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 tes

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

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?

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 écr

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

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,

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 th

Re: [ccp4bb] {Disarmed} AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

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

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

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:

Re: [ccp4bb] {Disarmed} AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

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 sof

[ccp4bb] AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

@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

[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 orienta

Re: [ccp4bb] Superpose program in CCP4

, October 31, 2016 10:14:12 AM Clement Angkawidjaja wrote: > Dear Wenhe, > > Have you looked at the Additional Log File from Superpose? > > Cheers, > Clement > > -Original Message- > From: WENHE ZHONG > Sent: Sunday, October 30, 2016 12:47 AM > To: CCP4BB@

Re: [ccp4bb] Superpose program in CCP4

Dear Wenhe, Have you looked at the Additional Log File from Superpose? Cheers, Clement -Original Message- From: WENHE ZHONG Sent: Sunday, October 30, 2016 12:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Superpose program in CCP4 Dear all, I always use the SUPERPOSE tool in

Re: [ccp4bb] Superpose program in CCP4

es, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP4 bulletin board on behalf of Edward Berry Sent: Sunday, October 30, 2016 9:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Super

Re: [ccp4bb] Superpose program in CCP4

WenHe, I'm not sure if you want to superimpose a number of structures (as rmsd would imply) or just compare two structures. If you want a complete list of the distances between corresponding atoms in two pdb files of identical sequence, you can use the fortran program http://www.cytbc1.net/berry/fo

Re: [ccp4bb] Superpose program in CCP4

I think superpose does not output CAs outwith a certain cut-off based on the quality of the superimposition. It does try to match as many as give reasonable RMSDs - but it is mainly focussed on the residues in matching secondary elements as this is where it starts the superimposition. A simpler ap

Re: [ccp4bb] Superpose program in CCP4

Dear Wenhe, Besides this advice, have a look at the http://webapps.embl-hamburg.de/rapido/ server. Sometimes its goodo to re-think of what you want to do, and wonder why its not easily doable in software (perhaps because its not the right thing to do …)

Re: [ccp4bb] Superpose program in CCP4

Dear Wenhe, No 3D superpose tool will always align/map all Calphas. If in the one protein the loop turns left, and in the other it turns right, then mapping those loops is meaningless and thus not done by good software. The other problem is that often two proteins that get compared do not eve

[ccp4bb] Superpose program in CCP4

Dear all, I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph (instead of using the graph automatically made by the program). However, there are many atoms missing in the RMSD list. In the set

Re: [ccp4bb] superpose bug?

Yes, certainly, guilty as sin :) Thanks, Eugene From: Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, November 19, 2014 11:22 AM To: Krissinel, Eugene (STFC,RAL,SC); ccp4bb Subject: Re: [ccp4bb] superpose bug? Hi Eugene, would you update the

Re: [ccp4bb] superpose bug?

gt; command-prompt options. > > Hope this helps, > > Eugene > > > > From: Lijun Liu [lijunli...@gmail.com] > Sent: Wednesday, November 19, 2014 12:17 AM > To: ccp4bb > Subject: [ccp4bb] superpose bug? > > Hi: > > I have a bunch of p

Re: [ccp4bb] superpose bug?

Subject: [ccp4bb] superpose bug? Hi: I have a bunch of pdb files and would like to superpose them to one of them based on secondary structure matching. I would like to get a script to do so (not a one-by-one job by hand). I tried superpose but it seemed to have some problems with output option

[ccp4bb] superpose bug?

Hi: I have a bunch of pdb files and would like to superpose them to one of them based on secondary structure matching. I would like to get a script to do so (not a one-by-one job by hand). I tried superpose but it seemed to have some problems with output option. Assuming C.pdb is the output p

Re: [ccp4bb] Superpose

My guess is that only atom pairs that are superposed to some measure of distance between them, are output. Can't say that I checked lsqkab code this weekend, but documentation does not suggest anything like that. Is this a problem for you? note that you can use other aligners/superposers in CCP

