>
> where X is the drive. Buried in the wincoot-faq.
Indeed possible but not the preferred way...
> I also found (from the BB) that I could simply create a file
>
>
> X:\YourWinCootDirectory\.coot-preferences\coot.py
>
> and stick that line in there.
This is a better place.. Alternatively put ".coot.py" in
X:\YourWinCootDirectory, just like on Linux.
> Bernard, maybe say this explicitly in the FAQ?
Just did. Thanks for pointing this out.
B
> HNY all!
> Frank
>
>
>
>
> On 04/01/2022 07:14, Frank von Delft wrote:
>
>
> Thanks Paul.
>
> I assume it's RTM to figure out where that startup script is? I
> confess I
> failed... I'm on Windows, and working out where startup lives tends to be
> torrid.
>
> Can I suggest an "edit-my-startup-script" feature from the GUI.
>
> Frank
>
>
> On 22/12/2021 17:08, Paul Emsley wrote:
>
>
> On 22/12/2021 15:37, Frank von Delft wrote:
>
>
> Hello - when I drag a bunch of files onto my wincoot, I
> end up with a long slew of dialogues, asking me if I wan to fix nomenclature
> errors.
>
> I've just realised I find it irritating, because I just
> want
> to look, not build.
>
> How do I turn it off by default?
>
>
>
> add this to your startup-script
>
> set_nomenclature_errors_on_read("ignore")
>
> Paul
>
>
> ##
> ##
>
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***
Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent
Div. Molecu
Re: [COOT] NCS tools copy ncs residue range to a particular slave chain
Hi Ahmad, > When I apply an ncs residue range from a master chain, it gets propagated to > all > slave chains, but I want the change to propagate to only a particular chain, > without having to undo all the changes in the other chains! > > Alternatively, I wonder if there's a way to build a segment from a template > that > could be a different chain in the same imol or from a different imol. You can use the corresponding scripting function (python or scheme; here python): copy_residue_range_from_ncs_master_to_chains (imol, master_chain_id, residue_range_start, residue_range_end, chain_id_list_in) chain_id_list_in is a python list (even if you copy only to one chain, e.g. ["B"]). HTH, B > Thank you. > > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.j > iscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohk > amp%40KI.SE%7Ca672263d8d224ba67be408d9b9822824%7Cbff7eef1cf4b4f > 32be3da1dda043c05d%7C0%7C0%7C637744791089510245%7CUnknown%7 > CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiL > CJXVCI6Mn0%3D%7C3000&sdata=ARPlOlt%2BOvaGvNkoMQxwg7H4CyKo5Wi > 2VX3LrTl38T8%3D&reserved=0> *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Coot on Windows
Hi Marie, > Is there a version of Coot that runs on 64-bit Windows machines? I'm a Mac Yes. Available from: https://bernhardcl.github.io/coot/ or from CCP4 of course. > and Linux user trying to get WinCoot installed on 64-bit Windows machines in a > teaching lab. I had planned to have the class fit models into a couple of > electron > density maps. > > I know about CCP4 Cloud but have never used it. Is that my only option on the > Windows machines? Cloud is easy since you do not need to bother about installations. Otherwise of course you can locally install CCP4 or run virtual machines with CCP4 (and Coot) on it. HTH, B ******* Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] How to display the rotamer error information while doing the real space refine in GUI
Hi, > I updated the coot version to 0.8.9.2. However, when I did the real sparce Blimey. This is not an upgrade but a downgrade... We are in the 0.9.6 series already > refinement, the rotamer error information didn't display. I remember there was > a ball at the alpha carbon atom in the peptide backbone. The colour of balls > are > different due to the validation of rotamer, which can tell me the condition > of the > rotamer. I wanted to know how to display this type of balls? This can only be done in the 0.9 series. So please do a "real" update of your Coot version. HTH, B ******* Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] "broken" pdb after merging the ligand
s issued to members of > > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j > > > iscmail.ac.uk%2FCOOT&data=04%7C01%7CBernhard.Lohkamp%40KI.SE > %7Ce25 > > > 8db3538694a8eeb6808d94b8db82d%7Cbff7eef1cf4b4f32be3da1dda043c05d > %7C0%7 > > > C0%7C637623894330730061%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4 > wLjAwMDAiLC > > > JQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9%2 > FM1O8 > > > pC0UI9%2FW4NB9%2FjaGesBwKU8vI3MhTwLVaqp1Q%3D&reserved=0, > a mailing > > list hosted by > > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.j > > > iscmail.ac.uk%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Ce2 > 58db3 > > > 538694a8eeb6808d94b8db82d%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C > 0%7C0%7 > > > C637623894330730061%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAw > MDAiLCJQIj > > > oiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=doGd3yf > 45tPt > > UJ5Uzui%2BAU%2BTAd33bACNqhgVLBwFxEs%3D&reserved=0, terms & > > conditions are available at > > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww. > > > jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7CBernhard.Loh > k > > > amp%40KI.SE%7Ce258db3538694a8eeb6808d94b8db82d%7Cbff7eef1cf4b4f > 32be3da > > > 1dda043c05d%7C0%7C0%7C637623894330730061%7CUnknown%7CTWFpb > GZsb3d8eyJWI > > > joiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3 > 000&a > > > mp;sdata=BU9H%2B0EpY0gCBIgLBi5QhIOV41nhUPua5kMXO66d6kY%3D&am > p;reserved > > =0 > > # > ### > > To unsubscribe from the COOT list, click the following link: > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jis > cmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard. > Lohkamp%40KI.SE%7Ce258db3538694a8eeb6808d94b8db82d%7Cbff7eef1cf > 4b4f32be3da1dda043c05d%7C0%7C0%7C637623894330730061%7CUnknow > n%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1ha > WwiLCJXVCI6Mn0%3D%7C3000&sdata=sww3cGiJWjIfh2mLaEqPSc5r16Z > 465dDDnZZ5vdFWxk%3D&reserved=0 > > This message was issued to members of > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2FCOOT&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7 > Ce258db3538694a8eeb6808d94b8db82d%7Cbff7eef1cf4b4f32be3da1dda04 > 3c05d%7C0%7C0%7C637623894330730061%7CUnknown%7CTWFpbGZsb3d > 8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3 > D%7C3000&sdata=9%2FM1O8pC0UI9%2FW4NB9%2FjaGesBwKU8vI3Mh > TwLVaqp1Q%3D&reserved=0, a mailing list hosted by > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Ce258 > db3538694a8eeb6808d94b8db82d%7Cbff7eef1cf4b4f32be3da1dda043c05d > %7C0%7C0%7C637623894330730061%7CUnknown%7CTWFpbGZsb3d8eyJW > IjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3 > 000&sdata=doGd3yf45tPtUJ5Uzui%2BAU%2BTAd33bACNqhgVLBwFxEs% > 3D&reserved=0, terms & conditions are available at > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jis > cmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7CBernhard.Lohk > amp%40KI.SE%7Ce258db3538694a8eeb6808d94b8db82d%7Cbff7eef1cf4b4f > 32be3da1dda043c05d%7C0%7C0%7C637623894330730061%7CUnknown%7 > CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiL > CJXVCI6Mn0%3D%7C3000&sdata=BU9H%2B0EpY0gCBIgLBi5QhIOV41nh > UPua5kMXO66d6kY%3D&reserved=0 *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] accept with space bar and dynamic validation
Dear Georg, > I am running coot on Windows10 (I guess on linux and mac it works). > However, > in past versions pressing the space bar after the Accept refinement? window > appeared, accepted the refinement, which was very handy because space is also > used to jump from one residue to the next one. Now pressing space in the > Accept Refinement? windows ticks the Auto-clear option. How can I change the > behaviour. See Paul's answer for this one... > In one of your video tutorial I became aware of dynamic validation. However it > is not pssoible to install it. The error is: > > debug:: curlew_install_extension() uninstall_button 0x25e3d930 > DEBUG:: in coot_get_url_and_activate_curl_hook > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbernhar > dcl.github.io%2Fcoot%2Fextensions%2Fcurlew_find_atom_overlap_baddies.py > &data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cae9748ef3f024245 > 39b008d935060d90%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C > 637599123135394740%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAw > MDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdat > a=wEmTmnAKxgoogMHV11YHBhum5a3%2F%2Fw9RLSTwIOwk8So%3D& > reserved=0 coot-download/curlew_find_atom_overlap_baddies.py > checksum compare 38143 5715 > WARNING:: Failure in checksum match coot- > download/curlew_find_atom_overlap_baddies.py 38143 vs 5715 My bad. Sorry. Somehow I forgot to update the checksum when I updated the file. It should work now. Please try again. In case there are issues please get in touch again. B > I am running wincoot 0.9.4.1 EL. > > Many thanks for all the effort you put in. > > Br, Georg. > > # > ### > > To unsubscribe from the COOT list, click the following link: > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jis > cmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard. > Lohkamp%40KI.SE%7Cae9748ef3f02424539b008d935060d90%7Cbff7eef1cf4 > b4f32be3da1dda043c05d%7C0%7C0%7C637599123135394740%7CUnknown > %7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haW > wiLCJXVCI6Mn0%3D%7C3000&sdata=iSv3HLcYXFHjJ5jWCMR%2FQI20RE > 0ZSTxFPtWBIHFeGF4%3D&reserved=0 > > This message was issued to members of > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2FCOOT&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7 > Cae9748ef3f02424539b008d935060d90%7Cbff7eef1cf4b4f32be3da1dda043 > c05d%7C0%7C0%7C637599123135394740%7CUnknown%7CTWFpbGZsb3d8 > eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D > %7C3000&sdata=ssvyHY4sSOVa1rxvHEU7elJrGfDVeuG1QYNGSOCqQ1g% > 3D&reserved=0, a mailing list hosted by > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jisc > mail.ac.uk%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cae97 > 48ef3f02424539b008d935060d90%7Cbff7eef1cf4b4f32be3da1dda043c05d% > 7C0%7C0%7C637599123135394740%7CUnknown%7CTWFpbGZsb3d8eyJWIj > oiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C30 > 00&sdata=m%2BDBuQKWDfFkEea%2B5Su7N%2BCiCIx6RFb8XrnqvnmJW > yk%3D&reserved=0, terms & conditions are available at > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jis > cmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7CBernhard.Lohk > amp%40KI.SE%7Cae9748ef3f02424539b008d935060d90%7Cbff7eef1cf4b4f3 > 2be3da1dda043c05d%7C0%7C0%7C637599123135404732%7CUnknown%7C > TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C3000&sdata=MHACVUb8%2Beqw4PRXJuQYDxxudN49 > 5sKyuMrdmzWArm0%3D&reserved=0 *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Release 0.9.4.1
WinCoot 0.9.4.1 is available now: http://bernhardcl.github.io/coot/ Should be part of CCP4 soon too. Apparently stereo works again (I cant test this myself but was told it does...). Stay safe! Bernhard On 04/02/2021 09:15, Bernhard Lohkamp wrote: Dear Erwin, indeed. It is ready but I will need to make some CCP4 specific adjustments. It should be ready in the next day(s). It will be available from: http://bernhardcl.github.io/coot/ ... and hopefully soon from CCP4 as well. B On 04/02/2021 08:37, Paul Emsley wrote: Dear Erwin, Bernhard will announce the new WinCoot release when he has done it. Paul. On 04/02/2021 07:34, Erwin Pannecoucke wrote: Dear Paul, Could you (again, unfortunately) point us towards the location of the Windows installer? To unsubscribe from the COOT list, click the following link: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cd50e0248ac5f4cac58c408d8c8e510cd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480233739970801%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=uOxbQfHtV3kwPN5yOa9uNW5wjwDQLw0BOHviuv5CW68%3D&reserved=0 This message was issued to members of https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCOOT&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cd50e0248ac5f4cac58c408d8c8e510cd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480233739970801%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=LJfZ1StOmnZ61%2FF7Ae79LACgb3plmJdDZpd1iO7t0fs%3D&reserved=0, a mailing list hosted by https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cd50e0248ac5f4cac58c408d8c8e510cd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480233739970801%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=3ssXSMdBJRZNHXgyILMCWjchySwSAG297ppN423BPPs%3D&reserved=0, terms & conditions are available at https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cd50e0248ac5f4cac58c408d8c8e510cd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480233739970801%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=tkXJI4E18eAuppV23%2FrEt2crFgfiFTOV7in%2BoOB1BR8%3D&reserved=0 -- ******* Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fki.se%2Fmedarbetare%2Fintegritetsskyddspolicy&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cd50e0248ac5f4cac58c408d8c8e510cd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480233739970801%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=com3tS%2Bl%2FDJNs6%2BUhT6sFIgyUNZXbRkc482k10jwWdg%3D&reserved=0>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cd50e0248ac5f4cac58c408d8c8e510cd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480233739980790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=GgG%2F%2B0MjDPXJ4iL0Iy%2BUo8z8u0akuyhSAYwBnwc3n%2BY%3D&reserved=0 This message was issued to members of https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCOOT&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cd50e0248ac5f4cac58c408d8c8e510cd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480233739980790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=DkMDKMvsifsr%2F%2FGYzF5g%2Bec2V6n5vCkc7kzhN6uU%2F%2FY%3D&reserved=0, a mailing list hosted by https://eur01.safelinks.protection.outlook.com/?url=http%3A%2
Re: [COOT] Release 0.9.4.1
Dear Erwin, indeed. It is ready but I will need to make some CCP4 specific adjustments. It should be ready in the next day(s). It will be available from: http://bernhardcl.github.io/coot/ ... and hopefully soon from CCP4 as well. B On 04/02/2021 08:37, Paul Emsley wrote: Dear Erwin, Bernhard will announce the new WinCoot release when he has done it. Paul. On 04/02/2021 07:34, Erwin Pannecoucke wrote: Dear Paul, Could you (again, unfortunately) point us towards the location of the Windows installer? To unsubscribe from the COOT list, click the following link: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C5fd14f690ea941a6dfaa08d8c8dfcb27%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480210949810300%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=AmpMNkdbu2dF41OUa44gWbtBk6Jr0%2Br3l%2FDxh6Mwfg4%3D&reserved=0 This message was issued to members of https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCOOT&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C5fd14f690ea941a6dfaa08d8c8dfcb27%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480210949810300%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=oEec7SATgkGQRHb5Zg7Xde%2BzZX3HBWUvPkUuWC4IpXo%3D&reserved=0, a mailing list hosted by https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C5fd14f690ea941a6dfaa08d8c8dfcb27%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480210949820300%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CLEvtCdOtBg8zshzj%2BltbFOpysJR2xUMPuiwDkbXCFY%3D&reserved=0, terms & conditions are available at https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C5fd14f690ea941a6dfaa08d8c8dfcb27%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637480210949820300%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=UDI%2FeCxlboSMmrGVVWx511YDiV22bNBHYBgIrAk%2BtIM%3D&reserved=0 -- ******* Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Keybindings to change contour map?
