1227:. The original scientific publication can be considered as both a primary source (since it was written by the researchers who collected and interpreted the data) and as a secondary source (since it was peer reviewed by two anonymous referees and the journal editor). The RCSB-PDB can also be considered as both a primary source (since the coordinates, structure factors, and experimental details are stored there) as well as a secondary source (since the deposited structures must undergo a quality check before they are released). PBDSum provides no additional quality checks above and beyond what the wwPDB has provided, therefore PDBSum could at most be considered a tertiary source. Adding additional links helps to interpret the experimental structure, but does nothing to verify it (e.g., does the structure adequate fit the electron density, are there any severe geometrical outliers, etc.).
1334:
data like structure factors is not. Furthermore these experimental details are more throughly reported in the "Materials and
Methods Report" tab in the RCSB-PDB. The RCSB-PDB also provides much more extensive searching and reporting capabilities including the ability to include experimental details as optional search parameters. This is important for example in locating the best structure(s) (highest resolution, crystallization pH close to physiological) to include in links from Knowledge (XXG). One last point: there is a link from the RCSB-PDB structure entry back to the corresponding PDBSum entry under the external links section. So for interpretation of the structure, they are available from the RCSB-PDB by clicking back to the PDBSum. "So, there are no important differences here." Cheers.
884:. What is being verified here? It is the experimentally determined structure. Many funding agencies and scientific journals require that the coordinates of structures be deposited in the PDB. The PDB has the task of insuring that these structures conform to certain quality standards, are properly documented, are assign a unique accession code (which by the way, is universally used by derivative databases including the PDBSum), and are made freely available to everyone. In addition, the PDB has the most complete on-line information about the experimental conditions under which the data was collected and this information is important in verification and in the interpretation of the structures. Furthermore the PDB is now requiring that
1279:. That is a misinterpretation of what I wrote above. I think it is important to distinguish between verification of the experimental structure which RCSB-PDB provides and interpretation of the structure which both the RCSB-PDB and PDBSum provide. I would agree that the PDBSum provides more links and therefore is better for interpreting the structure within a biological context, but the RCSB-PDB provides the essential minimum (PubMed citation + PFAM, SCOP and CATH). What the RCSB-PDB provides which the PDBSum does not is the hard data and experimental details which is essential for judging the quality and relevance of the structure.
1493:
this by a single click from the PDBsum link. However from an RCSB-PDB links, I should go first to "External links" (I have learned this from you only 30 minutes ago), then find PDBsum link at the bottom of a page, and so on. Only a WP reader who is more advanced than me (perhaps you) will ever do that. So, I still believe that PDBsum link is better. But let's simply keep all templates as they are right now, since we can not agree on that. Dan changed it to RCSB-PDB, so consider that your position prevailed. I do not care about WP users so much to continue this discussion. Thanks. No any hard feelings about that.
668:. It seems totally reasonable to format links differently for 'large scale' use in boxes (as argued above). And I can almost see the point of adding a link to the PDB also (although I still want to check through some articles to see if this is really necessary). However, with regard to link destination, I think it is confusing and wrong to have links pointing to different destinations. I think we should reach a consensus and harmonize the link destination (changing many thousands of articles if necessary - isn't that the whole point of templates?). --
980:. Specialists (like you or me) will never download protein structures by reaching them through WP articles, and non-specialists do not need to download anything. Remember that WP is designed for general public, high school students, etc. A common wikipedia reader only needs is a good portal to other internet resources and good graphics that shows various features of the proteins, such as subunit structure, secondary structure, ligands etc. That is where PDBsum much superior.
1651:
864:. The PDB does in fact provide text information. On the left hand side of any structure page in the PDB is an expandable list of "Download files" which includes the header text, full text (header + coordinates), and the coordinate data in a number of formats (xml, mmCIF, etc.). As far as I can see, PDBSum only provides the header information and not the coordinates. If you want the coordinates in PDBSum, you must follow the links back to the PDB.
1312:". What that suppose to mean? Both databases give an easy link to the same PDB file header which describes experimental conditions (it looks a little bit nicer in the PDBsum); both databases give the same R-factor, resolution, R-free, and so on (it seems that PDBsum is missing only the crystallographic group of symmetry). So, all experimental details are practically the same (there is a database of protein crystallization conditions
1027:. You might be surprised. Occasionally I might run into an WP protein article that interests me and I will want to down load the structure, if for no other reason than to produce a PyMol figure to add back to the article. Of course, I have a half dozen other ways to download the coordinates, but if I have a direct link right there right in front of me without having to double click through the PDBSum site, it is more convenient.
