Measure Electrostatic Potentials

User feeba8b156

28-08-2006 17:40:28

Hi,





When viewing the connoli structure of proteins, can Marvin space take the electrostatic potentials from a file and display it in terms of color on the protein surface?





If yes, how do we do it?





Thanks


Vidyashankara

ChemAxon 909aee4527

29-08-2006 07:53:50

Hi,





which file format would you use?


Probably only the specific file import is missing, we could implement this.





Thanks,


Judit

User feeba8b156

29-08-2006 15:56:05

Hey Judit,


I need to read the potentials from a PDB file





Vidyashankara

ChemAxon efa1591b5a

29-08-2006 21:15:30

Hello Vidyashankara,





are those potentials stored in a standard PDB record? If yes, then which one?


Or you mean partial atomic charges stored in the ATOM record?





Thanks,


Miklos

User feeba8b156

29-08-2006 21:21:55

Hey there,





You dont have the electrostatic potentials on the original PDB File. We are developing a program named CHARMM, which will calculate the electrostatic potential itself and write the values to a file. Now, I dont know the format in which Mspace reads the potentials. If you send me a file as an example it would be great. Also, Mspace doesnt read the PDBID 1KDX, any idea why?





Thanks


Vidyashankara

ChemAxon efa1591b5a

30-08-2006 21:27:16

Hi Vidyashankara,





I known that original PDB does not store EP data though there are extensions to the PDB format by the community of users that can include electrostatic potential too.





At present mspace can read EP from Gaussian cube file and we are ready to implement the format what you find the most suitable for your needs.


Standard formats that are widely used are certainly preferred.


Our ultimate goal, however, is to store volumetric data (as well as macromolecules, surfaces etc) in our Marvin Document File (MRV) format which is XML based.





Is your data atom center based or volumetric?





Regards,


Miklos

User feeba8b156

30-08-2006 22:17:12

Hey there,


Thanks for the promt reply. The file we use to store electrostatic potential is in binary format. The source code is at the bottom to help you implement the file format. The EP is stored in a 3D Grid format. The explanation of the terms are below





NCLX - Number of Grid Point along X- Axis


NCLY - Number of Grid Point along Y- Axis


NCLZ - Number of Grid Point along Z- Axis


DCEL - Grid Spacing


XBCEN - Center of Grid along X Axis


YBCEN - Center of Grid along Y Axis


ZBCEN - Center of Grid along Z Axis





-------------Source Code-----------------------


INTEGER UNIT


INTEGER NCLX,NCLY,NCLZ


REAL*8 DCEL


REAL*8 XBCEN,YBCEN,ZBCEN,EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM


REAL*4 SMTHNG(*)


REAL*4 PRFTR


C


C Local variable


INTEGER I





IF(UNIT.GT.0)THEN


WRITE(OUTU,'(3x,A)')


$ 'FIRST RECORD IS: NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN'


WRITE(OUTU,'(3x,A)')


$ ' EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM'


WRITE(UNIT) NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN


WRITE(UNIT) EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM


WRITE(UNIT)(PRFTR*SMTHNG(I),I=1,NCLX*NCLY*NCLZ)


ENDIF


-------------Source Code-----------------------








Also, for some reason, I am unable to visualize files such as 1kdx from pdb. any idea why?

ChemAxon efa1591b5a

31-08-2006 07:55:52

Hi, this binary format is fine, we will implement the loader for you and let you know when the updated distribution package is available for download.





Regarding 1KDX: thank you very much for the bug report. The root of the problem is that this molecule has multiple models and our PDB import code is not prepared to handle such situation.


We will implement the MODEL record handling procedures asap.


At the same time, the Charmm extension to PDB will also be implemented. I'll let you when it's done.





Regards,


Miklos

User feeba8b156

01-09-2006 17:37:40

Hi,





Thanks for the positive reply. Can you tell me about how long it might take to implement the CHARMM Extension? Its kind of urgent for our research project. If you can tell me the time required to make this work, it would be great!