http://w <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.york.ac.uk%2Fdocs%2Fdisclaimer%2Femail.htm&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C83df52bab9fc4c58754008d8a12f35ed%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637436572160236904%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=n7ChptypD2Pojg31ksJ1dcKOgnnC95QKJiCnpFTKFwI%3D&reserved=0>ww.york.ac.uk/docs/disclaimer/email.htm <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.york.ac.uk%2Fdocs%2Fdisclaimer%2Femail.htm&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C83df52bab9fc4c58754008d8a12f35ed%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637436572160236904%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=n7ChptypD2Pojg31ksJ1dcKOgnnC95QKJiCnpFTKFwI%3D&reserved=0> To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C83df52bab9fc4c58754008d8a12f35ed%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637436572160246906%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=HMAv%2F4MEcl9bho4AfuNrW35o4votwYYMBldCLkAZ5qk%3D&reserved=0> -- *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] [EXT] Re: Real space refinement of ds RNA
On 10/12/2020 05:05, manikandank wrote: On 2020-12-09 18:26, Paul Emsley wrote: On 09/12/2020 12:44, manikandank wrote: I would like to build a model of both single and double strand RNA into a 3A cryoEM map. In this regard, i would like to know the options in coot to do the following, How to do real space refinement of ds RNA (different kind of RNA secondary structures) , both strand together to the fit the map (bases come from different regions of RNA primary sequence) ? Have you watched the "Coot with RNA" video? https://www.youtube.com/watch?v=Zzim3SXnDSk <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DZzim3SXnDSk&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Ca2d4aa1fe7af4ffec8cc08d89cc0eebd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637431700167552678%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=A6EA9mPWfMucH2HCfblwotn0ekQ15SHdOr2l3GuJBMY%3D&reserved=0> See the comments. Paul. Hi Paul, Thank you very much for the quick response. I have now seen the video and the comments. As i have very long RNA (~2000 bases from ribosomal rna) that makes different secondary structures, i donot have often the ideal situation show in the video. First, i do not have the ProSMART menu for 'Generate Restraint' and i use wincoot 0.9.2 EL (please see the attachment). How to generate the restraint for a selected set of bases as they come from different chain? for ex. strand1: 10 to 25 from chain A and strand2: 40-55 chain B . I would like to restraint part of a ds strand or stem loop and fit only the selection using real space refine option. thank you very much for your suggestions There seems to be some bug (and some features missing) in the WinCoot version. Sorry about this. I will fix this for 0.9.3. In the meantime you can download the updated the extension file and replace the existing directory (yourwincoot/lib/python2.7/site-packages/coot/): https://raw.githubusercontent.com/bernhardcl/coot/refinement64/python/extensions.py Then you need to launch the module "Restraints". I will update this for 0.9.3. HTH, B with kind regards Mani. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Ca2d4aa1fe7af4ffec8cc08d89cc0eebd%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637431700167562630%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=rEi4aH%2F42BNhdjZVjxpy0Q7OzVvdFiNRg1b9GnvqlRk%3D&reserved=0> -- *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] WSL2 installation
et-colour-map-rotation-for-map 14.00) (set-active-map-drag-flag 1) (set-idle-function-rotate-angle 1.00) (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) WARNING: couldn't write to state file 0-coot-history.py WARNING: couldn't write to state file 0-coot-history.scm image.png To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7Cb4c1905213994845127908d88fb9c780%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637417375800455223%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=oxB09RBxf6AK0F8Xq0trRWBXWZlIkglkX09CpMAyIlU%3D&reserved=0> -- *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] WinCoot and Extension menu
Hi Marko, On 27/10/2020 12:50, Marko Hyvonen wrote: Hello Cooters, I was just installing latest WinCoot 0.9 beta2 and could not see the extensions menu. Is it missing from this version or did I do something wrong? Most extensions are distributed elsewhere in the menus now. Usually in places where they are more appropriate. Question has been asked (not specifically WinCoot though) before: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg49364.html And while on the topic of WinCoot, any idea why I often get a very long "program not responding" wait when opening a a new window, such as when opening new coordinates. Possibly just issue with my laptop when using external monitor, but any suggestions welcome. I can try to look into this but tricky since is not something I see. Previously there has been some issue depending on which compiler flags I have been using but this should have been resolved and was only an issue for startup not for other windows opening. Cheers and stay safe, B cheers, Marko -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk +44 (0)1223 766 044 @HyvonenGroup http://hyvonen.bioc.cam.ac.uk To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=04%7C01%7CBernhard.Lohkamp%40KI.SE%7C3dc7202db0b4471842bb08d87a703b5c%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637393970423592939%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=14Wv9f6xhSoLHOin7oMB%2BmyQwD4VKSF%2BZZFXOETgbGQ%3D&reserved=0> -- ******* Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] COOT on Windows using WSL2
e at https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=02%7C01%7CBernhard.Lohkamp%40KI.SE%7Cdad693385b5c49025f8508d84d9c7e94%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637344682319435870&sdata=vREOBd4xXxl9f0KZPFsLk1Gdo%2BRMMm5ykSpqidEAqi4%3D&reserved=0 -- *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] WinCoot & NVIDIA 3D Vision
Dear Shintaro, it seems you have tried the usual (see link below). You may try disable (uninstall) some XBOX features (GamesDVR). This was suggested by others: https://bernhardcl.github.io/coot/wincoot-faq.html#mozTocId906434 I am not sure if the 64bit version helps (*). Seems sadly usually not (still working on this one) but maybe in connection with the XBOX setting!? B (*) https://bernhardcl.github.io/coot/wincoot-releases.html On 31/08/2020 13:12, Shintaro Aibara wrote: Dear Coot-ers! With the observation that 3D vision works in a Windows environment without the need for a Quadro card, I was trying out all the usual 3D visualization programs to see if they could display a stereo image. I could get Chimera and Pymol to display a quad-buffered stereoscopic image using my current system in fullscreen mode (Windowed mode does not work, if you have any suggestions for this, that would be also great to hear) Graphics card: NVIDIA RTX 2070 NVIDIA driver: 425.31 (3D vision archive version) Windows Version: 10.0.17763 Build 17763 However WinCoot (0.8.9.2-pre EL rev. 7835) does not seem to want to do it. When I enable hardware stereo mode, I can see that the hardware indeed does engage 3D mode (the IR emitter shows green light, and my monitor gets darker), however there model/map that was displayed just disappears and only a black screen is in view. Going to full-screen mode does not change anything, and disabling the stereo mode brings the model/map back (in 2D). Opening a new model/map also shows nothing. I have already disabled Triple buffering, Threaded optimization, and Vsync in the NVIDIA control panel. I should note that in my version the "enable stereo" option is not present. However as Chimera and Pymol seem to be alright with it, I am inclined to think maybe something can be done to make it work in Coot too. Any suggestions would be much appreciated Best wishes Shintaro To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=02%7C01%7CBernhard.Lohkamp%40KI.SE%7Ccd941329ffb14cd718c508d84d9ec629%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637344692032197828&sdata=NCzC1gyDScY4WjoeGZKxG0y%2F3lYyDj07PWVDYqLonr8%3D&reserved=0> -- ******* Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Some issues about the installation of wincoot
On 01/08/2020 15:31, 程晨 wrote: To whom*it may concern,* The operating system of my PC is Win10. I tried to install coot but it always shows unsuccessful. I want to know which version of coot is suitable for Win10? WinCoot should work on Win10. If it doesnt then get in touch with some more information please. Note 1: I have seen errors upon installation, however, in all cases I vitnessed these can be ignored and WinCoot works fine. Note 2: WinCoot 0.9 doesnt come with an installer (yet), so you will have to make sure you have a dictionary and start from the correct bat file. B To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=02%7C01%7CBernhard.Lohkamp%40KI.SE%7C883c9f1028704d32671808d83621b80e%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637318866204781483&sdata=lmf4Dvv2nodKLxXZ0U%2BEtzjrRtN2M0NcqFqnhh7ZWcM%3D&reserved=0> -- ******* Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] WinCoot 0.9 beta2 - refinement setup failure
Hello, On 25/06/2020 18:05, Aleksandr Sverzhinsky wrote: Hello, I downloaded the WinCoot 0.9 beta2 folder to my C:\ directory as was done using the WinCoot 0.8.9.3 installer. Since there isn't an installer for this version, I don't have the shortcuts automatically created, but I found the wincoot64.bat file. Is this the correct way to install WinCoot 0.9? Yes and no. WinCoot 0.9 beta (2) is not an installer but just a zip archive, so it will just unpack all (WinCoot) files. You run it by running the wincoot64.bat file (or a link to it - or edit the old links to point to this new bat file). Now when I try real space refinement I get the error "Warning: Refinement setup failure. Failed to find restraints for: ALA"; this happens for all residues. Any help is appreciated. This can be expected especially if you dont have CCP4 installed. The current archive (!) ships without the dictionary so you will need to get this form elsewhere (old Coot, Phenix, CCP4). Maybe I should add some more instructions on this and/or add the dictionary... Maybe for 0.9 (still likely to be without an installer though). Too many covid-19 issues to deal with first though... HTH!? Stay safe, B -- *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Wincoot 0.9
There are quite a few bugs in the current 0.9 beta release. I am in the process of updating it. I will post some more instructions on how to "install" and run it then too. Sorry about the delay - blame the corona virus... and MS... and Paul ;-) B On 25/04/2020 01:56, Daniel Asarnow wrote: My apologies for the confusion! It was posted by Bernhard /Lohkamp/ 12 days ago: https://github.com/bernhardcl/coot/releases <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbernhardcl%2Fcoot%2Freleases&data=02%7C01%7CBernhard.Lohkamp%40KI.SE%7Cb227cc1373714a6d030008d7e8ab2f8a%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637233694250652773&sdata=bBZKCv6781ssG5AvigFExg0kzmyzTWKwoKDJxF0oA0s%3D&reserved=0> Best, -da On Fri, Apr 24, 2020 at 4:49 PM Bernhard Rupp mailto:hofkristall...@gmail.com>> wrote: If you could reveal where you got wincoot 0.9.x from, one could perhaps assist… See no message to this effect maybe got lost… __ __ Cheers, BR __ __ *From:* Mailing list for users of COOT Crystallographic Software mailto:COOT@JISCMAIL.AC.UK>> *On Behalf Of *Daniel Asarnow *Sent:* Friday, April 24, 2020 14:48 *To:* COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK> *Subject:* Wincoot 0.9 __ __ Hi all, Bernhard kindly posted a Wincoot build based on 0.9 recently. I was wondering if anyone was using it, and what is the correct way to use the package (with just /bin, /include, /lib provided). __ __ Thanks & best, -da __ __ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCOOT%26A%3D1&data=02%7C01%7CBernhard.Lohkamp%40KI.SE%7Cb227cc1373714a6d030008d7e8ab2f8a%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637233694250662769&sdata=q9chryiHfYg4jEmwdTSkSUKwPZR6puKhTzCkkxtr57E%3D&reserved=0> To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCOOT%26A%3D1&data=02%7C01%7CBernhard.Lohkamp%40KI.SE%7Cb227cc1373714a6d030008d7e8ab2f8a%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637233694250662769&sdata=q9chryiHfYg4jEmwdTSkSUKwPZR6puKhTzCkkxtr57E%3D&reserved=0> -- *** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