786:
the first site that will make available new structures and the first site that will publish corrections. The primary purpose of links in WP is verification and secondary purpose is additional education. WP articles should to the greatest extent possible be self explanatory and not rely on external links for understanding. Hence IMHO, reliability and timeliness should take precedence over adding additional understanding. Cheers.
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2130:
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1516:. That is to say, when the page writes the content from the template, it applies the markup in the wrong order. It takes the link text and makes a link before it looks at the outer brackets. I don't know what would be causing this, but it seems to be a rather technical error, since there is nothing obviously wrong with how the template is written. -
2345:
2223:
1744:
888:
be included in any structure that is deposited in the PDB. While it is highly unlikely that a
Knowledge (XXG) reader would check a structure using the structure factors, these factors provide the most rigorous level of verifiability that the data for the structure was collected and interpreted in an
122:
What kind of link is better for "PDB" is an open question. From WP perspective, it does not matter if a site is "official" or not. A lot of "official sites" are spam. We have no obligations to PDB and we are not affiliated with PDB in any way. The links must be "educational", convenient for a reader,
170:
That is easy to say, and I follow the argument above, but I would like to revisit this discussion. How / where are the above link options compared and contrasted? How do we keep that comparison up to date? Despite what you put above about the concept of an 'official' site, which I think is generally
1443:
Now I see... I should go from a RCSB-PDB entry (say 1gzm) to "External links" (this link does not work with mozilla on my SGI computer!), then find PDBsum at the bottom of a very long page, and click PDBsum. No WP reader will ever do that. In PDBsum however, all links to other databases (and a lot
1333:
Point #1 (verifiability) takes precedence over point # 3 (adding additional understanding) and you have not responded to that issue. While the crystallographic group symmetry and crystallization conditions are included in the header information (and therefore accessible from both databases), other
1068:
the corresponding paper is published in the scientific literature. In addition, the paper invariably references the coordinates deposited in the PDB. Hence for all practical purposes, the PDB becomes an inseparable part of the paper. Therefore to provide a complete citation, one not only needs to
988:
PDBsum provides quick link to standard PDB (and many other resources), whereas standard PDB does not provides link to PDBsum. So, the PDB is only one click away of PDBsum, but not vice versa. Finally let's not discuss "verifiability" issues to save some time. You would probably agree that PDB is no
746:
Good job! I think the question by Dan about the best destination is reasonable. As I noted above, there are huge advantages from educational/WP perspective to use PDBsum whenever possible, unless someone can explain why "official" PDB link is better - I think only crystallographic group of symmetry
1424:
much. The problem is: a reader goes to the standard PDB link, and he does not know anything about the existence of PDBsum and other protein structure databases. However if he follows PDBsum link (as I suggest), he will see the links to RCSB-PDB and 21 other protein structure/sequence databases. As
785:
Two points in favor of PDB. First is up time. As I write this, the PDB site is up and PDBsum is down. The PDB is mirrored, and to the best of my knowledge, PDBsum is not. The second is timeliness. When I want to download coordinates of a structure, I go to the primary source, the PDB. This is
237:
No. Only 3D coordinates of proteins come from RSCB PDB. In addition to 3D coordinates, the derivative databases (and partly RSCB PDB) include a lot of other data: amino acid sequences, ligands, chemical reactions catalyzed by enzymes, secondary structure, automatically generated pictures of ligand
1492:
a number of additional graphic representations (!) from the PDBsum link, but he will see only 3 immediate links to other databases from a PDB entry and nothing else. To clarify, let's consider a simple practical example. I want to see a
Uniprot annotation of subunit C from PDB file 2axt. I can do
943:
I have used the PDB for close to 20 years as a source of coordinates for structure based drug design. The coordinates can be downloaded from the PDB and not from the PDBSum. In other words, the PDBSum lacks essential data that is required for my work. I think the confusion here is that different
645:
And I strongly support Andrew. There is a reason for doing this. The PDB2 template is currently used in the
ProteinBox template (many thousands of articles). By creating the additional PDB2 template, Andrew makes sure that any changes of "main" PDB template (like you did) will not affect his work
175:
source of the data (note the lack of inverted commas around that last use of the word official). Is it possible to make a page listing the major PDB derived databases with comparisons according to key features? It seems like that is what we need to begin to address this question, but I don't know
1063:
Verifiability is the single most important issue, and on this point, there is no contest. As the original definitive source of the coordinates, structure factors, experimental details, the PDB is a far superior to PDBsum. The only verifiability that the PDBsum has is its links to the original
816:
The entire EBI site is down today, not only PDBsum. That can happen anywhere. Right, there are no mirrors except PDB iself, which can be easily accessed (if PDB is down, you do not get an instant access either with links from WP). Pleas note that PDB links do not verify anything, because this
646:
with
ProteinBox template. Same thing was done by WillowW (enzyme articles) and by me (PfamBox). This also creates an extra flexibility. If anyone of us decides to switch to MSD instead of standard PDB in all higher-level templates, one can easily do so without affecting anything else.
