Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to another
Dear Stuart Thank you for your reply Yes, you are right. The reports are not displayed for any project (not just the imported ones). What should I look at to solve the problem ? Stefano - Mail original - > De: "Stuart McNicholas" > À: "Stefano Trapani" > Cc: CCP4BB@jiscmail.ac.uk > Envoyé: Vendredi 23 Février 2024 11:08:09 > Objet: Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to > another > Dear Stefano, > I wonder if the problem is simply displaying any ccp4i2 reports on > the new computer, rather than just the imported ones. Have you tried > creating a completely new project and seeing if anything works in > that? There are some potential things to think about in the log file. > > Best wishes, > Stuart > > > On Fri, 23 Feb 2024 at 10:00, Stefano Trapani > wrote: >> >> Hi >> >> I am having troubles in transferring my ccp4i2 projects from one computer >> (MacOS) to another (Linux). >> First, I export my projects on the first computer by using the "Manage >> Projects >> / Export" tool. >> Then, I copy the .ccp4_project.zip files to the second computer. >> Finally, I import the .ccp4_project.zip files on the second computer by using >> the "Manage Projects / Import" tool (see screenshot 1.png) >> Import runs OK (see screenshot 2.png), but all job reports seem to disappear >> (see screenshot 3.png). After a while, the message "ERR_CONNECTION_TIMED_OUT" >> appears in the report frame (see 3.png). >> >> What could be the reason of that ? >> >> I am attaching a log file. >> >> Best >> >> Stefano Trapani >> >> Maître de Conférences >> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani >> - >> Centre de Biologie Structurale (CBS) >> 29 rue de Navacelles >> 34090 MONTPELLIER Cedex, France >> >> Tel : +33 (0)4 67 41 77 29 >> Fax : +33 (0)4 67 41 79 13 >> - >> Université de Montpellier >> CNRS UMR 5048 >> INSERM UMR 1054 >> - >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] superpose crystal objects in CCP4MG or other software
Hi This is more or less what I do in PyMOL, but I was looking for some quicker and more user-friendly tool. A (less cumbersome ?) procedure is the following (thanks to Arwen Pearson for the hint). It requires external manipulation of the PDB files and some matrix calculations (I have not tested it on pbdx/mmcif files): 1. get the rotation/translation matrix (R,t) one wants to apply 2. rotate/translate the coordinates in the PDB file 3. get the (S,U) matrix/vector from the SCALEn cards in the PDB header 4. change them according to the R,t transformation: newS = S·transpose(R) newU = U - S·transpose(R)·t 5. open the modified PDB file in the molecualr graphics program and symmetry expand. I have just checked that this works in Coot and CCP4MG, but not in PyMOL 2.2.0 (why ?). With UCSF Chimera, steps 1-4 seem to be already built-in in the superposition tools. I think that the possibility of easily performing steps 1-4 (i.e. changing the origin and orientation of a crystal with respect to the orthogonal reference frame) would be a valuable tool in CCP4MG (or any other graphics crystallographic software). Best regards. Stefano Trapani Le 2021-06-03 01:49, Jon Cooper a écrit : > I am thinking this could be done using pdbset to apply symops and origin > shifts, etc, with a bit of checking in Coot, creative chain-ID's and some > trial and error? Or using Coot to apply symops and save the resulting pdb's > with different chain ID's and then concatenate them into a mini-lattice? > Cheers, Jon.C. > > Sent from ProtonMail mobile > > Original Message ---- > On 2 Jun 2021, 15:42, Stefano Trapani wrote: > > Hi Boaz > > Thank you. > > That works in Chimera (first superpose, then symmetry expand) but not in > CCP4MG (independently of the order of the operations). > > It would be nice to have an equivalent option implemented in CCP4MG. > > Best regards > > Stefano Trapani > > Le 2021-06-02 16:20, Boaz Shaanan a écrit : > > Hi Stefano, > Did you try first to expand a unit cell in each lattice (using its symmops) > and then superimpose two molecules from each lattice? Perhaps the expanded > lattice wil move with the moving molecule? > I don't know how to do this in ccp4mg but I think it's possible in Chimera. > > My 2p. > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On Jun 2, 2021 16:59, Stefano Trapani wrote: > > Dear Stuart > > That does not work. > > "Transform coordinates" seems to move molecules, but not the crystal symmetry > elements (no update of the crystal symmetry operation matrices), so that > crystal symmetry expansion after "Transform coordinates" does not generate a > rotated/translated version of the "whole" crystal, but a new (different) > crystal packing. > > Stefano > > Le 2021-06-02 15:14, Stuart McNicholas a écrit : > > Dear Stefano, > It might be possible to do what you want in a roundabout way: > > i) Apply matrix to molecule: Molecule Icon -> Transform coordinates -> > Enter transformation > ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file. > iii) Load in the saved molecule > iv) For the new file: Molecule Icon -> Create crystal object. > > (Maybe ii) and iii) are not necessary.) > > Best wishes, > Stuart > > On Wed, 2 Jun 2021 at 13:50, Stefano