Re: [COOT] WinCoot-0.8.9.3-pre - comma instead of dot in coordinates
Hi Dorota, On 01/08/2019 10:54, Dorota Kubacka wrote: > Hi, > > Just to let you know that WinCoot-0.8.9.3-pre writes down coordinates with > comma not with dot. Mmmh. I guess this is rather a locale problem (*) since it works fine here. Make sure you have @set LANG=en in your wincoot.bat file. This should do the trick. Maybe it got lost somehow. There are some more convoluted ways to fix this (besides globally setting the Decimal symbol on your computer). Please get in touch if above doesnt fix it. B (*) your computer is set to use ',' (comma) instead of '.' (dot) as decimal separator. > Best > Dorota > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 > -- ******* Dr. Bernhard Lohkamp | Associate Professor/Docent Div. Molecular Structural Biology/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487695 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
Re: [COOT] Problem loading PDBx/mmCIF files for EM in Coot
Hi John, not sure if we have to discuss this on list (we can continue private after this if you wish). Coot, better mmdb, picks up _atom_site.auth_seq_id in the first instance as residue number. So, here we have 17 twice. Of course we have an insertion code but in the "strict" setting of Coot we do not allow this at the moment and warn of duplicated residues (see FAQ). I am not sure if this has ever been an issue with cif files, certainly for pdb files therefore the pedantry at the moment. HTH, B On 13/12/2018 10:05, John Berrisford wrote: Hi Andrea / Bernard Can you provide a more detailed report of the issue with these entries? i.e. which residue numbers are duplicated. Looking at 5lza are these the lines which are causing problems? ATOM 52209 P P . C V 22 17 ? 159.390 157.935 201.808 1.00 179.95 ? 17 C v P 1 ATOM 52210 O OP1 . C V 22 17 ? 160.558 157.192 201.304 1.00 163.34 ? 17 C v OP1 1 ATOM 52211 O OP2 . C V 22 17 ? 159.494 158.645 203.105 1.00 179.22 ? 17 C v OP2 1 ATOM 52212 O "O5'" . C V 22 17 ? 158.977 158.995 200.693 1.00 174.80 ? 17 C v "O5'" 1 ATOM 52213 C "C5'" . C V 22 17 ? 159.798 159.197 199.552 1.00 185.33 ? 17 C v "C5'" 1 ATOM 52214 C "C4'" . C V 22 17 ? 159.648 160.575 198.959 1.00 196.84 ? 17 C v "C4'" 1 ATOM 52215 O "O4'" . C V 22 17 ? 158.451 160.646 198.143 1.00 206.86 ? 17 C v "O4'" 1 ATOM 52216 C "C3'" . C V 22 17 ? 159.504 161.733 199.935 1.00 202.96 ? 17 C v "C3'" 1 ATOM 52217 O "O3'" . C V 22 17 ? 160.757 162.140 200.486 1.00 209.64 ? 17 C v "O3'" 1 ATOM 52218 C "C2'" . C V 22 17 ? 158.838 162.799 199.077 1.00 196.77 ? 17 C v "C2'" 1 ATOM 52219 O "O2'" . C V 22 17 ? 159.799 163.469 198.274 1.00 196.27 ? 17 C v "O2'" 1 ATOM 52220 C "C1'" . C V 22 17 ? 157.939 161.961 198.163 1.00 212.57 ? 17 C v "C1'" 1 ATOM 52221 N N1. C V 22 17 ? 156.526 161.937 198.609 1.00 203.47 ? 17 C v N11 ATOM 5 C C2. C V 22 17 ? 155.711 163.078 198.470 1.00 201.22 ? 17 C v C21 ATOM 52223 O O2. C V 22 17 ? 156.148 164.134 197.982 1.00 180.18 ? 17 C v O21 ATOM 52224 N N3. C V 22 17 ? 154.425 163.025 198.884 1.00 183.62 ? 17 C v N31 ATOM 52225 C C4. C V 22 17 ? 153.931 161.906 199.405 1.00 174.69 ? 17 C v C41 ATOM 52226 N N4. C V 22 17 ? 152.656 161.902 199.796 1.00 172.63 ? 17 C v N41 ATOM 52227 C C5. C V 22 17 ? 154.726 160.737 199.532 1.00 163.94 ? 17 C v C51 ATOM 52228 C C6. C V 22 17 ? 156.004 160.794 199.140 1.00 190.30 ? 17 C v C61 ATOM 52229 P P . U V 22 18 A 160.906 163.453 201.425 1.00 213.16 ? 17 U v P 1 ATOM 52230 O OP1 . U V 22 18 A 160.755 164.734 200.686 1.00 209.40 ? 17 U v OP1 1 ATOM 52231 O OP2 . U V 22 18 A 162.184 163.267 202.150 1.00 212.78 ? 17 U v OP2 1 ATOM 52232 O "O5'" . U V 22 18 A 159.749 163.307 202.511 1.00 198.92 ? 17 U v "O5'" 1 ATOM 52233 C "C5'" . U V 22 18 A 159.897 162.389 203.589 1.00 176.83 ? 17 U v "C5'" 1 ATOM 52234 C "C4'" . U V 22 18 A 159.052 162.761 204.784 1.00 178.19 ? 17 U v "C4'" 1 ATOM 52235 O "O4'" . U V 22 18 A 157.733 163.175 204.336 1.00 176.36 ? 17 U v "O4'" 1 ATOM 52236 C "C3'" . U V 22 18 A 158.780 161.634 205.775 1.00 201.36 ? 17 U v "C3'" 1 ATOM 52237 O "O3'" . U V 22 18 A 159.838 161.426 206.700 1.00 203.24 ? 17 U v "O3'" 1 ATOM 52238 C "C2'" . U V 22 18 A 157.454 162.045 206.411 1.00 198.91 ? 17 U v "C2'" 1 ATOM 52239 O "O2'" . U V 22 18 A 157.661 163.011 207.432 1.00 188.97 ? 17 U v "O2'" 1 ATOM 52240 C "C1'" . U V 22 18 A 156.743 162.726 205.237 1.00 181.84 ? 17 U v "C1'" 1 ATOM 52241 N N1. U V 22 18 A 155.810 161.824 204.513 1.00 214.12 ? 17 U v N11 ATOM 52242 C C2. U V 22 18 A 154.489 161.753 204.929 1.00 205.79 ? 17 U v C21 ATOM 52243 O O2. U V 22 18 A 154.048 162.398 205.865 1.00 184.59 ? 17 U v O21 ATOM 52244 N N3. U V 22 18 A 153.688 160.903 204.200 1.00 201.99 ? 17 U v N31 ATOM 52245 C C4. U V 22 18 A 154.063 160.125 203.123 1.00 187.09 ? 17
Re: [COOT] Problem loading PDBx/mmCIF files for EM in Coot
Hi Andrea, as Huw pointed out there are duplicated sequence numbers which Coot (mmdb) does not allow. The work around is the command: python: allow_duplicate_sequence_numbers() guile: (allow-duplicate-sequencenumbers) and have a look at the FAQ (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/docs/coot-faq.html#How-do-I-read-a-coordinates-file-with-duplicate-residue-numbers_003f) HTH, Bernhard On 13/12/2018 09:48, Andrea Thorn wrote: Thank you for pointing this out. The file came from PDBe - and I have a few dozens where this happens. So just fixing the CIF file in my download folder does not help the underlying problem. I basically want to find out if I did something wrong - or if I need to ask the PDB people to fix the PDBx/mmCIF files - or if it's Coot doing something it is not supposed to (bug report)... Best wishes Andrea. On 11/12/2018 17:35, Huw Jenkins wrote: On 11 Dec 2018, at 15:32, Andrea Thorn wrote: Can someone point out if the files for these entries are broken somehow, or if there is a bug in Coot? 5lza for me: There was an error reading 5lza.cif. ERROR 42 READ: Duplicate sequence number and insertion code. CIF ITEM: loop _atom_site.B_iso_or_equiv_esd row 52227 data [NULL] There was a coordinates read error looks like duplicate atom_site.auth_seq_id Huw To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 -- *** Dr. Bernhard Lohkamp | Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-17177 Stockholm Sweden +46 8 52487695 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
Re: [COOT] Coot usage
Dear Katja, there is no licence payment needed (although feel welcome to do so ;-) ). Please see "So I can just download it and use it, no questions asked?" and "Even if I'm part of a Big Pharma?" on https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ along with the licencing info... B On 26/11/2018 07:45, Galesa, Katja wrote: Dear Sirs, Is the licence for Coot payable in Pharmaceutical industry (Novartis)? Sorry to bother. I worked before at university, I used only basic and I enjoyed it. With best wishes, Katja Galeša To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 -- ******* Dr. Bernhard Lohkamp | Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-17177 Stockholm Sweden +46 8 52487695 bernhard.lohk...@ki.se | ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
Re: [COOT] set Coot download folder path in preferences
This is currently not possible. Maybe something for the wishlist... B On 19/03/2018 18:34, Xiao Lei wrote: Dear Coot users, I would like to change the default Coot download folder path (let's say after fetch a pdb, Coot saved the pdb in the default download folder). I looked into the Edit--> Preferences in Coot and I could not find a place to change the PATH. How could I find this option in Coot? Thanks ahead. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] COOT 0.89 crashes when Hardware-Stereo (Quad-buffered, NVIDIA 3Dvision2) is enabled
Have you tried running WinCoot in administrator mode? I had a report where this was required to run WinCoot in general. So not sure if this helps with the stereo. Unfortunately I dont have a Windows 10 machine with quad buffered stereo so it is difficult for me to test this issue. Another issue may be 32 vs 64 bit. I suspect that the issue lies there that somehow a 32 bit application (WinCoot) is not fully supported by the (3D) drivers. I shall make a 64 but version (*) B (*) it will come... Too much teaching currently On 19/03/2018 14:13, Pedro Matias wrote: Hi Christoph et al., We have had the same problem on several machines with Windows 10. I suspect this is caused by a recent update, to either Windows or the NVIDIA drivers. Like you, we have no problems with PyMOL, only COOT. We have tried several fixes and none have worked. Best regards, Pedro Às 12:48 de 19/03/2018, Christoph Parthier escreveu: I double-checked all three points. They were all set correctly. WinCoot crashes anyway as described... What pointed me to suspect WInCoot to be the culprit is the fact that NVIDIA quad-buffered stereo works in PyMOL on the same machine using these settings (also uses OpenGL). Christoph -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
[COOT] WinCoot 0.8.9 release
We are pleased to announce the availability of a Windows version of Coot-0.8.9. Binaries are available from WinCoot's new home: http://bernhardcl.github.io/coot/ and from Paul's binary site: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ as well as CCP4 in due time. Regards, Bernhard -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] WinCoot crashing when manipulating .mtz
On 07/12/2017 20:27, Paul Emsley wrote: On 07/12/2017 16:19, Thomas Laughlin wrote: I've been trying to build into an EM-density map using WinCoot and the program keeps crashing when manipulating the model or density. Using a .mrc seems to work fine, it is only when I use a .mtz that the program crashes upon manipulating objects. I'd prefer to use the .mtz for the ability to "on-the-fly" filter/sharpen. The computer I'm using has a dedicated nvidia quadro K2200, 64GB ram, and a Xeon E5-2630 v4. I was wondering is the size of the .mtz was overwhelming and if a solution would be to somehow segment it into more manageable pieces. I suspect that is what is happening. Yes, you can create map fragments based around the origin. WinCoot is 32bit and runs out of memory (2GB limit I think). Well, it uses large-adress-aware so can go up to 4GB. Having said this, this is not equal the size of the map and its still possibly your problem (*). I have been able to load 1.3GB map files but have no experience with large/EM mtz. Maybe you can provide it to me (confidentially) and I can test/debug. How can I check if the system resources are limiting WinCoot or if the crashes are for some other reason. What does coot say when it crashes? that will help in the diagnosis. Certainly ;-) Bernhard (*) there will be a real 64 bit at some point... -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Coot crashes on Windows 10
Dear Pedro, sorry, I didnt update the FAQ as I expected to have done. Please move everything from libexec to bin. That should do the trick. Bernhard On 20/11/2017 11:30, Pedro Matias wrote: Dear Bernhard, I don't use stereo in Windows. The graphics card is a GTX 1050. Which item in the list are you specifically referring to? Also, this happened only recently, possibly caused by a newer NVIDIA driver. Best regards, Pedro Às 10:13 de 20/11/2017, Bernhard Lohkamp escreveu: Dear Pedro, probably related to: http://bernhardcl.github.io/coot/wincoot-faq.html#mozTocId910462 please try this. It should solve your problem. Otherwise please get back to me. Bernhard On 20/11/2017 10:43, Pedro Matias wrote: Dear all, Very recently, COOT took to crashing on startup on my W10 desktop (see image below). Looking at the Windows Event Log, the culprit seems to be the 32-bit NVIDIA OpenGL driver: C:\WINDOWS\SYSTEM32\nvoglv32.DLL Anyone else had this problem? I noticed there's been no new WinCoot version for quite some time. Thanks in advance, Pedro -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email :mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8 -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Coot crashes on Windows 10