Re: [ccp4bb] Superpose

Hi Eugene, thanks for your response. Yes, the program is LSQKAB. No aligment is pursued, the aim is just to superpose models and get all the information as tables. Looking at old jobs (CCP4 6.2: LSQKAB version 6.2 : 13/03/09), it seems it always did the same, the results on xyz and B rms ju

Re: [ccp4bb] Superpose

I would say the guess is a wrong one. SS superposition is used only as a seed for further refinement. SSM (superpose) outputs all residues (not all atoms) and marks those which get aligned. Then, superposition is done using aligned residues. Alignment != superposition. As to LSQKAB, it's pure s

Re: [ccp4bb] Superpose

Dear H, you are referring to superpose, but your logfile lists the output from LSQKAB, which are two different programs. According to the man-page of superpose, it uses secondary structure elements for superposition, so maybe the missing atoms are those not part of a helix and not part of a strand

Re: [ccp4bb] Superpose

I should have said that this is the comparison of two crystaline states of the same molecule, the sequences are identical. Best H hbo...@pasteur.edu.uy ha escrito: Dear all, Why does (if it is suppossed to do so) Superpose output results for a subset of atoms only? See a summary of log fi

[ccp4bb] Superpose

Dear all, Why does (if it is suppossed to do so) Superpose output results for a subset of atoms only? See a summary of log file below (just the top lines, data on atoms, and final data and message). In the example, results for residues 69-76 are absent, other atoms are absent as well, but

Re: [ccp4bb] Superpose problem

.oli...@sussex.ac.uk> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 From: herohonan mailto:heroho...@163.com>> Reply-To: herohonan mailto:heroho...@163.com>> Date: Wed, 4 Jan 2012 21:16:41 +0800 To: mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] Superpose

Re: [ccp4bb] Superpose problem

Thank you for your reply! But I still wonder the differences between "Add superimposed PDB file to the ensemble" and "Add ensemble" in Phaser program and when to use the former. If I want to search for a complex model, I often just click the "Add ensemble" till completing the search model. --

Re: [ccp4bb] Superpose problem

You could use the Superpose program to generate superpositioned/superposed/superimposed models - i.e. to put your structures on top of each other. There are also a host of other programs available to do the same thing (!) In Phaser, you would then load each of these superimposed models, to gen

[ccp4bb] Superpose problem

Hello everyone: I am just learning how to use the CCP4 Program suite. When I use the MR approach --Phaser, there is a column say "Add superimposed PDB file to the ensemble". And there is another CCP4 supported program called "Superpose". I am afraid if my question is professional, but I wonder 1

Re: [ccp4bb] Superpose tool in CCP4_some residues missing in RMS output list

By default it only gives those with rms > mean. There is an option to ask for all to be output to a separate file.. E On 11/16/2011 11:48 AM, WENHE ZHONG wrote: Dear all, I am using the Molecular Suporpose tool under Coordinate Utilities list in CCP4 to superpose two similar structures. I tick

[ccp4bb] Superpose tool in CCP4_some residues missing in RMS output list

Dear all, I am using the Molecular Suporpose tool under Coordinate Utilities list in CCP4 to superpose two similar structures. I ticked the "Output all distances to a file" option, selected "Superpose specified atoms/residues", fit "CA atoms of Residues" to the other one. I wanted to see the RMS n

Re: [ccp4bb] Superpose, SSM

rd wrote: - > To: CCP4BB@JISCMAIL.AC.UK > From: Robbie Joosten > Sent by: CCP4 bulletin board > Date: 27-09-2011 05:22 > Subject: Re: [ccp4bb] Superpose, SSM > > One would assume that Windows software would read DOS/Windows type text > files... > Open the file in W

Re: [ccp4bb] Superpose, SSM

etin board wrote: - To: CCP4BB@JISCMAIL.AC.UK From: Robbie Joosten Sent by: CCP4 bulletin board Date: 27-09-2011 05:22 Subject: Re: [ccp4bb] Superpose, SSM One would assume that Windows software would read DOS/Windows type text files... Open the file in Wordpad. Unlike Notepad, it is able to