944:
users have different requirements. From a bioinformatics perspective, the PDBSum has some advantages. For structural biology, PDBSum lacks the most basic data (the coordinates). In short, I think PDBSum is a nice complement to but was never intended to replace the PDB. Cheers.
1245:. Yes, this is true. However, RCSB-PDB is only one click away of PDBsum (the link is there). Moreover, one would normally use searches in RCSB-PDB or more reliable scientific databases (such as SMART) rather than wikipedia to identify and download the PDB files of interest.
1133:. Yes, this is true. However, RCSB-PDB is only one click away of PDBsum (the link is there). Moreover, one would normally use searches in RCSB-PDB or more reliable scientific databases (such as SMART) rather than wikipedia to identify and download the PDB files of interest.
1184:
I could continue this list, but the overall picture is clear. Actually, this is a perfect example why a secondary source (PDBsum) is better than a primary source for WP. It provides references/links to numerous different primary sources, whereas the primary source does
222:
I don't think it is incorrect to do so. Where does structural data come from if not from the PDB? People add links to that data and pull in information from other resources to supplement that data, but ultimately it all comes from (stems from) the RSCB PDB. Dosn't it?
817:
database does not provide any information as text, except PDB headers (after a couple of extra clicks). This is contary to PDBsum which provides abstract of key articles, or UniProt which provides annotations. Therefore, PDBsum, or UniProt can be used for
630:
is preferable since it clearly indicates an external link. While I agree we should standardize and consolidate when appropriate, I don't think we need to be too aggressive about this if it means sacrificing these subtle (but important) differences.
316:
OK, I'll have a look and see what there is to see. I am slightly worried that you favour one site because you are more familiar with that site, but I'll have a look. I have also found many bugs on the PDB site, so I know where you are coming from.
876:. I have not done an exhaustive comparison, but it appears that the PDB provides many of the same links that are found in the PDBSum. The links in PDBSum may be organized better, but they are for the most part also included in the PDB.
1915:), in which case the extra space at the end of the template looks odd before the closing bracket. Currently it looks to me as though the two requirements (use in image caption vs use in brackets) are mutually exclusive. Any ideas?
870:. The PDB also provides the abstract as well as a link to the corresponding PubMed citaiton. In addition, the PDB provides a direct link to the relevant UniProt page under the "Sequence Details" tab on every structure page.
2077:
I can't imagine anyone needing to reference a list of more than 9 so that seems good. What do you think of the slightly more compact formatting and plainlinks style that I edited into the sandbox (similar format to
747:
is better in PDB than in PDBsum. On the other hand, let's respect opinions of people who are using PDB links in the more complicated templates. If AndrewGNF wants to use "official" PDB in
ProteinBox, so be it.
1567:
and that seems to have solved the problem. I am not sure what caused the problem in the first place or why adding a space fixes the problem. In any case, the problem in this article seems to now be resolved.
300:
of that can be found in the "standard" PDB. I could continue and make this list much longer. Just look yourself and trace the links provided in PDB and PDBsum. "Standard PDB" is a very poor job compare to
1031:
A common wikipedia reader only needs is a good portal to other internet resources and good graphics that shows various features of the proteins, such as subunit structure, secondary structure, ligands etc
929:
Boghog2, did you look and compared both sites? Did you ever use yourself these databases in your work? The difference between PDB and PDBsum is obvious and significant. Otherwise, I would not argue here.