Dear Pedro, probably related to: http://bernhardcl.github.io/coot/wincoot-faq.html#mozTocId910462 please try this. It should solve your problem. Otherwise please get back to me. Bernhard On 20/11/2017 10:43, Pedro Matias wrote: Dear all, Very recently, COOT took to crashing on startup on my W10 desktop (see image below). Looking at the Windows Event Log, the culprit seems to be the 32-bit NVIDIA OpenGL driver: C:\WINDOWS\SYSTEM32\nvoglv32.DLL Anyone else had this problem? I noticed there's been no new WinCoot version for quite some time. Thanks in advance, Pedro -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email :mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8 -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Ramachandran plot - atom-selection
Adding on a bit... On 23/10/2017 12:45, Karsten Dreifus wrote: Hi Paul, I am using the dev version coot 0.8.9-pre (revision 6956). Trying to use the Ramachandran plot atom-selection function. I used "/1/A/10-20" But does not filter. Any working examples? No. Its not functional. It is a placeholder and was meant to be filled but there is a new Ramachandran coming where it works ;-) In Paul's hands when... until then the current widget should probably be removed. B Many thanks, Karsten (from http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Ball-and-Stick-Representation ) -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] 3D annotation
On 06/05/2017 13:53, Luca Pellegrini wrote: I have created a 3D annotation with Extension -> Representations -> 3D Annotations -> Annotate position How do I delete it? Using: remove_text(int text_handle) There is currently no "nice" interface to this, but you can use attached python script (I would add commented lines into extensions.py as well - I will do for the next releases...). Bernhard def remove_annotation(rad=1.5) args = rotation_centre() + [rad] handle = text_index_near_position(*args) if handle > -1: remove_text(handle) remove_annotation() # add_simple_coot_menu_menuitem( # submenu, # "Remove annotation here...", # lambda func: remove_annotation()) -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Ligand definition
On 04/05/2017 13:30, Jan Stransky wrote: Hi, how does coot define what is ligand, namely for go_to_ligand()? Is it possible to tweak the definition? It is defined by the HETATM record in the pdb file. I have some small ligands in structure (acetate, sulphate, ...) and those are not recognised as ligand. I can imagine, it can be handy to skip those, when bigger more interesting things are present, but when they are only ligands in structure... I guess you will have to make sure that the ligand are HETATMs in the pdb file. You can use of course Coot to do so: Extensions-> Modelling-> Assign (Force) HETATMs for this Residue HTH, B -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] D shortcut in 0.8.8
Currently (newly) "D" is bound to "Display only Active" (*). This is hardcoded and hence cannot be overridden by a scripted key-board short-cut. The easiest is to change the letter from "D" to e.g. "F" (not to far away on the keyboard and not taken) in he templatekeybindings file (x). HTH, Bernhard (*) This should be mentioned in the keybindings list but isnt so far. (x) Usually in $HOME/.coot-preferences (on Windows in yourwincootinstalldirectory\.coot-preferences) On 06/04/2017 18:40, Jan Abendroth wrote: Thanks, Scott, something is odd. I installed 6699, ubuntu 14.04 and D is missing again. Btw. I don't think D removes anything currently, it hides molecules. Cheers, Jan On Thu, Apr 6, 2017 at 7:41 AM, Lovell, Scott W mailto:swlov...@ku.edu>> wrote: Hi Jan, __ __ I had also noticed this for the 0.8.8 release. As I recall, “D” would not delete water atoms but would delete other atoms that I was centered on. However, after I installed one of the subsequent nightly builds (6674) this function seems to be working fine. __ __ Thanks, Scott __ __ __ __ *From:*Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK>] *On Behalf Of *Jan Abendroth *Sent:* Wednesday, April 05, 2017 8:53 PM *To:* COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK> *Subject:* D shortcut in 0.8.8 __ __ Hi all, with version 0.8.8 the D key binding -delete this water- has disappeared. See below. D now seems change which molecules are displayed. Has this function been renamed? It was very handy. __ __ Cheers, Jan __ __ from our .coot file: (add-key-binding "Delete this water" "D" (lambda () (if (is-solvent-chain? (car (active-residue)) (cadr (active-residue))) (apply delete-atom (active-residue) __ __ -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com <http://Jan.Abendroth_at_gmail.com> work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com <http://www.emeraldbiostructures.com> -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com <http://Jan.Abendroth_at_gmail.com> work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487695 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Mutate to UNK?
For new amino acids you can use:
set_add_terminal_residue_default_residue_type("UNK")
Then you get an UNK (no CB) instead of ALA.
As for mutation, you have to go via ALA and then rename it.
Alternatively you can append UNK to your standard-residues.pdb (found in
$COOT_PREFIX/share/coot/). Then you can use UNK in "mutate" functions. I
(*) am reluctant to add it to the amino acids for all since the PDB
(nowadays) says
(http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_chem_comp.three_letter_code.html):
For ambiguous polymer components three-letter code should be given as 'UNK'.
So UNK is not only for (unknown) amino acids any more...
B
(*) Not sure what Paul thinks
On 27/06/2015 19:02, Ethan Merritt wrote:
On Saturday, 27 June 2015 04:39:56 PM Clarke, Oliver wrote:
I would still ultimately favor making it a standard residue with three letter
code UNK and single letter code X - it allows for easy specification of
ambiguity, and it is the PDB-sanctioned way of representing an amino acid of
unknown identity.
I would also suggest being able to set this as the default type for new
residues - it allows easy recognition of amino acids that are as yet
unassigned, and avoids confusion with alanine.
I like that idea a lot.
Ethan
Cheers,
Oliver.
--
*******
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Associate Professor/Docent
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
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S-17177 Stockholm
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phone: (+46) 08-52487651
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Re: [COOT] Mutate to UNK?
How about using: set_residue_name(int imol, const char *chain_id, int res_no, const char *ins_code, const char *new_residue_name) B On 26/06/2015 18:36, Oliver Clarke wrote: Hi all, Would it be possible to add "UNK" to the list of standard residues one can mutate to? Currently mutate doesn't seem to work using "UNK" as the target res type, and I would like to add it to a function for mutating a residue range to poly-UNK. This is useful where one has a structure containing regions that have assignable sequence, and regions where the sequence register is unclear, so as to differentiate the two. Cheers, Oliver. -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus
Re: [COOT] Override to accept RSR before convergence?
Hi Oliver, at the moment accepting the refinement prematurely using "enter" is only possible when the accept/reject dialog is active (hence the observed behaviour). What you can do is, make you own toolbutton. This is easily done using the toolbutton assistant "Add a user-defined Button" (although I guess you know how to do it from scratch) and define a button which calls: accept_regularizement() Then you can press the button and accept the refinement whenever you like. HTH B On 09/06/2015 23:31, Oliver Clarke wrote: Hi all, Would it be possible to change the behaviour of coot real space refinement such that I can accept the results of refinement regardless of whether Coot thinks the refinement has converged or not? Witness the following example of sphere refinement: https://www.dropbox.com/s/exza8yl27s8g5fu/coot_slow_refine.mov?dl=0 This is not the most dramatic example, but even in this case, the refinement has more or less converged to my satisfaction after 20 or 30s, but it is another minute before coot will pop up the little box that allows me to accept the refinement results. Now, if at that point I do a dragged refinement, Coot is perfectly happy for me to accept the results of refinement (by pressing Enter) before convergence, but not in the initial phase. In many cases it takes considerably longer than this to converge to Coot's satisfaction. I understand that this behavior might not be desirable all the time (it could easily be abused), but it would make refining large, low res structures **much** faster - perhaps Shift+Enter could allow override to accept, while Enter still results in the old behavior? Cheers, Oli. -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus
Re: [COOT] Dragged refinement fails with riding hydrogens
Hi Oliver, have you really dragged the methyl carbon far enough? I realised that it can be difficult to flip these with the hydrogens on (since these are "holding" it back). However, if you drag enough (maybe zoom out) it should work. In general it may be easier to drag one of the hydrogen (terminal atoms!) since these have less geometric restraints to go back immediately into the previous conformation. Bernhard On 27/05/2015 17:16, Oliver Clarke wrote: Hi all, dragged refinement doesn't seem to work for structures with riding hydrogens - see linked screen recording showing dragged refinement of the same structure with and without hydrogens. https://www.dropbox.com/s/15xs8ylhrx98ljk/dragged_refinement_H_bug.mov?dl=0 Would it be possible to alter this behaviour at some point such that hydrogens remain firmly attached during dragging, to remedy this? In the past I have got around this by just doing real space corrections in the absence of any hydrogens and adding them back in before every cycle of reciprocal space refinement, but this does not seem like the optimal way to be doing things. Cheers, Oliver. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] Default B-factor for new residues
This is fixed in r5695 (B-factors of side chain atoms having default B that is). Setting (refining?!) B-factors more intelligently is on the list, but requires a bit more sophistication than just adapting it from neighbouring residues (who says these are right(ish)?!). B On 16/05/2015 22:23, Oliver Clarke wrote: Also, on the same topic - the default B-factor for new atoms only seems to apply to add terminal residue... when a new sidechain is added, it defaults to a B-factor of 20. I think the same parameter should probably apply in both instances? Oliver -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] How to change directory sorting?
Hi Peter, this must be a GTK version/OS problem. Works perfectly fine for me (modern chooser). B On 19/03/2015 20:54, Peter Stogios wrote: Hi Paul, Thanks for the email. I tried both Modern and Classic and they behave the same. Within Modern view, clicking on the header to sort by name is able to sort files by name, but not directories. So I am unable to easily find the directory I want. In contrast, clicking on the header to sort by size or date modified worked fine. Peter From: Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> Date: Thursday, March 19, 2015 at 1:51 PM To: Peter Stogios mailto:p.stog...@utoronto.ca>> Cc: "COOT@JISCMAIL.AC.UK <mailto:COOT@JISCMAIL.AC.UK>" mailto:COOT@JISCMAIL.AC.UK>> Subject: Re: How to change directory sorting? On 17/03/15 14:10, Peter Stogios wrote: Hello, In Coot's directory/file open dialog window when opening any file type, the directory sorting doesn't make any sense and I cannot find what directory I need without pulling teeth. Directories are not sorted directories by "name", "date modified", "date created", or any sorting regularly utilized. Furthermore, the "Sort by Date" button doesn't apply to the directory listing, only to the file listing, so it is of no help. Can this be changed and how can this be done? Are you using Modern or Classic? Edit -> Preferences -> [General] -> File Selection Other than that it seems that thatś something of an oversight and needs to be fixed. Thanks, Paul. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] Setting MTZ resolution limits on the fly?