Re: [ccp4bb] **Possible spam**[ccp4bb] Superpose, SSM

Hi Matthias Thank you for your report. This is a genuine bug, lsqkab puts "\015\015\012" in the end of line instead of "\015\012" We will try to fix it. Andrey On 26 Sep 2011, at 20:42, Matthias Zebisch wrote: > Dear CCP4 users, > > I am using the ccp4i version 6.2.0 under windows 7. I've com

Re: [ccp4bb] Superpose, SSM

> other. You can also use Word to search and replace the linefeeds. > > Good luck with this very retro problem. > Cheers, > Robbie > > > Date: Mon, 26 Sep 2011 17:07:50 -0600 > > From: xtald...@gmail.com > > Subject: Re: [ccp4bb] Superpose, SSM > > To: C

Re: [ccp4bb] Superpose, SSM

, 26 Sep 2011 17:07:50 -0600 > From: xtald...@gmail.com > Subject: Re: [ccp4bb] Superpose, SSM > To: CCP4BB@JISCMAIL.AC.UK > > I think something in your workflow is inserting dos line feeds (\n\r or \r\n, > I can't remember which). > > If I have guessed correctly,

Re: [ccp4bb] Superpose, SSM

I think something in your workflow is inserting dos line feeds (\n\r or \r\n, I can't remember which). If I have guessed correctly, you want to remove those "\r"s before proceeding (or never let them get in there in the first place). You claim to open it with MS something, which would insert do

Re: [ccp4bb] Superpose, SSM

>>> The outputfile appears to have additional line feeds (see picture) which, >>> however are not seen in the windows notepad. What application ARE the extra lines seen in? Sounds like a problem with different newline conventions- vs vs - although I shouldn't have thought extra carriage return

Re: [ccp4bb] Superpose, SSM

Hi again, Thanks for your quick replies but I think I made myself not clear. here is what I'm doing: 1) superpose proteinA.pdb onto proteinB.pdb : works, but gives out proteinA_lsq1.pdb with extra empty lines (not the anisou lines ;o) ) 2) superpose proteinA_lsq1.pdb onto proteinC.pdb : do

Re: [ccp4bb] Superpose, SSM

I vaguely recall notepad doing something wacky with files in certain cases...why don't you get the excellent text editor NoteTab Light [sic] (I use it all the time--free and works great), then take a look at your files and see whether MS notepad altered the files. JPK On Mon, Sep 26, 2011 at 2:42

Re: [ccp4bb] Superpose, SSM

On Mon, 2011-09-26 at 20:42 +0100, Matthias Zebisch wrote: > However, it is not > possible to use it within CCP4, eg. for a subsequent superposition. What do you mean by that? Do you get an error when you use the superpose output pdb with some other program? -- "I'd jump in myself, if I wer

[ccp4bb] Superpose, SSM

Dear CCP4 users, I am using the ccp4i version 6.2.0 under windows 7. I've come across a problem with superpose. The outputfile appears to have additional line feeds (see picture) which, however are not seen in the windows notepad. The structure can also be opened in coot and pymol. However, it

[ccp4bb] superpose atom selection

Hello all, from the ccp4 manual: http://www.ccp4.ac.uk/html/superpose.html superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ] where [-s CID1/2] are optional selection strings in MMDB convention, and [foo_out.pdb] is optional output file. Please, could someone point me to docum

[ccp4bb] superpose structures .ssm or lsq which is better

Dear All, I am overlaying several structures using coot. There are two ways SSM or LSQ can be used in that package. But I got clearly different result form the two methods. In my opinion SSM only works on the secondary structures and LSQ can works on the whole atoms ,main chain or CA. So

Re: [ccp4bb] superpose

Hi Juan, This doesn't directly apply to Superpose -- but THESEUS (which does both conventional least-squares and maximum likelihood superpositions) puts RMSD values by default in the B-factor column of the PDB of the mean structure for a superposition. It is undocumented, but via the THE

[ccp4bb] superpose

Dear all I have three questions that might have been answered before but I haven't been able to find them. 1) I was wondering whether anyone could tell me what does (in the Superpose output) "RMS B DISPLACEMENT" stand for? 2) If "B" is B-factor how meaningful is it if the haven't been n