User talk:Valery Zapolodov
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June 2021
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Hello, I'm SoWhy. I noticed that you added or changed content in an article, Tor (network), but you didn't provide a reliable source. It's been removed and archived in the page history for now, but if you'd like to include a citation and re-add it, please do so. You can have a look at the tutorial on citing sources. If you think I made a mistake, you can leave me a message on my talk page. Thank you. SoWhy 18:44, 6 June 2021 (UTC)
Question
[edit][1] - Where is the access to the quaternary structures generated by AlphaFold and provided by Uniprot? I did not see it. My very best wishes (talk) 22:41, 29 July 2021 (UTC)
- Yes, it is not done yet, but certainly possible, so will revert it https://mobile.twitter.com/onoda_hiroki/status/1420068104239910915 Valery Zapolodov (talk) 23:03, 29 July 2021 (UTC)
- Good luck to people who will do it. Some of that can be done simply by combining AF2 models with crystal structures of the corresponding complexes available in PDB, for example, [2] and [3], i.e. one can just make a 3D superposition of two identical models, A and B, generated by AF2 with subunits A and B of the complex (this is a dimer in nature). But will they be compatible? Meaning that it could result in significant steric overlap of the A and B models after such superpositions (hence the refinement). Make such an excercise through the entire set of AF2 models and the corresponding structures of oligomeric structures from the PDB. Some of the complexes will be oligomeric. Is not that an interesting project? This is too obvious though. Someone is probably doing just that already, maybe even AF2 people. My very best wishes (talk) 23:29, 29 July 2021 (UTC)
- First of all there are some other proteins that do this concatenation in real life, not just chaperons, you can try emulating that. Second of all, you can just attach one protein to another in editor and then fold them together. See: https://mobile.twitter.com/Ag_smith/status/1417063635000598528 Valery Zapolodov (talk) 00:19, 30 July 2021 (UTC)
- "attach one protein to another" - you mean to treat them just as different domains of the same protein? Yes, that would make sense if AF2 was able to correctly dock domains. But unfortunately, it can only model individual water-soluble domains, but can not correctly dock them together - based on the results of the last CASP and models of thousands proteins they just made available. Solving protein docking problem might not be even possible in general using their approach, i.e. based on the multiple sequence alignments. If they will ever progress significantly with that, we will see it on CAPRI. My very best wishes (talk) 02:48, 30 July 2021 (UTC)
- It can do docking, that is the point: Google people missed that, they missed a lot of things. You apparently did too. There is a specially hacked colab for that, that works perfectly (the only thing that is still not quite there is DNA and robozymes): https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2_complexes.ipynb
- Also, a nice example of homo-6-mer! https://mobile.twitter.com/sokrypton/status/1418218396580208641 Valery Zapolodov (talk) 06:14, 30 July 2021 (UTC)
- Sure, it can do docking. But can it do docking correctly and consistently for a large number of cases that are not merely a homology modeling? If someone proves it in publications and/or in CAPRI, then it will worth attention. But looking at the models generated by AF2 right now [4],[5] I can say that whatever they have for docking in AF2 just produces nonsense, and looking at this model [6], I can say that they simply do homology modeling without even thinking if such model makes any sense for a single subunit (of course it does not). My very best wishes (talk) 11:39, 30 July 2021 (UTC)
- Wow. Uniprot has this insane bug that makes molstar viewer there broken. You should not even look into it. Instead use https://alphafold.ebi.ac.uk/entry/P0ADL6 only. Now, AS I SAID, google and EBI did not know about that hack when they started doing the database (database is said to be from 1st July). As for "single subunit", first of all of course it makes sense in many cases, because it either uses something to dock together (unstructured regions or other proteins) or it is stable even in single subunit, like hemoglobin. Valery Zapolodov (talk) 23:37, 30 July 2021 (UTC)