I think what you want is: molecule_name and make_and_draw_map_with_reso_with_refmac_params B P.S. Changing mtz resolution on the fly is currently not supported... On 18/03/2015 16:16, Oliver Clarke wrote: As an alternative solution to this query, is there any way to get the filename of a loaded map (or model) using the scripting interface? Because if that is the case I could write an extension myself to do this (just reloading another version of the mtz with different resolution limits), but I can't quite seem to find the appropriate function to grab the filename of an already loaded map. Best, Oliver. On Mon, 16 Mar 2015 17:00:04 +, Oliver Clarke wrote: Hi all, Would it be possible (or is it already possible) to set resolution limits for an mtz on the fly? I'm not sure whether this is feasible or not, but the fact that on the fly B-factor sharpening works makes me think it might be. This would be particularly handy when dealing with EM maps, where it is often desirable to look at the map filtered at say 8Å to reveal poorly ordered or very mobile domains, the position of which is lost in the noise when looking at the map with all the higher resolution terms present. Right now I just load the map several times with different resolution limits, but it would be nice to be able to do this on the fly, both for map interpretation and for fitting (One could fit domains several times using progressively higher resolution data, for example). I realize that using a positive B-factor in sharpening achieves a similar effect, but the map doesn't look nearly as good. Best, Oliver. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] Coot-Phenix boot
There was an issue with the python distributed with WinCoot. Please see: http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html#mozTocId910462 There is a new installer available which has the fix include. Hope this resolves your issue. Bernhard On 11/03/2015 21:49, Joel Tyndall wrote: Hi, I am running a windows 7 system and when I try and launch coot from phenix, Coot launches but no model or map (or phenix links in coot) can be seen. I read that this is because the Coot version is lacking python. As this is a windows install, how do I identify if the .exe has python for windows? When I launch it without Phenix I also see the error could not import coot.py Other than that Coot works well J _ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] molecule rubber banding not working in 8.1
Pressing Crtl with dragging will only move one atom. Without Crtl should drag/move everything "rubber-banded". Maybe its that. B On 11/03/2015 01:06, Kenneth Satyshur wrote: After using 7.1 for a while, it was easy to 'real space refi zone' a amino acid. Pull on it and it will drag everything else with it. On 8.1 when I try this, it just rips an atom away from the residue and does not move the whole residue. There must be a parameter that is not set right. How do I make the 'rubber banding' work again. It is not useful in its present form. thanks Kenneth A. Satyshur, M.S., Ph.D. University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] Coot- graphics issue
Hi Joel, although I dont run virtuawin (but dexpot) this may be the answer (note to self: add a comment on FAQ): https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1501&L=CCP4BB&P=R16628&1=CCP4BB&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 If this does not fix you problem please let me know and we can see if there are other solutions possible. B On 24/02/2015 21:30, Joel Tyndall wrote: Hi folks, I’ve been using Coot for several years now and its great. I have an issue where I am using multiple desktops on windows 8. The desktop software is virtuawin. When I start up Coot (0.8.1-pre(rev 5469) it works fine. When I switch desktops and then go back to the Coot desktop, the graphics window is white. Anyone seen this before? J _ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] Copy NCS residue range
Feature!? To make sure the master chain you set in the Ghost control and the one you use for copying are matching... Basically you can only change the master in the Ghost Control (or scripting), but not in the copy dialogs. B On 23/02/2015 15:14, Phil Evans wrote: In Extensions->NCS->Copy NCS Residue Range the first window asks for the Master chain, but this seems not to work. As far as I can see, you have to set the Master Chain in the Draw->NCS Ghost Control window This looks like a bug, I think Phil -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] new_molecule_by_smile_string bug
OK. This got messed up when introducing pyrogen, acedrg etc. (probably committed something which shouldnt have been...). I will clean this out. Sorry. B On 17/02/2015 17:50, Oliver Clarke wrote: Hi all, When I use the python scripting functions new_molecule_by_smiles_string or new_molecule_by_smiles_string_by_libcheck, I get an error stating that the global variable "three_letter_code" is not defined (and the molecule is not created - see first screenshot). Looking at coot_utils.py, it appears that new_molecule_by_smiles_string_by_libcheck has been defined twice, and three_letter_code referenced before definition in the second instance (see first screenshot). Cheers, Oliver. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] WinCoot: field 'Edit / Skeleton Parameters / Skeleton Radius' obscured
Thanks for pointing this out. It is fixed in revision 5503. B On 19/01/2015 16:06, Christoph Parthier wrote: Hi, This seems to be a WinCoot issue: whenever the value for the 'Skeleton Box Radius' (Menu 'Edit/Skeleton Parameters) is to be changed, the field shows the current value followed by a set of strange non-numerical characters. The input seems to be unaffected, though. Christoph -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] wincoot 8.1 - empty menus?
These are 2 different things. The screenshot is looking at the density fit (which is empty since you havent loaded anything -> no way to calculate a fit) whereas Frank was looking at the Extensions menus. These should be working for you as there are no errors in the startup. B On 14/01/2015 20:36, Anshul Bhardwaj wrote: Hello all, I am having similar empty extension sub-menus issue with recently released WinCoot-0.8.1. (snapshot is in attachment) Bernhard: I followed your suggestion of replacing coot_utils.py with revised version, nevertheless for me issue still seems to exist. It seems to be OS specific (or python path environment variable related) as new coot is running fine on my Linux boxes. I am running Windows Professional 64 bit with Service Pack 1. Frank: Is this bug resolved for you? Could you please share your Windows OS version? Let me know if it helps to provide a list of programs installed on my machine that uses python to resolve this issue. Thanks so much! Anshul Anshul Bhardwaj, PhD Faculty, Department of Biochemistry and Molecular Biology Manager, X-ray Crystallography and Molecular Interactions Sidney Kimmel Cancer Center Thomas Jefferson University 233 South 10th Street BLSB, Suite 822 Philadelphia, PA 19107 Tel: (215) 503-4587 anshul.bhard...@jefferson.edu http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/bhardwaj.html http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.htm From: Mailing list for users of COOT Crystallographic Software on behalf of Bernhard Lohkamp Sent: Monday, January 12, 2015 7:40 AM To: COOT@JISCMAIL.AC.UK Subject: Re: wincoot 8.1 - empty menus? A (crude, temporary) fix is available for this now. Please replace coot_utils.py in YOUR_WINCOOT_DIRECTORY\python27\lib\site-packages\coot\ with this one: https://coot.googlecode.com/svn/trunk/python/coot_utils.py This should do the trick. B On 09/01/2015 12:00, Frank von Delft wrote: Hi, I installed wincoot 8.1 but most of the Extensions sub-menus are empty... is it something I said? Screenshot below. Frank -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] wincoot 8.1 - empty menus?
A (crude, temporary) fix is available for this now. Please replace coot_utils.py in YOUR_WINCOOT_DIRECTORY\python27\lib\site-packages\coot\ with this one: https://coot.googlecode.com/svn/trunk/python/coot_utils.py This should do the trick. B On 09/01/2015 12:00, Frank von Delft wrote: Hi, I installed wincoot 8.1 but most of the Extensions sub-menus are empty... is it something I said? Screenshot below. Frank -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] wincoot 8.1 - empty menus?
Hi Frank, something must be wrong there. I assume some python related mishap which causes all python to fail (shouldnt of cause). I assume WinCoot somehow picks up the "wrong" python. Please send me the DOS console output from your startup (ideally starting WinCoot in the console rather than via the shortcuts). B On 09/01/2015 12:00, Frank von Delft wrote: Hi, I installed wincoot 8.1 but most of the Extensions sub-menus are empty... is it something I said? Screenshot below. Frank -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] Bugs related to insertion codes
Happy New Year indeed. we are aware that there are a few bugs with respect to loosing insertion codes. A fix I committed earlier got lost but will be available in the next pre-release... Bernhard On 03/01/2015 00:03, Dale Tronrud wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Happy New Year, I have been comparing the two PDB entries 2EWD and 4ND2 to try to figure out why the older was replaced by the latter. This task is surprising hard with Coot, but that is not my issue. When I SSM superimposed the A chain from each model a potion of the text printed to the terminal was confusing. (sorry but I can't figure out how to cut from a DOS window so I've attached a screen shot.) You will note that residue 208 matches 208 and 209 matches 209 but then 209 matches 209 again and then 210 matches 209 and then again 210 matches 209. The answer to this riddle is that on the left there really should be 209A, 209B, 210A, and 210B while on the right it should be 209 A through D and 210A and 210B. The SSM code is not writing the insertion codes to the output. A second issue becomes apparent when I open the "Go To Atom..." dialog box and select 2ewd!A|209A. All four 209 residues are properly shown in the residue table. The atom table, however shows the atoms for all four 209 residues. This table is identical when each of the 209 residues are selected. If I select 209A and double-click on the fourth CA atom I am, indeed, taken to 209D. Dale Tronrud -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlSnI7QACgkQU5C0gGfAG11ZyQCfXUIo8Jh5t9NzlUEKb42E5yrR liUAoJatGSTMU5tLZBp1DkTx7cUhgCKL =qsBa -END PGP SIGNATURE- -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] coot read-only switch
--no-guano ;-) B On 07/11/2014 11:50, Debreczeni, Judit wrote: -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: 07 November 2014 10:13 To: COOT@JISCMAIL.AC.UK Subject: [COOT] coot read-only switch Hello, does Coot have a 'read-only' command line option, i.e. so that it does not modify anything in the current directory? I often just want to look at a PDB-file and would prefer not to end up with coot-backup and all the other files. While these are not exactly what you are after, these may be of some help: 1. the backup dir can be set to be any directory, e.g. /tmp/, so that it doesn't fill the working dir with its droppings, by setting the relevant environment variable: https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Environment-Variables 2. backups can be switched off completely: https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Backup-Functions The options listed with 'coot --help' don't seem to list one of such kind. Regards, Tim -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
Re: [COOT] Display problem in coot _residue fit
Hi, as pointed out by Jan this should certainly not happen. If I understand the issue right then a LINK is created for every real space refinement. Which version of Coot are you using, which operating system, etc. I think we need some more information to fix this. BTW I assume your pdb file is free of (unwanted) LINK(R) records now (please check - maybe your refinement program created these...). Bernhard On 05/11/2014 06:16, ly wrote: Hi Jan, Thank you very much! It worked. Another problem is that the unexpected linker always formed during fit the residue to the map. Are there any parameter setting or python script using for the function of Real Space Refinement or Regularize zone to avoid this problem ? Dorothy -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
Re: [COOT] 2 bugs+1 question, OS X version
Just answering the question, not feeling qualified to comment on Mac... 3. Why does coot run .coot_preferences.py and then run .coot_preferences.scm ? Seems redundant. Should I have only one of them in the .coot-preferences folder? Yes, this is redundant but there for compatibility reasons. Although nowadays there is hardly a Coot without a Python so the scheme could go. Nevertheless, they certainly dont have to run both... B ___ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School 3040 Chemistry Building | sa...@umich.edu <mailto:sa...@umich.edu> | +1 (734) 764-3353 -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
Re: [COOT] Function for querying ramachandran probability?
Not there yet, unfortunately. On my list already... I started but got sidetracked. B On 27/08/2014 18:47, Oliver Clarke wrote: Hi all, Is there a built-in python or scheme function to return the Ramachandran probability of a given residue? I can't seem to find such a function but the data must be in there somewhere. I have written a couple of little jiffies to create copies of the active molecule colored by rotamer probability and "missing atoms" (see last two functions in linked script below - basically they assign rotamer score or missing atom factor to b-factor column and then color by B), which I find to be a useful guide during the later stages of building, and I would quite like to do the same for Ramachandran probability. I like having copies of the working molecule colored by the validation stats - it makes it easier to quickly identify problem regions comprised of residues that are nearby in space but not necessarily in sequence. I have hacked something together that sort of works, but if there was any possibility of including a proper implementation of the same (e.g. with dynamic updating of the relevant stats) in a future version of coot I think it would be a valuable feature. Script (contains a lot of junk, last two functions are the only ones relevant to this post): https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0 Cheers, Oliver. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
Re: [COOT] ccp4 QTMG
Hi, this looks odd. I am not entirely sure I follow how you produced and imported the map and what you figure shows. Anyway, the maps exported from Coot are written for one asymmetric unit which will (should) be expanded by symmetry in Coot and MG. In case you have a map not restricted to an asu this will not work (and you only see one map). I assume you are not centred on the ligand, so MG (and Coot as well) shows you the map parts in the different asus (clipped around the centre). Centred on the ligand everything should be in one place. Not necessarily a direct solution to this problem, but why dont you open you map from the mtz in MG and show (clip) only the map around the ligand. B On 19/08/2014 18:13, PC wrote: Hi, I used COOT mask map by atom selection and cut out a fragment of the map, then exported it and now I tried to open it in QTMG. It displays it as a unit cell, I want one for a presentation, how can I combine it to display one image ? Thank you, Patrick 3D Earth Screensaver Preview <http://www.inbox.com/earth> *Free 3D Earth Screensaver* Watch the Earth right on your desktop! Check it out at www.inbox.com/earth <http://www.inbox.com/earth> 3D Earth Screensaver Preview <http://www.inbox.com/earth> *Free 3D Earth Screensaver* Watch the Earth right on your desktop! Check it out at www.inbox.com/earth <http://www.inbox.com/earth> -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
Re: [COOT] Bug in python version of mutate_and_auto_fit()
Hi Oliver, thanks for the report. This is fixed in revision 5206 (must have been broken for years...). B On 18/08/2014 19:22, Oliver Clarke wrote: Hi all, The python version of mutate_and_auto_fit (used via the scripting interface) does not seem to work, where the same input works when used with the scheme version of the function. See attached screenshots showing the results of the same command applied via either schem or python to mutate Q58, chain A of 1BL8 to an arginine, as a test case. Scheme: https://www.dropbox.com/s/hs6w82x6s306j92/scheme.png Python: https://www.dropbox.com/s/yezwb2tkz3ikbrt/python.png I found this while writing a little extension to enable quick mutation of the active residue (hotkey + entering the single letter code - see https://www.dropbox.com/s/jzrjqvbk2oxj7jk/mutate_single_letter.py) - at the moment it uses simple mutate but I would rather use mutate_and_auto_fit if a refinement map is available. Best, Oliver. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com
Re: [COOT] Map selected for scrolling on Auto Open MTZ
Hi, this was due to some changes in the code when opening maps. For now I "fix" this to not make diff maps scrollable by default as before (some more sophistication may be used in the future). This is available from r5095. Bernhard On 12/06/2014 12:39, Huw Jenkins wrote: On 11 Jun 2014, at 11:30, Huw Jenkins wrote: Hi, The most recent pre-release of Coot I’ve compiled (revision 5094) has changed which map is set to scroll on Auto Open MTZ. I must stop replying to my own bug reports, but this appears to have been changed somewhere between r5047 and r5056. It affects the “View results of refinement in Coot” short-cut in CCP4i but not the “Open in Coot” function in the Phenix GUI. However Auto open-ing the output MTZ from phenix.refine also sets the second (Fo-Fc) map as scrollable. The “Fetch PDB and Maps from EDS”, however, works fine. Does that help to narrow down what’s changed? I know it’s hardly a massive burden to remember to change the scrollable map every time I auto open a new MTZ in Coot but it is a bit annoying... Thanks, Huw -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Syntax for Sphere refine + keybinding
Use:
sphere_refine_plus()
i.e. add the following lines to the keybindings file:
add_key_binding("Refine residue in a sphere", "T",
lambda: sphere_refine_plus(4.5))
B
On 30/05/2014 12:33, Joshi, Amar (Dr.) wrote:
Hi,
I am using Bernhard's keybinding file and I would like to add a sphere
refine + keybinding. Could anyone tell me the correct syntax for this?