Trapani wrote: > Dear all I would like to visually compare (using some molecular graphics > software) the crystal packing of two different crystal forms of the same > protein. In order to identify the similarities/differences between the > crystal packings, I need to change the default unit cell origin and > orientation of one of the crystal forms. Is there a way, in CCP4MG or other > molecular graphics software, to apply a given rotation/translation matrix to > a "crystal object" (not to a single molecular object), so that further > expansions of the object by crystal symmetry will be consistent with the new > origin/orientation ? If yes: can the transformation be defined by a > least-squares superposition between molecules from the two crystal objects ? > Best regards -- Stefano Trapani Maître de Conférences > http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] > - Centre de Biologie Structurale (CBS) 29 > rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - -- This message has been scanned for viruses and danger
Re: [ccp4bb] superpose crystal objects in CCP4MG or other software
Hi Boaz Thank you. That works in Chimera (first superpose, then symmetry expand) but not in CCP4MG (independently of the order of the operations). It would be nice to have an equivalent option implemented in CCP4MG. Best regards Stefano Trapani Le 2021-06-02 16:20, Boaz Shaanan a écrit : > Hi Stefano, > Did you try first to expand a unit cell in each lattice (using its symmops) > and then superimpose two molecules from each lattice? Perhaps the expanded > lattice wil move with the moving molecule? > I don't know how to do this in ccp4mg but I think it's possible in Chimera. > > My 2p. > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On Jun 2, 2021 16:59, Stefano Trapani wrote: > > Dear Stuart > > That does not work. > > "Transform coordinates" seems to move molecules, but not the crystal symmetry > elements (no update of the crystal symmetry operation matrices), so that > crystal symmetry expansion after "Transform coordinates" does not generate a > rotated/translated version of the "whole" crystal, but a new (different) > crystal packing. > > Stefano > > Le 2021-06-02 15:14, Stuart McNicholas a écrit : > > Dear Stefano, > It might be possible to do what you want in a roundabout way: > > i) Apply matrix to molecule: Molecule Icon -> Transform coordinates -> > Enter transformation > ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file. > iii) Load in the saved molecule > iv) For the new file: Molecule Icon -> Create crystal object. > > (Maybe ii) and iii) are not necessary.) > > Best wishes, > Stuart > > On Wed, 2 Jun 2021 at 13:50, Stefano Trapani wrote: > Dear all I would like to visually compare (using some molecular graphics > software) the crystal packing of two different crystal forms of the same > protein. In order to identify the similarities/differences between the > crystal packings, I need to change the default unit cell origin and > orientation of one of the crystal forms. Is there a way, in CCP4MG or other > molecular graphics software, to apply a given rotation/translation matrix to > a "crystal object" (not to a single molecular object), so that further > expansions of the object by crystal symmetry will be consistent with the new > origin/orientation ? If yes: can the transformation be defined by a > least-squares superposition between molecules from the two crystal objects ? > Best regards -- Stefano Trapani Maître de Conférences > http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] > - Centre de Biologie Structurale (CBS) 29 > rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 [2] -- This message has been scanned for viruses and dangerous content by MAILSCANNER [3], and is believed to be clean. - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 [2] On Jun 2, 2021 16:59, Stefano Trapani wrote: > Dear Stuart > > That does not work. > > "Transform coordinates" seems to move molecules, but not the crystal symmetry > elements (no update of the crystal symmetry operation matrices), so that > crystal symmetry expansion after "Transform coordinates" does not generate a > rotated/translated version of the "whole" crystal, but a new (different) > crystal packing. > > Stefano > > Le 2021-06-02 15:14, Stuart McNicholas a écrit : > > Dear Stefano, > It might be possible to do what you want in a roundabout way: > > i) Apply matrix to molecule: Molecule Icon -> Transform coordinates -> > Enter transformation > ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file. > iii) Load in the saved molecule > iv) For the new file: Molecule Icon -> Create crystal object. > > (Maybe ii) and iii) are not necessary.) > > Best wishes, > Stuart > > On Wed, 2 Jun 2021 at 13:50, Stefano Trapani wrote: > Dear all I would like to visually compare (using some molecular graphics > software) the crystal packing of two different crystal forms of
Re: [ccp4bb] superpose crystal objects in CCP4MG or other software