- These bugs do not matter because AF provides a button for downloading the coordinate file of the model and looking at it using PyMol or whatever on your PC (that is what I do). The issue here is the existence of large empty spaces between TM helices, which makes the model outright wrong. In other cases loops are passing though the lipid bilayer, etc. The models of monomeric subunits generated by homology will be physically unrealistic/unstable for all oligomeric complexes with intertwined structures. There are many: [7]. I respect the work by AF2 team greatly, and they did right thing and fantastic advance by making all these models available, but that allows to critically analyze their models that are far from perfect. This is good thing as it allows to understand the problems and potentially fix them. My very best wishes (talk) 02:14, 31 July 2021 (UTC)
- BTW, molstar and uniprot were fixed. Valery Zapolodov (talk) 09:42, 2 August 2021 (UTC)
- These bugs do not matter because AF provides a button for downloading the coordinate file of the model and looking at it using PyMol or whatever on your PC (that is what I do). The issue here is the existence of large empty spaces between TM helices, which makes the model outright wrong. In other cases loops are passing though the lipid bilayer, etc. The models of monomeric subunits generated by homology will be physically unrealistic/unstable for all oligomeric complexes with intertwined structures. There are many: [7]. I respect the work by AF2 team greatly, and they did right thing and fantastic advance by making all these models available, but that allows to critically analyze their models that are far from perfect. This is good thing as it allows to understand the problems and potentially fix them. My very best wishes (talk) 02:14, 31 July 2021 (UTC)
- Wow. Uniprot has this insane bug that makes molstar viewer there broken. You should not even look into it. Instead use https://alphafold.ebi.ac.uk/entry/P0ADL6 only. Now, AS I SAID, google and EBI did not know about that hack when they started doing the database (database is said to be from 1st July). As for "single subunit", first of all of course it makes sense in many cases, because it either uses something to dock together (unstructured regions or other proteins) or it is stable even in single subunit, like hemoglobin. Valery Zapolodov (talk) 23:37, 30 July 2021 (UTC)
- Sure, it can do docking. But can it do docking correctly and consistently for a large number of cases that are not merely a homology modeling? If someone proves it in publications and/or in CAPRI, then it will worth attention. But looking at the models generated by AF2 right now [4],[5] I can say that whatever they have for docking in AF2 just produces nonsense, and looking at this model [6], I can say that they simply do homology modeling without even thinking if such model makes any sense for a single subunit (of course it does not). My very best wishes (talk) 11:39, 30 July 2021 (UTC)
- "attach one protein to another" - you mean to treat them just as different domains of the same protein? Yes, that would make sense if AF2 was able to correctly dock domains. But unfortunately, it can only model individual water-soluble domains, but can not correctly dock them together - based on the results of the last CASP and models of thousands proteins they just made available. Solving protein docking problem might not be even possible in general using their approach, i.e. based on the multiple sequence alignments. If they will ever progress significantly with that, we will see it on CAPRI. My very best wishes (talk) 02:48, 30 July 2021 (UTC)
- First of all there are some other proteins that do this concatenation in real life, not just chaperons, you can try emulating that. Second of all, you can just attach one protein to another in editor and then fold them together. See: https://mobile.twitter.com/Ag_smith/status/1417063635000598528 Valery Zapolodov (talk) 00:19, 30 July 2021 (UTC)
- Good luck to people who will do it. Some of that can be done simply by combining AF2 models with crystal structures of the corresponding complexes available in PDB, for example, [2] and [3], i.e. one can just make a 3D superposition of two identical models, A and B, generated by AF2 with subunits A and B of the complex (this is a dimer in nature). But will they be compatible? Meaning that it could result in significant steric overlap of the A and B models after such superpositions (hence the refinement). Make such an excercise through the entire set of AF2 models and the corresponding structures of oligomeric structures from the PDB. Some of the complexes will be oligomeric. Is not that an interesting project? This is too obvious though. Someone is probably doing just that already, maybe even AF2 people. My very best wishes (talk) 23:29, 29 July 2021 (UTC)
Thank you!