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purposes, whereas PDB is not. The PDB/PDBsum links are mostly useful to provide some graphic information about proteins and to serve as "gates" to other internet resources, and that is where PDBsum much
606:
and would object to its disappearance. This template is well suited to the PBB infobox, in which the external link icon would really take up a substantial amount of space. (For example, the list for
1372:. And in that regard the PDBsum link provides much more information and options. One does not need any search facilities, since the proper link has been already provided in an WP article.
1488:
No, SGI has nothing to do with it. Everything boils down to a very simple thing (see
Argument#3, "Take two"). A WP reader will see easy links to 22 protein structure/sequence databases
1394:, 3D coordinates and structure factors) that are not stored in PDBSum database. To the extent that the PDBSum tertiary source links back to the primary/secondary source of the data (
874:
The PDB/PDBsum links are mostly useful to provide some graphic information about proteins and to serve as "gates" to other internet resources, and that is where PDBsum much superior
1398:, RCSB-PDB), both databases contain the same data. But why not link directly to the primary/secondary source of the data, the RCSB-PDB rather than a tertiary source like PDBSum?
238:
binding pockets, modeled protein movements or arrangements of proteins in membranes, and so on. Many of these data can be found only in derivative databases, but not in RSCB PDB.
1315:, but we are not talking about it). As about "hard data" - they are available by clicking "RSCB" or "MDB" links in the PDBsum menu. So, there are no important differences here.
1033:
You are making assumptions about what a reader might be interested in which might not apply in all cases. Furthermore, the PDB provides much the same information as PDBSum.
989:
better for verification purposes than PDBsum, and that link to PDB is not good for verification purposes (one should refer to publications in books and journals).
1168:, its topology diagram, amino acid sequence and regular secondary structure (please click further to "sequence" motifs, and so on). RCSB-PDB has nothing of that.
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RCSB-PDB provides which the PDBSum does not is the hard data and experimental details which is essential for judging the quality and relevance of the structure
40:
If this is not acceptable for some reason, we can instead add several off site links per PDB code, for example (taken from the list of links maintained at
279:
1057:
As a derivative database, it is natural that PDBsum would link to PDB. I agree that it would be nice if the PDB provided a link back to the PDBsum.
1003:
P.S. Of course I am not telling such stupid thing that PDBsum was intended to replace the PDB! We only discuss which link is better for WP purposes.
2051: Is 9 parameters sufficient? I can add support for additional parameters, but the template coding is a bit tedious. One probably could use
2291:
The Zero-width space solution has been implemented in the sandbox. Admins, if you agree, with the proposed change, could you implement it?
275:
and nice diagram with topology, amino acid sequence and regular secondary structure; please click further to "sequence" motifs, and so on
1209:
The original PDB link (let's call it RCSB-PDB) is better because this is a primary deposition site of data, a kind of "primary source".
1109:
The original PDB link (let's call it RCSB-PDB) is better because this is a primary deposition site of data, a kind of "primary source".
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PS: I have fond memories of SGI. I hope I don't start any OS religious wars, but in some ways, I still prefer the IRIX GUI to Linux.
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argument that RCSB-PDB has a better search facility. However this is irrelevant. Templates we are talking about make a reference to
1306:
PDBsum provides seven times more links than RCSB-PDB and a lot of additional graphical and other capabilities that RCSB-PDB does not
263:
Please compare "2axt" (as a random example) in PDB and PDBsum. The interface by PDBsum provides, among other things, the following:
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I think this is the wrong link for PDB codes, as the above database is just one example of many derived database based on the PDB.
177:
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I agree that the plain links is a good idea, but the list is a bit too compressed for my taste, so I have restored the spaces.
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2016:
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1940:​, ​, ​, ​, ​
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PDBsum provides quick link to standard PDB (and many other resources), whereas standard PDB does not provides link to PDBsum (
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I agree too. However, I don't think the story ends here. Lets be clear, there are two arguments to discuss here, one is link
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Changed protection, but I'll let you do the honors, since I'm not brave enough to edit a popular template from a tablet :)
1924:
I've though of a possible solution that solves the problem whilst avoiding inserting extra spaces about the place: Use the
549:(or vice-verse). It looks like the difference is minimal, the question is related to the general style of external links.
1429:. But if they follow PDBsum link, they will see a lot of them. If they follow RCSB-PDB, they will see only three of them.
155:
is better than "official site". PDB has enormous resources and does very poor job, probably due to management problems.
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5. PDBsum includes pictures with secondary structure and their topologies generated by PROMOTIF. RCSB-PDB has nothing.