Dear Stuart That does not work. "Transform coordinates" seems to move molecules, but not the crystal symmetry elements (no update of the crystal symmetry operation matrices), so that crystal symmetry expansion after "Transform coordinates" does not generate a rotated/translated version of the "whole" crystal, but a new (different) crystal packing. Stefano Le 2021-06-02 15:14, Stuart McNicholas a écrit : > Dear Stefano, > It might be possible to do what you want in a roundabout way: > > i) Apply matrix to molecule: Molecule Icon -> Transform coordinates -> > Enter transformation > ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file. > iii) Load in the saved molecule > iv) For the new file: Molecule Icon -> Create crystal object. > > (Maybe ii) and iii) are not necessary.) > > Best wishes, > Stuart > > On Wed, 2 Jun 2021 at 13:50, Stefano Trapani wrote: > >> Dear all I would like to visually compare (using some molecular graphics >> software) the crystal packing of two different crystal forms of the same >> protein. In order to identify the similarities/differences between the >> crystal packings, I need to change the default unit cell origin and >> orientation of one of the crystal forms. Is there a way, in CCP4MG or other >> molecular graphics software, to apply a given rotation/translation matrix to >> a "crystal object" (not to a single molecular object), so that further >> expansions of the object by crystal symmetry will be consistent with the new >> origin/orientation ? If yes: can the transformation be defined by a >> least-squares superposition between molecules from the two crystal objects ? >> Best regards -- Stefano Trapani Maître de Conférences >> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] >> - Centre de Biologie Structurale (CBS) >> 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 [2] Links: -- [1] http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [2] https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BBA=1 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] {Disarmed} AW: [ccp4bb] superpose crystal objects in CCP4MG or other software
Yes, that is the way I usually do, but it can be cumbersome. It would be easier if I could first superpose two molecules from the two crystals, and then decide in which directions to expand by crystal symmetry (I want to compare layers and rows of molecules). Best regards Stefano Le 2021-06-02 15:05, Schreuder, Herman /DE a écrit : > Dear Stefano, > > I do not know if it is possible, but as a workaround, you could first expand > your object by crystallographic symmetry and then do the superposition. > > Best, > > Herman > > VON: CCP4 bulletin board IM AUFTRAG VON Stefano > Trapani > GESENDET: Mittwoch, 2. Juni 2021 14:31 > AN: CCP4BB@JISCMAIL.AC.UK > BETREFF: [ccp4bb] superpose crystal objects in CCP4MG or other software > > Dear all > > I would like to visually compare (using some molecular graphics software) the > crystal packing of two different crystal forms of the same protein. > > In order to identify the similarities/differences between the crystal > packings, I need to change the default unit cell origin and orientation of > one of the crystal forms. > > * Is there a way, in CCP4MG or other molecular graphics software, to apply a > given rotation/translation matrix to a "crystal object" (not to a single > molecular object), so that further expansions of the object by crystal > symmetry will be consistent with the new origin/orientation ? > > * If yes: can the transformation be defined by a least-squares superposition > between molecules from the two crystal objects ? > > Best regards > > -- > Stefano Trapani > > Maître de Conférences > > http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] > > - > > Centre de Biologie Structurale (CBS) > > 29 rue de Navacelles > > 34090 MONTPELLIER Cedex, France > > Tel : +33 (0)4 67 41 77 29 > > Fax : +33 (0)4 67 41 79 13 > > - > > Université de Montpellier > > CNRS UMR 5048 > > INSERM UMR 1054 > > - > > -- > This message has been scanned for viruses and > dangerous content by MAILSCANNER [2], and is > believed to be clean. > > - > > To unsubscribe from the CCP4BB list, click the following link: > MAILSCANNER HAS DETECTED A POSSIBLE FRAUD ATTEMPT FROM > "EUR01.SAFELINKS.PROTECTION.OUTLOOK.COM" CLAIMING TO BE > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 [3] > -- > This message has been scanned for viruses and > dangerous content by MAILSCANNER [4], and is > believed to be clean. Links: -- [1] http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [2] https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mailscanner.info%2Fdata=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7Cc04bafa2734b43bcddee08d925c5059a%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C637582351009154508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000sdata=QKQlojah3a%2BPsIr%2FgVYZb93SbT98iOefgO%2FaAqM9ycM%3Dreserved=0 [3] https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7Cc04bafa2734b43bcddee08d925c5059a%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C637582351009154508%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000sdata=MpvO9vCcxjnH5sJrDptR3KPxlCl2hBMHhQJns8rSc80%3Dreserved=0 [4] http://www.mailscanner.info/ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] superpose crystal objects in CCP4MG or other software