[edit][8]. I see that Google Cloud has an API that should be enabled for translation using their Google Neural Machine Translation. Did you talk about this? Yes, that would be interesting to try. My very best wishes (talk) 00:07, 13 October 2021 (UTC)
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December 2021
[edit]
Please stop your disruptive editing. If you continue to add promotional or advertising material to Wikipedia, as you did at Vitamin D, you may be blocked from editing. This site is commercial and not a WP:SCIRS source. Do not put such promotional sites into the encyclopedia. Zefr (talk) 15:39, 16 December 2021 (UTC)
- How did you even understand German? Oh, what a genious! Anyway, you can link to a user manual for that thing. Also, considering you just reverted all my edits, you are being very disruptive yourself. All my edits were clarifying and IMHO you do not need a source for either one. Especially skin canser part, it is in UV article and is thus cited. Also, how is that promotional if it is German? Hahahaha! What a joke. Valery Zapolodov (talk) 15:50, 16 December 2021 (UTC)
- Google provides an automatic translator. The point remains: don't use commercial websites as if they were valid sources. Your edits were unconstructive, so were rightly reverted - that's how Wikipedia editing works. Also, you misspelled genius and cancer. Zefr (talk) 16:01, 16 December 2021 (UTC)
- I reverted your K2 revert, if there was some consensus on that before, well, sorry, not sorry. I am not going to reseatch all the WP:MEDRS on it. Valery Zapolodov (talk) 16:10, 16 December 2021 (UTC)
- If you find WP:MEDRS reviews for the K2 evidence, then it would be appropriate to add it. You could take up a discussion on the talk page to get the input of other editors. Meanwhile, do not edit war, WP:WAR. Zefr (talk) 16:14, 16 December 2021 (UTC)
- Maybe you should revert you violation notice here, since it does not look like you even pretend to respect any rules of reverting stuff yourself. Again, I am not going to research MEDRS on this, AS I SAID. Maybe, there is some problem with comprehending from your side and your snarky grammar comments do not help either. Instead you could have waited for some other editer to fix the cites for WP:MEDRS guidelines. And BTW, WP:ONUS is IMHO not on me, since I did provide for two cites of good quality and very wide coveredge on google. And it's quite simple to check that D3 is very often sold only with K2, even if without Mg. Maybe it was just news to you, I dunno. 109.252.90.54 (talk) 16:26, 16 December 2021 (UTC)
- If you find WP:MEDRS reviews for the K2 evidence, then it would be appropriate to add it. You could take up a discussion on the talk page to get the input of other editors. Meanwhile, do not edit war, WP:WAR. Zefr (talk) 16:14, 16 December 2021 (UTC)
- I reverted your K2 revert, if there was some consensus on that before, well, sorry, not sorry. I am not going to reseatch all the WP:MEDRS on it. Valery Zapolodov (talk) 16:10, 16 December 2021 (UTC)
- Google provides an automatic translator. The point remains: don't use commercial websites as if they were valid sources. Your edits were unconstructive, so were rightly reverted - that's how Wikipedia editing works. Also, you misspelled genius and cancer. Zefr (talk) 16:01, 16 December 2021 (UTC)
HDR video article naming
[edit]Hi, I noticed your edit about IPTPQc2. Thanks for it. You might also want to take a look at Talk:High-dynamic-range video#Requested move 18 December 2021. Can you give your opinion? Thanks. SH4ever (talk) 17:19, 18 December 2021 (UTC)
Double spaces at the end of the sentence.
[edit]Hi. I noticed that you removed the double spaces at the end of sentences in the article direct current. Double spaces are ignored when it comes to formatting the text for display. However, when looking at the source, the double spaces help editors find the ends of the sentences. Some editors get rather irritated when someone removes the double spaces. There are arguments for removing them, such as there is only one occurrence of a double space and all the other sentences end with a single space. If you change that, just be sure to explain it in the edit summary. If you have any question, feel free to ask me. I hope you enjoy editing Wikipedia. Constant314 (talk) 17:34, 25 March 2022 (UTC)
- Double spaces were common before 1998 and they are no longer acceptable in any form in source code or in html render. 2A00:1370:8184:164:2CB2:A1CD:4C7C:E243 (talk) 17:44, 25 March 2022 (UTC)
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December 2022
[edit]
Please stop your disruptive editing.