Many thanks,
Amar
-
Amar Joshi Ph.D
Bayliss Lab
Department of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Road, Leicester
LE1 9HN
Tel: 0116 229 7082
Email: aj...@leicester.ac.uk <mailto:aj...@leicester.ac.uk>
--
--
*******
Dr. Bernhard Lohkamp
Associate Professor/Docent
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487651
fax: (+46) 08-327626
email: bernhard.lohk...@ki.se
Re: [COOT] Extentions tab in WinCoot
Hi Mike, I just tested myself again (to be sure), but there doesnt seem to be a problem with either the pre-release nor 0.7.2.1 (assuming you got them from my website). I havent heard about this problem otherwise, so I suggest we communicate off-list to fix this. B On 14/05/2014 22:54, Mike Lucido wrote: Hello all, I've been successfully using Coot in an Ubuntu virtual machine, but decided to try migrating my crystallography packages to my Windows 7 OS recently. I've gone through several iterations of installing and uninstalling several different versions of WinCoot (0.7.2.1, 0.8-pre), with each attempt giving the same result: there is no "Extensions" tab in the menu bar upon opening the program. I tried opening through Phenix (recommended by a colleague, as this was a workaround for him), but the "Extensions" tab was still missing. Is this an issue with the WinCoot builds, an issue with the installer, or an issue with how my PC is set up? Any ideas or advice would be greatly appreciated. Thanks in advance, Mike Lucido -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] add_terminal_residue_using_phi_psi bug
"N" and "C" works fine for me. Actually "auto" as well, but what is missing is a resorting of the residues (they are in the wrong order after addition). So, do a sort_residues(imol) after addition and everything will be fine. B On 29/04/2014 15:08, Oliver Clarke wrote: Hi Bernhard, Thanks, but I’m not sure that’s the case - in the scheme manual that parameter is listed as residue_type, same as for add_terminal_residue, and in any case when I change it to “N” it still adds at the C-terminus. Also, even when adding at the C-terminus, it adds after the TER flag and whatever solvent molecules are part of the chain, which does not seem like the desired behaviour. Best, Oliver. On Apr 29, 2014, at 2:45 AM, Bernhard Lohkamp wrote: I believe what you call res_type is rather actually term_type and this function doesnt take "auto", only "N" and "C". So I am afraid you have to specify yourself which end you want to add. HTH, B On 28/04/2014 21:33, Oliver Clarke wrote: Hi all, I’ve used the add_terminal_residue_using_phi_psi function to make a little shortcut to force Coot to add a terminal residue (code below), which I can then refine into the density (sometimes Coot cannot find an acceptable position for a terminal residue, when I can clearly see appropriate density). It works fine, except that there seems to be a bug in add_terminal_residue_using_phi_psi - it always adds the new residue at the end of the chain, regardless of whether the N-term or C-term residue is clicked, and it also adds after the TER flag if present. This means that I can’t use this to add residues to the N-term, as Coot will not recognize that the adjacent residues are linked if they are not adjacent in the file. Thoughts? Oli. #Force addition of residue - useful when #Coot says "No acceptable position found" # but density is clear. def force_add_terminal_residue(): def force_addition(res1): mol_id=res1[1] ch_id=res1[2] res_no=res1[3] res_type="auto" add_terminal_residue_using_phi_psi(mol_id,ch_id,res_no, res_type,-64,-41) user_defined_click(1,force_addition) add_simple_coot_menu_menuitem(menu, "Forced addition of terminal residue (click terminus)", lambda func: force_add_terminal_residue()) -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Removing atom labels permanently
Of course for Windows ;-) (in python):
add_key_binding("Remove labels", "L", lambda: remove_all_atom_labels())
B
On 28/04/2014 18:00, Paul Emsley wrote:
This adds a key-binding (Shift+L) that removes all the current atom labels:
(add-key-binding "Remove labels" "L" (lambda () (remove-all-atom-labels)))
(Not for Windows, of course.)
HTH,
Paul
On 17/04/14 08:05, Bernhard Lohkamp wrote:
Hi Grant,
to remove all labels (via GUI Measures->Clear atom labels; or):
remove_all_atom_labels()
TO avoid labelling on recentre:
set_label_on_recentre_flag(state)
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Atom-Labeling
Note to self: This should be in preferences (put on list).
B
On 17/04/2014 03:54, Grant Mills wrote:
Dear all,
You may have read my concerns on the CCP4BB however I'm still looking
for an answer to turn off atom labels permanently. I've tried various
drivers, installs and updates and all I really want to do is get back
to work. The labels cause coot to grind to an almost halt but it runs
smoothly without them. If you have some time to help, it would be
greatly appreciated as I've been struggling with this issue for about
6 months or so.
Thanks you for your time,
Grant
--
*******
Dr. Bernhard Lohkamp
Associate Professor/Docent
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487651
fax: (+46) 08-327626
email: bernhard.lohk...@ki.se
Re: [COOT] add_terminal_residue_using_phi_psi bug
I believe what you call res_type is rather actually term_type and this function doesnt take "auto", only "N" and "C". So I am afraid you have to specify yourself which end you want to add. HTH, B On 28/04/2014 21:33, Oliver Clarke wrote: Hi all, I’ve used the add_terminal_residue_using_phi_psi function to make a little shortcut to force Coot to add a terminal residue (code below), which I can then refine into the density (sometimes Coot cannot find an acceptable position for a terminal residue, when I can clearly see appropriate density). It works fine, except that there seems to be a bug in add_terminal_residue_using_phi_psi - it always adds the new residue at the end of the chain, regardless of whether the N-term or C-term residue is clicked, and it also adds after the TER flag if present. This means that I can’t use this to add residues to the N-term, as Coot will not recognize that the adjacent residues are linked if they are not adjacent in the file. Thoughts? Oli. #Force addition of residue - useful when #Coot says "No acceptable position found" # but density is clear. def force_add_terminal_residue(): def force_addition(res1): mol_id=res1[1] ch_id=res1[2] res_no=res1[3] res_type="auto" add_terminal_residue_using_phi_psi(mol_id,ch_id,res_no, res_type,-64,-41) user_defined_click(1,force_addition) add_simple_coot_menu_menuitem(menu, "Forced addition of terminal residue (click terminus)", lambda func: force_add_terminal_residue()) -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] broken loggraph on 64 bit redhat: new style refmac graph popup after refmac from inside coot?
Sorry, didnt see this earlier... catching up with a massive backlog on
emails.
I dont have any solution to your loggraph problem, but Coot should
certainly allow (by default and if available) the use of qtrview. I put
this on my list to do (somewhere on the top ;-) ).
B
On 05/04/2014 15:04, hari jayaram wrote:
Hi all,
I like running my refmac from inside coot and having the loggraph blt
graphs popup on completion.
loggraph graph pop ups seem broken on 64 bit redhat enterprise running
ccp4 6.3 and ccp4 6.4 , both 64 bit versions. The window for the graph
pops up and then crashes with an error complaining of the loggraph.tcl
script( see below).
This script nor associated scripts have not changed in ccp4 for a while,
and everything works on 64 bit Ubuntu, so I am scared the error may like
with some redhat component.
I tried to compile a "native" blt instead of using the ccp4 supplied one
to see if that fixed things. Digging through the blt forums etc it seems
that many are abandoning blt to something like a replacement called
wize. Also judging from the forums several things in the blt 2.4 and
older seem to have issues with newer tk flavors like 8.5.
Regardless , given all this , are there any ways to auto popup the new
style qt based graphs when running refmac from within coot upon completion.
Sorry I am cross posting to coot, ccp4bb.
thanks for your help in advance.
hari
the error I see in refmac : view log graphs OR in coot on refmac
completion says:
"Error in startup script: syntax error in expression "10 11 12 + 12":
extra tokens at end of expression
while executing
"expr [string trim $ele] + $data(NCOLUMNS) "
(procedure "extract_tables_from_GRAPH" line 44)
invoked from within
"extract_tables_from_$filetype $input $arrayname"
(procedure "extract_tables_from_file" line 31)
invoked from within
"extract_tables_from_file $system(SCRIPT) $system(FORMAT) data"
invoked from within
"if { $system(SCRIPT) != "" } {
if { ![ElementExists system FORMAT] || $system(FORMAT) == "" } {
set system(FORMAT) [GetFileFormat $system(SCRI..."
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl"
line 2324)
invoked from within
"source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]"
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl" line 83)
"
--
***
Dr. Bernhard Lohkamp
Associate Professor/Docent
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487651
fax: (+46) 08-327626
email: bernhard.lohk...@ki.se
Re: [COOT] Help with mutate scm script
In scheme there are no "'" (comma) separators for arguments. B Hi, I am trying to write a scm script for mutating a residue (change A660 to ASP in this case). (read-pdb "inp.pdb") (mutate 0, A, 660, "", ASP) (write-pdb-file 0 "out.pdb") (coot-real-exit 0) This does not run. Could you please point the error and fix? -- Thanks, Abhinav __ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992 -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Removing atom labels permanently
Hi Grant, to remove all labels (via GUI Measures->Clear atom labels; or): remove_all_atom_labels() TO avoid labelling on recentre: set_label_on_recentre_flag(state) https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Atom-Labeling Note to self: This should be in preferences (put on list). B On 17/04/2014 03:54, Grant Mills wrote: Dear all, You may have read my concerns on the CCP4BB however I'm still looking for an answer to turn off atom labels permanently. I've tried various drivers, installs and updates and all I really want to do is get back to work. The labels cause coot to grind to an almost halt but it runs smoothly without them. If you have some time to help, it would be greatly appreciated as I've been struggling with this issue for about 6 months or so. Thanks you for your time, Grant -- ******* Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Delete chain
Hi Oliver, You can use the scripting function delete_residue_range (https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#index-delete_002dresidue_002drange-709): delete_residue_range(imol, chain_id, start_res, stop_res) Maybe not exactly what you want, but that works fine for this purpose (*). You can give a residue range outside what you have, just to make sure everything is deleted, i.e. delete_residue_range(0,"A", -100,10). B (*) Incidentally it has been on my todo list for quite some time to make a delete chain (etc) function... On 12/03/2014 00:51, Oliver Clarke wrote: Another one to chalk on the list of things that would be nice to have but not really needed - I feel like having a delete chain option in the ‘Delete item’ dialog would be very handy… I often find myself needing to delete a chain (from a complex or oligomer for example), and I always switch the color to Jone’s Rainbow and then hunt around for the N- and C- termini and use delete zone, which works but is a little cumbersome. Being able to click on a single atom from the desired chain to delete it would speed things up tremendously, for example when editing the kind of spaghetti-model that sometimes comes out of buccaneer or Arp/warp at low resolution (where there a lot of peptide fragments that need cleaning up). Best, Oliver. -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Real Space Refine waters - equivalent to Extensions: All Molecule: Fit Protein option?