Dear all I would like to visually compare (using some molecular graphics software) the crystal packing of two different crystal forms of the same protein. In order to identify the similarities/differences between the crystal packings, I need to change the default unit cell origin and orientation of one of the crystal forms. * Is there a way, in CCP4MG or other molecular graphics software, to apply a given rotation/translation matrix to a "crystal object" (not to a single molecular object), so that further expansions of the object by crystal symmetry will be consistent with the new origin/orientation ? * If yes: can the transformation be defined by a least-squares superposition between molecules from the two crystal objects ? Best regards -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de Biologie Structurale (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] matrix decomposition problem
Hi This is a linear-algebra question (with structural biology hidden behind...). I came across the following matrix equation : A = S X where : * A, S and X are real square matrices * A is a known (constant) matrix * S and X are unknown * S must be symmetric * X must be orthogonal I know there exist at least one solution to the equation --the polar decomposition of A-- and that this decomposition may not be unique (if A is singular). However, since S is not required to be positive-semidefinite (like in a polar decomposition), I was wondering if : * further solutions may exist * there is a criterion to establish the existence /number of these solutions * there is a practical way of calculating them -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] OT: Terminal Command-P
Le 2019-04-01 08:53, Paul Emsley a écrit : > Dear All, Sometime I use a Mac. A niggling issue I have is that, in a > Terminal, Command-P doesn't act like Alt-P in (say) a gnome-terminal try ESC-p (not simultaneously) --- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] collective term for hydrogen bonds and salt bridges
Sorry, I did not realised that. (I should have changed subject of the original post) Yes, we are not saying different things. Stefano Le 2018-09-19 17:06, Frank von Delft a écrit : > Okay. The original poster asked about hydrogen bonds and electrostatic > interactions. That's what I was referring to when I mentioned "enthalpic > interactions". > > And I think you're saying the same thing - which is cool. > > On 19/09/2018 15:06, Stefano Trapani wrote: >> Hi Frank > > I mean that, in my opinion, the term "enthalpic interaction" is >> not > appropriate to describe the hydrophobic effect, since the latter is > >> mainly driven by changes in the (system) entropy, not enthalpy. > > Table1 >> of the cited paper reports the thermodynamic functions for > transferring >> some nonpolar solutes from a few organic solvents to > water. The author >> says that: "The data collected in Table 1 clearly > show that the >> thermodynamic barrier to the solution process is > entropic rather than >> enthalpic". > > Also, after a brief description of two theoretical models >> (the > cavity-based model and the clathrate cage model) the author states: > >> "It is important to point out that both the cavity-based model and > the >> clathrate cage model rest upon the fact that the hydrophobic > effect is >> entropy, not enthalpy driven. The models differ only in how > they explain >> the source of the entropy loss." > > Best > > Stefano > > > > Le 2018-09-19 >> 14:41, Frank von Delft a écrit : >> >> Hi Stefano - could you elaborate? >> >> Certainly the medicinal chemists >> >> go on a great deal about how >> deltaH balances deltaS and how it's >> >> bloody hard to know what is >> what even when you try to measure it. >> >> Which is what that abstract >> also goes on about. >> >> >> >> On >> >> 19/09/2018 10:54, Stefano Trapani wrote: >>> >>> Le 2018-09-19 11:59, >> >> Frank von Delft a écrit : >>> >>> I believe medicinal chemists do indeed >> >> talk about "enthalpic >>> interactions". Frank >>> >>> Not a good choice >> >> either (à mon avis ...) >>> >>> >>> >>> >>> >>> The Real Reason Why Oil >> >> and Water Don't Mix >>> >>> Todd P. Silverstein Journal of Chemical >> >> Education *1998* /75/ >>> (1), 116 >>> >>> DOI: 10.1021/ed075p116 >>> >>> >> >> https://pubs.acs.org/doi/abs/10.1021/ed075p116 [1] >>> >>> >>> Stefano >> >> >>> >>> >>> >>> On 19/09/2018 10:40, Stefano Trapani wrote: >>> >>> Le >> >> 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : >>> >>> (where >> >> hydrophobic interactions result from van der Waals forces >>> in an aqueous environment). >>> >>> Hi >>> >>> I am not sure that, if one is to give a concise definition of >>> hydrophobic "interactions", this would be a convenient one, >>> because it may lead someone to identify vdW forces as the main >>> factor that maintains apolar aggregated molecules together in >>> aqueous environment. I have seen many students (and PhD's) >>> believing to the equality: hydrophobic 'forces'=vdW forces (and >>> not understanding, for example, that the side chains of a Ser and >>> an Ile can also establish vdW interactions). >>> >>> It is true that apolar groups that aggregate establish van der >>> Waals interactions (like any molecule in contact with another >>> one) but these microscopic (real) forces are not (as far as I >>> know) the main reason of aggregation in aqueous environment. >>> >>> The hydrophobic effect seem to be of a mainly entropic nature >>> (and it has much more to do with hydrogen bonds than van der >>> Waals forces): >>> >>> https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [2] >>> >>> https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [3] >>> >>> Being mainly of an entropic nature, hydrophobic "contacts" are >>> not the direct result of real microscopic "forces" that act >>> between apolar groups. The terms "forces" and "interactions" in >>> wide