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If you continue to disrupt Wikipedia, as you did at Kanye West, you may be blocked from editing. Throast {{ping}} me! (talk | contribs) 04:49, 3 December 2022 (UTC)
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Please stop your disruptive editing.
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If you continue to disrupt Wikipedia, as you did at Elon Musk, you may be blocked from editing. Disruptive--maybe, but careless, certainly. Drmies (talk) 02:00, 17 December 2022 (UTC)
- Liar. "blocked for a week for blatantly misrepresenting sources" I did not do such a thing. You MUST be perma blocked on a GLOBAL level on all wikipedia subdomains for after a "crazy stalker" attacked a car carrying his young son.
- I.e his son was attacked. Is https://news.sky.com/story/crazy-stalker-attacks-elon-musks-car-as-twitter-boss-threatens-legal-action-against-account-tracking-his-private-jet-12768404 not WP:RSPS? Valery Zapolodov (talk) 03:17, 17 December 2022 (UTC)
- @HAL333:, BTW, I have 500 edits, so your extended confirmed protection comment was illogical. Valery Zapolodov (talk) 05:56, 17 December 2022 (UTC)
If you believe this block is unjustified, please read the guide to appealing blocks (specifically this section) before appealing. Place the following on your talk page: {{unblock|reason=Please copy my appeal to the [[WP:AE|arbitration enforcement noticeboard]] or [[WP:AN|administrators' noticeboard]]. Your reason here OR place the reason below this template. ~~~~}}. If you intend to appeal on the arbitration enforcement noticeboard, I suggest you use the arbitration enforcement appeals template on your talk page so it can be copied over easily. You may also appeal directly to me (by email), before or instead of appealing on your talk page.
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Valery Zapolodov (block log • active blocks • global blocks • contribs • deleted contribs • filter log • creation log • change block settings • unblock • checkuser (log))
Request reason:
Please copy my appeal to the arbitration enforcement noticeboard or administrators' noticeboard. I did not do anything wrong, why? How is this allowed on wikipedia? I did not misrepresent the sources. "after a "crazy stalker" attacked a car carrying his young son." I.e his son was attacked. Is https://news.sky.com/story/crazy-stalker-attacks-elon-musks-car-as-twitter-boss-threatens-legal-action-against-account-tracking-his-private-jet-12768404 not WP:RSPS? Valery Zapolodov (talk) 03:04, 17 December 2022 (UTC)
Decline reason:
Transferring this to AE or AN would only waste people's time, including yours, as you don't think you did anything wrong- when you clearly did. 331dot (talk) 07:56, 17 December 2022 (UTC)
If you want to make any further unblock requests, please read the guide to appealing blocks first, then use the {{unblock}} template again. If you make too many unconvincing or disruptive unblock requests, you may be prevented from editing this page until your block has expired. Do not remove this unblock review while you are blocked.
