Re: [COOT] Build-it cannot find self-build guile
Hi Paul Dne 10/26/2021 v 4:37 PM Paul Emsley napsal(a): > On 20/10/2021 14:12, Jan Stransky wrote: >> Update, no-guile build version passed, but I dont see the icons :-) > > > I don't think that those things are related. I don't know much about > icons, maybe there something of interest in the console output. > I have cleared the build directories, and now I got working coot without guile and with icons. It loads also the CCP4 modules, when i2 is pointed on the binary > >> >> Jan >> >> On 10/20/21 14:04, Jan Stransky wrote: >>> Hi, >>> >>> since CCP4-bundled Coot is not working in the second latest Ubuntu >>> (21.04), I went into the adventure of building it my own, using the >>> build-it script. >>> >>> Everything builds an works (as far as I can tell) up to the point of >>> building Coot it self. The log congratulates me on using Guile, and >>> then >>> it fails to find it: >>> >>> checking for mmdb2... yes >>> checking for ssm... yes >>> no >>> checking for non-prefixed single-precision FFTW2 (fftw.h)... yes >>> checking for Clipper... yes >>> Congratulations, you are using Guile >>> checking for guile... no >>> configure: error: guile required but not found >>> make: *** No targets specified and no makefile found. Stop. >>> make failed. >>> >>> Any ideas? Let me know in which log would you be interested. > > > I wonder if it is the same problem as we are having on Debian > Bullseye. I haven't resolved it yet. > > >>> >>> Thanks, >>> >>> Jan >>> >>> P.S. list of packages installed based on various sources: >>> >>> cmake libxext-dev libxmu-dev libxt-dev libc6-dev libncurses5-dev >>> libglu1-mesa-dev libjpeg-dev mesa-common-dev libgtk2.0-dev >>> libgnomecanvas2-dev gfortran libtinfo-dev > > These are in the build-it script. > > > Paul. > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/ -- Jan Stránský, PhD. Institute of Biotechnology, AS CR Centre of Molecular Structure Průmyslová 595 252 50 Vestec Czech Republic Email: jan.stran...@ibt.cas.cz Phone: +420 325 873 788 - Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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] Build-it cannot find self-build guile
Update, no-guile build version passed, but I dont see the icons :-) Jan On 10/20/21 14:04, Jan Stransky wrote: > Hi, > > since CCP4-bundled Coot is not working in the second latest Ubuntu > (21.04), I went into the adventure of building it my own, using the > build-it script. > > Everything builds an works (as far as I can tell) up to the point of > building Coot it self. The log congratulates me on using Guile, and then > it fails to find it: > > checking for mmdb2... yes > checking for ssm... yes > no > checking for non-prefixed single-precision FFTW2 (fftw.h)... yes > checking for Clipper... yes > Congratulations, you are using Guile > checking for guile... no > configure: error: guile required but not found > make: *** No targets specified and no makefile found. Stop. > make failed. > > Any ideas? Let me know in which log would you be interested. > > Thanks, > > Jan > > P.S. list of packages installed based on various sources: > > cmake libxext-dev libxmu-dev libxt-dev libc6-dev libncurses5-dev > libglu1-mesa-dev libjpeg-dev mesa-common-dev libgtk2.0-dev > libgnomecanvas2-dev gfortran libtinfo-dev > > -- > Jan Stránský, PhD. > Institute of Biotechnology, AS CR > Centre of Molecular Structure > Průmyslová 595 > 252 50 Vestec > Czech Republic > > Email: jan.stran...@ibt.cas.cz > Phone: +420 325 873 788 > > - > > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová > zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její > přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu > nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření > smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným > právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá > předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. > > Disclaimer: If not expressly stated otherwise, this e-mail message (including > any attached files) is intended purely for informational purposes and does > not represent a binding agreement on the part of Institute of Biotechnology > of the Czech Academy of Sciences. The text of this message and its > attachments cannot be considered as a proposal to conclude a contract, nor > the acceptance of a proposal to conclude a contract, nor any other legal act > leading to concluding any contract, nor does it create any pre-contractual > liability on the part of Institute of Biotechnology of the Czech Academy of > Sciences. > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/ > - > > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová > zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její > přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu > nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření > smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným > právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá > předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. > > Disclaimer: If not expressly stated otherwise, this e-mail message (including > any attached files) is intended purely for informational purposes and does > not represent a binding agreement on the part of Institute of Biotechnology > of the Czech Academy of Sciences. The text of this message and its > attachments cannot be considered as a proposal to conclude a contract, nor > the acceptance of a proposal to conclude a contract, nor any other legal act > leading to concluding any contract, nor does it create any pre-contractual > liability on the part of Institute of Biotechnology of the Czech Academy of > Sciences. -- Jan Stránský, PhD. Institute of Biotechnology, AS CR Centre of Molecular Structure Průmyslová 595 252 50 Vestec Czech Republic Email: jan.stran...@ibt.cas.cz Phone: +420 325 873 788 - Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá před
[COOT] Build-it cannot find self-build guile
Hi, since CCP4-bundled Coot is not working in the second latest Ubuntu (21.04), I went into the adventure of building it my own, using the build-it script. Everything builds an works (as far as I can tell) up to the point of building Coot it self. The log congratulates me on using Guile, and then it fails to find it: checking for mmdb2... yes checking for ssm... yes no checking for non-prefixed single-precision FFTW2 (fftw.h)... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile... no configure: error: guile required but not found make: *** No targets specified and no makefile found. Stop. make failed. Any ideas? Let me know in which log would you be interested. Thanks, Jan P.S. list of packages installed based on various sources: cmake libxext-dev libxmu-dev libxt-dev libc6-dev libncurses5-dev libglu1-mesa-dev libjpeg-dev mesa-common-dev libgtk2.0-dev libgnomecanvas2-dev gfortran libtinfo-dev -- Jan Stránský, PhD. Institute of Biotechnology, AS CR Centre of Molecular Structure Průmyslová 595 252 50 Vestec Czech Republic Email: jan.stran...@ibt.cas.cz Phone: +420 325 873 788 - Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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] Changing scroll map keybinding
Hi, I believe, I have seen somewhere a keybinding, which cycle through maps attached to scroll wheel (basicaly moving the radio button "Scroll" in Display Manager). However, I can't find anywhere what key does that... Any ideas? Or do you know a coot function which does that? Best regards, Jan
[COOT] Ligand definition
Hi, how does coot define what is ligand, namely for go_to_ligand()? Is it possible to tweak the definition? 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... Jan
[COOT] Bug in jiggle fit (Coot 0.8.8 from CCP4)
A jiggle fit, at least under keybinding, refuse to work. I can see
following error message:
In /local/protein/ccp4/ccp4-7.0/share/guile/gtk-2.0/gtk.scm:
147: 0* [apply # ()]
In unknown file:
?: 1 [#]
...
?: 2 [format:out # ...]
In /local/protein/ccp4/ccp4-7.0/share/guile/1.8/ice-9/format.scm:
193: 3 (let ((arg-pos #) (arg-len #)) (cond (# # # #) (else # #t)))
193: 4* [format:format-work "WARNING:: placeholder for non-scheme
function: ~s~%" ...]
209: 5 (letrec (# # # # ...) (set! format:pos 0) (set!
format:arg-pos 0) ...)
805: 6* [anychar-dispatch]
289: 7 (if (>= format:pos format-string-len) arg-pos ...)
...
323: 8 (case (char-upcase #) (# # # #) (# # # #) ...)
336: 9* [format:out-obj-padded #f ...
337: 10* [next-arg]
263: 11* (if (>= arg-pos arg-len) (begin # #))
264: 12 (begin (set! format:arg-pos #) (format:error "missing
argument(s)"))
In unknown file:
...
?: 13 [scm-error misc-error #f "~A" ("error in format") #f]
: In procedure scm-error in expression (scm-error (quote
misc-error) #f ...):
: error in format
It is 0.8.8 from ccp4 package. Haven't tested on nightlies as I am
affecetd by haswell-GPU-dynamic-library bug.
Cheers,
Jan
Re: [COOT] Caps lock feature
Well, when it is as keybinding/shorcut, it is a bit unexpected... And I have seen colleges confused because of that with coot... Jan On 01/25/2017 02:17 PM, Tim Gruene wrote: Dear Jan, this is the very behaviour I would expect from Caps Lock: it acts as though you would continuosly keep the Shift-Key pressed. Do you think this is unexpected? Best, Tim On Wednesday 25 January 2017 01:39:19 PM Jan Stransky wrote: Hi, I don't know, if call it bug, or feature... We (me and my college) have just found, that when you use keybinding with Caps Lock On, it behaves as you would press Shift + key binding normally with Caps Lock Off. Just letting know, as it can puzzle some one... Best regards, Jan -- Jan Stransky, PhD student Institute of Biotechnology, CAS Laboratory of structure and function of biomolecules Prumyslova 595 Vestec Czech Republic +420325873759 -- Jan Stransky, PhD student Institute of Biotechnology, CAS Laboratory of structure and function of biomolecules Prumyslova 595 Vestec Czech Republic +420325873759
Re: [COOT] CHO H-bonds.