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Here is an example call to each of the five different PDB templates that I have found in common usage, namely 1)
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1308:? Good. Then we can agree at least on something. But you tell that I am missing the following point of yours: "
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6. PDBsum has pictures with chemical reactions for enzymes and links to enzyme databases. PDB-RCSB has nothing.
322:
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1271:. No, that is not the case. This is main point and should be explained in detail (see 2axt as an example):
1147:. No, that is not the case. This is main point and should be explained in detail (see 2axt as an example):
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2. PDBsum usually includes an
Abstract of key crystallography paper with key Figures. RCSB-PDB does not.
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Specialists (like you or me) will never download protein structures by reaching them through WP articles
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Sorry, but your point #1 (verifiability) is groundless because we are talking about different links to
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The current usage is ... 212, 903, 4, 2986, and 166 times, respectively (as of a couple of days ago).
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http://en.wikipedia.org/search/?title=Human_leukocyte_antigen&diff=556740430&oldid=553201860
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optimal way and the PDB to my knowledge in general the only place where this data can be obtained.
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better interface than the official PDB (I can easily explain why). We discussed this question with
1750:. The /doc subpage isn't protected though - next time you can just do it yourself. Best regards —
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reasonable, somehow when it comes to data providers I think we have an obligation to link to the
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PDB links do not verify anything, because this database does not provide any information as text
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I am going to update the template to point at the appropriate page of the official PDB website;
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to provide support for unlimited number of parameters, but this is beyond my coding knowledge.
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2035:
2010:
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and add value to WP articles. In that regards PDBsum is the way to go, because it provides a
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The sandbox has been modified to allow up to 9 parameters: {{PDB/sandbox|3BSE|1OBB|3TRA}} →
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885:
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2180:). I would appreciate if the main template were synched with the sandbox. Better yet, if
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1512:
This template does not render correctly. For example, I see the following in an article:
1039:. I agree that PDBSum has a nice layout, but I think you are overstating the superiority.
582:. i.e. is that call to the PDB article really needed on the pages that use this template.
284:
Pictures with secondary structures, including beta-sheet topologies produced by PROMOTIF;
1425:
you can see from the discssion above, many people (like Dan) do not know much about the
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Link to each subunit (row at the left) - click there and you will see the picture of an
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I think such a suite of links in addition to the official link could be quiet nice. --
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PDBsum which provides abstract of key articles, or UniProt which provides annotations
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I just added a space between the pdb template and the closing image bracket in this
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You would probably agree that PDB is no better for verification purposes than PDBsum
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and the result (wrong; link broken; extra ] is shown after image as wikitext) is
25:
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1xyz
2359:
looks like a good solution so I have implemented it. Thanks for the suggestion!
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1154:(!) other biological databases, including RCSB-PDB. RCSB-PDB has only links to
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3. PDBsum has link to each subunit (row at the left) - with the picture of an
1069:
cite the scientific literature, but also the coordinates deposited in the PDB.
1064:
literature plus the PDB. Please note that structures often appear in the PDB
1460:
So the whole argument now boils down to whose cross link is most accessible?
278:
List of ligands - click at any ligand - and you will see something like that
2328:
2184:
rights were added to this template, I can make the changes myself. Thanks.
1795:
Hello. There is a problem with usage PDB template in images. Here the diff:
1664:
1171:
4. PDBsum has diagrams of ligand binding pockets. PDB-RCSB has none of that.
106:
1868:
1830:
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1043:
What user would prefer link to PDB rather than to PDBsum from WP articles?
982:
What user would prefer link to PDB rather than to PDBsum from WP articles?
976:
Yes, the PDB database is more convenient for downloading the coordinates.
2157:
The two requests immediately above have been implemented in the sandbox:
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1991:
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Where did you see a link from PDB entries to PDBsum? I do not see any.
1052:
but the PDB does provide links to many of the same third party sources
441:
433:
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204:, just like PDB itself. Calling them "PDB derived" would be incorrect.
101:
PDB templates right now: "PDB2" ("official site"), in
ProteinBox (see
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1239:. RCSB-PDB is better for downloading the 3D coordinates of proteins.
1127:. RCSB-PDB is better for downloading the 3D coordinates of proteins.
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1055:). So, the PDB is only one click away of PDBsum, but not vice versa.
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and transcluded it from the various PDB templates above. thoughts?