Thanks


Vidyashankara

ChemAxon efa1591b5a

04-09-2006 08:49:11

Hi,





1. MODEL record in PDB: this feature is being implemented, it should be available within a few days.





2. CHARMM extension to PDB (ATOM record carries extra information): we can implement the new PDB reader within a few days, however, a sample file would be a great help. I suppose column start-end positions are the same as in standard PDB, except for the extra columns.


I also suppose, that the line length limit to 80 columns is exceeded in this extension, is that correct?





3. 3D grid file for volumentric EP data: Judit will implement it in few days time.





So, altogether: you can get all these new features (along with the new applet API call for hiding chains - see other topic at http://www.chemaxon.com/forum/viewtopic.php?p=7763#7763) will be available for you by the end of this week.


Is this o.k.?





Thanks and regards,


Miklos

ChemAxon 909aee4527

05-09-2006 09:05:56

Hi Vidyashankara,





I'd like to ask about the 3D grid format:


- are there any comments in the file, if yes how can they recognized (special place or sign)?


- are there any special descriptors? e.g. version number, processor architecture, byte ordering?


- should the fields EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM be taken care of, if yes, can you give a brief description about them?


- can you give a sample file?





Thanks for all,


Judit

User feeba8b156

05-09-2006 23:11:58

EPSW : Dielectric Constant of solvent


EPSP : Dielectric Constant of protein interior.


CONC: Concentration of Salt


TMEMB : Thickness of Membrane


ZMEMB : Center of membrane along Z Axis


EPSM : dielectric constant of membrane





Let me know if you need anything else, i am attached CHARMM PDB format file and a electostatic potential file for your assistance. but the electrostatic file is in binary format, i dont know how you will be able to read it





you have to rename the extension of the electrostatic potention file to phi80 and that extension isnt allowed and i renamed it to pdb

User feeba8b156

05-09-2006 23:13:11

mvargyas wrote:
Hi,





1. MODEL record in PDB: this feature is being implemented, it should be available within a few days.





2. CHARMM extension to PDB (ATOM record carries extra information): we can implement the new PDB reader within a few days, however, a sample file would be a great help. I suppose column start-end positions are the same as in standard PDB, except for the extra columns.


I also suppose, that the line length limit to 80 columns is exceeded in this extension, is that correct?





3. 3D grid file for volumentric EP data: Judit will implement it in few days time.





So, altogether: you can get all these new features (along with the new applet API call for hiding chains - see other topic at http://www.chemaxon.com/forum/viewtopic.php?p=7763#7763) will be available for you by the end of this week.


Is this o.k.?





Thanks and regards,


Miklos



The following is the CHARMM PDB format:





WRITE(IUNIT,


& '(A,I5,1X,A4,1X,A4,2X,A4,3X,3F8.3,2F6.2,6X,A4)')


& 'ATOM ',I,ATYPE,REN,ARID,X(I),Y(I),Z(I),1.0,WMAIN(I)


& ,SID





where


I - atom number


ATYPE - atom type


REN - reside name


(Note CHARMM uses HSD, HSP, and HSE for HIS protonation states, so they


should be included)


ARID - reside ID


(which is the same as residue number in PDB, but here it is a character


format, although they are mostly numbers)


X,Y,Z - XYZ coordinates


WMAIN - an extra CHARMM array


(you may think this corresponds to B-factor in PDB X-ray structures)


SID - Segment ID


(This is equivalent to CHAIN ID in PDB, although it has 4 character


format while PDB has only one character)

ChemAxon efa1591b5a

06-09-2006 06:46:50

Thanks for the info and sample files. We will let you know when the new version supporting these features is ready for download.

User feeba8b156

06-09-2006 19:46:53

Also, In the CHARMM PDB File, Water residue name is TIP3 and not HOH (as in original PDB).

ChemAxon efa1591b5a

07-09-2006 10:43:01

O.k. that's fine, pdb import will recognise it.


thanks.

ChemAxon 909aee4527

12-09-2006 14:06:20

Hi,





just to keep you informed, we are getting on with the grid mapping and the pdb import:


http://www.chemaxon.com/marvinspace/gallery/phi80.png


It will be available for test soon.