About the unit cell shrinkage: I have heard a lecture (I believe it was Andrea Thorn form G. Sheldrick group on one of CCP4 meetings), where she mentioned a mistake in X-ray wavelenght input (swaped 3rd and 4th digit), which no program from integration to structure solution did not recognised. It appeared in structure refinement in wrong bond distances. Worth of checking. Jan On 07/01/2015 10:58 AM, Ian Tickle wrote: Paul, as an aside to this, would it be possible to have it so that if the relevant boxes in the Environment Distances menu are checked then H-bonds and.or bumps are automatically re-calculated on re-centering? Currently it's necessary to check off on one of the boxes every time the view is re-centered. If I forget to do that it's very easy to miss bumps (and I don't have a great deal of faith in MP's concept of what constitutes a bump)! Cheers -- Ian On 30 June 2015 at 14:33, Ian Tickle ianj...@gmail.com mailto:ianj...@gmail.com wrote: Hello All I guess this is really a question about MolProbity (and possibly about autoBuster) but I assume that most Coot users will be using the MolProbity validation tools. I am in the process of depositing 4 structures of the same protein (different ligands) and I noticed that MP seems to be reporting an unusually large number of bumps in both the small overlap and bad overlap classes. In each case the resolution is 2 Ang., the structures have been refined by autoBuster and the density seems to be unequivocal, see e.g.: https://drive.google.com/file/d/0B4H4H-DyO60-SEQwS1k5S3RIVG8/view?usp=sharing A lot of the bumps are main-chain CHalpha to main-chain carbonyl O H-bonds, but there are also some CH...O side-chain H-bonds, again with clear density. The C...O distances are in the range 3.0 to 3.2 Ang., so too short for a vdW contact. The H...O distances are ~ 2.2 Ang. which is definitely shorter than the sum of the vdW radii ( H: 1.2 + O: 1.5 = 2.7). I found this survey of CH...O H-bonds but it's restricted to CH...O bonds at the end of helices and I see them mostly in sheets. http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pdfs/chapter1.pdf This reports 11 examples (i.e. H-bonds, not structures) in the 3.0-3.2 range for the whole of the PDB (admittedly as it was in 2001 when the article appears to have been written). I have about the same number in one structure! One possibility I considered was that the unit cells had all somehow 'shrunk'. This can be tested with WhatCheck: however it only reports a very small shrinkage which translates to an error of ~ 0.02 Ang. in a 3 Ang. distance, which is nowhere near enough to explain a discrepancy of 0.5 Ang. So I guess my question is has anyone else noticed this in their MP dot-plots; also does anyone know what criteria does MP uses for testing bumps and specifically what value is it using for CH...O H-bonds? And of course I'd like to know whether this will affect my percentile ranking in the clashscore from the PDB validation! Cheers -- Ian -- Jan Stransky, PhD student Institute of Biotechnology, CAS Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
Re: [COOT] CHO H-bonds.
Dear Tim, I know that it cause rescaling and you don't have to input the number manually most of the time recently. I just wanted to point out that it can obviously happend. The question reminded me Andrea's lecture. Jan On 07/02/2015 10:34 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jan, when you input the wrong wavelength during data processing, you rescale the Ewald sphere construction, i.e. it will result in a different unit cell and crystal to detector distance. I am not sure what you mean by 'which no program from integration to structure solution did not recognised'. How should the downstream software detect the human mistake? The wavelength you enter should of course be double checked. Nowadays this seldomly occurs because the experimental settings are usually transferred automatically and reliably between the beamline software and the processing tools. Cheers, Tim On 07/02/2015 09:27 AM, Jan Stransky wrote: About the unit cell shrinkage: I have heard a lecture (I believe it was Andrea Thorn form G. Sheldrick group on one of CCP4 meetings), where she mentioned a mistake in X-ray wavelenght input (swaped 3rd and 4th digit), which no program from integration to structure solution did not recognised. It appeared in structure refinement in wrong bond distances. Worth of checking. Jan On 07/01/2015 10:58 AM, Ian Tickle wrote: Paul, as an aside to this, would it be possible to have it so that if the relevant boxes in the Environment Distances menu are checked then H-bonds and.or bumps are automatically re-calculated on re-centering? Currently it's necessary to check off on one of the boxes every time the view is re-centered. If I forget to do that it's very easy to miss bumps (and I don't have a great deal of faith in MP's concept of what constitutes a bump)! Cheers -- Ian On 30 June 2015 at 14:33, Ian Tickle ianj...@gmail.com mailto:ianj...