- I cleary did not do anything wrong, but please do continue your revenge flash mob for the 7 day ban of journalists by banning me for 7 days. Copium. Valery Zapolodov (talk) 21:48, 17 December 2022 (UTC)
WGS 84 Standard
[edit]This change [9] restored a link that is now redundant with the first one in the External Links section. That was in fact an old version of the standard; the new link points to the current version instead (and is a live page). Davidpward (talk) 13:46, 24 December 2022 (UTC)
- What do you mean by "is a live page"? You need to use USA VPN to access the link. I can archive it if you want. Valery Zapolodov (talk) 13:58, 24 December 2022 (UTC)
- I meant that the old link is dead; it was removed from the server. Davidpward (talk) 16:13, 24 December 2022 (UTC)
- It is not dead. Download this VPN https://play.google.com/store/apps/details?id=octohide.vpn and select Poland. Now it will work. .mil is geoblocked for many countries. See also my comment here: https://wiki.riteme.site/wiki/Talk:.mil Valery Zapolodov (talk) 03:08, 25 December 2022 (UTC)
- Ok it seems there was a temporary server outage before. Regardless, why is that old link still needed? It is for an outdated version of the standard. The section already contains a link to the current version of the standard. Davidpward (talk) 20:52, 25 December 2022 (UTC)
- The current version of the standard technically is this (even though we already have G2238, using ITRF2020 since 27 November 2022) https://earth-info.nga.mil/php/download.php?file=(U)WGS%2084(G2139).pdf Valery Zapolodov (talk) 03:17, 26 December 2022 (UTC)
- Your change [10] added a link to the 1991 version of the standardization document. Is there a particular reason that is needed? It's not the original version or the latest version. The section already has a link to the 2014 standardization document (which yes is itself updated by G2139). If not can we please undo that change? Davidpward (talk) 03:50, 26 December 2022 (UTC)
- And your change removed it. Yes, it says "The original WGS 84 is documented in versions prior to 1996", that means later standard may be inadecvate for older items in the ensemblies. The way it works is that it has epoch that changes both inside one frame realisation and also realisations change with epoch as described by WKT2 of the ensembly. You also deleted G1762' info cause you thought it is one without prime. But if you look into https://earth-info.nga.mil/php/download.php?file=(U)WGS%2084(G2139).pdf it talks about one with a prime. Valery Zapolodov (talk) 04:57, 26 December 2022 (UTC)
- This isn't answering my question.
- WP:EL says external links should be kept to a minimum. I intentionally deleted the link to the 1991 revision of a document and replaced it with a link to the 2014 revision. I believe the current version of the full standardization document, for the significant majority of readers, has higher value for learning about (let alone implementing) WGS 84. Why specifically does including two versions of the same document here meet the burden described in WP:EL? Davidpward (talk) 13:47, 26 December 2022 (UTC)
- That is not why you deleted it in the first place, you mistakenly thought the link was dead. I already told you why it meets WP:EL. Valery Zapolodov (talk) 13:53, 26 December 2022 (UTC)
- I deleted it for both reasons. Davidpward (talk) 14:24, 26 December 2022 (UTC)
- As an example, the older document talks in depth about EGM96 (just EGM, cause EGM2008 did not exist yet). Modern documents only mention EGM96. Valery Zapolodov (talk) 14:06, 26 December 2022 (UTC)
- We have separate articles about EGM and WMM. This article and its links are about WGS 84. Davidpward (talk) 14:21, 26 December 2022 (UTC)
- WGS 84 requires EGM and WMM and vice versa, just like it requires new IERS prime meridian, or ITRF2020's reference stations require new ANTEX files... Valery Zapolodov (talk) 14:24, 26 December 2022 (UTC)
- If the reason for linking to the 1991 revision is because it contains information related to EGM96, can we move the link to the EGM page instead? Davidpward (talk) 14:26, 26 December 2022 (UTC)
- But we talk about EGM96 on the WGS page too. Valery Zapolodov (talk) 16:07, 26 December 2022 (UTC)
- I'm moving this discussion to the article's talk page since I don't think we will reach concensus here. Davidpward (talk) 00:07, 27 December 2022 (UTC)
- Go ahead. Valery Zapolodov (talk) 08:53, 27 December 2022 (UTC)