Regards,


Judit

User feeba8b156

15-09-2006 23:25:04

Hey,





That looks great! around when is it gonna be out?





Thanks


Vidyashankara

ChemAxon 909aee4527

18-09-2006 15:02:08

It will be available in a few days, the end of the week for sure.

ChemAxon 909aee4527

19-09-2006 15:09:36

It would be good to have some tests before launching a version that contains the new features.


I've created a test page for testing: http://www.chemaxon.com/marvinspace/1_3_2.


If you found this solution inconvenient, please let us know.





PDB import is much better, you can see if you load pdb files that failed to load before. E.g. 1kdx.pdb can be loaded or even 1kdx_charmm.pdb.





To map the grid, you need to create a surface first, then File->Open property file..., and choose the 1kdx_ep.phi80 file. After mapping you may wish to adjust the minimum and maximum values on the toolbar.


(I think this component needs an update it seems a bit hard to use.)


The image I pasted in my previous post was made by creating a Connolly surface with manual precision 0.2 and setting the minimum and maximum values to -1, +1.





Please test the applet a bit and give us a feedback so we can further improve it.





Regards,


Judit

User feeba8b156

19-09-2006 21:07:37

Hey Judit,





I am not able to open any CHARMM PDB files. Its open the file and displays the chains on the right. But I can see any structure. It kinda hangs. Just a grey box shows in the black space. whats wrong?





Vidyashankara

ChemAxon efa1591b5a

19-09-2006 21:38:26

Hi Vidyashankara,





we've got only one charmm pdb file, 1kdx. I tried that and it loads and displays properly. Did you try that one too.


Could you please send us some of the troublesome files to help us identify the problems?





Thanks,


Miklos

User feeba8b156

19-09-2006 22:14:55

Hi,


The applet just doesnt display the structure. I am adding a screenshot.

ChemAxon 909aee4527

20-09-2006 14:21:22

Hi,





Yes, I can reproduce this when I load a huge structure. The file is loaded (otherwise it wouldn't appear at the selection panel), but the rendering takes some time. I think it will be displayed after a few secs (15-20 sec with ~100.000 atoms), but certainly this is not an acceptable behaviour.





This case haven't occured yet (well, at least not significantly), but I will add progressing to the rendering phase, and I saw some refreshing problem too that will be corrected.


Until then, will you try it again and see if it appears in half a minute? If it doesn't, could you send us the file you're trying, please?


Btw the missing progress bar is now added to the applet.





A question: in case of having more models in a pdb file what is the expected displaying behaviour for you: display all models, display the first model only, or adjustable on-the-fly?





Judit

User feeba8b156

20-09-2006 20:02:13

Judit, I cant see the structure even after 5 mins. It just has the grey screen.





Incase you have many models, It should display all, the user should be able to select just one model from the selection panel.

ChemAxon efa1591b5a

20-09-2006 20:45:21

Thanks for the PDB files, these will be great help to fix the load/display problem.


We'll get back to you soon.


Regards,


Miklos

ChemAxon 909aee4527

22-09-2006 13:54:22

Hi Vidyashankara,


the http://www.chemaxon.com/marvinspace/1_3_2 is updated, the pdb files are recognized.


Will you check it?


Thanks a lot,


Judit

User feeba8b156

22-09-2006 17:48:04

Hey judit!





The applet works great now. I just have one problem. When i generate the secondary structure, the structure is really thin. I guess the rendering is done using the SEQRES and HELIX values from the original pdb. Since the Charmm file doesnt contain these values, is it possible for you to make the chain thick and good looking in the charmm file too?

User feeba8b156

22-09-2006 17:56:29

you will probably need to generate the secondary structure information for the charmm PDB like rasmol does.

ChemAxon efa1591b5a

25-09-2006 06:25:11

Indeed, Vidyashankara, you are right. We take the info from the PDB file and at present we do not recognize secondary structure from the coordinates.





We'll work on that... how urgently do you need it?





Cheers


Miklos

User feeba8b156

25-09-2006 06:38:41

Hey Miklos,


The feature is very important for visualisation of the charmm files. So the sooner the better, how long will it take to implement the feature?