@gmail.com wrote: Hello All I guess this is really a question about MolProbity (and possibly about autoBuster) but I assume that most Coot users will be using the MolProbity validation tools. I am in the process of depositing 4 structures of the same protein (different ligands) and I noticed that MP seems to be reporting an unusually large number of bumps in both the small overlap and bad overlap classes. In each case the resolution is 2 Ang., the structures have been refined by autoBuster and the density seems to be unequivocal, see e.g.: https://drive.google.com/file/d/0B4H4H-DyO60-SEQwS1k5S3RIVG8/view?usp=sharing A lot of the bumps are main-chain CHalpha to main-chain carbonyl O H-bonds, but there are also some CH...O side-chain H-bonds, again with clear density. The C...O distances are in the range 3.0 to 3.2 Ang., so too short for a vdW contact. The H...O distances are ~ 2.2 Ang. which is definitely shorter than the sum of the vdW radii ( H: 1.2 + O: 1.5 = 2.7). I found this survey of CH...O H-bonds but it's restricted to CH...O bonds at the end of helices and I see them mostly in sheets. http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pdfs/chapter1.pdf This reports 11 examples (i.e. H-bonds, not structures) in the 3.0-3.2 range for the whole of the PDB (admittedly as it was in 2001 when the article appears to have been written). I have about the same number in one structure! One possibility I considered was that the unit cells had all somehow 'shrunk'. This can be tested with WhatCheck: however it only reports a very small shrinkage which translates to an error of ~ 0.02 Ang. in a 3 Ang. distance, which is nowhere near enough to explain a discrepancy of 0.5 Ang. So I guess my question is has anyone else noticed this in their MP dot-plots; also does anyone know what criteria does MP uses for testing bumps and specifically what value is it using for CH...O H-bonds? And of course I'd like to know whether this will affect my percentile ranking in the clashscore from the PDB validation! Cheers -- Ian - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1 iD8DBQFVlPeFUxlJ7aRr7hoRAuQXAJ4gYxRxL/BELbrDGpAxUXbUErBPgwCghcsv nEVcp0relCBO/HVt9poCnYE= =V1FJ -END PGP SIGNATURE- -- Jan Stransky, PhD student Institute of Biotechnology, CAS Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
Re: [COOT] two suggestions
You can already click on residue symbols in Coot's Ramachandran, which will focus you on that residue... A table you can get from Molprobity webservice, but it is not clickable though... Cheers, Jan On 05/25/2015 06:22 PM, Shane Caldwell wrote: If I might add as well to Oliver's suggestions, an option to jump to questionable/bad ramachandrans would be useful at the validation stage. A list like the residues with missing atoms / residues with alt confs functions would be a quick way to inspect these without having to track them down in a busy 2d plot. Shane Caldwell McGill University On Mon, May 25, 2015 at 11:05 AM, Oliver Clarke oc2...@columbia.edu mailto:oc2...@columbia.edu wrote: Also along the same lines, I would love to see a local ramachandran - a ramachandran plot, but only displaying those residues within a certain distance from the center of rotation, say 20 Å. The ramachandran plot is very handy for validation and identification of troublesome regions, but it gets very crowded for large, multi chain structures, and I feel like this would be a handy aid during refinement. Cheers, Oliver. -- Jan Stransky, PhD student Institute of Biotechnology, CAS Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
Re: [COOT] help regarding using jiggle fit in COOT
Dear Shivu, you can define a keybinding for jiggle fit like this: def key_binding_func_7(): using_active_atom(fit_to_map_by_random_jiggle, aa_imol, aa_chain_id, aa_res_no, aa_ins_code, 100, 1.0) add_key_binding(Jiggle Fit, J, lambda: key_binding_func_7()) and put it to my_keybindings.py in ~/.coot-preferences Best regards, Jan On 04/29/2015 01:35 AM, onetwo wrote: Dear All, I have a query related to the jiggle fit option in Coot. I want to use it to fit the model in the map obtained by electron microscopy. My query may seem very lame and naive, but how we can use this option, do we have to go to scripts via: calculate scripting scheme and enter the values in: fit-to-map-by-random-jiggle imol chain_id resno ins_code n_trials jiggle_scale_factor I am not able to use it though. is there any other option in GUI available. what does the ins_code here refer to ? and if by resno is the residue number or the number of residues, how we can specify the residues to use for the jiggle fit. I have converted the mrc map to ccp4 format using em2em, when I open it in coot, i am able to do the model/fit/refine but the undo option doesn't work. Kindly help. Looking forward for the help -- Shivu https://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? Get your own *FREE* website, *FREE* domain *FREE* mobile app with Company email. *Know More * http://track.rediff.com/click?url=___http://businessemail.rediff.com?sc_cid=sign-1-10-13___cmp=hostlnk=sign-1-10-13nsrv1=host -- Jan Stransky, PhD student Institute of Biotechnology, AS CR Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