- I'm moving this discussion to the article's talk page since I don't think we will reach concensus here. Davidpward (talk) 00:07, 27 December 2022 (UTC)
- But we talk about EGM96 on the WGS page too. Valery Zapolodov (talk) 16:07, 26 December 2022 (UTC)
- If the reason for linking to the 1991 revision is because it contains information related to EGM96, can we move the link to the EGM page instead? Davidpward (talk) 14:26, 26 December 2022 (UTC)
- WGS 84 requires EGM and WMM and vice versa, just like it requires new IERS prime meridian, or ITRF2020's reference stations require new ANTEX files... Valery Zapolodov (talk) 14:24, 26 December 2022 (UTC)
- We have separate articles about EGM and WMM. This article and its links are about WGS 84. Davidpward (talk) 14:21, 26 December 2022 (UTC)
- That is not why you deleted it in the first place, you mistakenly thought the link was dead. I already told you why it meets WP:EL. Valery Zapolodov (talk) 13:53, 26 December 2022 (UTC)
- And your change removed it. Yes, it says "The original WGS 84 is documented in versions prior to 1996", that means later standard may be inadecvate for older items in the ensemblies. The way it works is that it has epoch that changes both inside one frame realisation and also realisations change with epoch as described by WKT2 of the ensembly. You also deleted G1762' info cause you thought it is one without prime. But if you look into https://earth-info.nga.mil/php/download.php?file=(U)WGS%2084(G2139).pdf it talks about one with a prime. Valery Zapolodov (talk) 04:57, 26 December 2022 (UTC)
- Your change [10] added a link to the 1991 version of the standardization document. Is there a particular reason that is needed? It's not the original version or the latest version. The section already has a link to the 2014 standardization document (which yes is itself updated by G2139). If not can we please undo that change? Davidpward (talk) 03:50, 26 December 2022 (UTC)
- The current version of the standard technically is this (even though we already have G2238, using ITRF2020 since 27 November 2022) https://earth-info.nga.mil/php/download.php?file=(U)WGS%2084(G2139).pdf Valery Zapolodov (talk) 03:17, 26 December 2022 (UTC)
- Ok it seems there was a temporary server outage before. Regardless, why is that old link still needed? It is for an outdated version of the standard. The section already contains a link to the current version of the standard. Davidpward (talk) 20:52, 25 December 2022 (UTC)
- It is not dead. Download this VPN https://play.google.com/store/apps/details?id=octohide.vpn and select Poland. Now it will work. .mil is geoblocked for many countries. See also my comment here: https://wiki.riteme.site/wiki/Talk:.mil Valery Zapolodov (talk) 03:08, 25 December 2022 (UTC)
- I meant that the old link is dead; it was removed from the server. Davidpward (talk) 16:13, 24 December 2022 (UTC)
Please review this change [11]. It's very unclear what this sentence means: "Solution for Earth orientation parameters consistent with ITRF2014 is also needed (IERS EOP 14C04)." Is something needed on the page (is this a statement that belongs on the talk page?) Is something needed in the standard that is not defined? This statement also needs to cite a source.
Also regarding IGS 20: the date 27 November 2022 is in the past (and was when the edit was made); it's unclear what relationship this has directly to WGS (the cited source never mentions WGS once). This text needs further explanation. Thank you. Davidpward (talk) 13:08, 15 January 2023 (UTC)
- Yes, the date is in the past. GPS and control segment moved to G2238, which is almost ITRF2020. EPSG should soon update the 3 ensemblies. They require PSD to work too, new in ITRF2020. As for Earth parameters, there is a presentation on the topic, Polynomial Model defined in ICD of GPS. See page 4. https://www.unoosa.org/documents/pdf/icg/2018/icg13/wgd/wgd_12.pdf here is another presentation which talks about G1762', with a prime. https://www.unoosa.org/pdf/icg/2016/icg11/wgd/02wgd.pdf Valery Zapolodov (talk) 13:30, 15 January 2023 (UTC)
CS1 error on Uranium-238
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Removal of content at List of presidents who did not win reelection
[edit]Wikipedia is not a crystal ball - let's wait for the election. FifthFive (talk) 04:34, 23 October 2024 (UTC)
- (and even if Trump wins, the content would still be valid - but would probably need a note mentioning that he won a later election) FifthFive (talk) 04:36, 23 October 2024 (UTC)