Thanks


Vidyashankara

ChemAxon efa1591b5a

26-09-2006 07:44:11

Hi Vidyashankara,





I believe it takes a day to implement the secondary structure element identification. However, we cannot schedule the task this week, perhaps middle of next week.


We will inform you!





Regards,


Miklos

ChemAxon 909aee4527

02-10-2006 11:38:04

Hi Vidyashankara,





can I ask you if you managed to map Charmm grid files to surfaces?


We would like to make sure that the grid is processed correctly. Would you like us to test it with more files, and in this case could you send us input files?


Or would you prefer test it yourself and give us feedback?





MarvinSpace 1.3.2 will be released soon with the changes we made recently (Charmm pdb&grid import, water display, bugfixes).





We will implement the secondary structure recognition and correct nucleic acid visualization soon as agreed, and will be released as MSpace 1.3.3.





In case you find any problems (pdb import, grid mapping or any other) please report us and we will fix them.





Regards,


Judit

User feeba8b156

03-10-2006 21:46:57

Hey Judit,





The mapping works great with 1kdx.





however, i tried it with 3gb1, it says error mapping.


i am attaching both the files

ChemAxon 909aee4527

05-10-2006 08:20:38

Hi,





thank you very much!


Sorry, there was a mix-up with the read and processed grid sizes.


1kdx worked only because the grid size was equal in all directions.


It is corrected, and the applet is updated.





Judit

User feeba8b156

09-10-2006 21:53:22

Hi Judit,


When are you planning on releasing 1.3.2?





Thanks


V

ChemAxon 909aee4527

10-10-2006 14:18:25

Hi Vidyashankara,





we could release mspace 1.3.2 though marvin 4.1.2 is still in test version.


You can download it from http://www.chemaxon.com/test/marvin.


If something is wrong with it we can still correct it until the final marvin 4.1.2 relase.





The secondary structure representation of dna is also available in 1.3.2.





Hope you will find it useful,


Judit

User feeba8b156

10-10-2006 20:05:18

a few fixes





1. I hope you know that Charmm differentiates between protein, dna and rna chains.





a protein chain will show up at PROA,PROB etc... DNA chain will show up as DNAA, DNAB etc... RNA chains will show up as RNAA, RNAB etc...





So when i try to read a dna chain, it gives me a macromolecule error.





2. When i generate crystals, the image of the crystal generated by mspace isnt very clear.





3. We need to add a parameter to open the property file for electrostatic potentials in the following manner


document.MSpaceApplet.setProperty("Property_file", "1kdx.phi80", "0.2","-1","1");





where 1kdx.phi80 = property file


0.2 = manual precision


-1 and +1 are the maximum values





this param will be added right below, after defining the pdb file and generating the conolly struture for that molecule.





4. We need to generate secondary struture.





If you need to test the applet, you can goto http://www.charmm-gui.org/pdbreader/index.php





type the PDBID (1KDX, 1ORS etc...), keep clicking next and click on view structure in the CHARMM PDB file.





to check the crystal, you can type an xray pdbid like 1av1 or 2a01 and click on generate crystal in the options page. you could also test by clicking generate biologically functional unit.








At times, mspace says not enough memory.I have over 1 gb ram. is it possible to set this right?

ChemAxon 909aee4527

11-10-2006 14:50:35

Hi,





thank you for the valuable feedback!


The first 3 points are easy to fix, they can be done quickly.


The 4th point requires us some more time to implement.


In case it will not be ready by the 4.1.2 release we can give a "test release" (like yesterday) a few days later if it is ok.





Judit

User feeba8b156

11-10-2006 15:11:50

Thanks a lot Judit. you guys rock! When are you out with 4.1.2?

ChemAxon efa1591b5a

12-10-2006 16:43:13

Marvin is planned to be released tomorrow (13 October, 2006) - keep fingers crossed.





However, I am not sure that we can squeeze the marvinspace bug fixes and the new API call in that release. We'll try, but I am the bottleneck here (AFAIK Judit did a lot of API work /she's great!).