Re: [COOT] RSR behavior in coot 0.8.1
It is good to have this elasticity configurable, but I agree with dr Roberts, that preferable default value should be to give usage as previous. Draging a single atom is always possible with pressing Ctrl. However, what would be sometimes useful, is possibility to drag several atom - not one, but not whole residue. Good for fitting long sidechains like Arg or Lys. Maybe possible with temporarily changed this new value... Jan Dne 24. 3. 2015 v 23:01 Roberts, Sue A - (suer) napsal(a): I'm wondering why this was changed. Does the optimum elasticity change with resolution, map quality, or another experimental limitation? Or does it more of a user preference? Over the years, I've gotten used to being able to drag a loop that is out of density into density and watch as it magically sorts itself into the (often) proper conformation in less time that I could build it myself. I miss this behavior and would like COOT to, again, do such things for me. (OK, that's a lazy approach, but there's always undo, so it's often worth a try). I've tried various settings of refinement_drag_elasticity and I need to lower it to 0.5 or so before any semblance of earlier behavior appears. Sue On Mar 24, 2015, at 1:53 PM, Kevin Jude wrote: We've noticed a new behavior in real space refinement in coot 0.8.1 whereby dragged atoms are more tightly restrained to their initial positions than in earlier versions. This seems to be described in the release notes by: o BUG-FIX: The amount that the other atoms ove with moving the picked atom has been reduced (but is configurable) The old behavior was often useful for moving out of a local minimum. How can I configure this? Best wishes Kevin Jude Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 or 520 621 4168 s...@email.arizona.edu http://www.cbc.arizona.edu/facilities/x-ray_diffraction -- Jan Stransky, PhD student Institute of Biotechnology, AS CR Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
[COOT] Water check without map
Dear all, it is not possible to run Check/Delete waters from Validation menu without choosen map. Even though I switch off criterias which actually needs map (r.m.s.d. map level and difference map check). I know, minor issue, but it is a bit illogical and can be useful to check contacts even without map... Best regards, Jan -- Jan Stransky, PhD student Institute of Biotechnology, AS CR Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
[COOT] Sekvence Alignmutate
Hi all, I have experienced strange behavior of Alignmutate tool. I wanted to correct few differences in sequence with it, and there is a place in the sequence looking like this: orginal sequence: XYZDSUVW new sequence: XYZSPUVW which ends after Alignmutate like this: XYZDS-UVW XYZ-SPUVW and more over numbering of residues changes because of it. And that is wrong. Therefore, I suggest to incorporate an option Treat sequence rigid or something like that, which would just found best match without any missing residues. Yes, Mutate residue range did the trick, but it has slightly different purpose, I think. The second problem I have noticed, that it seems that with both mutate-sequence tools (Alignmutate, Mutate residue range), it mutates all the residues, including those which remains same. That cause displacement of correctly placed residues. Best regards, Jan -- Jan Stransky, PhD student Institute of Biotechnology, AS CR Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
Re: [COOT] get difference map peak values
Hi, setting the difference map as scroll and scrolling around the peak visibility won't help? You can see current level in r.m.s.d. and e/A^3 on the top of window when scrolling map. In my opinion getting more precise number then with this way is nonsense anyway, because the map numbers change with every refmac5/phenix.refine run. Jan On 11/04/2014 01:31 AM, Murpholino Peligro wrote: Hi everybody. Can I get difference map peak values with a single click? (clicking on a negative/positive density) How? (I think I read this somewhere, but google or looking at the mailing list is not helping) Thanks -- Jan Stransky, PhD student Institute of Biotechnology, AS CR Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
Re: [COOT] Display problem in coot _residue fit
It really looks like a bug. Or it has something to do with molecule libraries and it happend somehow that those links are defined in CIF file. Then they would be applied with those two operations. May be try to update both coot and libs? On 11/05/2014 06:16 AM, 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 -- Jan Stransky, PhD student Institute of Biotechnology, AS CR Laboratory of structure and function of biomolecules Nad Safinou II 366 Vestec Czech Republic Tel.: +420226201570