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281:- "standard PDB" also has links to ligand structure (please compare)
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Request disabled pending discussion of the best solution. — Martin
1304:
So, you do not dispute my last and the only important argument 3:
1865:] (no space between "}}" and "]]" which now renders correctly as:
529:
The question remains as to whether it does any harm to convert
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1360:. Same data have identical "verifiability". But you have made
1947:
Does anyone know of any issues that would stop it working?
36:
http://www.rcsb.org/pdb/explore/explore.do?structureId=1XYZ
1895:
Apologies for being difficult, but I've just noticed that
1841:
683:
In the interest of keeping everything straight, I created
1632:
It really does help when translating articles. Thanks :)
1313:
708:
Looks good. Lets move some of the other information from
596:
From the PBB perspective, I very much support the use of
984:
Certainly not a student, and not a specialist like me.
293:
Links to many other databases that are not linked to PDB
1796:
1564:
972:
Sorry, but I can not agree. There are two main points.
268:
Abstract of key crystallography paper with key
Figures;
1847:
Is it possible to add some spacing into the template?`
1265:. PDBsum has no significant advantages over RCSB-PDB.
1215:. No, we have to provide best "secondary" sources per
1141:. PDBsum has no significant advantages over RCSB-PDB.
1115:. No, we have to provide best "secondary" sources per
978:
But a wikipedia reader does not need these coordinates
109:), and "PDB link" (PDBsum site) in enzyme articles by
1358:
the same coordinates (3D structure) and the same data
44:
1997:It would be great to be able to use something like
1966:Can we make this template take multiple PDB codes?
1201:
Which PDB link is better for wikipedia? Take three.
1680:Edit request from Jacopo Werther, 26 November 2012
1368:PDB file. So, the only important question is what
1253:. I would agree that this is not a critical issue.
1098:Which PDB link is better for wikipedia? Take two.
1801:When PDB template is used in image description:
1588:Edit request from MindZiper, 13 September 2011
1102:I guess Boghog2 made the following arguments.
290:Links to UniProt records (this is important);
287:Pictures with chemical reactions for enzymes;
8:
1971:({{PDB|3BSE}}, {{PDB2|1OBB}}, {{PDB2|3TRA}})
761:I'm agnostic, so if you guys want to change
610:is already quite long -- imagine that using
858:The following points need to be clarified:
2305:, since he is familiar with this issue. --
1444:of other options) are immediately vizible.
1420:If there was such link, I would not argue
178:Comparison of online PDB derived databases
105:), "PDB3" (PDBsum site) - in PfamBox (see
2162:
1765:Sorry, you are right! Thank you so much!
1061:Finally let's not discuss "verifiability"
620:.) However, I imagine for inline links,
2001:to make something that looks like (PDB
1550:That's the use that doesn't work. See
2176:And the changes work as expected (see
1158:other databases (PFAM, SCOP and CATH).
1075:. On this point, I strongly disagree.
585:Just a dump of my current thinking. --
202:and a lot of other databases/resources
138:Please do explain why, I am curious.--
192:I would recommend to create articles
7:
1716:Please add the missing interwikies:
1862:Error fixed in the sandbox version:
1807:it will be expanded as: (note ]]])
1526:Try {{PDB|2G9H}} which renders as
1416:With regard to your last argument.
115:Category:Enzymes of known structure
21:Currently this template points to;
2169:
1037:That is where PDBsum much superior
732:... but ... well... lets try... --
14:
1552:Human_leukocyte_antigen#Functions
1045:Oh, I don't know, me perhaps? ;-)
771:to PDBsum, I have no objection.
353:Comparing different PDB templates
176:where such a page should live...
2343:
2262:
2221:
2128:
1905:is often used in brackets e.g. (
1742:
1687:
1649:
1595:
1719:] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ]
1952:06:22, 16 September 2015 (UTC)
1674:14:49, 13 September 2011 (UTC)
1644:05:22, 13 September 2011 (UTC)
200:. Structure databases use PDB
1:
1772:14:37, 26 November 2012 (UTC)
1761:11:17, 26 November 2012 (UTC)
1737:08:50, 26 November 2012 (UTC)
728:. I am going to try to write
562:can be similarly merged onto
2369:03:56, 7 October 2015 (UTC)
2338:11:28, 6 October 2015 (UTC)
2321:16:00, 5 October 2015 (UTC)
2296:09:19, 5 October 2015 (UTC)
2285:to reactivate your request.