Re: [ccp4bb] collective term for hydrogen bonds and salt bridges
Hi Frank I mean that, in my opinion, the term "enthalpic interaction" is not appropriate to describe the hydrophobic effect, since the latter is mainly driven by changes in the (system) entropy, not enthalpy. Table1 of the cited paper reports the thermodynamic functions for transferring some nonpolar solutes from a few organic solvents to water. The author says that: "The data collected in Table 1 clearly show that the thermodynamic barrier to the solution process is entropic rather than enthalpic". Also, after a brief description of two theoretical models (the cavity-based model and the clathrate cage model) the author states: "It is important to point out that both the cavity-based model and the clathrate cage model rest upon the fact that the hydrophobic effect is entropy, not enthalpy driven. The models differ only in how they explain the source of the entropy loss." Best Stefano Le 2018-09-19 14:41, Frank von Delft a écrit : > Hi Stefano - could you elaborate? > > Certainly the medicinal chemists go on a great deal about how deltaH balances > deltaS and how it's bloody hard to know what is what even when you try to > measure it. Which is what that abstract also goes on about. > > On 19/09/2018 10:54, Stefano Trapani wrote: > > Le 2018-09-19 11:59, Frank von Delft a écrit : > > I believe medicinal chemists do indeed talk about "enthalpic interactions". > Frank > > Not a good choice either (à mon avis ...) > > > > THE REAL REASON WHY OIL AND WATER DON'T MIX > > Todd P. Silverstein > Journal of Chemical Education 1998 _75_ (1), 116 > > DOI: 10.1021/ed075p116 > > https://pubs.acs.org/doi/abs/10.1021/ed075p116 [2] > > Stefano > > On 19/09/2018 10:40, Stefano Trapani wrote: > > Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : > > (where hydrophobic interactions result from van der Waals forces in an > aqueous environment). > > Hi > > I am not sure that, if one is to give a concise definition of hydrophobic > "interactions", this would be a convenient one, because it may lead someone > to identify vdW forces as the main factor that maintains apolar aggregated > molecules together in aqueous environment. I have seen many students (and > PhD's) believing to the equality: hydrophobic 'forces'=vdW forces (and not > understanding, for example, that the side chains of a Ser and an Ile can also > establish vdW interactions). > > It is true that apolar groups that aggregate establish van der Waals > interactions (like any molecule in contact with another one) but these > microscopic (real) forces are not (as far as I know) the main reason of > aggregation in aqueous environment. > > The hydrophobic effect seem to be of a mainly entropic nature (and it has > much more to do with hydrogen bonds than van der Waals forces): > > https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [3] > > https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [4] > > Being mainly of an entropic nature, hydrophobic "contacts" are not the direct > result of real microscopic "forces" that act between apolar groups. The terms > "forces" and "interactions" in widely used expressions like "hydrophobic > forces" and "hydrophobic interactions" are somehow misleading. > > Best > > --- > Stefano Trapani > > Maître de Conférences > http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] > - > Centre de Biochimie Structurale (CBS) > 29 rue de Navacelles > 34090 MONTPELLIER Cedex, France > > Tel : +33 (0)4 67 41 77 29 > Fax : +33 (0)4 67 41 79 13 > - > Université de Montpellier > CNRS UMR 5048 > INSERM UMR 1054 > - > > -- > This message has been scanned for viruses and > dangerous content by MAILSCANNER [5], and is > believed to be clean. > > - > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 [6] -- This message has been scanned for viruses and dangerous content by MAILSCANNER [5], and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MAILSCANNER [5], and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MAILSCANNER [5], and is believed to be clean. Links: -- [1] http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [2] https://pubs.acs.org/doi/abs/10.1021/ed075p116 [3] https://en.wikipedia.org/wiki/Hydrophobic_effe
Re: [ccp4bb] collective term for hydrogen bonds and salt bridges