Regarding the recognition of the secondary structure: we are aware of the importance of proper identification of the elements of the secondary structure, so please be assured that it will be implemented in the near future. But unfortunately, we cannot give you even vague time line of this development due to many other commitments (and some of them are overdue).


And also because we have not studied how difficult it is to perceive helices and sheets in proteins at least in theory (making the code is not the big job here, I reckon). If you can give us any clue that would certainly help us a lot.





Regards,


Miklos

ChemAxon 909aee4527

13-10-2006 11:56:20

The new API calls will be included in the following form:


Code:
document.MSpaceApplet.mapPropertyFile("3gb1.phi80", -30, 20 );


document.MSpaceApplet.mapPropertyFile("1kdx.phi80", -5.45, 1.23, 0.2 );



This call generates the Connolly surface and maps the property file on it.


The first will use the default surface precision, the second sets the surface precision manually.


Note that the default precisions were changed recently, and they usually generate fairly smooth surfaces.





Judit

User feeba8b156

13-10-2006 18:32:19

Thanks judit! Thats great news! Is is already implimented and available for download?





Thanks again!





To make your job simpler with the generation on the secondary structure, you can use what rasmol does. I think, rasmol calculates phi and psi backbone dihedral angles of each


residue, and assign the secondary structure based on its location in the


Ramanchandran plot.





Till you implement it, i will simply copy the helix and seqres lines from the original pdb to the charmm pdb.

ChemAxon efa1591b5a

13-10-2006 20:43:09

It's implemented, but Marvin has not yet been released. Perhaps Monday? - We'll try to push the Marvin developer team.





Thanks for the secondary structure hints - it does sound fairly simple.





Regards,


Miklos

User feeba8b156

13-10-2006 21:19:45

Hi,





Just one tiny problem. When i view the crystal structure, I see only the chains from the parent pdb. Is it possible to display all the chains in the crystal file between 73-76 colums? Now, we use PROA, PROB etc... for out conveineince. Many people use different abbreviations. So you might want to generalize it so that everyone can use it. You should take the chain name from the four columns. If a pdb file has 25 chains, mspace must displays the 25 different chains.





also, if i open mspace about 3-4 times without restarting the browser, it comes up with some memory problem. is it possible to fix this?





Thanks


Vidyashankara

ChemAxon efa1591b5a

17-10-2006 10:26:13

Quote:
Just one tiny problem. When i view the crystal structure, I see only the chains from the parent pdb. Is it possible to display all the chains in the crystal file between 73-76 colums? Now, we use PROA, PROB etc... for out conveineince. Many people use different abbreviations. So you might want to generalize it so that everyone can use it. You should take the chain name from the four columns. If a pdb file has 25 chains, mspace must displays the 25 different chains.
O.K. we will implement it.


Just to clarify: all chains are displayed in the current implementation, but the chain identifiers are dislayed as A, B, C etc, but you'd like to see PROA, PROB etc on the right hand side selection panel. Is that correct?


Or you mean that some chains (i.e. atoms, bonds) are completely missing from the 3d view?
Quote:



also, if i open mspace about 3-4 times without restarting the browser, it comes up with some memory problem. is it possible to fix this?


We will check this (later). Probably knowing your browser + operating system would be useful information.





Thanks,


Miklos

ChemAxon 909aee4527

20-10-2006 08:57:13

Hello Vidyashankara,





Marvin 4.1.2 is released, and is ready to dowload at


http://www.chemaxon.com/marvin/download.html.





2 applet examples have been created to demonstrate the api usage, but unfortunately there is a problem with the second one. There are some streaming errors with reading the property file which I don't understand yet, since it works from the menu correctly.





The examples are located here:


http://www.chemaxon.com/marvinspace/applet/chapplet.html


http://www.chemaxon.com/marvinspace/applet/chapplet2.html.





We will fix it asap and give you a new release.





Judit

ChemAxon 909aee4527

01-12-2006 08:34:31

I've split this topic, the latest posts are moved to the topics below:


http://www.chemaxon.com/forum/ftopic2356.html


http://www.chemaxon.com/forum/ftopic2357.html





Hope, it's not a problem.


Judit