2273:has been answered. Set the
2151:to reactivate your request.
2139:has been answered. Set the
1710:to reactivate your request.
1698:has been answered. Set the
1618:to reactivate your request.
1606:has been answered. Set the
1427:Protein structure databases
1370:this specific link provides
730:Protein structure databases
552:The final question whether
335:So, did you look at PDBsum?
194:Protein structure databases
2387:
2027:Evolution and evolvability
1828:Correct result should be:
1503:21:37, 14 April 2008 (UTC)
1470:20:46, 14 April 2008 (UTC)
1454:16:28, 14 April 2008 (UTC)
1439:15:59, 14 April 2008 (UTC)
1408:20:46, 14 April 2008 (UTC)
1382:14:50, 14 April 2008 (UTC)
1344:06:45, 14 April 2008 (UTC)
1325:01:28, 14 April 2008 (UTC)
1299:21:20, 13 April 2008 (UTC)
1195:13:05, 13 April 2008 (UTC)
1090:19:03, 12 April 2008 (UTC)
1013:16:57, 12 April 2008 (UTC)
999:16:52, 12 April 2008 (UTC)
954:15:13, 12 April 2008 (UTC)
939:18:29, 11 April 2008 (UTC)
899:15:13, 12 April 2008 (UTC)
832:22:14, 10 April 2008 (UTC)
796:21:08, 10 April 2008 (UTC)
781:17:31, 10 April 2008 (UTC)
757:16:21, 10 April 2008 (UTC)
345:16:08, 10 April 2008 (UTC)
248:20:45, 12 April 2008 (UTC)
198:Protein sequence databases
131:and decided to use PDBsum.
2247:09:07, 28 June 2015 (UTC)
2216:08:58, 28 June 2015 (UTC)
2194:09:07, 27 June 2015 (UTC)
2113:06:45, 26 June 2015 (UTC)
2095:04:23, 26 June 2015 (UTC)
2065:04:04, 26 June 2015 (UTC)
2020:07:28, 7 April 2015 (UTC)
1920:04:10, 23 July 2015 (UTC)
1578:15:09, 15 July 2011 (UTC)
1559:14:21, 15 July 2011 (UTC)
1546:17:55, 11 July 2011 (UTC)
1521:15:48, 11 July 2011 (UTC)
738:20:54, 5 April 2008 (UTC)
703:20:15, 5 April 2008 (UTC)
674:20:54, 5 April 2008 (UTC)
656:16:58, 5 April 2008 (UTC)
641:01:22, 5 April 2008 (UTC)
608:Cyclin-dependent_kinase_2
591:15:50, 4 April 2008 (UTC)
327:15:31, 4 April 2008 (UTC)
311:03:53, 4 April 2008 (UTC)
233:15:31, 4 April 2008 (UTC)
214:03:53, 4 April 2008 (UTC)
186:20:36, 3 April 2008 (UTC)
165:15:53, 3 April 2008 (UTC)
144:20:36, 3 April 2008 (UTC)
92:09:59, 3 April 2008 (UTC)
1999:({{PDB|3BSE|1OBB|3TRA}})
1857:15:29, 25 May 2013 (UTC)
1554:, first image caption. -
1390:RCSB-PDB includes data (
1150:1. PDBsum has links to
2178:Template:PDB/testcases
1886:
1844:
1837:CORRECT: description,
516:can be converted into
492:can be converted into
1874:
1836:
1821:
1822:WRONG: description,
1366:a single and defined
664:, the other is link
103:Histone H2B type 1-C
2163:space after last ]
1624:Add the interwiki:
502:, and it certainly
1887:
1845:
1780:space after last ]
1166:individual subunit
723:PDB_template_usage
688:PDB_template_usage
273:individual subunit
2353:T.Shafee(Evo﹠Evo)
2336:
2293:T.Shafee(Evo﹠Evo)
2289:
2288:
2172:" feature request
2155:
2154:
2092:T.Shafee(Evo﹠Evo)
2017:T.Shafee(Evo﹠Evo)
1949:T.Shafee(Evo﹠Evo)
1917:T.Shafee(Evo﹠Evo)
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886:structure factors
258:PDB versus PDBsum
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1969:Currently I use
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1936:ZERO WIDTH SPACE
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1926:Zero-width space
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1872:
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1755:Mr. Stradivarius
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1724:Template:PDB/doc
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1628:es:Plantilla:PDB
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1217:WP:Verifiability
1117:WP:Verifiability
881:WP:Verifiability
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97:In fact we have
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2182:template editor
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149:
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84:
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23:
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2281:parameter to
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2240:
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2179:
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2170:Multiple PDBs
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2158:
2150:
2147:parameter to
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2114:
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1973:to produce (
1968:
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1556:Theanphibian
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2165:" error fix
1661:. — Martin
1207:Argument 1.