Le 2018-09-19 11:59, Frank von Delft a écrit : > I believe medicinal chemists do indeed talk about "enthalpic interactions". > Frank Not a good choice either (à mon avis ...) THE REAL REASON WHY OIL AND WATER DON'T MIX Todd P. Silverstein Journal of Chemical Education 1998 _75_ (1), 116 DOI: 10.1021/ed075p116 https://pubs.acs.org/doi/abs/10.1021/ed075p116 [6] Stefano > On 19/09/2018 10:40, Stefano Trapani wrote: > > Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : > > (where hydrophobic interactions result from van der Waals forces in an > aqueous environment). > > Hi > > I am not sure that, if one is to give a concise definition of hydrophobic > "interactions", this would be a convenient one, because it may lead someone > to identify vdW forces as the main factor that maintains apolar aggregated > molecules together in aqueous environment. I have seen many students (and > PhD's) believing to the equality: hydrophobic 'forces'=vdW forces (and not > understanding, for example, that the side chains of a Ser and an Ile can also > establish vdW interactions). > > It is true that apolar groups that aggregate establish van der Waals > interactions (like any molecule in contact with another one) but these > microscopic (real) forces are not (as far as I know) the main reason of > aggregation in aqueous environment. > > The hydrophobic effect seem to be of a mainly entropic nature (and it has > much more to do with hydrogen bonds than van der Waals forces): > > https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [2] > > https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [3] > > Being mainly of an entropic nature, hydrophobic "contacts" are not the direct > result of real microscopic "forces" that act between apolar groups. The terms > "forces" and "interactions" in widely used expressions like "hydrophobic > forces" and "hydrophobic interactions" are somehow misleading. > > Best > > --- > Stefano Trapani > > Maître de Conférences > http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] > - > Centre de Biochimie Structurale (CBS) > 29 rue de Navacelles > 34090 MONTPELLIER Cedex, France > > Tel : +33 (0)4 67 41 77 29 > Fax : +33 (0)4 67 41 79 13 > - > Université de Montpellier > CNRS UMR 5048 > INSERM UMR 1054 > - > > -- > This message has been scanned for viruses and > dangerous content by MAILSCANNER [4], and is > believed to be clean. > > - > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 [5] -- This message has been scanned for viruses and dangerous content by MAILSCANNER [4], and is believed to be clean. Links: -- [1] http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [2] https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [3] https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [4] http://www.mailscanner.info/ [5] https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BBA=1 [6] https://pubs.acs.org/doi/abs/10.1021/ed075p116 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] collective term for hydrogen bonds and salt bridges
Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : > (where hydrophobic interactions result from van der Waals forces in an > aqueous environment). Hi I am not sure that, if one is to give a concise definition of hydrophobic "interactions", this would be a convenient one, because it may lead someone to identify vdW forces as the main factor that maintains apolar aggregated molecules together in aqueous environment. I have seen many students (and PhD's) believing to the equality: hydrophobic 'forces'=vdW forces (and not understanding, for example, that the side chains of a Ser and an Ile can also establish vdW interactions). It is true that apolar groups that aggregate establish van der Waals interactions (like any molecule in contact with another one) but these microscopic (real) forces are not (as far as I know) the main reason of aggregation in aqueous environment. The hydrophobic effect seem to be of a mainly entropic nature (and it has much more to do with hydrogen bonds than van der Waals forces): https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [1] https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [2] Being mainly of an entropic nature, hydrophobic "contacts" are not the direct result of real microscopic "forces" that act between apolar groups. The terms "forces" and "interactions" in widely used expressions like "hydrophobic forces" and "hydrophobic interactions" are somehow misleading. Best --- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - Links: -- [1] https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [2] https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] definition of "apo" and alternatives?
See also the IUPAC reccomandations : https://goldbook.iupac.org/html/A/A00417.html https://goldbook.iupac.org/html/H/H02836.html --- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - Le 2018-01-31 15:43, F.Xavier Gomis-Rüth a écrit : > Hi Johannes, > > this is normal textbook knowledge, which got perverted over time and > misusage. Just check with a serious dictionary like Merrian Webster or > > even the Wikipedia (see below). > > Best regards, > > Xavier > > https://www.merriam-webster.com/dictionary/apoenzyme [1] > > https://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Apoenzyme_and_Holoenzyme > [2] > > https://www.biology-online.org/dictionary/Apoenzyme [3] > > https://en.wikipedia.org/wiki/Enzyme [4] > > On 31/1/18 15:33, Johannes Cramer wrote: > >> Dear collegues, >> >> a while ago, there was a discussion in the board on the term apo-structure >> as a way to descibe a native, free, or unbound protein (no ligands). I think >> the conclusion