You can by using an extra argument (True or #t to get the animation) fit_waters(imol, True) or (fit-waters imol #t) Bernhard > Dear Joe, > > We'll need info from the experts, but as far as I'm aware it's not > possible to get the animation. > > Venlig hilsen/best regards > Folmer Fredslund > > On Feb 5, 2014 7:05 PM, "Joseph Noel" <mailto:n...@salk.edu>> wrote: > > Dear Folmer! > > Thanks! That is the one I am familiar with but wasn't sure how I > could animate it like for the protein. I guess maybe its not possible. > > Best- > > Joe > > __ > Joseph P. Noel, Ph.D. > Arthur and Julie Woodrow Chair > Investigator, Howard Hughes Medical Institute > Professor, The Jack H. Skirball Center for Chemical Biology and > Proteomics > The Salk Institute for Biological Studies > 10010 North Torrey Pines Road > La Jolla, CA 92037 USA > > Phone: (858) 453-4100 extension 1442 > > Cell: (858) 349-4700 > Fax: (858) 597-0855 > E-mail: n...@salk.edu <mailto:n...@salk.edu> > > Publications & Citations: > http://scholar.google.com/citations?user=xiL1lscJ > > Homepage Salk: http://www.salk.edu/faculty/noel.html > Homepage HHMI: http://hhmi.org/research/investigators/noel.html > > __ > > On Feb 4, 2014, at 10:15 PM, Folmer Fredslund <mailto:folm...@gmail.com>> wrote: > >> Dear Joseph, >> >> Yes, it's possible, but not you don't get any real time updates >> like you do for the protein. >> >> Here's a link to the fine manual: >> >> http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Refine-All-Waters >> >> Venlig hilsen >> Folmer Fredslund >> >> On Feb 5, 2014 12:05 AM, "Joseph Noel" > <mailto:n...@salk.edu>> wrote: >> >> Is there a way in COOT to automate the real space refine of >> waters - something equivalent to the Extension, All Molecule, >> Fit Protein? >> >> __ >> Joseph P. Noel, Ph.D. >> Arthur and Julie Woodrow Chair >> Investigator, Howard Hughes Medical Institute >> Professor, The Jack H. Skirball Center for Chemical Biology >> and Proteomics >> The Salk Institute for Biological Studies >> 10010 North Torrey Pines Road >> La Jolla, CA 92037 USA >> >> Phone: (858) 453-4100 extension 1442 >> >> Cell: (858) 349-4700 >> Fax: (858) 597-0855 >> E-mail: n...@salk.edu <mailto:n...@salk.edu> >> >> Publications & Citations: >> http://scholar.google.com/citations?user=xiL1lscJ >> >> Homepage Salk: http://www.salk.edu/faculty/noel.html >> Homepage HHMI: http://hhmi.org/research/investigators/noel.html >> >> __ >> > -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Changing map/molecule names.
For now, please use the scripting command: set_molecule_name(imol, name) B > Hi all > > I think I've asked this before, but a cursory search in the coot archives > doesn't yield an answer. > > Is there a way to change the name of specific maps and molecules (as > displayed under the Display Manager) ? > > Thanks, > > F > > > > - > Francis E. Reyes PhD > 215 UCB > University of Colorado at Boulder > > Publications & Citations: > http://scholar.google.com/citations?user=FW4-CaQJ&hl=en > ------ > -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] what python command to mutate with "stub" ?
The function you want is
delete_residue_sidechain()
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#delete_002dresidue_002dsidechain
For keybindings, pythonics (old version), please see ("Kill Sidechain"):
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Bernhards_key_bindings_for_coot.py
HTH
B
> Hello Cootaholics
>
> I'd like to add a custom button (or key binding, or both) that will
> do a simple mutate, keep the residue type the same, and trim it back
> to the beta carbon. This would be the same as the "stub" function in
> the Simple Mutate dialogue box. I am finding that I repeat this
> action often and would like to make it quicker and easier. Can
> someone help me out with the proper python command?
>
> Thanks, Scott
>
>
--
*******
Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487651
fax: (+46) 08-327626
email: bernhard.lohk...@ki.se
Re: [COOT] COOT 3D
Use the toolbutton swap stereo: Main Toolbar -> right mouse click-> Manage buttons-> select Swap Stereo Or for the script minded: switch_stereo_sides() This will toggle the stereo images left and right. HTH, B > Dear Coot list, > > I have build a couple of active 3D computers recently. One of them is > miss behaving and invert left/right images. > > Our work around is to wear the goggles upside down... not very comfortable. > > I have not yet found the source of the problem but Is there a command in > coot to invert left and right images (similar to the pymol command > invert sides)? > > Cheers, > Arnaud > -- ******* Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Atoms with zero occupancy
I have added this in the python Extensions. For now you can start this for your "imol" in the python scripting window: zero_occ_atoms_gui(imol) NB There may be better way in the future and to make this a more permanent feature. B > I would like the coot option - find residues with missing atoms to at > least have the option to pick those residues where there are atoms > with occupancy set to 0.00. > > Do others feel this would be helpful? > > Eleanor Dodson > -- ******* Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Adding a metal - ZN in fact
This should not happen indeed. I fix this a few month back, but I am afraid it seems it didnt make it into 0.7.x. Sorry. It is certainly fixed in 0.8-pre. B > I have added an atom at pointer - asked to have it called ZN (selected > Other option for atom type and put in ZN) and the output file assigns > no atom type or residue type.. > >I dont think this should happen? > Eleanor > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] faster coot?
Have a look at these: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration Some of these can be configured in preferences. B > Hi all, > > I'm on a 2.4 intel core i7, Radeon HD 6770M . I'm working on a 0.5 MDa > complex with a unit cell 250 x 250 x 100 , P222. Coot 0.7.2 on Mac. > > I need to be able to pan around a map radius of at least 100A . coot-real > only shows two threads. > > Unfortunately, panning around is slow. Any tips on speeding up coot? > > Thanks, F > > > > > - > Francis E. Reyes PhD > 215 UCB > University of Colorado at Boulder > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Problems with COOT_PYTHON_EXTRAS_DIR on WinCoot 0.7 rev 4459 on Windows 7
Ok. I tracked down what's going wrong and fixed it (r4758) (*). This has been broken for a while (since r3273) it seems. So you must have been using a very old WinCoot ;-) B (*) You may have to wait until this is available for Windows since I am fiddling with my build system at the moment. Sorry. So please use the previous fix I sent for now. > Hi, > > This is probably more a question for Bernhard: > > After upgrading to Windows 7 I am no longer able to read in a custom coot.py > located in a startup directory outside of the WinCOOT directory. > The error message is as follows > > Coot Python Scripting GUI code found and loaded. > WARNING:: no directory "C" in COOT_PYTHON_EXTRAS_DIR C:\COOT-Startup > WARNING:: no directory "\COOT-Startup" in COOT_PYTHON_EXTRAS_DIR > C:\COOT-Startup > INFO:: loading preferences file > C:\WinCoot/.coot-preferences/coot_preferences.py > > Running python script C:/WinCoot/.coot-preferences/coot_preferences.py > > The relevant setting in runwincoot.bat is: > set COOT_PYTHON_EXTRAS_DIR=C:\COOT-Startup > > I tried various iterations of C:\\; C://; C::/ to get Python separate the > drive component from the directory component but to no avail. I even placed > the COOT-Startup directory in the WinCOOT folder and used > set COOT_PYTHON_EXTRAS_DIR=%COOT_PREFIX%\COOT-Startup > but still nothing works. > > BTW I am using CMD.exe, but it does not work under PowerShell either. > > Any insights? > > Thanks > > Carsten > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Problems with COOT_PYTHON_EXTRAS_DIR on WinCoot 0.7 rev 4459 on Windows 7
Whilst I am looking into this (not too obvious just from the email), the quick solution is to put your coot.py file in your C:/WinCoot/.coot-preferences directory. It should be read in from there. B > Hi, > > This is probably more a question for Bernhard: > > After upgrading to Windows 7 I am no longer able to read in a custom coot.py > located in a startup directory outside of the WinCOOT directory. > The error message is as follows > > Coot Python Scripting GUI code found and loaded. > WARNING:: no directory "C" in COOT_PYTHON_EXTRAS_DIR C:\COOT-Startup > WARNING:: no directory "\COOT-Startup" in COOT_PYTHON_EXTRAS_DIR > C:\COOT-Startup > INFO:: loading preferences file > C:\WinCoot/.coot-preferences/coot_preferences.py > > Running python script C:/WinCoot/.coot-preferences/coot_preferences.py > > The relevant setting in runwincoot.bat is: > set COOT_PYTHON_EXTRAS_DIR=C:\COOT-Startup > > I tried various iterations of C:\\; C://; C::/ to get Python separate the > drive component from the directory component but to no avail. I even placed > the COOT-Startup directory in the WinCOOT folder and used > set COOT_PYTHON_EXTRAS_DIR=%COOT_PREFIX%\COOT-Startup > but still nothing works. > > BTW I am using CMD.exe, but it does not work under PowerShell either. > > Any insights? > > Thanks > > Carsten > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Feature request
As with so many things. This is already available, but currently only via scripting: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/doc/coot-faq.html#How-do-I-do-a-superposition-on-just-a-part-of-my-structure_003f HTH, B > > Hi Paul, hi all, > > let me add a request for a feature that I would find of great help in > comparing structures. > > In the "Calculate --> SSM Superpose..." menu, I would find extremely > useful having a "residue range" just like in the "LSQ superpose..." menu. > > That would help when comparing a couple of single chains, composed each > by two domains, and wants to superpose the first two domains, or the > second two. > > It'll be great if you could implement it in future versions of the programs. > > Thanks a lot, > ciao, > Sebastiano > > -- > *Sebastiano Pasqualato, PhD* > Crystallography Unit > Department of Experimental Oncology > European Institute of Oncology > IFOM-IEO Campus > via Adamello, 16 > 20139 - Milano > Italy > > tel +39 02 9437 5167 > fax +39 02 9437 5990 > > > > > > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Wrong Leucine rotamer in Coot 0.7
Dear Dirk, I am not sure which program you are using ;-) , but Coot uses LEU mt Chi1 -65deg and Chi2 174deg and hence CD2 is not anywhere near N. Of course if you use chi2 angle of 51 the situation is different... I assume something else is going wrong here. B > Dear Tim, > > the mt rotamer in Coot is simply wrong: I really need quite frequently > the correct mt rotamer from Richardson's penultimate rotamer library, > which Coot should be using, according to its documentation. The Coot mt > Chi angles -65, 51 lead to a close contact of CD2 with N of 2.9 A. > The correct mt rotamer with Chi-angles -65, 175 have no close contacts: > CD1-N: 3.7 A, CD2-N: 4.6 A. And it really "looks" correct. > > Best regards, > > Dirk. > > Am 18.06.13 22:52, schrieb Tim Gruene: >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> Dear Dirk, >> >> it may simply be a different definition of the angles - when I set >> chi2 to 175 degree in the coot mt-rotamer, the CD1 atom is in eclipse >> position with the N atom, so this is probably not a rotamer! You may >> have a reason for flagging one setting wronger than another? >> >> Best, >> Tim >> >> On 06/18/2013 08:11 PM, Dirk Kostrewa wrote: >>> Dear Paul, >>> >>> the leucine "mt" rotamer in Coot 0.7 appears to be wrong: the >>> Richardson penultimate rotamer library says for leucine "mt" >>> Chi1=-65, Chi2=175, but if I choose the leucine "mt" rotamer in >>> Coot, the resulting Chi angles are Chi1=-65, Chi2=51. Could you >>> please check this? >>> >>> Best regards, >>> >>> Dirk. >>> >> - -- >> 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/ >> >> iD8DBQFRwMigUxlJ7aRr7hoRAhgAAJ9HkEUZE1NZwI2c8a5Mtwf28zr1xwCfdm9g >> XfIDotbnr8ZMP/s+hDlHxlE= >> =hGeD >> -END PGP SIGNATURE- > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] dna restraints
Sorry, just quickly: load user-define-restraints (scm or py) there are several function to make own restraints (incl DNA/RNA as well as some simple, experimental ProSMART interface - which is the way to go for secondary structure restraints, I believe). B > Is there some non-convoluted way to force Watson-Crick hydrogen bonds > during real space refinement? And a related question - is there some > way to define secondary structure (helices/sheets) for the whole > molecule (maybe based on header) and then enforce it? > > One way I see right now is to supply LINK records (which I assume coot > will honor but I may be wrong) for every hydrogen bond that defines > secondary structure. It would also probably require adjusting parameter > files to provide distance restraints? That would take some scripting, > which is no big deal. But I don't want to invent something that coot > may already have a tool for. > > This stuff may be useful at low resolution, which is pretty much what > one generally gets with protein-DNA complexes. > > Cheers, > > Ed. > -- ******* Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Coot update refmac output map as map to use for real-space refinement after each run
There was indeed a bug when trying to swap the map colours after running refmac, but only in the pythonic version (*). However, you appear to be using the scheme version and this seems to be OK. Maybe there is problem earlier in your .coot file and the command doesnt even get executed. What does the console output say upon start-up? Have you tried the command in the Scheme Scripting window to see if it works from there? (we can discuss this in more detail off-list). B (*) Fixed in revision 4651 > On a related note..I do have the following setting > (set-keep-map-colour-after-refmac 1) in my .coot file , but it does not > seem to be getting picked up and the refmac produced map color does > change after the run and the . I am running coot version > > 0.7.1-pre (revision 4549) [with guile 1.8.8 embedded] [with python > 2.7.0 embedded] > > My setting /home/hari/.coot reads.. > > (set-keep-map-colour-after-refmac 1) > > Any ideas on what I am doing wrong. > Thanks again > Hari > > > > On Tue, May 21, 2013 at 5:31 AM, Bernhard Lohkamp > mailto:bernhard.lohk...@ki.se>> wrote: > > > Hi Hari, > > sorry for getting back late. There was indeed a bug (in the scheme > scripting). This is fixed in r4647 (just downloading refmac.scm from the > repository should be ok). > > B > > > Hi all, > > I generally run refmac from inside coot. > > > > The "older" coot version would automatically pick the newest maps > that > > resulted from refmac as the map to use for refinement..so it would go > > from one FWT map (say map 0) to the newest FWT (map 2) map that > > resulted after refmac.. > > > > However the auto picking of the newest map is no longer happening > > > > Is there someplace in the .coot settings file I can use to set > the old > > coot behavior and I am hoping that there is a setting that will > pick the > > newest map as the one to be used. > > > > Thanks for your help > > > > Hari > > > > > > > -- > *** > > Dr. Bernhard Lohkamp > Assistant Professor > Div. Molecular Structural Biology > Dept. of Medical Biochemistry and Biophysics (MBB) > Karolinska Institutet > S-17177 Stockholm > Sweden > > phone: (+46) 08-52487651 > fax: (+46) 08-327626 > email: bernhard.lohk...@ki.se <mailto:bernhard.lohk...@ki.se> > > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Coot update refmac output map as map to use for real-space refinement after each run
Hi Hari, sorry for getting back late. There was indeed a bug (in the scheme scripting). This is fixed in r4647 (just downloading refmac.scm from the repository should be ok). B > Hi all, > I generally run refmac from inside coot. > > The "older" coot version would automatically pick the newest maps that > resulted from refmac as the map to use for refinement..so it would go > from one FWT map (say map 0) to the newest FWT (map 2) map that > resulted after refmac.. > > However the auto picking of the newest map is no longer happening > > Is there someplace in the .coot settings file I can use to set the old > coot behavior and I am hoping that there is a setting that will pick the > newest map as the one to be used. > > Thanks for your help > > Hari > > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] coot rev4630 builds (and runs) but fails test?