1107:Argument 1.
666:destination
76:Proteopedia
66:NCBI Entrez
2275:|answered=
2141:|answered=
1700:|answered=
1608:|answered=
1263:Argument 3
1237:Argument 2
1139:Argument 3
1125:Argument 2
487:PDB enzyme
461:PDB enzyme
456:Note that
382:PDB enzyme
1636:MindZiper
1289:Cheers.
822:superior.
773:AndrewGNF
695:AndrewGNF
633:AndrewGNF
482:Clearly,
397:, and 5)
107:C2 domain
2301:Pinging
2237:Thanks!
1728:Thanks,
625:PDB link
615:PDB link
567:PDB link
534:PDB link
521:PDB link
372:PDB link
173:official
1495:Biophys
1462:Boghog2
1446:Biophys
1431:Biophys
1400:Boghog2
1374:Biophys
1336:Boghog2
1317:Biophys
1291:Boghog2
1187:Biophys
1082:Boghog2
1080:Cheers
1005:Biophys
991:Biophys
946:Boghog2
931:Biophys
891:Boghog2
824:Biophys
788:Boghog2
749:Biophys
648:Biophys
337:Biophys
303:Biophys
301:PDBsum.
240:Biophys
206:Biophys
157:Biophys
61:JenaLib
51:PDBWiki
42:PDBWiki
2361:Boghog
2355:: The
2307:Ahecht
2239:Boghog
2202:Boghog
2186:Boghog
2105:Boghog
2073:Boghog
2057:Boghog
1932:U+200B
1784:": -->
1570:Boghog
1538:Boghog
1066:BEFORE
662:format
180:??? --
81:TOPSAN
56:PDBsum
2279:|ans=
2269:This
2145:|ans=
2135:This
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1704:|ans=
1694:This
1655:Added
1612:|ans=
1602:This
1269:Reply
1243:Reply
1213:Reply
1145:Reply
1131:Reply
1113:Reply
718:into
539:into
506:like
504:looks
387:, 4)
377:, 3)
367:, 2)
151:Even
113:(see
2365:talk
2349:Done
2333:talk
2329:MSGJ
2315:PAGE
2313:TALK
2243:talk
2227:Done
2212:talk
2190:talk
2109:talk
2084:PDB2
2061:talk
2048:3TRA
2044:1OBB
2040:3BSE
2011:3TRA
2007:1OBB
2003:3BSE
1992:3TRA
1986:1OBB
1980:3BSE
1912:1LVM
1853:talk
1786:edit
1748:Done
1669:talk
1665:MSGJ
1640:talk
1574:talk
1565:edit
1542:talk
1533:2G9H
1499:talk
1466:talk
1450:talk
1435:talk
1422:that
1404:talk
1396:i.e.
1392:e.g.
1378:talk
1340:talk
1321:talk
1295:talk
1191:talk
1185:not.
1086:talk
1009:talk
995:talk
950:talk
935:talk
895:talk
828:talk
792:talk
777:talk
766:PDB2
753:talk
699:talk
652:talk
637:talk
601:PDB2
577:PDB2
544:PDB2
511:PDB3
450:1xyz
442:1xyz
434:1xyz
424:1xyz
417:1xyz
402:PDB3
392:PDB2
341:talk
323:talk
307:talk
298:None
244:talk
229:talk
210:talk
196:and
161:talk
125:much
99:four
17:link
2277:or
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2036:PDB
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1989:,
1983:,
1976:PDB
1908:PDB
1900:PDB
1882:123
1878:PDB
1849:a5b
1842:123
1839:PDB
1824:PDB
1722:to
1702:or
1657:to
1610:or
1536:.
1529:PDB
1514:PDB
1490:and
734:Dan
713:PDB
670:Dan
587:Dan
572:or
557:PDB
526:.
497:PDB
471:PDB
430:PDB
413:PDB
362:PDB
182:Dan
153:MSD
140:Dan
88:Dan
71:OCA
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2367:)
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