Re: [COOT] How to mask a map considering the symmetric operations?
Or to put it slightly differently: the masking of symmetry-related density works (only) when the cell and symmetry of the map is the same as the cell and symmetry of the atoms for the mask. Paul. Bernhard Lohkamp wrote: Hi, you dont say how you obtained you map. Usually in Coot, thanks to clipper, the maps extend over the whole crystal space, i.e. you have the same map in all asu. However this only works if the map is either generated by Coot itself (from an mtz file) or if you read a map file which covers only/exactly the asu (or unit cell). I assume you didnt use either of these. So, please try that and you will get the same, masked map around all molecules incl the symmetry related ones. Alternatively you could write out the symmetry related molecules and masked them again. B Hi all, I am looking for a strategy to obtain a density map which only contain densities where no assignment was made in the model. When I load a PDB file and its corresponding density map to coot, I can mask all regions contain the model. And then several parts were left around the edge of the model. However, these parts are not totally the one where no assignments was made, because some of them belong to the adjacent asymmetric unit part. I can display these parts by using cell and symmetry function in coot and can see the model overlap with the map. But how can I also make masks on them and let only the part where no assignments was made left from the whole map. That is how to mask the model and also its images. Thanks
Re: [COOT] [ccp4bb] [COOT] 120hz LCDs and coot stereo
On Thu, 2009-12-17 at 18:25 -0500, Ajit Datta wrote: I just talked to the NVIDIA pre-sales people and they told me that this driver (195.22 beta) should work with 120Hz lcd monitors together with Nvidia 3D vision kit on a quadro graphics card. Ajit B. http://www.phoronix.com/scan.php?page=news_itempx=NzczOQ NVIDIA Pushes Out 195.22 Beta Linux Driver ... Other changes include... support for NVIDIA 3D Vision Stereo on Linux with Quadro GPUs... -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[COOT] deleting atoms from alternate conformations
Hi all, judging from what I see being used by my colleagues, COOT is well on its way to world domination. Time to learn how to use it myself then... Anyway, suppose I have split a residue, say lysyl, to model alternate conformations of its side chain. Suppose further that I would like to remove NZ from conformer B. Upon doing so, the current COOT implementation will remove the atom. Good. It will also remove the confID from what was conformer A's NZ atom and re-set its occupancy to 1. On the latter part, intuition tells me that instead, conformer A's atoms should be unaffected, namely keep their confID and sub-unity occupancy. My questions: 1) What behavior is expected by other COOT users in comparable situations? 2) Should a few folks align themselves with my opinion, can COOT's behavior be modified without unintended side effects? Specifically, I like COOT's current behavior when Delete Residue is applied to alternative conformations: Delete the conformer completely and set the remaining conformer's atoms to Occ=1 and remove the confID. Thank you for your consideration. Happy Holidays to everyone! Wolfram Tempel
Re: [COOT] deleting atoms from alternate conformations
wtempel wrote: Hi all, judging from what I see being used by my colleagues, COOT is well on its way to world domination. Like Linux (haha). Anyway, suppose I have split a residue, say lysyl, to model alternate conformations of its side chain. Suppose further that I would like to remove NZ from conformer B. Upon doing so, the current COOT implementation will remove the atom. Good. It will also remove the confID from what was conformer A's NZ atom and re-set its occupancy to 1. On the latter part, intuition tells me that instead, conformer A's atoms should be unaffected, namely keep their confID and sub-unity occupancy. My questions: 1) What behavior is expected by other COOT users in comparable situations? Would the answer be different if a C or an O had been deleted? I'd rather ask: is Coot doing the right thing in such a case? I suspect that Garib or Pavel may know. 2) Should a few folks align themselves with my opinion, can COOT's behavior be modified without unintended side effects? Yes. Specifically, I like COOT's current behavior when Delete Residue is applied to alternative conformations: Delete the conformer completely and set the remaining conformer's atoms to Occ=1 and remove the confID. I think that that is just doing the above for many atoms. Paul.