was that an apo-form is a halo enzyme lacking a cofactor and >> should not be used as a substitute for "unbound". >> We were recently asked by a reviewer to change "unbound" to "apo" in a text. >> We are weighing our options at the moment. Just comply and change it or >> "teach" the reviewer something... >> Can anyone share experiences with similar situations? Can anyone point out a >> publication on the term? >> >> Cheers, >> Johannes > > -- > > -- > This message has been scanned for viruses and > dangerous content by MAILSCANNER [5], and is > believed to be clean. Links: -- [1] https://www.merriam-webster.com/dictionary/apoenzyme [2] https://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Apoenzyme_and_Holoenzyme [3] https://www.biology-online.org/dictionary/Apoenzyme [4] https://en.wikipedia.org/wiki/Enzyme [5] http://www.mailscanner.info/ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] Some TLS issues in REFMAC5
sin refine.1.tls # tlsout refine.2b.tls # ./refine.2b.log: Data line--- refi type rest reso 1.6 ./refine.2b.log: Data line--- refi bref iso ./refine.2b.log: Data line--- refi tlsc 1 ./refine.2b.log: Data line--- ncycl 1 ./refine.2b.log: Data line--- END ./refine.2b.log: Data line--- REFMAC_5.8.0158 ./refine.2b.log: Data line--- TLS From REFMAC ./refine.2b.log: Data line--- RANGE 'A 1.' 'A 83.' ALL ./refine.2b.log: Data line--- ORIGIN 14.408 -11.294 0.204 ./refine.2b.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 -0.0132 0.0145 ./refine.2b.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 -1.0778 0.8265 ./refine.2b.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 0.2451 0.0292 0.2475 -0.3305 ./refine.2b.pdb:REMARK 3 U VALUES : RESIDUAL ONLY ./refine.2b.pdb:ATOM 1 N ALA A 1 19.624 -3.183 8.094 1.00 11.31 N ./refine.2b.pdb:ATOM 2 CA ALA A 1 19.857 -4.525 7.537 1.00 10.72 C ./refine.2b.pdb:ATOM 3 CB ALA A 1 19.749 -5.555 8.682 1.00 11.14 C ./refine.2b.pdb:ATOM 4 C ALA A 1 18.904 -4.806 6.397 1.00 10.38 C ./refine.2b.pdb:ATOM 5 O ALA A 1 17.697 -4.379 6.389 1.00 11.21 O ## RUN 2c : run 1 TLS cycle + 0 REFI cycle starting from run 1 output # refmac5 xyzin refine.1.pdb # hklin 2pm1_unique.mtz # xyzout refine.2c.pdb # hklout refine.2c.mtz # tlsin refine.1.tls # tlsout refine.2c.tls # ./refine.2c.log: Data line--- refi type rest reso 1.6 ./refine.2c.log: Data line--- refi bref iso ./refine.2c.log: Data line--- refi tlsc 1 ./refine.2c.log: Data line--- ncycl 0 ./refine.2c.log: Data line--- END ./refine.2c.log: Data line--- REFMAC_5.8.0158 ./refine.2c.log: Data line--- TLS From REFMAC ./refine.2c.log: Data line--- RANGE 'A 1.' 'A 83.' ALL ./refine.2c.log: Data line--- ORIGIN 14.408 -11.294 0.204 ./refine.2c.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 -0.0132 0.0145 ./refine.2c.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 -1.0778 0.8265 ./refine.2c.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 0.2451 0.0292 0.2475 -0.3305 ./refine.2c.pdb:REMARK 3 U VALUES : RESIDUAL ONLY ./refine.2c.pdb:ATOM 1 N ALA A 1 19.625 -3.182 8.099 1.00 24.22 N ./refine.2c.pdb:ANISOU 1 N ALA A 1 3456 2974 2771 -686 -241 -1002 N ./refine.2c.pdb:ATOM 2 CA ALA A 1 19.856 -4.525 7.538 1.00 21.45 C ./refine.2c.pdb:ANISOU 2 CA ALA A 1 2928 2783 2437 -578 -335 -755 C ./refine.2c.pdb:ATOM 3 CB ALA A 1 19.748 -5.559 8.676 1.00 22.64 C ./refine.2c.pdb:ANISOU 3 CB ALA A 1 3156 3160 2286 -496 -469 -696 C ./refine.2c.pdb:ATOM 4 C ALA A 1 18.899 -4.809 6.397 1.00 18.57 C ./refine.2c.pdb:ANISOU 4 C ALA A 1 2540 2292 2220 -439 -161 -563 C ./refine.2c.pdb:ATOM 5 O ALA A 1 17.699 -4.379 6.386 1.00 19.18 O ./refine.2c.pdb:ANISOU 5 O ALA A 1 2718 2262 2304 -345 8 -562 O ## RUN 2d : run 0 TLS cycle + 1 REFI cycle starting from run 1 output # refmac5 xyzin refine.1.pdb # hklin 2pm1_unique.mtz # xyzout refine.2d.pdb # hklout refine.2d.mtz # tlsin refine.1.tls # tlsout refine.2d.tls # ./refine.2d.log: Data line--- refi type rest reso 1.6 ./refine.2d.log: Data line--- refi bref iso ./refine.2d.log: Data line--- refi tlsc 0 ./refine.2d.log: Data line--- ncycl 1 ./refine.2d.log: Data line--- END ./refine.2d.log: Data line--- REFMAC_5.8.0158 ./refine.2d.log: Data line--- TLS From REFMAC ./refine.2d.log: Data line--- RANGE 'A 1.' 'A 83.' ALL ./refine.2d.log: Data line--- ORIGIN 14.408 -11.294 0.204 ./refine.2d.log: Data line--- T 0.0146 0.0216 0.0348 -0.0171 -0.0132 0.0145 ./refine.2d.log: Data line--- L 5.7967 6.9434 7.6528 -0.1751 -1.0778 0.8265 ./refine.2d.log: Data line--- S -0.1069 0.0961 0.0131 -0.1165 0.2451 0.0292 0.2475 -0.3305 ./refine.2d.pdb:REMARK 3 U VALUES : RESIDUAL ONLY ./refine.2d.pdb:ATOM 1 N ALA A 1 19.621 -3.183 8.093 1.00 11.24 N ./refine.2d.pdb:ATOM 2 CA ALA A 1 19.857 -4.524 7.537 1.00 10.69 C ./refine.2d.pdb:ATOM 3 CB ALA A 1 19.748 -5.555 8.682 1.00 11.10 C ./refine.2d.pdb:ATOM 4 C ALA A 1 18.905 -4.806 6.397 1.00 10.36 C ./refine.2d.pdb:ATOM 5 O ALA A 1 17.698 -4.380 6.390 1.00 11.19 O -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction
Dear Pascal have a look at : https://doi.org/10.1107/S0907444910002763 Acta Cryst. (2010). D66, 514-521 Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions S. Trapani, G. Schoehn, J. Navaza and C. Abergel Best, --- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani - Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 - Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 - Le 2016-10-25 03:49, Pascal Egea a écrit : > Dear All, > > I would like to know if it is possible to use a low resolution EM > reconstruction of a complex obtained in negative stain EM (not cryo EM) to > help molecular replacement in a 4.5A resolution X-ray diffraction data set of > the same complex > I am aware of the possibility of using low resolution cryoEM maps for MR as > described in the review from Jackson et al in Nature Protocols but I was > wondering if there is an intrinsically impossibility for negative stain > reconstructions. > > Any thoughts or advice will be greatly appreciated. > > Best, > -- > > Pascal F. Egea, PhD > Assistant Professor > UCLA, David Geffen School of Medicine > Department of Biological Chemistry > Boyer Hall room 356 > > 611 Charles E Young Drive East > Los Angeles CA 90095 > office (310)-983-3515 > lab (310)-983-3516 > email pegea at mednet.ucla.edu [1] > -- > This message has been scanned for viruses and > dangerous content by MAILSCANNER [2], and is > believed to be clean. Links: -- [1] http://mednet.ucla.edu [2] http://www.mailscanner.info/ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] AMoRe fails to use model coordinates
You could try the stand-alone version of AMoRe from Jorge Navaza's web site. http://mem.ibs.fr/JORGE/index.html Stefano TRAPANI Maître de Conférences Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM1; UM2; INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 http://www.cbs.cnrs.fr/spip.php?rubrique182PERS=Stefano%20Trapani On Wed, April 27, 2011 13:14, Chris Richardson wrote: One of our group was having trouble getting AMoRe to use model coordinates as a trial model. I've replicated this using the data from the tutorial at http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial-amore.html It fails using CCP4 6.1.13 on OS 10.6.7 (compiled from Fink) and Ubuntu 8.0.4 LTS (binary installation from ccp4.ac.uk). The tutorial uses a PDB file of model coordinates (model.pdb). As I understand it, AMoRe is supposed to generate an SF table file from this. Instead, AutoAMoRe seems to be looking for an mtz file. The logs look like this: *** * Information from CCP4Interface script *** There is no SF Table file for the map of the model coordinates Generating the file /home/foop/temp/amoretest/AmoreModel_MR_trial.tab *** File: /home/foop/temp/amoretest/AmoreModel_MR_trial.mtz Cannot be opened for reading CCP4 library signal ccp4_general:Cannot find input file (Error) raised in ccp4setenv amore: Cannot find input file Times: User: 0.0s System:0.0s Elapsed: 0:00 *** * Information from CCP4Interface script *** The program run with command: /sw/share/xtal/ccp4-6.1.13/bin/amore HKLIN /home/foop/temp/amoretest/AmoreModel_MR_trial.mtz HKLPCK0 /tmp/foop/AmoreTest_1_3_hkl.tmp TABLE1 /home/foop/temp/amoretest/AmoreModel_MR_trial.tab has failed with error message Last system error message: No such file or directory amore: Cannot find input file *** The command script generating this is: *** /tmp/foop/AmoreTest_1_4_com.tmp *** title AmoreTest sortfun - MODEL - resolution 60.0 - 3.0 labin FC=FC PHIC=PHIC ## This script run with the command ## # /sw/share/xtal/ccp4-6.1.13/bin/amore HKLIN /home/foop/temp/amoretest/AmoreModel_MR_trial.mtz HKLPCK0 /tmp/foop/AmoreTest_1_3_hkl.tmp TABLE1 /home/foop/temp/amoretest/AmoreModel_MR_trial.tab If anyone can suggest a way around this problem (other than using an alternative MR program), I'd be grateful. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Passerelle antivirus CBS -- Passerelle antivirus CBS
[ccp4bb] theta
A trivial question about terms. What should be called scattering angle in Bragg's low: theta or 2*theta ? In my view, the scattering angle is 2*theta (the angle between the incident and the scattering directions), while theta is the reflection angle (the angle between the incident or diffracted ray and the reflecting crystal planes). However, I hear sometimes calling theta the scattering angle. Is this just a misuse of the term ? Stefano TRAPANI Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM1; UM2; INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13
[ccp4bb] Alternative origin list in CCP4 documentation
Dear all In the CCP4 documentation about alternative origins for spacegroups (http://www.ccp4.ac.uk/dist/html/alternate_origins.html) one can find the following table: _ P 1 m 1 SG No: 6 (Standard short HM symbol: Pm) Number of alternate origins: 2 This is a polar spacegroup: the origin is not fixed along the C axis Norigin Xo Yo Zo 1 0. 0. ?? 2 0. 0.5000 ?? _ However, I would expect that the choice of the origin for this space group be arbitrary on the mirror plane, i.e.: _ The origin is not fixed in the AC plane Norigin Xo Yo Zo 1 ?? 0. ?? 2 ?? 0.5000 ?? _ Similarly, I would expect that the tables for space group P1c1 (No 7), C1m1 (No 8) be different from those in the documentation (I have not checked for other space groups ...) Is it correct what I am saying or am I missing something? Thank you --- Stefano TRAPANI Centre de Biochimie Structurale (CBS) CNRS UMR 5048; UM 1; UM 2; INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13