Hi Kip, difficult to tell where the tests fail without further information. Most likely one or the other test fails because you dont have the required files (coordinates, etc), which are not distributed. This is nothing for you to worry about, but for us (if it fails for us - currently doesnt for me ;-) so you are save). B > Hi All, > > I am trying to build revision 4630 (on Fedora 17 64-bit) from sources > using the autobuild script -- coot building seems to pass (and the > binary seems to run perfectly fine on my machine) but the logs show that > it is failing the first test. I am running Fedora 17 64-bit > > Any and all advice on how to proceed would be greatly appreciated! > > The last few lines of gtk2-python-build.log are: > > BUILDING coot: version coot-0.7.1-pre-revision-4630, python=yes > coot build was good. > done coot build. > INSTALLING refmac monomer library... > GETTING reference structures tar... > INSTALLING reference structures... > we are slimming directory > /home/kip/Software/coot-build_20130511/autobuild/Linux-xray-pre-release-gtk2-python > fat_dir is > /home/kip/Software/coot-build_20130511/autobuild/Linux-xray-pre-release-gtk2-python > clear_type is clear-static > cleaned_dir is > /home/kip/Software/coot-build_20130511/autobuild/coot-Linux-x86_64-fedora-17-gtk2-python > rsyncing... > /home/kip/Software/coot-build_20130511/autobuild/Linux-xray-pre-release-gtk2-python/etc > does not exist > /home/kip/Software/coot-build_20130511/autobuild/Linux-xray-pre-release-gtk2-python/html > does not exist > > first coot test failed > > greg test status: 1 > python test status: 1 > finished > > > On a related note, are there any recent pre-built binaries available for > download (I can't seem to find any)? > > Thank you! > Kip -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Fetch PDB doesn't work
You dont say which version you are using. Anyway, this has been discussed before https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1302&L=coot&P=R1936&1=coot&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 ...and we are working on updates. Several servers have changed, so we are trying to keep up. B > Hi all, > i'm recently experiencing that "File->Fetch PDB using acession code" > doesn't work. It downloads file with *.pdb extension, but inside there > is html code with link to the structure. > > Is that our bad local setup of coot, or is it global feature? > > "Fetch PDB & map using EDS" works properly. > > Thanks > > Jan > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] copy fragment command
For merging use: merge_molecule([list of things to merge], imol_to_be_merged_into) As for renaming chains: change_chain_id(imol, new_chain_id, chain_id_in, use_res_range_flag, resno_from, resno_to) or change_chain_id_with_result(imol, new_chain_id, chain_id_in, use_res_range_flag, resno_from, resno_to) You have to be careful when chaining chain ids as Coot wont allow you to insert doublicate residue numbers in the same chain. So you may have to renumber residues first. Hope this helps, B > Hey, > > I have been trying to find the script command that would do the same thing as > gui "copy fragment", but no success. > I have to copy hundreds of fragments and merge them to new molecule. With gui > it would take long time, then I was thinking to try to make a script. I only > found the copy_molecule or copy_chain, but I do not want to copy whole chain, > only a "fragment" (specific residues). Is there command (python) to copy > fragment? > I could use: > copy_residue_range > then I would change the chain id and renumber. I see the renumbering command, > but no command for changing chain id? > > > Best, > Arto > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] refining/regularizing a ligand I built
The reminiscence to the procheck plot comes from the default 10 degree block size in Coot rather than using a smooth curve as in molprobity. But you can change this if you like. It wont change your outliers though (*) ;-) . See: http://www.biop.ox.ac.uk/coot/doc/coot/Ramachandran-Plots.html B (*) but may be a bit slower... > Ok, sorry for that...it was just that the picture of the Ramachandran, > with the allowed and disallowed regions, reminds > strongly of the one in PROCHECK. It actually does not look like the > one from MOLPROBITY (see attachments). > > > On 4/4/13 9:18 PM, Bernhard Lohkamp wrote: >> The Ramachandran plot in Coot is not based on PROCHECK, it never was!!! >> It is based on the molprobity one, however it needs updating and >> currently not based on the latest distribution (*). >> >> B >> >> (*) a Clipper/Kevin thing for the interested... >> >>> Paul, is it planned to replace the Ramachandran check based on PROCHECK with >>> one based on MOLPROBITY? At least in v. 0.7 for Mountain Lion it was >>> still not available >>> Best, >>> Xavier >>> >>> >>> On 25/3/13 5:33 PM, Paul Emsley wrote: >>>> On Wed, 2013-03-20 at 13:24 +, Anat Bashan wrote: >>>>> Hi All, >>>>> >>>>> I build a ligand that is partly RNA and Partly a protein chain. In >>>>> between I have a special nucleotide with a N bound to C3' (instead of >>>>> O3'). it is : CC-PPU-Ala-Phe-Val. I have links in the .pdb file and the >>>>> PPU is a known ligand to COOT. My links connect the N3' of the PPU with >>>>> the C of Ala. nevertheless, if I try to regularize or refine the Ala >>>>> keeps moving away from the PPU. The other link I defined between the C >>>>> and the PPU works fine. >>>>> What am I missing here ? >>>>> Do I need to specify anything else than the LINK? >>>>> I attached the .pdb file of my ligand for you to be able to load into >>>>> coot and try playing with it yourself. >>>> Sorry for the delay (I was a bit disconnected and distracted at the CCP4 >>>> dev meeting). >>>> >>>> So, what you are missing, it seems to me, is the use of JLigand (that's >>>> the best tool AFAIK) to define the link between the Ala and the PPU. >>>> This link is not in the refmac monomer library and you have to tell Coot >>>> (and Refmac) exactly what you mean (libcheck helps out). >>>> >>>> You do not need to explicitly make the link, Coot will do that for you >>>> as you use JLigand. >>>> >>>> HTH, >>>> >>>> Paul. >>>> >>> -- > > -- -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] refining/regularizing a ligand I built
The Ramachandran plot in Coot is not based on PROCHECK, it never was!!! It is based on the molprobity one, however it needs updating and currently not based on the latest distribution (*). B (*) a Clipper/Kevin thing for the interested... > Paul, is it planned to replace the Ramachandran check based on PROCHECK with > one based on MOLPROBITY? At least in v. 0.7 for Mountain Lion it was > still not available > Best, > Xavier > > > On 25/3/13 5:33 PM, Paul Emsley wrote: >> On Wed, 2013-03-20 at 13:24 +, Anat Bashan wrote: >>> Hi All, >>> >>> I build a ligand that is partly RNA and Partly a protein chain. In between >>> I have a special nucleotide with a N bound to C3' (instead of O3'). it is : >>> CC-PPU-Ala-Phe-Val. I have links in the .pdb file and the PPU is a known >>> ligand to COOT. My links connect the N3' of the PPU with the C of Ala. >>> nevertheless, if I try to regularize or refine the Ala keeps moving away >>> from the PPU. The other link I defined between the C and the PPU works fine. >>> What am I missing here ? >>> Do I need to specify anything else than the LINK? >>> I attached the .pdb file of my ligand for you to be able to load into coot >>> and try playing with it yourself. >> Sorry for the delay (I was a bit disconnected and distracted at the CCP4 >> dev meeting). >> >> So, what you are missing, it seems to me, is the use of JLigand (that's >> the best tool AFAIK) to define the link between the Ala and the PPU. >> This link is not in the refmac monomer library and you have to tell Coot >> (and Refmac) exactly what you mean (libcheck helps out). >> >> You do not need to explicitly make the link, Coot will do that for you >> as you use JLigand. >> >> HTH, >> >> Paul. >> > > -- -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Add other solvent molecules setting
Just for completeness, there is actually an extra function for this: (define *additional-solvent-ligands* '()) which can be added to the .coot file. B On 14/02/2013 17:10, Debreczeni, Judit wrote: Yes, it can be added to the .coot file like this: (append! *solvent-ligand-list* (list "TRS")) or like this for multiple molecules: (append! *solvent-ligand-list* (list "TRS" "XXX" "YYY")) -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Ulrich Gohlke Sent: 14 February 2013 10:48 To: COOT@JISCMAIL.AC.UK Subject: [COOT] Add other solvent molecules setting Dear crystalleagues, in Extensions -> Modelling -> Add Other Solvent Molecules..., is there a way to add common compounds such as TRS to the pre-selected molecules permanently, i.e. one doesn't have to "Add a new Residue Type" every time Coot is started? Can this be added to the .coot file or something? Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc- berlin.de/en/research/research_teams/macromolecular_structure_and_inter action/ -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Trying to build coot from source
Hi Ethan, build logs are in: $HOME/public_html/build-logs/ ... some subdirectory depending on computer name, OS, etc. This will give you some hints where it stopped (and why). Otherwise manual continuation is of course possible (providing everything else got correctly compiled and installed), but you may want to pass some more information to configure (check config.log - if there - or the autobuild script for flags). But then the usual: make, make install B On 06/02/2013 02:11, Ethan Merritt wrote: Since the pdbe has apparently changed its URL, breaking the download capability in the version of coot I've been running, I decided to try to build a current copy from source. I downloaded the autobuild.sh script, customized AUTOBUILD_BUILD and AUTOBUILD_INSTALLED, stuck a #!/bin/bash at the top, and ran ./autobuild.sh python It downloaded and built lots of support libraries but not, unfortunately, coot itself. The last thing output by the script was Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 16160810 (15M) [application/x-tar] Server file no newer than local file “/home/local/coot/autobuild/sources/coot-0.7.1-pre-revision-4552.tar.gz” -- not retrieving. I can't find any error messages or log files. All I know is that the autobuild process seems to have stopped at that point and not built an executable. Is there some follow-on command I need to run? Do I need to manually ./configure and make in a subdirectory? Ethan -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
Re: [COOT] Coot and JLigand
You are (most likely) missing the goocanvas libraries on your system. Once you installed this (and recompiled coot with it), it should work. B On 22/01/2013 12:32, "ing. Jan Stránský" wrote: Hello (again), I've get closer where is the problem: I'm missing Coot Ligand Builder. The button in Calculate -> Ligand builder is disabled. But I'm unable to google it. Where do I get it? Best regards Jan On 01/08/2013 01:47 PM, Paul Emsley wrote: On 08/01/13 12:27, "ing. Jan Stránský" wrote: Hi everybody, I think, I have some problem with JLigand. Recently on CCP4-weekend's lunch bytes I saw in Bernhard's (or Paul's) JLigand window one extra toolbar (see my window in attachment). I remember ther was icon with "+" to show close contacts of ligand and button for direct sending of ligand to coot (or to update it). I have JLigand 1.0.37 and coot 0.7 runing under Fedora. Where is the problem? Hello (again) Jan, We suspect that you are remembering the "+" environment button in the Lidia window (to get a better analysis of the interactions, you should hydrogenate region first (this needs molprobity probe)). Regards, Paul and Bernard. -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
